RetrogeneDB ID:

retro_cpor_113

Retrocopy
location
Organism:Guinea Pig (Cavia porcellus)
Coordinates:scaffold_170:750091..751963(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSCPOG00000013496
Aliases:None
Status:KNOWN_PROTEIN_CODING
Parental gene
information
Parental gene summary:
Parental gene symbol:UBQLN1
Ensembl ID:ENSCPOG00000004849
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_cpor_113
ATGGCTGAGAATGGCGAGAGCAGCGGCCCCCCGCGCCCCTCCCGCGGTCCTGCTGCGGCCCAAGGTTCAGCCGCTGCCCC
AGCTGAGCCCAAAATCATCAAAGTAACTGTAAAGACCCCCAAAGAGAAAGAGGAGTTTGCGGTGCCCGAGAACAGCTCAG
TCCAGCAGTTTAAGGAAGCGATTTCTAAGCGCTTCAAATCCCAAACCGATCAGCTAGTGTTGATTTTTGCCGGAAAGATC
TTAAAAGATCAAGATACCTTGCTCCAGCATGGCATCCATGATGGGCTGACTGTTCACCTAGTCATCAAAAGCCAGAACAG
ACCTCAGGGCCAGTCTACCACACAGCCTAGCAATGCCGCGGGAACTAATACTACCACGGCGTCAACTCCCAGGAGTAACT
CCACACCTATTTCCACAAATAGCCCGTTTGGGTTGGGGAGCCTGGGAGGACTTGCAGGCCTTAGTAGCCTGGGTTTGAGC
TCCACCAATTTCTCCGAGCTCCAGAACCAGATGCAGCAGCAGCTCATGGCCAGCCCTGAGATGATGATCCAAATCATGGA
AAATCCCTTTGTTCAGAGCATGCTTTCAAATCCTGATCTGATGAGGCAGCTCATTATGGCCAATCCACAAATGCAACAAT
TGATTCAGAGAAACCCAGAAATCAGTCACCTGCTCAACAACCCAGATATAATGAGGCAGACTCTTGAAATCGCCAGGAAT
CCAGCCATGATGCAAGAGATGATGAGAAATCAAGACCTGGCTCTCAGCAATCTCGAAAGCATCCCAGGTGGCTACAATGC
TTTAAGGCGCATGTACACTGACATTCAAGAACCCATGCTGAATGCTGCACAAGAGCAGTTTGGGGGTAATCCATTTGCCT
CAGTGGGAGGCAGTTCCTCCTCTGGAGAAGGTACTCAGCCTTCCCGCACAGAAAATCGTGATCCATTGCCCAATCCATGG
GCCCCACCACCAACGACTCAGAATTCTGCCACTACCAGCACTACCACAAGCAGTGGCAATGGATCTGGCAGTAGCTCCAG
TAATGCTGCTGGAAGCACTGTGGCTGCAGCTAATTATGTGGCTAGCATCTTCAGTACCCCAGGAATGCAGAGCCTGCTGC
AACAGATAACTGAAAACCCTCAGTTGATTCAGAATATGCTGTCTGCACCCTACATGAGAAGCATGATGCAGTCCTTGAGC
CAGAATCCGGATTTGGCTGCACAGATGATGCTGAATAGCCCGCTGTTTACTGCAAATCCTCAGCTGCAGGAGCAGATGCG
GCCTCAGCTCCCAGCTTTCTTGCAGCAGATGCAGAATCCAGACACACTATCAGCCATGTCCAACCCAAGAGCAATGCAGG
CTTTAATGCAGATACAGCAGGGGCTACAGACATTAGCCACTGAAGCACCTGGCCTGATTCCAAGCTTCACTCCAGGTGTG
GGTGTGGGGGTGCTGGGAACCACCATAGGTCCTGTAGGCCCAGTCACTCCCATAGGCCCTATAGGCCCTATAGTCCCTTT
TACCCCAATAGGCCCCATTGGGCCCATAGGACCCACTGGCCCTGCAGGACCCACTGGCTCCACAGGCTCTGGTGGCCCCA
CTGCACCCACTGTGTCCAGTTCTGCACCCAGTGAAACCACAATTGCAACATCAGAATCTGGAACCAACCAGCAATTCATT
CAGCAGATGGTGCAGGCTCTGGCTGGAGCAAATCCTCCACAGCTGCCGAATCCAGAAGTCAGATTTCAGCAACAACTGGA
ACAGCTCAACGCCATGGGGTTCTTAAACCGTGAGGCAAACTTGCAGGCCCTAATAGCAACAGGAGGCGACATCAATGCAG
CCATTGAGAGGCTGCTGGGCTCCCAGCAATCT

ORF - retro_cpor_113 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 77.34 %
Parental protein coverage: 85.23 %
Number of stop codons detected: 0
Number of frameshifts detected: 0


Retrocopy - Parental Gene Alignment:

ParentalMAESGESGGPPGSQDNAATAEDAGAPSAAASTEPKIMKVTVKTPKEKEEFAVPENSSVQQFKEEISKRFK
MAE.GES.GPP......A.A......SAAA..EPKI.KVTVKTPKEKEEFAVPENSSVQQFKE.ISKRFK
RetrocopyMAENGESSGPPRPSRGPAAAQG----SAAAPAEPKIIKVTVKTPKEKEEFAVPENSSVQQFKEAISKRFK
ParentalSHTDQLVLIFAGKILKDQDTLSQHGIHDGLTVHLVIKTQNRSQDHSAQQTNNPGG-NVSPSSTSNSNSTS
S.TDQLVLIFAGKILKDQDTL.QHGIHDGLTVHLVIK.QNR.Q..S..Q..N..G.N....ST..SNST.
RetrocopySQTDQLVLIFAGKILKDQDTLLQHGIHDGLTVHLVIKSQNRPQGQSTTQPSNAAGTNTTTASTPRSNSTP
ParentalGSATGNPFGLGGLGGLAGLSSLGLNTTNFSELQSQMQRQLLSNPEMMVQIMENPFVQSMLSNPDLMRQLI
.S.T..PFGLG.LGGLAGLSSLGL..TNFSELQ.QMQ.QL...PEMM.QIMENPFVQSMLSNPDLMRQLI
RetrocopyIS-TNSPFGLGSLGGLAGLSSLGLSSTNFSELQNQMQQQLMASPEMMIQIMENPFVQSMLSNPDLMRQLI
ParentalMANPQMQQLIQRNPEISHMLNNPDIMRQTLELARNPAMMQEMMRNQDRALSNLESIPGGYNALRRMYTDI
MANPQMQQLIQRNPEISH.LNNPDIMRQTLE.ARNPAMMQEMMRNQD.ALSNLESIPGGYNALRRMYTDI
RetrocopyMANPQMQQLIQRNPEISHLLNNPDIMRQTLEIARNPAMMQEMMRNQDLALSNLESIPGGYNALRRMYTDI
ParentalQEPMLSAAQEQFGGNPFASLVSNTSSGEGSQPSRTENRDPLPNPWAPQTSQTSSASSGTTNTVSGTAGSA
QEPML.AAQEQFGGNPFAS.....SSGEG.QPSRTENRDPLPNPWAP......SA...TT.......GS.
RetrocopyQEPMLNAAQEQFGGNPFASVGGSSSSGEGTQPSRTENRDPLPNPWAPPPTTQNSATTSTTTSSGNGSGSS
ParentalTSGTSGQSTTGPNLVPGVGASMFNTPGMQSLLQQITENPQLMQNMLSAPYMRSMMQSLSQNPDLAAQMML
.S...G......N.V....AS.F.TPGMQSLLQQITENPQL.QNMLSAPYMRSMMQSLSQNPDLAAQMML
RetrocopySSNAAGSTVAAANYV----ASIFSTPGMQSLLQQITENPQLIQNMLSAPYMRSMMQSLSQNPDLAAQMML
ParentalNNPLFAGNPQLQEQMRQQLPTFLQQMQNPDTLSAMSNPRAMQALLQIQQGLQTLATEAPGLIPGFTPGLG
N.PLF..NPQLQEQMR.QLP.FLQQMQNPDTLSAMSNPRAMQAL.QIQQGLQTLATEAPGLIP.FTPG.G
RetrocopyNSPLFTANPQLQEQMRPQLPAFLQQMQNPDTLSAMSNPRAMQALMQIQQGLQTLATEAPGLIPSFTPGVG
ParentalTLGSTGSSPGTNG
..G..G...G..G
Retrocopy-VGVLGTTIGPVG

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
SRP017611_brain 89 .96 RPM 121 .01 RPM
SRP017611_kidney 29 .42 RPM 165 .09 RPM
SRP017611_liver 17 .11 RPM 189 .30 RPM
SRP040447_lung 29 .46 RPM 102 .12 RPM
SRP040447_skeletal_muscle 26 .94 RPM 61 .60 RPM

ChIP-Seq - click to see more details

Cavia porcellus was not studied using ChIP-Seq data.

EST - click to see more details

No EST(s) were mapped for retro_cpor_113 retrocopy.

TSS - click to see more details

Cavia porcellus was not studied using FANTOM5 data.

Lab - click to see more details

retro_cpor_113 was not experimentally validated.

Retrocopy orthology:
Cavia porcellus does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.
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 ENSCAFG000000014351 retrocopy
retro_cfam_236,
Callithrix jacchus ENSCJAG000000036092 retrocopies
retro_cjac_3977, retro_cjac_4067,
Cavia porcellus ENSCPOG00000004849 1 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,


Copyright © RetrogeneDB 2014-2017