RetrogeneDB ID: retro_ptro_876

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 13:75152372..75153904(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CTAGE5
• Ensembl ID: ENSPTRG00000006297
• Aliases: None
• Description: None

Sequence

>retro_ptro_876
AATCACATCAAGACTCTGACTGGACACTTGCTAAAGATGAAAGATCAGGCTGCTATGCTTGAAGAAGACACAACGGATGA
TGATAACTTGGAATTAGAAGTGAACAGTCAATCAGAAAATGGTGCTTATTTAGATGATCCTCCAAAAGGAGCTTTGAAGA
AACTGATTCATGCTGCTAAGTTAAATGTTTCTTTAAAAACCTTAGAAGGAGAAAGAAACCACATTATTATTCAGTTATCT
GAAGTGGACAAAACAAAGGAAGAGCTTACAGAGCATATTAAAAATCTTCAGACTCAACAAGCATCTTTGCAGTCAGAAAA
CATATATTTTGAAAGAATCAGAAGCTTCAACAGAAACTTAAAATAATGACTGAATTATATCAAGAAAATGAAATGACACT
CCACAGGAAATTGACAATAGAGGAAAATTACCGGATAGAGGAAGAAGAGAAGCTTTCTAAAGTGGAAGAAAAGATCAGCC
ATGCCACTGAAGAGCTGGAGACCTATAGAAAGCTAGCCAAAGATCTTGAAGAAGAATTGGAGAGAACTGTTCATTTTTAT
CAAAAGCAGGTTATTTCCTACGAGAAAAAAGGACATGATAATTGGTTGGCAGCTCGGACTGCTGAAAGAAACCTCAATGA
TTTAAGGAAAGAAAATGCTCACAACAAACAAAAATTAACTGAAACAGAGTTTAAATTTGAAGTTTTAGAAAAAGATCCTA
ATGCACTTGATGTTTCAAATACAGCATCTGGCAGAGAGCATTCCCCATATGGTCCCTCACCATTGGGTCGGCCTTCATCT
GAAACGAGGACTTTTCTCTCTCCTCAAACTTTGTTGGAGGATCCACTCAGACTCTCACCTGTGCTTCCAGGGAGAGGAGG
GAGAAGCCCAAGCGGCCGAGAGAATCCTCTGGACCATCAGATTACCAATGAAAGATGAGAACCAAGCTGTGATAGGTTAA
CTGATCCTCACAGAGCTCCTTCTGACACTGGGTCCCTGTCATCTCCATGGGAACAGGACCATAGGATGATGTTTCCTCCA
CCAGGACAATCATATCCTGATTCAGCTCTTCCTCCACAAAGGGAAGACAGATTTTATTCTAATTCTGATAGACTGCCTGG
ACCAGCAGAACTCAGAAGTTTTAATATGCCTTCTTTGGATAAAATGGATGGGTCAATGCCTTCAGAAATGGAATCCACTA
GAAATGATGCCGAAGACGATCCTGGTAGTTTAAATGTGCCTGATTCATCTCTCCCTGCTGAAAATGAAGCAACTGGCCCC
GGCTTTATTCCTCCACCTCTTGCTCCAATCAGTGGTCCATTGTTTCCAGTGGACACAAGGTGCCCGTTCATGAGAAGAGG
ACCCCTTTTCCCCCAACCTCCTCCAGGAACGATGTTTGGAGCTTCACGAGGTTATTTTCCACCAAGGGATTTCCCAGGTC
CACCACATGCTCCATTTGCAATGAGAAACATCTGTCCACCAAGGGGTTTACCTGCTTACTTTCATCCAAGACCTGGATTT
TACCCCAACCCC

Alignment

ORF - retro_ptro_876 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.85 %
• Parental protein coverage: 63.68 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  SHIKTLTERLLKMKDWAAMLGEDITDDDNLELEMNSESENGAYLDNPPKGALKKLIHAAKLNASLKTLEG
          .HIKTLT..LLKMKD.AAML.ED.TDDDNLELE.NS.SENGAYLD.PPKGALKKLIHAAKLN.SLKTLEG
Retrocopy NHIKTLTGHLLKMKDQAAMLEEDTTDDDNLELEVNSQSENGAYLDDPPKGALKKLIHAAKLNVSLKTLEG

Parental  ERNQIYIQLSEVDKTKEELTEHIKNLQTEQASLQSENTHFENENQKLQQKLK-VMTELYQENEMKLHRKL
          ERN.I.IQLSEVDKTKEELTEHIKNLQT.QASLQSEN..FE.........LK..MTELYQENEM.LHRKL
Retrocopy ERNHIIIQLSEVDKTKEELTEHIKNLQTQQASLQSENIYFE-RIRSFNRNLK<IMTELYQENEMTLHRKL

Parental  TVEENYRLEKEEKLSKVDEKISHATEELETYRKRAKDLEEELERTIHSYQGQIISHEKKAHDNWLAARNA
          T.EENYR.E.EEKLSKV.EKISHATEELETYRK.AKDLEEELERT.H.YQ.Q.IS.EKK.HDNWLAAR.A
Retrocopy TIEENYRIEEEEKLSKVEEKISHATEELETYRKLAKDLEEELERTVHFYQKQVISYEKKGHDNWLAARTA

Parental  ERNLNDLRKENAHNRQKLTETELKFELLEKDPYALDVPNTAFGREHSPYGPSPLGWPSSETRAFLSPPTL
          ERNLNDLRKENAHN.QKLTETE.KFE.LEKDP.ALDV.NTA.GREHSPYGPSPLG.PSSETR.FLSP.TL
Retrocopy ERNLNDLRKENAHNKQKLTETEFKFEVLEKDPNALDVSNTASGREHSPYGPSPLGRPSSETRTFLSPQTL

Parental  LEGPLRLSPLLPGGGGRGSRGPGNPLDHQITNERGESSCDRLTDPHRAPSDTGSLSPPWDQDRRMMFPPP
          LE.PLRLSP.LPG.GGR...G..NPLDHQITNER.E.SCDRLTDPHRAPSDTGSLS.PW.QD.RMMFPPP
Retrocopy LEDPLRLSPVLPGRGGRSPSGRENPLDHQITNER*EPSCDRLTDPHRAPSDTGSLSSPWEQDHRMMFPPP

Parental  GQSYPDSALPPQRQDRFCSNSGRLSGPAELRSFNMPSLDKMDGSMPSEMESSRNDTKDDLGNLNVPDSSL
          GQSYPDSALPPQR.DRF.SNS.RL.GPAELRSFNMPSLDKMDGSMPSEMES.RND..DD.G.LNVPDSSL
Retrocopy GQSYPDSALPPQREDRFYSNSDRLPGPAELRSFNMPSLDKMDGSMPSEMESTRNDAEDDPGSLNVPDSSL

Parental  PAENEATGPGFVPPPLAPIRGPLFPVDTRGAFLRRGPPFPPPPPGAMFGASRDYFPPRDFPGPPPAPFAM
          PAENEATGPGF.PPPLAPI.GPLFPVDTR..F.RRGP.FP.PPPG.MFGASR.YFPPRDFPGPP.APFAM
Retrocopy PAENEATGPGFIPPPLAPISGPLFPVDTRCPFMRRGPLFPQPPPGTMFGASRGYFPPRDFPGPPHAPFAM

Parental  RNVYPPRGFPPYLPPRPGFFPPP
          RN..PPRG.P.Y..PRPGF.P.P
Retrocopy RNICPPRGLPAYFHPRPGFYPNP

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	0.00 RPM	10.90 RPM
SRP007412_cerebellum	0.00 RPM	9.86 RPM
SRP007412_heart	0.03 RPM	11.02 RPM
SRP007412_kidney	0.00 RPM	54.97 RPM
SRP007412_liver	0.00 RPM	36.20 RPM
SRP007412_testis	3.79 RPM	20.44 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_876 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_876 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_876 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pongo abelii	retro_pabe_1060

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 41 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000016105	4 retrocopies	retro_cjac_1747, retro_cjac_2711, retro_cjac_3217, retro_cjac_921,
Cavia porcellus	ENSCPOG00000026514	2 retrocopies	retro_cpor_189, retro_cpor_727,
Homo sapiens	ENSG00000150527	3 retrocopies	retro_hsap_1201, retro_hsap_3691, retro_hsap_640,
Homo sapiens	ENSG00000258941	1 retrocopy	retro_hsap_78,
Gorilla gorilla	ENSGGOG00000011990	1 retrocopy	retro_ggor_936,
Nomascus leucogenys	ENSNLEG00000004121	10 retrocopies	retro_nleu_1218, retro_nleu_1690, retro_nleu_2087, retro_nleu_2103, retro_nleu_2148, retro_nleu_2600, retro_nleu_2951, retro_nleu_3017, retro_nleu_3077, retro_nleu_688,
Pongo abelii	ENSPPYG00000005768	9 retrocopies	retro_pabe_1001, retro_pabe_1002, retro_pabe_1007, retro_pabe_1055, retro_pabe_1060, retro_pabe_1588, retro_pabe_2119, retro_pabe_29, retro_pabe_3024,
Pan troglodytes	ENSPTRG00000006297	10 retrocopies	retro_ptro_1286, retro_ptro_1712, retro_ptro_2503, retro_ptro_2580, retro_ptro_2880, retro_ptro_466, retro_ptro_821, retro_ptro_826, retro_ptro_868, retro_ptro_876 ,
Ictidomys tridecemlineatus	ENSSTOG00000015890	1 retrocopy	retro_itri_95,