Spreadsheet: 557f1f10-c74d-42ec-9b10-3d9dd80cbc5c
Sheet: Sheet1

Table S3-1. Primer pairs for the Air locus. | Unnamed: 1 | Unnamed: 2 | Unnamed: 3 | Unnamed: 4 | Unnamed: 5 | Unnamed: 6
The amplified loci (Position name), the genome positions (Start and End), size of the amplified fragments (Length), sequence of primers and PCR efficiency using 10 ng genome DNA (Genome) are shown.
position name | Start | End | Length | Sequence of upstream primer | Sequence of downstream primer | Genome (Ct)
position-01 | 12135844 | 12136003 | 160 | ATAACGGCAGTTGGACTTGG | CACACCCATGCAGTTAAACG | 25.4
position-02 | 12147902 | 12148077 | 176 | TGGGTAGGGAGCAGGTACAG | AGGTTCCATTTGCACAGAGG | 25.7
position-03 | 12150002 | 12150178 | 177 | TGCATACTCTGCATCCAAGC | AGAGGAACACCAGAGAGACCAG | 25.4
position-04 | 12160126 | 12160284 | 159 | ATTTGAAACAAATGCAGCCC | GGGTTTCAGTGAACTGCCTG | 26.7
position-05 | 12170064 | 12170263 | 200 | TTGAAGGTCTGAGGTCAGGG | GAGAGGTAAGGCCTCTTGGG | 26.5
position-06 | 12180027 | 12180210 | 184 | TTCCATTCCTTCACTCCACG | CACTGACAACACTTGCCTGC | 26.4
position-07 | 12192058 | 12192224 | 167 | CTAGGAAGCCAGCAGTCAGC | TGGTGGCATGTGTGTTTACC | 25.4
position-08 | 12200109 | 12200264 | 156 | CTGCAAATGGAAGAATGTGG | TCCCAGGAGCTCTGGTAATC | 26
position-09 | 12211078 | 12211232 | 155 | GGGTTTATAGGGCCTCCTG | AACTTTCCCTGGCTGTTCTTC | 28.1
position-10 | 12220095 | 12220255 | 161 | TCATCTGGAATGTAAGGCCC | CCTGGCAGACAGGCATAAAC | 26.3
position-11 | 12230109 | 12230276 | 168 | [NAME] | GGCAAGGCCTTAGGAGAAAG | 26.3
position-12 | 12234033 | 12234191 | 159 | GATTCCTTAATGCCTGCCAC | GCATGAGGATCAGCACAGTC | 24
position-13 | 12247085 | 12247267 | 183 | TGAGTACGTGCTTCTGCTGG | GACCAGTAGCTTGGAGAAGGG | 25.2
position-14 | 12250062 | 12250256 | 195 | GGCTTGTACCTTAGACAAGCATC | TTGAAAGTGTGCTCATTGCC | 26.1
position-15 | 12253116 | 12253288 | 173 | ACACAGTGTGCTGCAACCTC | TTCTTACAATCCACGAGTGCC | 25.6
position-16 | 12261063 | 12261257 | 195 | TACAATGGTGGGCTACCCTG | ACCTAGGAGAGCAGCTGTGG | 26.1
position-17 | 12275076 | 12275272 | 197 | AGATGTCTCAGCGGGCAC | TCTCAGTGGAATGTGTGAATTTG | 26
position-18 | 12279128 | 12279285 | 158 | CTAGGGAGCTTGCGAATGAC | GCTGGTGAGGGAGTAGTTGG | 26.1
position-19 | 12291029 | 12291218 | 190 | TACACCTCAGGCTTCAAACG | AGGCTGGAGGGACTTGAAAC | 25.6
position-20 | 12295106 | 12295256 | 151 | AGGCAGTTTGTACATTCACACC | TCAGAGAGCTACCCAATGCC | 25.5
Table S3-2. Primer pairs for ENOR28.
Position name | Start | End | Length | Sequence of upstream primer | Sequence of downstream primer | Genome (Ct)
position-01 | 49820055 | 49820228 | 174 | CAGGGTGAGTGACATTTATTTCC | TGCAAATGGTTAGGGTAGGG | 25.098
position-02 | 49835118 | 49835269 | 152 | TGCAGCATGAAAGCAGAGAG | CTAGGGATCCATCCCATCTG | 25.204
position-03 | 49850048 | 49850201 | 154 | TTACTTCACTGCTGTTAACTATTTGG | GTTAAGGCTGTAACACACACACAC | 25.989
position-04 | 49865286 | 49865448 | 163 | AAGTAAAGGCATCCTAATTTCTGAAG | TTAGGCCAGTCATTGGGTTC | 24.687
position-05 | 49875256 | 49875419 | 164 | CTTCTCTGCTGGCATCTGTG | AATGACAAGGAATGGATTTGTG | 25.207
position-06 | 49885293 | 49885472 | 180 | GACACAATTATCCTAACCAAAGGC | TCATAATGAGCCATATACAAGGTG | 25.456
9330197I23 | 49897635 | 49897784 | 150 | CAAGAAGTCAGATGATATTCAGGG | TTTCCTCTATGAGAAAGGCATTG | 27.631
position-07 | 49909982 | 49910156 | 175 | GAGGTAAAGCTAGGTATCTCTGGG | TAAGTATGAGGCGTGGGAGG | 23.465
position-08 | 49920005 | 49920154 | 150 | AGTAATGTTGTGACTGAAAGAAGGC | ATCAATCTAGGGATGAAGTAAGGTC | 24.709
A730038J21 | 49931448 | 49931603 | 156 | AATGCTTCCATGAGACCCAC | TGCTTACTGGATTGCTTCCC | 24.02
position-09 | 49939946 | 49940136 | 191 | TTGGCCACCTTAAAGTTATTGAC | TTGGGAAGAATTAGCCCAAC | 24.303
B230105K17 | 49946786 | 49946928 | 122 | TCAATCCTTTCAGCTTCGTG | TCTGGGACAGTGGAGGAACT | 24.9343845
[NAME] | 49949811 | 49949952 | 142 | GGCACAAATATTACATTCTTCTTGG | [NAME] | 24.004
position-10 | 49954390 | 49954575 | 186 | TTTGACTCAGTTAGAGGCTGTTTG | GGTATCATGAGACAGCAACACTG | 24.519
D130067E14 | 49959037 | 49959181 | 145 | TGATGCAGAGTCAGTGGAGG | TGGGATTCTCTCAGAGGAGG | 24.06
position-11 | 49970680 | 49970854 | 175 | CCTCTACTGACATTGGCTTGC | TGACCATCTCTATGCCAAGG | 24.044
position-12 | 49980633 | 49980802 | 170 | GCGGTCTCGATTCTGACTTC | CCTGCCAGTCCCACTCTTAC | 23.237
position-13 | 49990764 | 49990917 | 154 | ATGTCTCTGGAAGAGAGGCG | GCTGGGAATTGAAACTTAGGTC | 23.218
7120471J24 | 50001599 | 50001743 | 145 | CCATGAATGGGAACAGAATG | CCCAGGCTTTGTCTTCACTC | 27.403
position-14 | 50012458 | 50012616 | 159 | GATCAAGTGGAGGGATGGG | [NAME] | 24.892
6430540B20 | 50025156 | 50025304 | 149 | GGTTGGCAATAGACATGCTG | CTGGAGGGTGTGTGATGTTG | 23.806
position-15 | 50036346 | 50036526 | 181 | [NAME] | GCTGGCTTTCTATTGCTGTG | 23.386
position-16 | 50046377 | 50046548 | 172 | CCCTTGGATAATGGGCTAGTG | TTTAAAGGGTCAGGATTAAGATAGG | 26.836
position-17 | 50057069 | 50057265 | 197 | TGAGCCTTTCAGATGCTGTG | ACTTGCGCCACTGGTATAGG | 23.656
7120448I12 | 50071187 | 50071344 | 158 | TTCTTCTATGTATGCTCTCTCTGTGTC | CGCTCTTCAGGGAGGTTTAG | 26.123
position-18 | 50081657 | 50081851 | 195 | TCCCGTGACACAGTGATTTC | TCCAGAGAGGCGCTATATGTG | 24.001
position-19 | 50091683 | 50091874 | 192 | AAGCAGAAGGCAGAGATAGCC | GGGTGGAATTAGAAGGTGTGTG | 23.514
position-20 | 50108305 | 50108458 | 154 | AGAGGAAGGAACAATGGAGC | CTCCTCTCTATCCCATCTCTCC | 25.741
position-21 | 50121762 | 50121911 | 150 | ACCAATGAGGGTACCTGAGC | CTGCGTCCACAGAACCTTTG | 25.851
position-22 | 50135336 | 50135504 | 169 | TGATTGACAGGGACTTCTGC | TCCCAGGTAATCTACATCAAAGTTC | 25.153
Table S3-3. Primer pairs for ENOR31.
position name | Start | End | Length | Sequence of upstream primer | Sequence of downstream primer | Genome (Ct)
position-01 | 56917651 | 56917802 | 152 | CAAGGGTTACAGGCACATCC | GAAGGGAAGTGACTTATGAGTGAAG | 25.165
position-02 | 56930613 | 56930789 | 177 | ACCAACCATATCACAAGCCC | GTCAAGCAGGAGTAATCGGC | 25.057
position-03 | 56954712 | 56954888 | 177 | TGACCCAGAGAGGGATTCTG | TCCTTTCCCTAAGGAGTCCC | 26.662
position-04 | 56962829 | 56962980 | 152 | AAAGGAGGAAGGAGTGTAGGG | ATGGGCAGATCAAACACCAC | 23.36
position-05 | 56972855 | 56973015 | 161 | [NAME] | AATATGAACCAGCCAGACAGG | 24.499
position-06 | 56982302 | 56982452 | 151 | GGTGGGTCTGTAGATTTGTAGGG | CACAATTGCACAGGATCAGG | 23.728
B230370O04 | 56993505 | 56993674 | 170 | TGGTGTATGGTTGTTTATTTCCC | TTCCCAGGCAATATTTGTCAC | 25.836
A330054M17 | 56997393 | 56997544 | 152 | GCCAGCACACTGGTATTTCTG | AGTGTGCTTGACCTCAGTGC | 23.649
C230076G20 | 57002497 | 57002638 | 141 | TGATTCAAGAGGTGAAGAAAACC | TCCAATCGCTACTGTCTCCA | 25.64132266666667
position-07 | 57010876 | 57011052 | 177 | [NAME] | TGTTAACACTACCAATCCATGAGC | 23.737
position-08 | 57018318 | 57018501 | 184 | CATGACCCACATGAAAGCTG | CTAACCTAACCGTTGGCCC | 25.243
D130039M01 | 57026876 | 57027015 | 140 | [NAME] | GACCTCATACTTCCAGACAGACC | 26.373
position-09 | 57037817 | 57037974 | 158 | GAGCCTCACTCATTCCATGC | GTTAGAGGTCTCTAGGCTCATGC | 23.896
position-10 | 57047920 | 57048072 | 153 | GACTACGAATTTGGCTTGTACATC | AACCTGTGAAGACTTAAATCACTGG | 25.315
position-11 | 57059362 | 57059511 | 150 | AAGAAAGCACACTTTGAAGGC | GAATCATTTATGAAGGTTTCCTCC | 24.904
position-12 | 57067946 | 57068098 | 153 | TGTGTAGCTCTTCTGGAATTTGC | CCCATTTATTCCATCCTCTACTC | 26.432
position-13 | 57077901 | 57078064 | 164 | TGGTCTTCCTCTCTTGTGTGG | AATCTCTGGCTCCTGAATGC | 23.487
7120464J01 | 57086728 | 57086883 | 155 | CTTGCTGAATCTGCTTGCTG | GCTTCCATTGAGCTGTCCAC | 24.416105
position-14 | 57090007 | 57090171 | 165 | TGCTAGTTCCTTAAATACAGCAAAC | GCCTCATTACCTCTAGTGAAGCTC | 24.451
C030047J05 | 57093397 | 57093536 | 140 | TAAGTGTCCAACTTCGGTTTCTG | ACATACTCTGTAATTCATGTGGTGC | 25.105
position-15 | 57104334 | 57104532 | 199 | GGAGTTTCAGATGGTTGTGAAC | GCCTAGAGAAATGGCTTAGCAG | 24.487
position-16 | 57114239 | 57114423 | 185 | GGCACCTCTAGGCAAGTCTG | TGGGCATGCTTAATCACATC | 23.396
position-17 | 57124278 | 57124475 | 198 | ACCATTACGGCAAGAAGCAC | CCCTTTCTTCCTGAACTTGC | 27.316
position-18 | 57139472 | 57139627 | 156 | ATAAACACAAGCCACCGGG | AAGAATAACAGGACCCAGGC | 25.647
position-19 | 57153387 | 57153579 | 193 | GGGATCATCTTAGGGTAGAAATTAAAC | ACAGCAGCATGACACTGGAG | 25.354
position-20 | 57172411 | 57172562 | 152 | AATTTCTTACTGCCCACTGAGG | GGATAAATTGCATAAAGACAACACTG | 26.641
Table S3-4. Primer pairs for long PCR.
amplified fragments | Start | End | Length | Sequence of upstream primer | Sequence of downstream primer
A | 57087542 | 57090171 | 2630 | AGATAGAGGTGTGCAGCATCAG | GCCTCATTACCTCTAGTGAAGCTC
B | 57090007 | 57092476 | 2470 | TGCTAGTTCCTTAAATACAGCAAAC | GAGCACAGAACAGGATACCATC
C | 49951466 | 49954575 | 3110 | TGGTGGTGGAAATCACTTCTC | GGTATCATGAGACAGCAACACTG
D | 49954390 | 49957564 | 3175 | TTTGACTCAGTTAGAGGCTGTTTG | CAGGATCCACATGTATAGGGC
Table S3-5. Primer pairs for probe synthesis for Northern analysis.
Primer pairs were designed to amplify unique regions in ENORs or Air. The probes from the primer pairs, color coded by light blue, were also used for the examination, which revealed consistent result with that using probes in the same ENORs shown in Figure 6.
Probe name | Resource | Chromosome | Length | Sequence of forward primer | Sequence of revers primer
ENOR62 | C230073G13 | 17 | 569 | TGTTGGTTTTCTTTGCGATG | AACTTCAGCCCACATCACCT
ENOR54 | 7120420E17 | 15 | 811 | TGACACTTGAATTCCCTTTTGA | TGGAAGTTTGCATGAGGTTTC
ENOR2 | A430083K03 | 1 | 1298 | TTATGCGAGATGTGCAGGAT | ATTACTCATGCTGCGGTCCT
[NAME] | A630062C24 | 17 | 857 | CGTGGCAAATGATCACATCT | TGGAGAGTAGGTGGGTCCTG
ENOR16 | A330078N10 | 5 | 1199 | GCGAGTCTCAGGTGAGAAGG | TTTTGCCTGCTATTGGTGGT
ENOR14 | C130081G07 | 4 | 762 | GGCCCCATGAGAAAAAGAAC | GCCTCCAGTGACAGCCTTTA
ENOR14' | C030029H13 | 4 | 447 | AGCTGTCCATAGGGAGGAGA | CCTGGCAAAATCAAGGACAT
ENOR28 | 6430540B20 | 8 | 559 | TTACCCACCAAGATCAACCTG | TCATGTCTAAGCAGACCCTTGA
ENOR31 | D130039M01 | 8 | 1017 | GCATGATCATCAGGTTCTCAAA | CAGTCTGTGGGATTTGTGGTT
Air (ENOR60) | Genome DNA | 17 | 927 | TTTGCAACTCTGAGGGTTTTT | TGTGCATAAGTGCAGGTGCT
[NAME] | [NAME] | 17 | 1190 | TTCCTCTTGTCGTTGTTTGC | ACCGTCGACGTGTTTGCTAC
ENOR28 | D130067E14 | 8 | 691 | TGCATAATACAGTTACAGAATGGGTA | TGTGCTCAATATGAATCACTCCA
ENOR31 | A330054M17 | 8 | 801 | TGCCGGTAGTACACTCTGATTT | CGTGAGTCGGATACCTGTGA
Table S3-6. Primer pairs for RNA localization experiments.
The primer pairs, color coded by light blue, were also used for the examination, which revealed consistent result with that of transcripts shown in Figure 7.
 | Probe name | RNA/Chrom. | Length | Sequence of forward primer | Sequence of revers primer | Genome (Ct)
 | [NAME] | mRNA | 140 | CGGAAACAAGAAGGGGATCT | GTCTGCTTCCGAAACACTGG | 25.6
 | Rian (ENOR44) | 12 | 139 | CCCGTAGAGGTTTAACTGCAC | TGATCCAACATCAGTCCTCCT | 25.6
 | ENOR62 | 17 | 196 | AATGGCACAAACTTGGGAAG | CCTTCCAGGGAAAGAGATCC | 26.267
 | ENOR54 | 15 | 164 | ACCTGGGAAGAGCAGAAACC | TTCCTTTCCACAGAATGGATG | 24.092
 | ENOR2 | 1 | 168 | CATGCCATGAATCTGACAGC | GATGCCAGCCCAAATGTAAC | 23.891
 | [NAME] | 17 | 168 | GAGTGGTCTCAGGCTTCAGG | TGTGGAGAGTAGGTGGGTCC | 24.308
 | ENOR16 | 5 | 175 | TGTAGAGGCACTGATGCAGG | CCCTCCGTGTCTCTCTGAAG | 27.051
 | ENOR14 | 4 | 187 | CAGGGTGTCCTTGCTTTCTC | AGAACAGCTTCTGCCTTTGG | 25.5595
 | ENOR28 | 8 | 145 | TGGGATTCTCTCAGAGGAGG | TGATGCAGAGTCAGTGGAGG | 24.06
 | ENOR31 | 8 | 155 | CTTGCTGAATCTGCTTGCTG | GCTTCCATTGAGCTGTCCAC | 24.416105
 | GAPDH | mRNA | 141 | GTGGACCTCATGGCCTACAT | GGTCTGGGATGGAAATTGTG | 19.8
 | b-actin | mRNA | 109 | GGTACCACCATGTACCCAGG | AGTACTTGCGCTCAGGAGGA | 23.4
 | Rian (another set) | 12 | 130 | GCAAAGTTCTTGCTCACCTCA | AGGTAACTGCATTCCGTCTGC | 25.7
 | ENOR62 | 17 | 188 | CAAGTTCTTCCTCTGGCTGG | AGGCAACAAAGATTTGACCG | 24.2245
 | ENOR54 | 15 | 195 | AGACCTGGGTGGGCTTAGAC | TAAATGCTGCCATTACGGTG | 23.9915
 | ENOR2 | 1 | 168 | CTGACGGGTTGGCTAAGATG | CAGAGCAGACACAGCTCCAC | 25.3555
 | [NAME] | 17 | 158 | ATTGTATGTGGAGCGAAGGC | CCGACAGAAGAGGACCTGAC | 24.6385
 | ENOR16 | 5 | 194 | AGTGCTTTGTGGGAAGATGG | TGGGAGTGGTAAGATTTGGG | 24.0635
 | ENOR14 | 4 | 166 | GTCTAAAGGTGGCGCTCAAG | TTAAACTTCGCAGCATGCAC | 24.2565
 | ENOR28 | 8 | 142 | [NAME] | GGCACAAATATTACATTCTTCTTGG | 24.004
 | ENOR31 | 8 | 140 | ACATACTCTGTAATTCATGTGGTGC | TAAGTGTCCAACTTCGGTTTCTG | 25.105