From biomedicine to natural history research: EST resources for ambystomatid salamanders

Putta, Srikrishna; Smith, Jeramiah J; Walker, John A; Rondet, Mathieu; Weisrock, David W; Monaghan, James; Samuels, Amy K; Kump, Kevin; King, David C; Maness, Nicholas J; Habermann, Bianca; Tanaka, Elly; Bryant, Susan V; Gardiner, David M; Parichy, David M; Voss, S Randal

doi:10.1186/1471-2164-5-54

BMC Genomics

Table 6 Ambystoma contigs that show sequence similarity to rat spinal cord injury genes.

From: From biomedicine to natural history research: EST resources for ambystomatid salamanders

Ambystoma Contig ID	RAT cDNA clone	E-value
MexCluster_7440_Contig1	gi\|1150557\|c-myc, exon 2	E^-29
MexCluster_4624_Contig1	gi\|1468968\| brain acyl-CoA synthtase II	E^-09
TigCluster_4083_Contig1		E^-09
TigSingletonClusters_Salamander_4_G20_ab1	gi\|1552375\| SKR6 gene, a CB1 cannabinoid recept.	E^-08
MexSingletonClusters_NT009B_B04	gi\|17352488\| cyclin ania-6a	E^-46
TigCluster_3719_Contig1		E^-114
TigCluster_8423_Contig1	gi\|1778068\| binding zyginI	E^-102
TigCluster_7064_Contig1	gi\|1836160\| Ca2+/calmodulin-dependent	E^-20
MexCluster_3225_Contig1	gi\|1906612\| Rattus norvegicus CXC chemokine	E^-68
TigSingletonClusters_Salamander_13_F03_ab1		E^-38
MexSingletonClusters_BL285B_A06	gi\|203042\| (Na+, K+)-ATPase-beta-2 subunit	E^-63
TigCluster_6994_Contig1		E^-65
MexSingletonClusters_BL014B_F12	gi\|203048\| plasma membrane Ca2+ ATPase-isoform 2	E^-112
TigSingletonClusters_Salamander_5_F07_ab1		E^-92
MexCluster_1251_Contig1	gi\|203167\| GTP-binding protein (G-alpha-i1)	E^-110
TigSingletonClusters_Salamander_3_P14_ab1		E^-152
TigSingletonClusters_Salamander_22_B01_ab1	gi\|203336\| catechol-O-methyltransferase	E^-47
TigSingletonClusters_Salamander_17_N04_ab1	gi\|203467\| voltage-gated K+ channel protein (RK5)	E^-08
MexSingletonClusters_v1_p8_c16_triplex5ld_	gi\|203583\| cytosolic retinol-binding protein (CRBP)	E^-77
TigCluster_6321_Contig1		E^-18
MexCluster_5399_Contig1	gi\|204647\| heme oxygenase gene	E^-67
TigCluster_2577_Contig1		E^-67
MexCluster_4647_Contig1	gi\|204664\| heat shock protein 27 (Hsp27)	E^-83
TigSingletonClusters_Salamander_12_M05_ab1		E^-51
MexSingletonClusters_BL285C_F02	gi\|205404\| metabotropic glutamate receptor 3	E^-41
TigSingletonClusters_Salamander_2_B24_ab1	gi\|205508\| myelin/oligodendrocyte glycoprotein	E^-26
TigCluster_5740_V2_p10_M20_TriplEx5ld_	gi\|205531\| metallothionein-2 and metallothionein 1	E^-08
TigSingletonClusters_V2_p5_A2_TriplEx5ld_	gi\|205537\| microtubule-associated protein 1A	E^-59
MexCluster_1645_Contig1	gi\|205633\| Na, K-ATPase alpha-2 subunit	E^-149
TigSingletonClusters_Contig328		0
TigSingletonClusters_Contig45	gi\|205683\| smallest neurofilament protein (NF-L)	E^-63
MexSingletonClusters_NT016A_A09	gi\|205693\| nerve growth factor-induced (NGFI-A)	E^-95
TigSingletonClusters_I09_Ag2_p9_K24_M13R		E^-24
MexSingletonClusters_NT007A_E07	gi\|205754\| neuronal protein (NP25)	E^-64
TigCluster_7148_Contig1		E^-57
MexCluster_9504_Contig1	gi\|206161\| peripheral-type benzodiazepine receptor	E^-73
MexSingletonClusters_BL016B_B02	gi\|206166\| protein kinase C type III	E^-36
TigCluster_981_Contig1		E^-27
MexSingletonClusters_nm_19_k3_t3_	gi\|206170\| brain type II Ca2+/calmodulin-dependent	E^-117
MexSingletonClusters_v11_p42_j20_t3_049_ab1 gi\|207138\| norvegicus syntaxin B		1e^-079
MexSingletonClusters_nm_14_h19_t3_	gi\|207473\| neural receptor protein-tyrosine kinase	E^-40
TigSingletonClusters_Contig336		E^-34
TigSingletonClusters_E10_Ag2_p18_O19_M13	gi\|2116627\| SNAP-25A	E^-123
MexCluster_211_Contig1	gi\|220713\| calcineurin A alpha	E^-63
TigSingletonClusters_Salamander_7_K14_ab1		E^-87
MexSingletonClusters_NT014A_G03	gi\|220839\| platelet-derived growth factor A chain	E^-21
TigSingletonClusters_Salamander_9_M15_ab1		E^-56
TigSingletonClusters_Salamander_19_M06_ab1	gi\|2501807\| brain digoxin carrier protein	E^-55
MexSingletonClusters_Contig100	gi\|2746069\| MAP-kinase phosphatase (cpg21)	E^-108
TigSingletonClusters_Salamander_11_A16_ab1		E^-70
MexCluster_8345_Contig1	gi\|2832312\| survival motor neuron (smn)	E^-40
TigCluster_8032_Contig1		E^-49
MexCluster_3580_Contig1	gi\|294567\| heat shock protein 70 (HSP70)	0
TigCluster_8592_Contig2		E^-161
TigSingletonClusters_Salamander_17_N08_ab1	gi\|2961528\| carboxyl-terminal PDZ	E^-10
MexSingletonClusters_BL286C_D09	gi\|298325\| sodium-dependent neurotransmitter tran.	E^-12
TigSingletonClusters_Contig95		E^-22
MexSingletonClusters_Contig461	gi\|2996031\| brain finger protein (BFP)	E^-08
TigSingletonClusters_Salamander_11_O19_ab1		E^-23
TigSingletonClusters_E16_Ag2_p8_O20_M13R	gi\|3135196\| Ca2+/calmodulin-dependent	E^-33
MexSingletonClusters_Contig188	gi\|3252500\| CC chemokine receptor protein	E^-15
MexCluster_6961_Contig1	gi\|3319323\| suppressor of cytokine signaling-3	E^-08
MexSingletonClusters_nm_14_p15_t3_	gi\|349552\| P-selectin	E^-16
TigCluster_218_Contig2		E^-99
MexSingletonClusters_Contig506	gi\|3707306\| Normalized rat embryo, cDNA clone	E^-14
TigSingletonClusters_I16_Ag2_p5_N7_M13R	gi\|3711670\| Normalized rat muscle, cDNA clone	E^-35
MexSingletonClusters_V1_p1_a10_Triplex5Ld	gi\|3727094\| Normalized rat ovary, cDNA clone	E^-15
TigSingletonClusters_v2_p1_D20_triplex5ld		E^-16
MexSingletonClusters_NT005B_F02	gi\|3811504\| Normalized rat brain, cDNA clone	E^-35
TigSingletonClusters_Salamander_22_I04_ab1		E^-34
TigSingletonClusters_Ag2_p34_N23_M13R	gi\|405556\| adenylyl cyclase-activated serotonin	E^-17
TigSingletonClusters_Salamander_1_H02_ab1	gi\|4103371\| putative potassium channel TWIK	E^-22
MexCluster_4589_Contig1	gi\|4135567\| Normalized rat embryo, cDNA clone	E^-32
TigSingletonClusters_Contig220		E^-09
TigCluster_4093_Contig1	gi\|4228395\| cDNA clone UI-R-A0-bc-h-02-0-UI	E^-104
MexSingletonClusters_nm_21_2_m7_t3_	gi\|425471\| nuclear factor kappa B p105 subunit	E^-22
TigCluster_8535_Contig1		E^-11
MexSingletonClusters_v6_p1_j6_triplex5_1ld_	gi\|430718\| Sprague Dawley inducible nitric oxide	E^-13
TigSingletonClusters_Salamander_15_D22_ab1		E^-41
MexCluster_3498_Contig1	gi\|436934\| Sprague Dawley protein kinase C rec.	0
TigCluster_6648_Contig1		0
MexSingletonClusters_BL279A_B12	gi\|464196\| phosphodiesterase I	E^-49
TigSingletonClusters_Salamander_25_P03_ab1		E^-75
MexCluster_8708_Contig1	gi\|466438\| 40kDa ribosomal protein	E^-168
TigCluster_5877_Contig1		E^-168
MexSingletonClusters_nm_14_a9_t3_	gi\|493208\| stress activated protein kinase alpha II	E^-51
TigSingletonClusters_Salamander_11_A13_ab1	gi\|517393\| tau microtubule-associated protein	E^-44
TigSingletonClusters_Salamander_12_J14_ab1	gi\|55933\| c-fos	E^-26
MexSingletonClusters_nm_21_2_l13_t3_	gi\|56822\| major synaptic vesicel protein p38	E^-39
TigCluster_2065_Contig1		E^-50
MexCluster_10965_Contig1	gi\|56828\| nuclear oncoprotein p53	E^-75
TigCluster_5315_Contig1		E^-66
MexCluster_4245_Contig1	gi\|56909\| pJunB gene	E^-50
TigSingletonClusters_G05_Ag2_p9_G8_M13R		E^-09
MexSingletonClusters_NT013D_C12	gi\|56919\| region fragment for protein kinase C	E^-33
TigSingletonClusters_Salamander_21_H19_ab1		E^-24
MexCluster_9585_Contig1	gi\|57007\| ras-related mRNA rab3	E^-61
TigCluster_4885_Contig1		E^-63
TigSingletonClusters_Salamander_1_M03_ab1	gi\|57238\| silencer factor B	E^-13
MexSingletonClusters_NT008B_D05	gi\|57341\| transforming growth factor-beta 1	E^-13
TigSingletonClusters_Salamander_24_I16_ab1		E^-20
MexCluster_9533_Contig1	gi\|57479\| vimentin	0
TigCluster_5768_Contig1		0
MexSingletonClusters_BL283B_A11	gi\|596053\| immediate early gene transcription	E^-12
TigSingletonClusters_Salamander_13_J19_ab1		E^-16
MexSingletonClusters_v6_p4_j2_triplex5_1ld_	gi\|790632\| macrophage inflammatory protein-1alpha	E^-22
TigCluster_2146_Contig1	gi\|951175\| limbic system-associated membrane prot.	E^-11
MexSingletonClusters_v11_p54_o4_t3_	gi\|971274\| neurodegeneration associated protein 1	E^-09
TigSingletonClusters_Salamander_2_J12_ab1		E^-11

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ISSN: 1471-2164

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