RetrogeneDB ID:

retro_cjac_1737

Retrocopy
location
Organism:Marmoset (Callithrix jacchus)
Coordinates:19:19649897..19651543(-)
Located in intron of:ENSCJAG00000004930
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:WBP11
Ensembl ID:ENSCJAG00000021611
Aliases:None
Description:WW domain binding protein 11 [Source:HGNC Symbol;Acc:16461]


Retrocopy-Parental alignment summary:






>retro_cjac_1737
ATGGGACAGAGATCTACATTATCCACTAAGAGTGGAAAATTTATGAACCCCACAGACCAAGCCTGAAAGGAAGCCCAGAA
GAGAGAATTAAAGAACAAAAATAAGCGCACGATGGTTCAAGCTGCAGTTTTAAAGATGAAGGATCCAAAACAGATTATCT
GAGACATGGAGAAACTGGATGAAATGGAGTTTAACCCAGTGCAACAGCCACAATTAAATGAGAAAGTACTGAAAAGACCA
GCGTAAAAAGCTGCGTGAAACCTCTGAATGTATTCTACGACTCTATGAAAAAGAGAATCCAGATATCTACAAAGAATTGA
GAGCGCTAGAAGTAGAGTAAGAACAGAAGAGGGCTCAACTTAGTCAGTATTTTGATGCTGTCAAGAATGCTCAGCGCGTG
GAAGTGGAGAGTATTCCTTTGCCAGATATGCCACATGCTCCTTCCAACATTTTGATCCAGGACATTCCACTTCCTAGCTC
CCAGCCACCCTCCACCCTAAAGAAAACCTCAGGCCATGGACCTCCAATTTGGGCAGTTTCTATCCTTCCTCTTCTTGGAG
ATGGTGTTCCACATTTGCCCCCTGGCAGAAAACCTCCGGGCCCTCCTCTGGTCCACCTCCTCCAAGTTGTGCAGATGTAT
GGCCGTAAAGTTGGTTTTGCCCTAGATCTTACCCCTCGTAGGCGAGATGAAGACGTGTTATATAGTCCTGAACTTGCCCA
GCGAGGCCATGATGATGATGTTTCTAGCACCAGTGAAGATGATGGCTATCCTGAGGACATGGATCAAGATAAGCATGTTG
ACAGTACTGATGGCAGTGACACTGACAAATCAGATGGAGAAAGTGAGGGGGATGAATTTGTGCACTGTGATGATGGTGAA
AGAGAACAATGAAGAAAAGAAGGTGTGAGTGTACGGTTTACAGATATGCCTGGAAAATCAAGGAAGAAAAAAAAAGAATA
GGAAGGAACTGACTCCTCTTCAAGCCATGATGCTATGTATGGCAGGTCAAGAAATCCCTGAGGGATGGGAAGCAGAGGAA
TTTTCAGAAAATAATGATGATGACTCTGATGACTCTGAAGCAGAAAAGCAACCACAAAAACAACATAGAGAGGAATCCCA
TTCCGATGGCACATCCTTCCTCCTTCTCAGATACAAGCATTCCCAAGCCAGGACCACCACCTCTTGGACCACCACCTGCT
CCACCATTACGGCCTTCTGGGCCACCTACAGGCCTTCCTCCTGGTCCATCTCCCAGAGCTCCTCCATTCCTGAGGCCACC
TGGAATGCCAGGACTCCAAGGGCCTTTACCCCGACTTTTACCTCCAGGACCACCAACAGGCTGACCCGCTGGCCCTCCCT
GAGGTCCACCTCCAGGTCTGCCTCCTGGCACCCCTCCTTGAGGACCCCCACCAAGGATACCTCCCCCTGCACCTCCAGGT
ATTGCTCCTCCACCTCGTACTGGCATGATGCACCCACCTTTGGTGCCTCCCCTTGGACCTGCCCCCACCACCCTGGGCTT
TTCCCACCAGCTCCCTTGCCAAACCCTGGGGTTTTAAGTGCCCCACCCAACTTGATTCAGAGACCCAAGGTGGTTGATAC
GAGTGCAGCCACCATTGAGAAGAAAGCCACAGCAACCATCAGCGCC

ORF - retro_cjac_1737 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 68.37 %
Parental protein coverage: 85.96 %
Number of stop codons detected: 7
Number of frameshifts detected 6


Retrocopy - Parental Gene Alignment:

ParentalMGRRSTSSTKSGKFMNPTDQAGKEARKRELKKNKKQRMMVRAAVLKMKDPKQIIRDMEKLDEMEFNPVQQ
MG.RST.STKSGKFMNPTDQA.KEA.KRELK.NK..R.MV.AAVLKMKDPKQII.DMEKLDEMEFNPVQQ
RetrocopyMGQRSTLSTKSGKFMNPTDQA*KEAQKRELK-NKNKRTMVQAAVLKMKDPKQII*DMEKLDEMEFNPVQQ
ParentalPQLNEKVLK-DKRKKLRETFERILRLYEKENPDIYKELRKLEVEYEQKRAQLSQYFDAVKNAQHVEVESI
PQLNEKVLK.D.RKKLRET.E.ILRLYEKENPDIYKELR.LEVE.EQKRAQLSQYFDAVKNAQ.VEVESI
RetrocopyPQLNEKVLK>DQRKKLRETSECILRLYEKENPDIYKELRALEVE*EQKRAQLSQYFDAVKNAQRVEVESI
ParentalPLPDMPHAPSNILIQDIPLPGAQPPSILKKTSAYGPPTRAVSILPLLGHGVPRLPPGRKPPGPPP-GPPP
PLPDMPHAPSNILIQDIPLP..QPPS.LKKTS..GPP..AVSILPLLG.GVP.LPPGRKPPG.PP...PP
RetrocopyPLPDMPHAPSNILIQDIPLPSSQPPSTLKKTSGHGPPIWAVSILPLLGDGVPHLPPGRKPPG-PP<SGPP
ParentalP-QVVQMYGRKVGFALDLPPRRRDEDMLYSPELAQRGHDDDISSTSEDDGYPEDMDQDKHDDSTDDSDTD
P.QVVQMYGRKVGFALDL.PRRRDED.LYSPELAQRGHDDD.SSTSEDDGYPEDMDQDKH.DSTD.SDTD
RetrocopyP>QVVQMYGRKVGFALDLTPRRRDEDVLYSPELAQRGHDDDVSSTSEDDGYPEDMDQDKHVDSTDGSDTD
ParentalKSDGESEGDEFVHRDDGERDNNEEKKSGLSVRFADMPGKSRK-KKKNMKELTPLQAMMLRMAGQEIPEEG
KSDGESEGDEFVH.DDGER......K.G.SVRF.DMPGKSRK.KKKN.KELTPLQAMML.MAGQEIP.EG
RetrocopyKSDGESEGDEFVHCDDGERE--Q*RKEGVSVRFTDMPGKSRK>KKKNRKELTPLQAMMLCMAGQEIP-EG
ParentalREVEEFSEDD-DEDDSDDSEAEKQSQKQHKEESHSDGTS-TASSQQQAPPQSVPP-SQIQAPPM-PGPPP
.E.EEFSE...........E...Q.Q..H.EESHSDGTS....S....P....PP.....APP..P..PP
RetrocopyWEAEEFSENNXXXXXXXXAEKQPQKQ--HREESHSDGTS>SSFSDTSIPKPGPPPLGPPPAPPLRPSGPP
ParentalLGPPPAPPLRPPGPPTGLPPGPP--PGAPPFLRPPGMPGLRGPLPRLLPP-GPPPGRPP-GPPPGPPPGL
.G.PP.P...P..PP...PPG.P...G..P.L.PPG.P......P...PP.G.PPG.PP.GPPP..PP..
RetrocopyTGLPPGP--SPRAPPFLRPPGMPGLQGPLPRLLPPGPPTG*PAGPP*GPPPGLPPGTPP*GPPPRIPPPA
ParentalPPGPPPRGPPPRLPPPAPPGIPPPRPGMM-RPPLVPPLGPAPPGLF--PPAPLPNPGVLSAPPNLIQRPK
PPG..P...PPR.....PP..PP..P.....P.L.PP.....PG....PP.....P.V.......I....
RetrocopyPPGIAP---PPRTGMMHPPLVPPLGPAPT<HPGLFPPAPLPNPGVLSAPPNLIQRPKVVDTSAATIEKKA
ParentalADDTSA
....SA
RetrocopyTATISA

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
SRP051959_colon 1 .53 RPM 15 .95 RPM
SRP051959_heart 1 .74 RPM 20 .54 RPM
SRP051959_kidney 1 .29 RPM 20 .90 RPM
SRP051959_liver 0 .95 RPM 15 .44 RPM
SRP051959_lung 2 .08 RPM 24 .86 RPM
SRP051959_lymph_node 4 .16 RPM 26 .03 RPM
SRP051959_skeletal_muscle 1 .64 RPM 24 .35 RPM
SRP051959_spleen 2 .04 RPM 22 .44 RPM

ChIP-Seq - click to see more details

Callithrix jacchus was not studied using ChIP-Seq data.

EST - click to see more details

No EST(s) were mapped for retro_cjac_1737 retrocopy.

TSS - click to see more details

Callithrix jacchus was not studied using FANTOM5 data.

Lab - click to see more details

retro_cjac_1737 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_cjac_1737 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 22 parental genes, and 34 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG000000147591 retrocopy
retro_btau_20,
Canis familiaris ENSCAFG000000129262 retrocopies
retro_cfam_1369, retro_cfam_1911,
Callithrix jacchus ENSCJAG00000021611 1 retrocopy
retro_cjac_1737 ,
Homo sapiens ENSG000000844632 retrocopies
retro_hsap_1878, retro_hsap_4719,
Gorilla gorilla ENSGGOG000000044483 retrocopies
retro_ggor_1375, retro_ggor_1711, retro_ggor_2932,
Macropus eugenii ENSMEUG000000139711 retrocopy
retro_meug_1952,
Myotis lucifugus ENSMLUG000000152161 retrocopy
retro_mluc_1074,
Macaca mulatta ENSMMUG000000192991 retrocopy
retro_mmul_1329,
Monodelphis domestica ENSMODG000000179491 retrocopy
retro_mdom_143,
Mustela putorius furoENSMPUG000000116191 retrocopy
retro_mputfur_280,
Mus musculus ENSMUSG000000302161 retrocopy
retro_mmus_2740,
Nomascus leucogenys ENSNLEG000000039261 retrocopy
retro_nleu_2651,
Oryctolagus cuniculus ENSOCUG000000171771 retrocopy
retro_ocun_974,
Otolemur garnettii ENSOGAG000000105181 retrocopy
retro_ogar_207,
Ochotona princeps ENSOPRG000000150083 retrocopies
retro_opri_107, retro_opri_1159, retro_opri_678,
Pongo abelii ENSPPYG000000043233 retrocopies
retro_pabe_1558, retro_pabe_2099, retro_pabe_3663,
Pan troglodytes ENSPTRG000000047243 retrocopies
retro_ptro_1260, retro_ptro_1637, retro_ptro_3136,
Rattus norvegicus ENSRNOG000000055053 retrocopies
retro_rnor_1287, retro_rnor_2726, retro_rnor_741,
Rattus norvegicus ENSRNOG000000495931 retrocopy
retro_rnor_740,
Sorex araneus ENSSARG000000070851 retrocopy
retro_sara_753,
Sarcophilus harrisii ENSSHAG000000166491 retrocopy
retro_shar_81,
Tupaia belangeri ENSTBEG000000033941 retrocopy
retro_tbel_2213,




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