RetrogeneDB ID:

retro_cfam_236

Retrocopy
location
Organism:Dog (Canis familiaris)
Coordinates:X:47861216..47863088(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSCAFG00000016509
Aliases:None
Status:KNOWN_PROTEIN_CODING
Parental gene
information
Parental gene summary:
Parental gene symbol:UBQLN1
Ensembl ID:ENSCAFG00000001435
Aliases:None
Description:ubiquilin 1 [Source:HGNC Symbol;Acc:12508]


Retrocopy-Parental alignment summary:






>retro_cfam_236
ATGGCTGAGAACGGCGAGAGTAGCGGCCCCCCGCGCCCCTCCCGCGGCCCTGCCGCGGCCCAAGGCCCTGCCTCTGCCCC
GGCCGAGCCCAAAATCATCAAAGTTACTGTGAAGACCCCCAAAGAGAAAGAGGAGTTCGCGGTGCCCGAGAATAGCTCAG
TCCAGCAGTTTAAGGAAGCGATTTCAAAACGCTTCAAATCCCAAACCGACCAGCTAGTGTTGATTTTTGCCGGAAAAATC
TTAAAAGATCAAGATACCTTGATTCAGCATGGCATCCATGATGGACTGACTGTTCATCTTGTAATTAAAAGCCAGAACCG
ACCTCAGGGCCAGTCCACACAGCCTAGTAATGCCGCGGGAACTAATACTACCTCCGCGTCGACTCCCAGGAGTAACTCCA
CATCTGTTTCCACAAATAGCAACCCGTTTGGGCTGGGGAGCTTAGGAGGACTTGCAGGCCTTAGCAGCCTGGGCTTGAGC
TCGACCAACTTCTCTGAGCTCCAGAACCAGATGCAGCAGCAGCTCCTGTCCAGCCCTGAGATGATGATTCAAATCATGGA
AAATCCCTTTGTTCAGAGCATGCTTTCAAATCCCGATCTAATGAGGCAGCTCATTATGGCCAATCCACAGATGCAGCAGT
TGATTCAGAGAAATCCAGAAATCAGTCACCTGCTCAACAACCCAGATATAATGAGACAGACCCTGGAAATTGCCAGGAAT
CCAGCCATGATGCAAGAGATGATGAGAAATCAAGATTTGGCTCTCAGCAATCTTGAAAGCATCCCAGGTGGCTACAATGC
TCTACGACGCATGTACACTGATATTCAAGAACCCATGCTGAATGCTGCACAAGAGCAGTTTGGGGGTAATCCATTTGCCT
CGGTGGGAAGCAGTTCCACCTCTGGGGAAGGTACACAACCTTCCCGCACAGAAAATCGAGATCCACTACCCAATCCATGG
GCACCACCACCGGCTACCCAGAGTTCTGCAACCACCAGCACAACCTCCAGCAGTGGCAGTGGCTCTGGCAGTAGCTCCAG
CAGTGCTACTGGGAACACCGTGGCTGCAGCCAACTATGTTGCCAGCATCTTCAGTACCCCAGGAATGCAGAGCTTGCTGC
AACAGATAACTGAAAACCCTCAACTGATCCAGAATATGCTGTCTGCACCCTACATGAGAAGCATGATGCAGTCGCTGAGC
CAGAATCCAGATTTAGCTGCACAGATGATGCTGAATAGCCCGGTGTTTACTGCAAATCCTCAGTTGCAGGAGCAGATGCG
TCCACAGCTCCCAGCTTTCCTGCAGCAGATGCAGAATCCAGACACACTATCAGCCATGTCAAACCCAAGAGCAATGCAGG
CTTTAATGCAGATCCAGCAGGGGCTACAGACATTAGCCACTGAAGCTCCTGGCCTCATTCCAAGCTTCACTCCAGGTGTG
GGGGTAGGGGTGCTGGGAACCGCTATAGGCCCTGTAGGCCCAGTCACACCCATAGGCCCCATAGGCCCCATAGTCCCATT
TACTCCCATAGGCCCCATTGGGCCCATAGGACCCACCGGCCCTGCAGGCCCTGGCTCTACTGGCTCTGGAGGCCCCCCTG
GGCCCACTGTTTCTAGCTCTACACCCACCGAAACCACTAGCCCAACATCAGAATCTGGACCCAACCAGCAGTTCATTCAG
CAAATGGTGCAGGCTCTGGCTGGGGCAAGTCCTCCACAGCTGCCGAATCCAGAAGTCAGATTTCAGCAACAACTGGAACA
GCTCAACGCAATGGGGTTCTTAAACCGTGAGGCAAACTTGCAGGCTCTAATAGCAACAGGAGGCGACATCAATGCTGCCA
TTGAAAGGCTGCTGGGCTCCCAGCCATCCTAA

ORF - retro_cfam_236 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 78.49 %
Parental protein coverage: 85.23 %
Number of stop codons detected: 0
Number of frameshifts detected: 0


Retrocopy - Parental Gene Alignment:

ParentalMAESGESGGPPSSQDGAAAAEGAGAPAAAASAEPKIMKVTVKTPKEKEEFAVPENSSVQQFKEEISKRFK
MAE.GES.GPP....G.AAA.G.....A.A.AEPKI.KVTVKTPKEKEEFAVPENSSVQQFKE.ISKRFK
RetrocopyMAENGESSGPPRPSRGPAAAQGP----ASAPAEPKIIKVTVKTPKEKEEFAVPENSSVQQFKEAISKRFK
ParentalSHTDQLVLIFAGKILKDQDTLSQHGIHDGLTVHLVIKTQNRPQDHSAQQTNTSGSNVTTSSAPSTNSTSG
S.TDQLVLIFAGKILKDQDTL.QHGIHDGLTVHLVIK.QNRPQ..S.Q..N..G.N.T..S.P..NSTS.
RetrocopySQTDQLVLIFAGKILKDQDTLIQHGIHDGLTVHLVIKSQNRPQGQSTQPSNAAGTNTTSASTPRSNSTSV
ParentalSATSNPFGLGGLGGLAGLSSLGLNTTNFSELQSQMQRQLMSNPEMMVQIMENPFVQSMLSNPDLMRQLIM
S..SNPFGLG.LGGLAGLSSLGL..TNFSELQ.QMQ.QL.S.PEMM.QIMENPFVQSMLSNPDLMRQLIM
RetrocopySTNSNPFGLGSLGGLAGLSSLGLSSTNFSELQNQMQQQLLSSPEMMIQIMENPFVQSMLSNPDLMRQLIM
ParentalANPQMQQLIQRNPEISHMLNNPDIMRQTLELARNPAMMQEMMRNQDRALSNLESIPGGYNALRRMYTDIQ
ANPQMQQLIQRNPEISH.LNNPDIMRQTLE.ARNPAMMQEMMRNQD.ALSNLESIPGGYNALRRMYTDIQ
RetrocopyANPQMQQLIQRNPEISHLLNNPDIMRQTLEIARNPAMMQEMMRNQDLALSNLESIPGGYNALRRMYTDIQ
ParentalEPMLSAAQEQFGGNPFASLVSNTSSGEGSQPSRTENRDPLPNPWAPQASQSSSASSSTTSAVGGTGGSAA
EPML.AAQEQFGGNPFAS..S...SGEG.QPSRTENRDPLPNPWAP.....SSA..STTS......GS..
RetrocopyEPMLNAAQEQFGGNPFASVGSSSTSGEGTQPSRTENRDPLPNPWAPPPATQSSATTSTTSS----SGSGS
ParentalSGTSGQSSSAPNLGPGVGASMFNTPGMQSLLQQITENPQLMQNMLSAPYMRSMMQSLSQNPDLAAQMMLN
...S..............AS.F.TPGMQSLLQQITENPQL.QNMLSAPYMRSMMQSLSQNPDLAAQMMLN
RetrocopyGSSSSSATGNTVAAANYVASIFSTPGMQSLLQQITENPQLIQNMLSAPYMRSMMQSLSQNPDLAAQMMLN
ParentalNPLFAGNPQLQEQMRQQLPTFLQQMQNPDTLSAMSNPRAMQALLQIQQGLQTLATEAPGLIPGFTPGLGA
.P.F..NPQLQEQMR.QLP.FLQQMQNPDTLSAMSNPRAMQAL.QIQQGLQTLATEAPGLIP.FTPG.G.
RetrocopySPVFTANPQLQEQMRPQLPAFLQQMQNPDTLSAMSNPRAMQALMQIQQGLQTLATEAPGLIPSFTPGVG-
ParentalLGSTGGSSGSNG
.G..G...G..G
RetrocopyVGVLGTAIGPVG

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






RNA-Seq - click to see more details

(Hint: click retrocopy or parental gene accession number on the plot's legend, to show / hide expression level values)

Expression validation based on RNA-Seq data:
Library Retrocopy expression Parental gene expression
SRP012049_cerebellum 77 .28 RPM 117 .39 RPM
SRP017611_brain 68 .20 RPM 137 .98 RPM
SRP017611_kidney 18 .42 RPM 62 .54 RPM
SRP017611_liver 9 .79 RPM 73 .38 RPM

ChIP-Seq - click to see more details

Canis familiaris was not studied using ChIP-Seq data.

EST - click to see more details

1 EST(s) were mapped to retro_cfam_236 retrocopy
EST ID Start End Identity Match Mis-match Score
DN368349 47861537 47862213 99.9 675 0 673

TSS - click to see more details

Canis familiaris was not studied using FANTOM5 data.

Lab - click to see more details

retro_cfam_236 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_cfam_236 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 20 parental genes, and 23 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG000000148272 retrocopies
retro_btau_1087, retro_btau_188,
Canis familiaris ENSCAFG00000001435 1 retrocopy
retro_cfam_236 ,
Callithrix jacchus ENSCJAG000000036092 retrocopies
retro_cjac_3977, retro_cjac_4067,
Cavia porcellus ENSCPOG000000048491 retrocopy
retro_cpor_113,
Dasypus novemcinctus ENSDNOG000000126871 retrocopy
retro_dnov_14,
Dipodomys ordii ENSDORG000000152661 retrocopy
retro_dord_680,
Equus caballus ENSECAG000000191101 retrocopy
retro_ecab_1063,
Echinops telfairi ENSETEG000000028221 retrocopy
retro_etel_39,
Felis catus ENSFCAG000000150491 retrocopy
retro_fcat_83,
Homo sapiens ENSG000001350181 retrocopy
retro_hsap_58,
Myotis lucifugus ENSMLUG000000020362 retrocopies
retro_mluc_1774, retro_mluc_33,
Mustela putorius furoENSMPUG000000020281 retrocopy
retro_mputfur_55,
Mus musculus ENSMUSG000000053121 retrocopy
retro_mmus_83,
Nomascus leucogenys ENSNLEG000000033061 retrocopy
retro_nleu_31,
Otolemur garnettii ENSOGAG000000129471 retrocopy
retro_ogar_276,
Pongo abelii ENSPPYG000000193231 retrocopy
retro_pabe_87,
Pan troglodytes ENSPTRG000000210551 retrocopy
retro_ptro_93,
Rattus norvegicus ENSRNOG000000192821 retrocopy
retro_rnor_339,
Ictidomys tridecemlineatus ENSSTOG000000134621 retrocopy
retro_itri_157,
Tursiops truncatus ENSTTRG000000046961 retrocopy
retro_ttru_1475,


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