BMC Genomics 2004, 5:54 http://www.biomedcentral.com/1471-2164/5/54 Table 6: Ambystoma contigs that show sequence similarity to rat spinal cord injury genes. (Continued) TigSingletonClusters_E16_Ag2_p8_O20_M13R MexSingletonClusters_Contig188 MexCluster_6961_Contig1 MexSingletonClusters_nm_14_p15_t3_ TigCluster_218_Contig2 MexSingletonClusters_Contig506 TigSingletonClusters_I16_Ag2_p5_N7_M13R MexSingletonClusters_V1_p1_a10_Triplex5Ld TigSingletonClusters_v2_p1_D20_triplex5ld MexSingletonClusters_NT005B_F02 TigSingletonClusters_Salamander_22_I04_ab1 TigSingletonClusters_Ag2_p34_N23_M13R TigSingletonClusters_Salamander_1_H02_ab1 MexCluster_4589_Contig1 TigSingletonClusters_Contig220 TigCluster_4093_Contig1 MexSingletonClusters_nm_21_2_m7_t3_ TigCluster_8535_Contig1 MexSingletonClusters_v6_p1_j6_triplex5_1ld_ TigSingletonClusters_Salamander_15_D22_ab1 MexCluster_3498_Contig1 TigCluster_6648_Contig1 MexSingletonClusters_BL279A_B12 TigSingletonClusters_Salamander_25_P03_ab1 MexCluster_8708_Contig1 TigCluster_5877_Contig1 MexSingletonClusters_nm_14_a9_t3_ TigSingletonClusters_Salamander_11_A13_ab1 TigSingletonClusters_Salamander_12_J14_ab1 MexSingletonClusters_nm_21_2_l13_t3_ TigCluster_2065_Contig1 MexCluster_10965_Contig1 TigCluster_5315_Contig1 MexCluster_4245_Contig1 TigSingletonClusters_G05_Ag2_p9_G8_M13R MexSingletonClusters_NT013D_C12 TigSingletonClusters_Salamander_21_H19_ab1 MexCluster_9585_Contig1 TigCluster_4885_Contig1 TigSingletonClusters_Salamander_1_M03_ab1 MexSingletonClusters_NT008B_D05 TigSingletonClusters_Salamander_24_I16_ab1 MexCluster_9533_Contig1 TigCluster_5768_Contig1 MexSingletonClusters_BL283B_A11 TigSingletonClusters_Salamander_13_J19_ab1 MexSingletonClusters_v6_p4_j2_triplex5_1ld_ TigCluster_2146_Contig1 MexSingletonClusters_v11_p54_o4_t3_ TigSingletonClusters_Salamander_2_J12_ab1 gi|3135196| Ca2+/calmodulin-dependent gi|3252500| CC chemokine receptor protein gi|3319323| suppressor of cytokine signaling-3 gi|349552| P-selectin gi|3707306| Normalized rat embryo, cDNA clone gi|3711670| Normalized rat muscle, cDNA clone gi|3727094| Normalized rat ovary, cDNA clone gi|3811504| Normalized rat brain, cDNA clone gi|405556| adenylyl cyclase-activated serotonin gi|4103371| putative potassium channel TWIK gi|4135567| Normalized rat embryo, cDNA clone gi|4228395| cDNA clone UI-R-A0-bc-h-02-0-UI gi|425471| nuclear factor kappa B p105 subunit gi|430718| Sprague Dawley inducible nitric oxide gi|436934| Sprague Dawley protein kinase C rec. gi|464196| phosphodiesterase I gi|466438| 40kDa ribosomal protein gi|493208| stress activated protein kinase alpha II gi|517393| tau microtubule-associated protein gi|55933| c-fos gi|56822| major synaptic vesicel protein p38 gi|56828| nuclear oncoprotein p53 gi|56909| pJunB gene gi|56919| region fragment for protein kinase C gi|57007| ras-related mRNA rab3 gi|57238| silencer factor B gi|57341| transforming growth factor-beta 1 gi|57479| vimentin gi|596053| immediate early gene transcription gi|790632| macrophage inflammatory protein-1alpha gi|951175| limbic system-associated membrane prot. gi|971274| neurodegeneration associated protein 1 E-33 E-15 E-08 E-16 E-99 E-14 E-35 E-15 E-16 E-35 E-34 E-17 E-22 E-32 E-09 E-104 E-22 E-11 E-13 E-41 0 0 E-49 E-75 E-168 E-168 E-51 E-44 E-26 E-39 E-50 E-75 E-66 E-50 E-09 E-33 E-24 E-61 E-63 E-13 E-13 E-20 0 0 E-12 E-16 E-22 E-11 E-09 E-11 moderate (identified in 10–30% of the EST sequences) and high frequencies (identified in at least 30% of the EST sequences). Within the A. mexicanum contigs, 0.49% and 0.06% of positions were polymorphic at moderate and high frequency, while higher levels of polymorphism were observed for A. t. tigrinum (1.41% and 0.20%). Higher levels of polymorphism are expected for A. t. tigri- num because they exist in larger, out-bred populations in nature. To identify SNPs between species, we had to first identify presumptive, interspecific orthologues. We did this by performing BLASTN searches between the A. mexicanum and A. t. tigrinum assemblies, and the resulting alignments Page 8 of 17 (page number not for citation purposes)