RetrogeneDB ID: retro_ptro_2880

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 9:28002639..28004252(-)
• 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_2880
TCTGAACGCTTGCTAAAAATGAAAGATCAGGCTGCTATGCTTGGAGAAGACATAACGGATGATGGTAACTTGGAATTAGA
AATGAACAGTGAATCGGAAAATGGTGCTTACTTAGATAATCCTCCAAAAGGAGCTCTGAAGAAACTGATTTATGCTGCTA
AGTTAAATGCTTCTTTAAAAACCTTAGAAGGAGAAAGAAACCAAATTTATAGTCAGTTATCTGAAGTTGATAAAACAAAG
GAAGAGCTTACAGAGCATATTAAAAATCTTCAGACTGAACAAGCATCTTTGCAGTCAGAAAACATACATTTTGAAAGTGA
GAATCAGAAGCTTCAACAAAAACTTAAAGTAATGATTGAATTTTATCAAGAAAATGAAATGAAACTCCAGAGGAAATTAA
CAGTAGATGAAAATTACCGGTTAGAGAAGGAAGAAAAACTTTCTAAAGTACACGAAAAGATTAACCATGCCACTGAAGAG
TTGGAGACCTATAGAAAGTGAGCCAAAGATCTTGAAGAAGAGTTGGCGAGAACTATTCATTCTTATCAAGGATGGATTAT
TTCCCACGAGAAGAAAGCACATAATAATTGGTTGGCAGCTTGGACTGCTGAAAGAAACCTCAATGATTTAAGGAAAGAAA
GTGCTCACAACAGACAAAAATTAACTGAAGCAGAGTTTAAATTTGAACTTTTAGAAAAAGATCCTTATGCACTTCATGTT
CCAAATACAGCATTTGGCAGAGAGCATTCCCCATATGGTCCCTCACCATTGGGTCGGCCTTTATCCTAAACAAGAGCTTT
TCTCTATCCTCCAACTTTGTTGGAGGGCCCACTGAGACTCTCATCTTTGCTAATAGGAGGAGGAGGAGGAAGAGGCTCAA
GAGGTCCAGGGAATCCTCTGGACCATCAGATTACCAATGAAAGAGGAGAATCAAAATGTGACAGGTTAACCAGTCCTCAC
AGGGCTTCTTCTGACACTGGGTCCCTGTCACCTCCATGGGAACAGGACCGTAGGATGATGTTTCTTCCACCAGGACAATC
ATATCCTGATTCAGCTCTTCCTCCACAAAGGCAAGACAGGTTTTATTCTAATTCTGGCACACTGTCTGGACCAGCAGAAC
TCAGAAGGTTTAATATGACTTCTTTGGATAAAGTGGATGGGTCAATGCTTTCAGAAATGGAATCCAGTAGAAATGATACC
GAAGATGACCTTGGTAATTTAAGTGTGCCTGATTCATCTCTCCCCGCTGAAAATGAAGCTACTGGCCCTGACTTTTCTCC
TCCACCTCTTGCTCCAATCAGAGGTCCATCGTTTCCGGGGGATACAAGGGGCCTGTTCATGAGAAGAGGACCTCCTTCCC
CCCACCTCCTCCAGGAACCATGTTTGGAGCTTCTCAAGATTATTTTCCACCAAGGGATTTCCCAGATCCACCACATGCTC
CATTTGCAATGAGAAATGTCTATCCAGCGAGGGGTTTCCTCCTTACCTTCCCCCAAAACCTGGATTTTTCCCCATAAACC
CCACATTCTGAAGGTAGAAGTGAGTTCCCTGCAGGGCTGATTCTGCCTTCAAATGAGCCTGCTACTGAACTTCCAGAACC
ACAGCAAGAAACC

Alignment

ORF - retro_ptro_2880 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.35 %
• Parental protein coverage: 66.79 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  TERLLKMKDWAAMLGEDITDDDNLELEMNSESENGAYLDNPPKGALKKLIHAAKLNASLKTLEGERNQIY
          .ERLLKMKD.AAMLGEDITDD.NLELEMNSESENGAYLDNPPKGALKKLI.AAKLNASLKTLEGERNQIY
Retrocopy SERLLKMKDQAAMLGEDITDDGNLELEMNSESENGAYLDNPPKGALKKLIYAAKLNASLKTLEGERNQIY

Parental  IQLSEVDKTKEELTEHIKNLQTEQASLQSENTHFENENQKLQQKLKVMTELYQENEMKLHRKLTVEENYR
          .QLSEVDKTKEELTEHIKNLQTEQASLQSEN.HFE.ENQKLQQKLKVM.E.YQENEMKL.RKLTV.ENYR
Retrocopy SQLSEVDKTKEELTEHIKNLQTEQASLQSENIHFESENQKLQQKLKVMIEFYQENEMKLQRKLTVDENYR

Parental  LEKEEKLSKVDEKISHATEELETYRKRAKDLEEELERTIHSYQGQIISHEKKAHDNWLAARNAERNLNDL
          LEKEEKLSKV.EKI.HATEELETYRK.AKDLEEEL.RTIHSYQG.IISHEKKAH.NWLAA..AERNLNDL
Retrocopy LEKEEKLSKVHEKINHATEELETYRK*AKDLEEELARTIHSYQGWIISHEKKAHNNWLAAWTAERNLNDL

Parental  RKENAHNRQKLTETELKFELLEKDPYALDVPNTAFGREHSPYGPSPLGWPSSETRAFLSPPTLLEGPLRL
          RKE.AHNRQKLTE.E.KFELLEKDPYAL.VPNTAFGREHSPYGPSPLG.P.S.TRAFL.PPTLLEGPLRL
Retrocopy RKESAHNRQKLTEAEFKFELLEKDPYALHVPNTAFGREHSPYGPSPLGRPLS*TRAFLYPPTLLEGPLRL

Parental  SPLL-PGGGGRGSRGPGNPLDHQITNERGESSCDRLTDPHRAPSDTGSLSPPWDQDRRMMFPPPGQSYPD
          S.LL..GGGGRGSRGPGNPLDHQITNERGES.CDRLT.PHRA.SDTGSLSPPW.QDRRMMF.PPGQSYPD
Retrocopy SSLLIGGGGGRGSRGPGNPLDHQITNERGESKCDRLTSPHRASSDTGSLSPPWEQDRRMMFLPPGQSYPD

Parental  SALPPQRQDRFCSNSGRLSGPAELRSFNMPSLDKMDGSMPSEMESSRNDTKDDLGNLNVPDSSLPAENEA
          SALPPQRQDRF.SNSG.LSGPAELR.FNM.SLDK.DGSM.SEMESSRNDT.DDLGNL.VPDSSLPAENEA
Retrocopy SALPPQRQDRFYSNSGTLSGPAELRRFNMTSLDKVDGSMLSEMESSRNDTEDDLGNLSVPDSSLPAENEA

Parental  TGPGFVPPPLAPIRGPLFPVDTRGAFLRRGPP-FPPPPPGAMFGASRDYFPPRDFPGPPPAPFAMRNVYP
          TGP.F.PPPLAPIRGP.FP.DTRG.F.RRGPP.FPPPPPG.MFGAS.DYFPPRDFP.PP.APFAMRNVYP
Retrocopy TGPDFSPPPLAPIRGPSFPGDTRGLFMRRGPP<FPPPPPGTMFGASQDYFPPRDFPDPPHAPFAMRNVYP

Parental  PR-GFPPYLPPRPGFFPP-PPHSEGRSEFPSGLIPPSNEPATEHPEPQQET
          .R.GFPPYLPP.PGFFP...PHSEGRSEFP.GLI.PSNEPATE.PEPQQET
Retrocopy AR<GFPPYLPPKPGFFPI>TPHSEGRSEFPAGLILPSNEPATELPEPQQET

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	0.04 RPM	10.90 RPM
SRP007412_cerebellum	0.04 RPM	9.86 RPM
SRP007412_heart	0.00 RPM	11.02 RPM
SRP007412_kidney	0.05 RPM	54.97 RPM
SRP007412_liver	0.03 RPM	36.20 RPM
SRP007412_testis	0.00 RPM	20.44 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_2880 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2880 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2880 has 0 orthologous retrocopies within eutheria group .

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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,