RetrogeneDB ID: retro_ptro_1542

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 2A:53398255..53399713(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: CRTC1
• Ensembl ID: ENSPTRG00000010719
• Aliases: None
• Description: CREB regulated transcription coactivator 1 [Source:HGNC Symbol;Acc:16062]

Sequence

>retro_ptro_1542
ACCCCCTTCCAATCCTTGGGCCTGGACACCAGCCTGACTACCAGGCACCATGGGCTGGTGAACAGGGTGTACCGGGAACG
CGGCCGGCTACGCTCCCAGCACTGCCTGCACCTGTCAAAGGACAAACACGGATAGCAGGCCAACAGCTGCCCATATGGCA
CCGTGTACCTCTTGCCACCCACGGACACCAGCTGGAGAAGGACCAATTCTGACTCGCCCTGCACCAGAGCACAATGACGC
CCATGCAGCCAGAATCCTTTACTAGTGGGTCCCAGGACGTGCACCAGAAAAAAGTCTTACTATTAACAGTCCCAGGAATG
GAAGAGACCATATCAGAGGCAGACAAAAACCTTTCCAAGCAAGCGTGGGGAAACCAAGAAGACTGGATCCAGGACCAAGT
CCTGCGCGGAATCAACGAATCAACATCTTCCCGTCCGCCGACCAGGAAAACACTACAGCCCTGATCTCCGCCACTCACAA
TACTGGGGGCTCCCTGCAGCGCCTGACCAGCATCCACTTCCCTTCCCCGCTCGACTCCGAGGAGCCCACCTTCCCCGCAC
TCAGTAGCTCCAGCAGCACCGACAACGTCTCGGCCAACCTGATGCACCTGGGCATCAGCGGCGCCGGCCGGGGGATGAGC
ACACTCGGCTCCCCTCCGCTGCACCGTCCAGCCGGCGTCAGCCCCCCTGTCCCTGAGCACAGAGACGGGGCATCAGCAGT
CATCGCCCACTCTGTCCCCGCTGTCATACATCACTCAGGTCATACATCATGAATGCCCTGTCTCTGGAGCAGCAGCTACC
CTACGCCTTCTTCACCCAGACGGACTCCCAGCAGCCGCTGCCGCAGCCCCAGCCTCCGCCGCCCCCTTAGCCTGGGTCTC
AGCCGCCGCCAACCCCACCGCCCCTACAGGCGCCCATCCGCCTGCCCCCCCGGCAGCCCCTGTTGCCCAGCACCAACCTG
AATCGTGGGCCACAGCCGCCCCCGCTCGCGGTCACGGTACCGTCCTCTCTCTTCCAATCCCCACGGAGAATCCCGGCCAA
CAGTCGATGGGGATCGACATCGCCTCGGCGCCGCCTCTGCAGCAGTAGCGGCACTAGCCCCGGCTCCTCGGCCAACCAGT
CTCCCACCTCGCCAGTCTCCAATGAAGGCTTCTCCCCAGGGAGCTCCCCGCAACACACTTCCACTCTGGGCAGCGTGTTT
GGGGACGCGTACTATGAGCAGCAGATGGCGTTCAGGCAGGCCAATGCTCCGTCCCACCAGCTGGAGCAGTTCAACATGAT
GGAGAACGCCATCAGCTCCCTATACAACAGGGGCTCCACGCTCAACTACTCGCAGGCGGTCATGATAGGCCTCACCCACA
GCCACGGGAGCCTGCTGAACTCGCAGCAGCTGGGCTACACCAGCCACAGTGGCATCCCCAACATCATCCTCATAGTGACA
GGACAGTCTCCCCCGGCC

Alignment

ORF - retro_ptro_1542 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.52 %
• Parental protein coverage: 75.54 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 7

Retrocopy - Parental Gene Alignment:

Parental  TPFQSSGLDTSRTTRHHGLVDRVYRERGRLGSPHRRPLSVDKHGRQADSCPYGTVYLSPPADTSWRRTNS
          TPFQS.GLDTS.TTRHHGLV.RVYRERGRL.S.H...LS.DKHG.QA.SCPYGTVYL.PP.DTSWRRTNS
Retrocopy TPFQSLGLDTSLTTRHHGLVNRVYRERGRLRSQHCLHLSKDKHG*QANSCPYGTVYLLPPTDTSWRRTNS

Parental  DS-ALHQSTMTPTQPESFSSGSQDVHQKRVLLLTVPGMEETTSEADKNLSKQAW-DTKKTGSR-PKSCEV
          DS.ALHQSTMTP.QPESF.SGSQDVHQK.VLLLTVPGMEET.SEADKNLSKQAW..TKKTGSR.P.....
Retrocopy DS<ALHQSTMTPMQPESFTSGSQDVHQKKVLLLTVPGMEETISEADKNLSKQAW>ETKKTGSR>PSPARN

Parental  PGINIFPSADQENTTALIPATHNTGGSLPDLTNIHFPSPLPTPLDPEEPTFPALSSSSSTGNLAANLTHL
          ..INIFPSADQENTTALI.ATHNTGGSL..LT.IHF....P.PLD.EEPTFPALSSSSST.N..ANL.HL
Retrocopy QRINIFPSADQENTTALISATHNTGGSLQRLTSIHF----PSPLDSEEPTFPALSSSSSTDNVSANLMHL

Parental  GIGGAGQGMSTPGSSPQHRPAGVSP-LSLSTEARRQQASPTLSPLSPITQAV-AMDALSLEQQLPYAFFT
          GI.GAG.GMST.GS.P.HRPAGVSP.LSLSTE...QQ.SPTLSPLS.ITQ....M.ALSLEQQLPYAFFT
Retrocopy GISGAGRGMSTLGSPPLHRPAGVSP>LSLSTETGHQQSSPTLSPLSYITQVI>IMNALSLEQQLPYAFFT

Parental  QAGSQQPPPQPQPPPPPPPASQQPPPPPPPQAPVRLPPGGPLLPSASLTRGPQPPPLAVTVPSSLPQSP-
          Q..SQQP.PQPQPPPPP.P.SQ.PP.PPP.QAP.RLPP..PLLPS..L.RGPQPPPLAVTVPSSL.QSP.
Retrocopy QTDSQQPLPQPQPPPPP*PGSQPPPTPPPLQAPIRLPPRQPLLPSTNLNRGPQPPPLAVTVPSSLFQSP<

Parental  PENPGQPSMGIDIASAPALQQYR-TSAGSPANQSPTSPVSNQGFSPGSSPQHTSTLGSVFGDAYYEQQMA
          .ENPGQ.SMGIDIASAP.LQQ.R.TS.GS.ANQSPTSPVSN.GFSPGSSPQHTSTLGSVFGDAYYEQQMA
Retrocopy TENPGQQSMGIDIASAPPLQQ*R>TSPGSSANQSPTSPVSNEGFSPGSSPQHTSTLGSVFGDAYYEQQMA

Parental  ARQANALSHQLEQFNMMENAISSSSLYSPGSTLNYSQAAMMGLTGSHGSLPDSQQLGYASHSGIPNIILT
          .RQANA.SHQLEQFNMMENAI..SSLY..GSTLNYSQA.M.GLT.SHGSL..SQQLGY.SHSGIPNIIL.
Retrocopy FRQANAPSHQLEQFNMMENAI--SSLYNRGSTLNYSQAVMIGLTHSHGSLLNSQQLGYTSHSGIPNIILI

Parental  VTGESPPS
          VTG.SPP.
Retrocopy VTGQSPPA

Legend:

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

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP007412_brain_prefrontal_cortex	0.02 RPM	116.15 RPM
SRP007412_cerebellum	0.07 RPM	155.87 RPM
SRP007412_heart	0.00 RPM	4.28 RPM
SRP007412_kidney	0.00 RPM	19.59 RPM
SRP007412_liver	0.03 RPM	11.03 RPM
SRP007412_testis	0.53 RPM	6.11 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_1542 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_1542 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_1542 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2102

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000007421	3 retrocopies	retro_cjac_2682, retro_cjac_595, retro_cjac_666,
Homo sapiens	ENSG00000105662	1 retrocopy	retro_hsap_2102,
Pan troglodytes	ENSPTRG00000010719	1 retrocopy	retro_ptro_1542 ,