RetrogeneDB ID:

retro_cjac_1254

Retrocopy
location
Organism:Marmoset (Callithrix jacchus)
Coordinates:14:13145969..13147620(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:PPP1R12A
Ensembl ID:ENSCJAG00000019271
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_cjac_1254
GCAGCAGCTCGAAAGGAAGAACGGATCGTGCTTAGAGATGCCAGGCAGTGGCTAAATAGTGGTCATATAAATGATGTCCG
ACATGCAGAATCTGGAGGTACAGCACTTCACGTTGCAGCTGCTAAAGGCTATACGGAAGTTTTAAAACTTTTAATACAGG
CAGGATATGATACTAATATTAAAGACTATGATGGCTGGACACCTCTTCATGCTGCAGCTCATTGGGGTAAAGAAGAAGCA
TGTCGAATTTTAGTGGACAATCTCTGTGATGAGATGGTCAACAAAGTGGGCCAAACAGCCTTTGATGTAGCAGATGAAGA
CATTTTAGGATATTTAGAAGAGCTGCAAAAGAAACAAAATCTGCTCCATAGTGAAAAACGGGATAAGAAATCTCCACTAA
TTGAATCTACAGCAAATATGGACAATAATCAGTCACAGAAGACCTTTAAAAACAAAGAGACATTGATTATTGAGCCAGAG
AAAAATGCATCCCATATTGAATCTCTGGAACAAGAAAATGTTGATGAAGAAGAAGAACGAAAGAAAGATGAGTCTAGCTG
CTCTAGGGAAGAAGATGAGGAAGATGACTTGGAATCAGAAGCTGAAACAGATAAGACAAAACCCTGACTTCTGTAACTAA
TGTCAACACTTCTAGTACACAAGCAGCTACTGTAGCTGTTACAACACCTACTGTGTTATCAGGTCAAGCAACACCTACAT
CGCCTATTAAAAAGTTTCCAACTACAGCTACAAAAATTTCTCCCAAAGAAGAAGAGAGAAAAGATGAGTCTCCTGCCACT
TGGAGGTTAGGACTTAGAAAGGCCGGCAGTTATGGCACACTTGCTGAAATCACAGCATCAAAAGAGGGTCAGAAAGAAAA
AGATACTGCAGGTGTTACACGTTCAGCTTCGAGTCCCAGACTTTCCTCCTCTTTGGATAATAAAGAAAAGGAGAAAGATA
GTAAAGGAACTAGGCTTGCATATGTCGCGCCTACAATACCAAGATGACTAGTCAGTACATCTGACGTTGAAGAGAAAGAA
AACAGAGATTCTTCAAGTTTGCGAACAAGTAGTTCATATACAAGGAGAAAATGGGAAGATGATCTTAAAAAAATAGCTCA
ATTAATGAAGGATCAACTTATCATAAAAGTTGCTCCTTTGGTAGAAGACAAGATGATTTGATTAGTTCCAGTGTTCCAAG
CACCACGTCAACACCAACAGTTACCTCTGCAGCTGGGCTTCAGAAAAGTCTGCTTTCCAGCACAAGCACTGCTACAAAGA
TTACAATCAGTTCTTCCTCAGCAGGCACACAAAGCAGTACCTCAAATCGTTTGTGGGCTGAGGATAGTATAGAAAAAGAA
AAGGACAGTGTTCCTACATCAGTGACCATTCCCATTGCTCCAACTGTTGTAAATGCTGCAGCTTCTACCACAACCCTGAC
TACAACTACTGCTGGCACTGTCTCCTCCACAACAGAGGTCAGGGAGAGACACAGATCATACCCTACTCCTGTTAGGGATG
AAGAGTCTGAATCCCAAAGAGAAGCAAGATCTAGACAAGCAAGGCAATCTAGAAGATCAACACAGGGAGTGACATTAACT
GATCTTCAAGAAGCTGGGAAAACTATAGGAAGAAGTCGTTCTACCAGAACC

ORF - retro_cjac_1254 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 94.4 %
Parental protein coverage: 53.59 %
Number of stop codons detected: 1
Number of frameshifts detected 2


Retrocopy - Parental Gene Alignment:

ParentalAARKEEERIMLRDARQWLNSGHINDVRHAKSGGTALHVAAAKGYTEVLKLLIQAGYDVNIKDYDGWTPLH
AA...EERI.LRDARQWLNSGHINDVRHA.SGGTALHVAAAKGYTEVLKLLIQAGYD.NIKDYDGWTPLH
RetrocopyAAARKEERIVLRDARQWLNSGHINDVRHAESGGTALHVAAAKGYTEVLKLLIQAGYDTNIKDYDGWTPLH
ParentalAAAHWGKEEACRILVDNLCDMEMVNKVGQTAFDVADEDILGYLEELQKKQNLLHSEKRDKKSPLIESTAN
AAAHWGKEEACRILVDNLCD.EMVNKVGQTAFDVADEDILGYLEELQKKQNLLHSEKRDKKSPLIESTAN
RetrocopyAAAHWGKEEACRILVDNLCD-EMVNKVGQTAFDVADEDILGYLEELQKKQNLLHSEKRDKKSPLIESTAN
ParentalMDNNQSQKTFKNKETLIIEPEKNASRIESLEQEKVDEEEEGKKDESSCSSEEDEEDDSESEAETDKTKP-
MDNNQSQKTFKNKETLIIEPEKNAS.IESLEQE.VDEEEE.KKDESSCS.EEDEEDD.ESEAETDKTKP.
RetrocopyMDNNQSQKTFKNKETLIIEPEKNASHIESLEQENVDEEEERKKDESSCSREEDEEDDLESEAETDKTKP<
ParentalLASVTNVNTSSTQAATVAVTTPTVSSGQATPTSPIKKFPTTATKISPKEEERKDESPATWRLGLRKTGSY
L.SVTNVNTSSTQAATVAVTTPTV.SGQATPTSPIKKFPTTATKISPKEEERKDESPATWRLGLRK.GSY
RetrocopyLTSVTNVNTSSTQAATVAVTTPTVLSGQATPTSPIKKFPTTATKISPKEEERKDESPATWRLGLRKAGSY
ParentalGALAEITASKEGQKEKDTAGVTRSASSPRLSSSLDNKEKEKDSKGTRLAYVAPTIPRRLASTSDIEEKEN
G.LAEITASKEGQKEKDTAGVTRSASSPRLSSSLDNKEKEKDSKGTRLAYVAPTIPR.L.STSD.EEKEN
RetrocopyGTLAEITASKEGQKEKDTAGVTRSASSPRLSSSLDNKEKEKDSKGTRLAYVAPTIPR*LVSTSDVEEKEN
ParentalRDSSSLRTSSSYTRRKWEDDLK-KNSSINEGSTYHKSCSFGRRQDDLISSSVPSTTSTPTVTSAAGLQKS
RDSSSLRTSSSYTRRKWEDDLK.KNSSINEGSTYHKSCSFGRRQDDLISSSVPSTTSTPTVTSAAGLQKS
RetrocopyRDSSSLRTSSSYTRRKWEDDLK<KNSSINEGSTYHKSCSFGRRQDDLISSSVPSTTSTPTVTSAAGLQKS
ParentalLLSSTSTTTKITTGSSSAGTQSSTSNRLWAEDSTEKEKDNVPTSVTIPVAPTVVNAAASTTTLTTTTAGT
LLSSTST.TKIT..SSSAGTQSSTSNRLWAEDS.EKEKD.VPTSVTIP.APTVVNAAASTTTLTTTTAGT
RetrocopyLLSSTSTATKITISSSSAGTQSSTSNRLWAEDSIEKEKDSVPTSVTIPIAPTVVNAAASTTTLTTTTAGT
ParentalVSSTTEVRERRRSYLTPVRDEESESQRKARSRQARQSRRSTQGVTLTDLQEAEKTIGRSRSTRT
VSSTTEVRER.RSY.TPVRDEESESQR.ARSRQARQSRRSTQGVTLTDLQEA.KTIGRSRSTRT
RetrocopyVSSTTEVRERHRSYPTPVRDEESESQREARSRQARQSRRSTQGVTLTDLQEAGKTIGRSRSTRT

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 .09 RPM 84 .82 RPM
SRP051959_heart 0 .09 RPM 127 .17 RPM
SRP051959_kidney 0 .04 RPM 63 .72 RPM
SRP051959_liver 0 .02 RPM 26 .86 RPM
SRP051959_lung 0 .07 RPM 113 .74 RPM
SRP051959_lymph_node 0 .11 RPM 101 .53 RPM
SRP051959_skeletal_muscle 0 .04 RPM 40 .09 RPM
SRP051959_spleen 0 .06 RPM 99 .24 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_1254 retrocopy.

TSS - click to see more details

Callithrix jacchus was not studied using FANTOM5 data.

Lab - click to see more details

retro_cjac_1254 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_cjac_1254 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 1 parental gene, and 1 retrocopy.

Species Parental gene accession Retrocopies number
Callithrix jacchus ENSCJAG00000019271 1 retrocopy
retro_cjac_1254 ,


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