RetrogeneDB ID:

retro_tgut_15

Retrocopy
location
Organism:Zebrafinch (Taeniopygia guttata)
Coordinates:10:1806958..1808566(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSTGUG00000003852
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:SNW1
Ensembl ID:ENSTGUG00000012340
Aliases:None
Description:SNW domain containing 1 [Source:HGNC Symbol;Acc:16696]


Retrocopy-Parental alignment summary:






>retro_tgut_15
CTCAGCAGCTTTTTGCCAGCTCCAACCCAGCTGTCCCCAGATCAGCTGGAACTAGAAGAAAGAGCAAGAGCTCAGAGATC
CAGGCAGAGTGCTCTGGCCTCCTCACAAAGGGAACCTCCCCCATATGGTGACCGGAAGGGATGGATACCACAGGTGCTAG
AGGATTTTGGAGATGGGGGTGCCTTCCCAGAAATTCACGTGGCCCAATATACATTGGATATGGGCCAAAAGAAGAAAATT
TCCAATGCTTTGGCTCTTCAGGTGGATGCAGAAGGAAAAATAAAATATGATGCAATTGCTCGACAAGGACAGTCAAAGGA
CAAGGTTATTTACACAAAGTACACAGATCTTGTGCCAAAAGAAGTCATGAATGTGGGTGATCCTGAACTGCAAAGACCAG
ATGACAAGGCAATTAGAGAGGTAACAAAGAAGACAAGAGCAGCCTTGGAGAAATTAGTCTCCCAAAAAGTTGCAGCAGCC
ATGCCAGTTCGAGCTGCTGACGAGCCAGCTCTGGCACAATACATTCGGTACACACCATCTCAGCAAGGAGCTGCATTCAA
CTCTGGAGCAAGGCAGAGAGTTATTCGGGTAGTGGAAATGCAGAAGGACCCTATGGAGCCTCCAAGATTCAAAATCAACA
AGAAGATTCCACAAGGACCACCATCTCCTCCAGCACCTGTAATGCACTCTCCGAGTAGAAAGATGACTGTGAGAGAGCAG
CAAGAGTGGAAAATTCCTCCATGCATTTCAAACTGGAAGAATGCAAAGGGTTACACCGTTCCCTTGGAGAAGCGTCTGGC
TGCAGATGGCAGAGGATTGCAGGCTGTTCATATTAATGAAAACTTTGCCAAACTTGCTGAGGCGCTCTATATTGCTGACA
GAAAGGCTCGTGAGGCAGTAGAGATGCGTGCCCAGTTGGAGAGGAAAATGGCTCAGAAAGAAAAGGAGAAACACGAGGAA
AAGCTCCGAGAAATGGCTCAGAAAGCCAGGGAGAGAAGAGCAGGGATCAAAACACGTGTTGAAAAAGAGGATGGAGCAGC
TAGAGAAAGGGATGAAATCAGACGTGACTGGCGCAAAGAAAGACAACATGACAGAAATCTTTCCCGGGCAGCTCCTGATA
AAAGGTCAAAGCTGCAAAGGAATGAGAACAGAGATATCAGTGAAGTTATTGCCCTGGGGGTACCCAACCACAGGCCATCC
AATGAAATCCAATATGACCAGAGGCTGTTCAACCAGAGCAAGGGTATGGACAGTGGCTTTGCTGGTGGAGACGATGAAAT
TTATAATGTTTATGACCAGCCATGGAGAAGTGGCAAGGATATGGCCCAGAACATCTACAGGCCAAGTAAAAATATGGATA
AGGACATGTATGGTGATGATCTAGAGGCTCAAATAACGATCAGCAGGTTTGCTCCTGACAAAGAGTTTTCTAACTCAGAT
CGTAACACCGGAGGAAGGGGCAGAGATGGACCAGTTCAATTTGAGGAGGATCCATTTGGTTTGGACAAGTTTCTGGAAGA
AGCCAAGCAACACGGTGGTTCTAAACAGCCATCAGGCAGCAGCGGCCCTAAGGAACATGAGCATCAGAGCAAAAAGAGGA
GGAAGGAC

ORF - retro_tgut_15 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 91.04 %
Parental protein coverage: 99.81 %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalVSSFLPAPTQLSQDQLELEERARAQRSRQAALVSSRREPPPYGYRKGWIPRALEDFGDGGAFPEIHVAQY
.SSFLPAPTQLS.DQLELEERARAQRSRQ.AL.SS.REPPPYG.RKGWIP..LEDFGDGGAFPEIHVAQY
RetrocopyLSSFLPAPTQLSPDQLELEERARAQRSRQSALASSQREPPPYGDRKGWIPQVLEDFGDGGAFPEIHVAQY
ParentalPLDMGRKKKMSNALAVQVDAEGKIKYDAIARQGQSKDKVIYSKYTDLVPKEVMNVDDPELQRPDEEAIRE
.LDMG.KKK.SNALA.QVDAEGKIKYDAIARQGQSKDKVIY.KYTDLVPKEVMNV.DPELQRPD..AIRE
RetrocopyTLDMGQKKKISNALALQVDAEGKIKYDAIARQGQSKDKVIYTKYTDLVPKEVMNVGDPELQRPDDKAIRE
ParentalITEKTRAALEKSVSQKVAAAMPVRAADKLAPAQYIRYTPSQQGVAFNSGAKQRVIRMVEMQKDPMEPPRF
.T.KTRAALEK.VSQKVAAAMPVRAAD..A.AQYIRYTPSQQG.AFNSGA.QRVIR.VEMQKDPMEPPRF
RetrocopyVTKKTRAALEKLVSQKVAAAMPVRAADEPALAQYIRYTPSQQGAAFNSGARQRVIRVVEMQKDPMEPPRF
ParentalKINKKIPRGPPSPPAPVMHSPSRKMTVKEQQEWKIPPCISNWKNAKGYTIPLDKRLAADGRGLQTVHINE
KINKKIP.GPPSPPAPVMHSPSRKMTV.EQQEWKIPPCISNWKNAKGYT.PL.KRLAADGRGLQ.VHINE
RetrocopyKINKKIPQGPPSPPAPVMHSPSRKMTVREQQEWKIPPCISNWKNAKGYTVPLEKRLAADGRGLQAVHINE
ParentalNFAKLAEALYIADRKAREAVEMRAQVERKMAQKEKEKHEEKLREMAQKARERRAGIKTHVEKEDGEARER
NFAKLAEALYIADRKAREAVEMRAQ.ERKMAQKEKEKHEEKLREMAQKARERRAGIKT.VEKEDG.ARER
RetrocopyNFAKLAEALYIADRKAREAVEMRAQLERKMAQKEKEKHEEKLREMAQKARERRAGIKTRVEKEDGAARER
ParentalDEIRHDRRKERQHDRNLSRAAPDKRSKLQRNENRDISEVIALGVPNPRPSNEIQYDQRLFNQSKGMDSGF
DEIR.D.RKERQHDRNLSRAAPDKRSKLQRNENRDISEVIALGVPN.RPSNEIQYDQRLFNQSKGMDSGF
RetrocopyDEIRRDWRKERQHDRNLSRAAPDKRSKLQRNENRDISEVIALGVPNHRPSNEIQYDQRLFNQSKGMDSGF
ParentalAGGEDEIYNVYDQPWRSGKDMAQNIYRPSKNLDKDMYGDDLEARIKTNRFVPDKEFSNSDRNTRGRGRDG
AGG.DEIYNVYDQPWRSGKDMAQNIYRPSKN.DKDMYGDDLEA.I...RF.PDKEFSNSDRNT.GRGRDG
RetrocopyAGGDDEIYNVYDQPWRSGKDMAQNIYRPSKNMDKDMYGDDLEAQITISRFAPDKEFSNSDRNTGGRGRDG
ParentalPVQFEEDPFGLDKFLEEAKQHGGSKRPSDSSRPKEHEHESKKRRKD
PVQFEEDPFGLDKFLEEAKQHGGSK.PS.SS.PKEHEH.SKKRRKD
RetrocopyPVQFEEDPFGLDKFLEEAKQHGGSKQPSGSSGPKEHEHQSKKRRKD

Legend:
*Stop codon
>Forward frameshift by one nucleotide
<Reverse frameshift by one nucleotide






RNA-Seq - click to see more details

Taeniopygia guttata was not studied using RNA-Seq expression data.

ChIP-Seq - click to see more details

Taeniopygia guttata was not studied using ChIP-Seq data.

EST - click to see more details

No EST(s) were mapped for retro_tgut_15 retrocopy.

TSS - click to see more details

Taeniopygia guttata was not studied using FANTOM5 data.

Lab - click to see more details

retro_tgut_15 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_tgut_15 has 0 orthologous retrocopies within neognath group .

Parental genes homology:
Parental genes homology involve 21 parental genes, and 33 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000039762 retrocopies
retro_amel_163, retro_amel_912,
Canis familiaris ENSCAFG000000304091 retrocopy
retro_cfam_195,
Callithrix jacchus ENSCJAG000000169472 retrocopies
retro_cjac_2932, retro_cjac_576,
Dipodomys ordii ENSDORG000000123803 retrocopies
retro_dord_693, retro_dord_781, retro_dord_782,
Felis catus ENSFCAG000000016371 retrocopy
retro_fcat_635,
Homo sapiens ENSG000001006031 retrocopy
retro_hsap_174,
Gorilla gorilla ENSGGOG000000260161 retrocopy
retro_ggor_257,
Loxodonta africana ENSLAFG000000034822 retrocopies
retro_lafr_474, retro_lafr_787,
Myotis lucifugus ENSMLUG000000052282 retrocopies
retro_mluc_387, retro_mluc_805,
Monodelphis domestica ENSMODG000000052521 retrocopy
retro_mdom_1841,
Mustela putorius furoENSMPUG000000087241 retrocopy
retro_mputfur_551,
Mus musculus ENSMUSG000000210392 retrocopies
retro_mmus_1022, retro_mmus_387,
Nomascus leucogenys ENSNLEG000000167711 retrocopy
retro_nleu_982,
Otolemur garnettii ENSOGAG000000298251 retrocopy
retro_ogar_1404,
Ochotona princeps ENSOPRG000000075681 retrocopy
retro_opri_737,
Pongo abelii ENSPPYG000000060311 retrocopy
retro_pabe_454,
Pan troglodytes ENSPTRG000000065871 retrocopy
retro_ptro_165,
Sorex araneus ENSSARG000000022793 retrocopies
retro_sara_403, retro_sara_568, retro_sara_727,
Tupaia belangeri ENSTBEG000000140743 retrocopies
retro_tbel_2575, retro_tbel_2927, retro_tbel_3536,
Taeniopygia guttata ENSTGUG00000012340 2 retrocopies
retro_tgut_15 , retro_tgut_30,
Tarsius syrichta ENSTSYG000000109511 retrocopy
retro_tsyr_1871,


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