RetrogeneDB ID:

retro_cjac_2964

Retrocopy
location
Organism:Marmoset (Callithrix jacchus)
Coordinates:7:17378899..17380437(-)
Located in intron of:ENSCJAG00000008267
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:KPNA7
Ensembl ID:ENSCJAG00000015943
Aliases:None
Description:Importin subunit alpha [Source:UniProtKB/TrEMBL;Acc:F7I329]


Retrocopy-Parental alignment summary:






>retro_cjac_2964
ATGCTGAGCTTAGATGCTCCAGAAGAGAGGCTGAGAAAATTTAAGTACCGAGGCAAAGATGCATCTCTGAGGCGACAGCA
GAGGATGGCAGCCAGCCTGAAGCCCTGAAAGGCTGAGAAAGATGAACAGACCTTAAAGAGAAGGAATATCACCAGCTTCT
GCCCTGACACACCTTCTGAAAAAACAGCCAAAGGGGTGGCGGTCAGCCTCACTCTGGGTGAAATAATCCAAGGTGTGAAT
AGCTCAGATCCAGCCCTGTGTTTCCAGGCCACCCAGACAGCCAGAAAAATGCTATCGCAGGAAAAGAACTCCCCTCTGAA
ATTGGTCGTCCAAGCGGGCCTCATTCTCAGGATGGTGGAGTTCCTGAAGTCATCTCTTTCCCTCTTCTTGCAGTTAAAGG
CCTCCTGGGCCCTCACCAACATTGCTGCAGGGACTTCGGAGCAGACTCGAGCTGTGGTAGAAGGGGGAGCCATCCAGCCC
TTGATCGCGCTCCTGTCTCTCCCCAACCTGGCTGTGTGTGAACAGGCAGTGTGGGCTCTTGGTGGTAACATAGCTGGTGA
TGGCCCAGAGTTCAGAGATAAGATCATCTCAAGCAATGGTATCCCACATCTGCTGGCCTTGATTTCACACACCCTCCAAT
CACATTCCTGCAGAATATCACGTGGACCTTATCGAACCTTTGCGGAAACAAGAACCCGTACCCTTGCGATACTGCGGTGA
AGCAGATACTGCCGTCCCTCCTCCACCTCCGACAGCACCATGACAGTGAGGTTCTCTCCGACGCCTGCTGGCACTACCTC
ACTGACAGCTGCAGCAAGCGCATCGGACAAGTGTTTGACACGGGATTCCTGCCCTGGCTGGTGGCGCTCTTGATCAGCTT
AGAGCTCAACGTCTTGACCCCTTCTCTCCGCTCCGTGGGGAACATTGTCATGGGCACAGATGAACAGACGCAGAGAGCCA
TAGACACGGTCATACTGAACGTGCTCCCCTAGCTCCTCCAGCACAACAAGCCCTCTATTCAGAAGGAGGCAGCCTGGGCC
CTGAGCAACGTGGCGGCAGGACCCTGTCACCACATCCAGAAGCTGCTTGCCTACAACGTCTTGCCTCTCTTGGTGGCTGT
GCTAAAACATGGAGAATTTAAAGTCCAGAAAGAGGCTATCTGGACAGTGGCAAACTTTGTAACGGGGCCACCATGGTTCA
GCTGATCCAGCTCGTCCATTCTGGGATCCTGGATCCCCTGGTGAATCTGCTCACCTCCCGAGATGTTAAAATTGTTCATC
ATCCTCGATGTCATCTCTTTCATCCTCAAGGTGGCAGAGAAACTGTCTGAGAAGGAAAACGTGTGTCTTCTGATAGAAGA
ACTCGGTGGAATTGATAGAATTGAAGCTTTACAACTGCATGAGAACCGTCAGATTAGCCTGTCAGCTTTGAACATCATGG
AGAAGCACTTTAGCGAGGAAGAAGAGAGCCTAATGTTACTGAGCCAAGTCGTAGACCAAGATTGTGAATTTATAAACAGT
GACTGCTTAGCAAAAAAA

ORF - retro_cjac_2964 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 86.15 %
Parental protein coverage: 100.0 %
Number of stop codons detected: 2
Number of frameshifts detected: 3


Retrocopy - Parental Gene Alignment:

ParentalMPSLDAPEERLRKFKYRGKDASLRRQQRMAVSLKLRKAKKDEQTLKRRNITSFCPDTPSEKTAKGVTVSL
M.SLDAPEERLRKFKYRGKDASLRRQQRMA.SLK..KA.KDEQTLKRRNITSFCPDTPSEKTAKGV.VSL
RetrocopyMLSLDAPEERLRKFKYRGKDASLRRQQRMAASLKP*KAEKDEQTLKRRNITSFCPDTPSEKTAKGVAVSL
ParentalTLGEIIQGVNSSDPALCFQATQTARKMLSQENNPPLKLVVDAGLIPRMVEFLKSSLYPCLQFEAAWALTN
TLGEIIQGVNSSDPALCFQATQTARKMLSQE.N.PLKLVV.AGLI.RMVEFLKSSL...LQ..A.WALTN
RetrocopyTLGEIIQGVNSSDPALCFQATQTARKMLSQEKNSPLKLVVQAGLILRMVEFLKSSLSLFLQLKASWALTN
ParentalIAAGTSEQTRAVVEGGAIQPLIALLSSPNLAVCEQAVWAL-GNIAGDGPEFRDKIISSNAIPHLLALISH
IAAGTSEQTRAVVEGGAIQPLIALLS.PNLAVCEQAVWAL.GNIAGDGPEFRDKIISSN.IPHLLALISH
RetrocopyIAAGTSEQTRAVVEGGAIQPLIALLSLPNLAVCEQAVWALGGNIAGDGPEFRDKIISSNGIPHLLALISH
ParentalTL-PVSIFFFLFIFLXXXCRNKNPDPCDAAVKQILPALLHLLQHHDTEVLSDACWALSYLTDSCSKRIGQ
TL.P..........L...C.NKNP.PCD.AVKQILP.LLHL.QHHD.EVLSDACW...YLTDSCSKRIGQ
RetrocopyTL<PITFLQNITWTLSNLCGNKNPYPCDTAVKQILPSLLHLRQHHDSEVLSDACW--HYLTDSCSKRIGQ
ParentalVVDTGVLPRLVALLNSSELNVLTPSLRTVGNIVTGTDEQTQRAIDTGILNVLPQLLQHNKPSIQKEAAWA
V.DTG.LP.LVALL.S.ELNVLTPSLR.VGNIV.GTDEQTQRAIDT.ILNVLP.LLQHNKPSIQKEAAWA
RetrocopyVFDTGFLPWLVALLISLELNVLTPSLRSVGNIVMGTDEQTQRAIDTVILNVLP*LLQHNKPSIQKEAAWA
ParentalLSNVAAGPCHHIQQLLAYDVLPPLVAVLKHGDFKVQKEAIWTVANFVM-GATLDQLIQLVHSGILEPLVN
LSNVAAGPCHHIQ.LLAY.VLP.LVAVLKHG.FKVQKEAIWTVANFV..GAT..QLIQLVHSGIL.PLVN
RetrocopyLSNVAAGPCHHIQKLLAYNVLPLLVAVLKHGEFKVQKEAIWTVANFVT<GATMVQLIQLVHSGILDPLVN
ParentalLLTAPDVKIV-LIILDVISFILEAAEKLSEKENVCLLIEELGGIDRIEALQLHENRQISLSALNIIEKHF
LLT..DVKIV..I..DVISFIL..AEKLSEKENVCLLIEELGGIDRIEALQLHENRQISLSALNI.EKHF
RetrocopyLLTSRDVKIV>IIL-DVISFILKVAEKLSEKENVCLLIEELGGIDRIEALQLHENRQISLSALNIMEKHF
ParentalSEKEEESLMLLSQVVDQDCEFINCDCLATK
SE.EEESLMLLSQVVDQDCEFIN.DCLA.K
RetrocopySE-EEESLMLLSQVVDQDCEFINSDCLAKK

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 0 .00 RPM 0 .02 RPM
SRP051959_heart 0 .00 RPM 0 .00 RPM
SRP051959_kidney 0 .00 RPM 0 .00 RPM
SRP051959_liver 0 .00 RPM 0 .00 RPM
SRP051959_lung 0 .00 RPM 0 .05 RPM
SRP051959_lymph_node 0 .00 RPM 0 .02 RPM
SRP051959_skeletal_muscle 0 .02 RPM 0 .00 RPM
SRP051959_spleen 0 .00 RPM 0 .00 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_2964 retrocopy.

TSS - click to see more details

Callithrix jacchus was not studied using FANTOM5 data.

Lab - click to see more details

retro_cjac_2964 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_cjac_2964 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 14 parental genes, and 23 retrocopies.

Species Parental gene accession Retrocopies number
Canis familiaris ENSCAFG000000151252 retrocopies
retro_cfam_459, retro_cfam_861,
Choloepus hoffmanni ENSCHOG000000042431 retrocopy
retro_chof_805,
Callithrix jacchus ENSCJAG00000015943 1 retrocopy
retro_cjac_2964 ,
Equus caballus ENSECAG000000005541 retrocopy
retro_ecab_981,
Echinops telfairi ENSETEG000000000961 retrocopy
retro_etel_1548,
Homo sapiens ENSG000001854671 retrocopy
retro_hsap_3337,
Mus musculus ENSMUSG000000387702 retrocopies
retro_mmus_2844, retro_mmus_3301,
Nomascus leucogenys ENSNLEG000000108271 retrocopy
retro_nleu_1680,
Otolemur garnettii ENSOGAG000000311063 retrocopies
retro_ogar_1289, retro_ogar_3237, retro_ogar_353,
Ochotona princeps ENSOPRG000000154342 retrocopies
retro_opri_1101, retro_opri_118,
Pongo abelii ENSPPYG000000173691 retrocopy
retro_pabe_2750,
Pan troglodytes ENSPTRG000000194462 retrocopies
retro_ptro_102, retro_ptro_2142,
Tupaia belangeri ENSTBEG000000090073 retrocopies
retro_tbel_1475, retro_tbel_3862, retro_tbel_3962,
Tursiops truncatus ENSTTRG000000029982 retrocopies
retro_ttru_1426, retro_ttru_430,


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