RetrogeneDB ID:

retro_cjac_2734

Retrocopy
location
Organism:Marmoset (Callithrix jacchus)
Coordinates:6:71230010..71230876(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:USP12P1
Ensembl ID:ENSCJAG00000019344
Aliases:USP12P1, USP12
Description:Ubiquitin carboxyl-terminal hydrolase [Source:UniProtKB/TrEMBL;Acc:F7FL24]


Retrocopy-Parental alignment summary:






>retro_cjac_2734
AGAAGGAAAATTTTAATGTGCTCAGCAACTTTCTTCCATAGTATAGCCACACAGAAGGGAAAGGTTGAAGTAATATCTCC
TGAGAAGTTCAAAACAAGATTAGAGAAAGAAAATGAGCTTTTCTGCATGCAACAAGATGCCCATGGATTCTTAAATTACC
TACTAAATACAATTGCTGATACTTTACAAGAAGAAAGAAGTCAGGATAAACAAAATGATTGCTTACCAAATGGTAATATT
GACACTGAAAATAACAACAGCACTCCGGACACAATGTAGGTTCATGAAATTTTTCAGGAACAATTAACTAATAAAACCAG
ATGTCTTACTTGTGAAACTATAACAGCAAAGATGAAGATTTTAAGGAACTTCCTGTGATGTAGAACAAAATGTATCAGTT
ATTCACTGTTTAAGTGTTTTTTAGCAAGACAGAAACTCTGTGAAGTGAATACAGACATTACTGTGAAGAGTGTTGTAGCA
AACAGGAAGCACACAAATGAATGAATGCTTAAAAACCACCCATGATTCCAGCTCTACATCTGAAAAGATTTAAATGTGTG
GATTAACTTCACTGATGTATGCAACTTTCTTACTAGGTAGTTTTTCATTTAGAACTTTGTCTGTGTAACACTTCCGATGA
TGCAAGTAATCCAGACAGAATCCAGGGCCTTGTGGGTATTATGATTCAATGTGGAAGTGGTCACAGGTAAGGCCATTATA
TTGCAATTTAATGAGTTAAGAAATCAAGATTTCTGCTTGTTGTTTGATGACACTGTAGAAAAAAAAATGAATTGCACAAG
TTACTGAAGAATTCCATGGATTGAAATCAGATTATCTTGAAGAACTCAGAGTCTGGTTACATTCTG

ORF - retro_cjac_2734 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 67.23 %
Parental protein coverage: 77.84 %
Number of stop codons detected: 10
Number of frameshifts detected 6


Retrocopy - Parental Gene Alignment:

ParentalKESLLTCLADLFHSIATQKKKVGVIPPKKFITRLRKENELFDNYMQQDAHEFLNYLLNTIADILQEERKQ
....L.C.A..FHSIATQK.KV.VI.P.KF.TRL.KENELF...MQQDAH.FLNYLLNTIAD.LQEER.Q
RetrocopyRRKILMCSATFFHSIATQKGKVEVISPEKFKTRLEKENELF--CMQQDAHGFLNYLLNTIADTLQEERSQ
ParentalEKQNGRLPNGNIDNENNNSTPDPTWVHEIFQGTLTNETRCLTCETI-SSKDEDFLDL-SVDVEQNTSITH
.KQN..LPNGNID.ENNNSTPD...VHEIFQ..LTN.TRCLTCETI..SKDEDF..L.S.DVEQN.S..H
RetrocopyDKQNDCLPNGNIDTENNNSTPDTM*VHEIFQEQLTNKTRCLTCETI<NSKDEDFKEL<SCDVEQNVSVIH
ParentalCLR-GFSNTETLCSEYKYYCEECRSKQEAHKRMKVKKLPMILALHLKRFKYMDQLHRYTKLSYRVVFPLE
CL...FS.TETL.SEY..YCEEC.SKQEAHK.M...K.PMI.ALHLKRFK..D.LH....LSY.VVF.LE
RetrocopyCLS>FFSKTETL*SEYRHYCEECCSKQEAHK*MNA*KPPMIPALHLKRFKCVD*LH*CMQLSY*VVFHLE
ParentalLRLFNTSGDATNPDRMYDLVAVVVHCGSGPNRGHYIAI--VKSHDF-WLLFDDDIVEKID-AQAIEEFYG
L.L.NTS.DA.NPDR...LV.....CGSG...GHYIAI..VK...F..LLFDD....K...AQ..EEF.G
RetrocopyLCLCNTSDDASNPDRIQGLVGIMIQCGSGHR*GHYIAI**VKKSRF>CLLFDDTVEKKMN>AQVTEEFHG
ParentalLTSD-ISKNSESGYIL
L.SD.I.KNSESGYIL
RetrocopyLKSD>ILKNSESGYIL

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






(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 0 .29 RPM 58 .04 RPM
SRP051959_heart 0 .49 RPM 52 .78 RPM
SRP051959_kidney 0 .42 RPM 54 .11 RPM
SRP051959_liver 0 .26 RPM 39 .70 RPM
SRP051959_lung 0 .46 RPM 46 .79 RPM
SRP051959_lymph_node 0 .41 RPM 30 .82 RPM
SRP051959_skeletal_muscle 0 .13 RPM 30 .44 RPM
SRP051959_spleen 0 .44 RPM 35 .32 RPM
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_2734 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_2734 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_cjac_2734 has 5 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Homo sapiens retro_hsap_2328
Pan troglodytes retro_ptro_1701
Gorilla gorilla retro_ggor_1767
Pongo abelii retro_pabe_2110
Macaca mulatta retro_mmul_937

Parental genes homology:
Parental genes homology involve 9 parental genes, and 24 retrocopies.

Species Parental gene accession Retrocopies number
Callithrix jacchus ENSCJAG00000019344 5 retrocopies
Homo sapiens ENSG000001524844 retrocopies
Microcebus murinus ENSMICG000000062692 retrocopies
Macaca mulatta ENSMMUG000000214251 retrocopy
Nomascus leucogenys ENSNLEG000000003233 retrocopies
Otolemur garnettii ENSOGAG000000306391 retrocopy
Pongo abelii ENSPPYG000000052323 retrocopies
Pan troglodytes ENSPTRG000000057273 retrocopies
Tupaia belangeri ENSTBEG000000129602 retrocopies



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