RetrogeneDB ID: retro_ptro_1712

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 2B:172063494..172065583(-)
• 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_1712
TATGAAGTACAGTCATCTTTAGAGGATGCCAGCTTTGAGAAGGCGGCAGCAGAAGCACGAAGTTTGGAGGCAACCTGTGA
AAAGCTGAACAGGTCCAATTCTGAACTTGAGGATGAAATCCTCTGTCTAGAAATAGAGTTAAAAGAAGAGAAATCTAAAC
ATTCTCAACAAGATGAACTGATGGCGGATATTTCAAAAAGGATACAATCTCTAGAAGATGAGTCAAAATCCCTCAAATCA
CAAATAGCTGAAGCCAGAATCATCTGCAAGATTCTTCCAGTGACTGAAGAACGACGGGCGATAGCAATAAAAGATGCTTT
GAGTGAAAATTCTCAACTTCAGGAAAGCCAGAAACAGCTTTTGCAAGAAGCTGAAGTATGGAAAGAACAAGTGAGTGAAC
TTAATAAACAGAAAATAACATTTGAAGACTCCAAAGTGTACGCAGAACAAGTTCTAAATGATAAAGAAAATCACAACAAG
ACTCTGACTGGACAGTTGCTAAAGATGAAAGATCAGGCTGCTATGCTTGAAGAAGACACAACGGATGATGATAACTTGGA
ATTAGAAGTGAACAGTCAATCGGAAAATGGTGCTTACTTAGATGATCCTCCCAAACGAGCTTTGAAGAAACTGATTCATG
CTACTAAGTTAAATGTTTCTTTAAAAGCCTTAGAAGGAGAAAGAAACCACATTATTATTCAGTTATCTGAAGTGGACAAA
ACAAAGGAAGAGCTTACAGAGCATATTAAAAATCTTCAGACTCAACAAGCATCTTTGCAGTCAGAAAACATATATTTTGA
AAGTGAGAATCAGAAGCTTCAACAGAAACTTAAAATAATGACTGAACTATATCAAGAAAATGAAATGACACTCCACAGGA
AATTGACAATAGAGGAAAATTACCGGATAGAGGAAGAAGAGAAGCTTTCTAAAGTGGAAGAAAAGATCAGCCATGTCACT
GAAGAGCTGGAGACCTATAGAAAGCTAGCCAAAGATCTTGAAGAAGAATTGGAGAGAACTGTTCATTTTTATCAAAAGCA
GGTTATTTCCTACGAGAAAAAAGGACGTAATAATTGGTTGGCAGCTCGGACTGCTGAAAGAAACCTCAATGATTTAAGGA
AAGAAAATGCTCACAACAAACAAAAATTAACTGAAACAGAGTTTAAATTTGAACTTTTAGAAAAAGATCCTAATGCACTT
GATGTTTCAAATACAGCATTTGGCAGAGAGCTTTCGCCATATGGTCCCTCACCATTGGGTCAGCCTTCATCTGAAACGAG
AGCTTTTCTCTCTCCTCAAACTTTGTTGGAGGATCCACTCAGACTCTCACCTGTGCTTCCAGGGGGAGGAGGAAGCCCAA
GCAGCCCAGGGAATCCTCTGGACCATCAGATTACCAATAAAAGAGGAGAACCAAGCTGTGATAGGTCAACTGATGCTCAC
AGGGCTCCTTCTGACACTGGGTCCCTCTCATCTCCATGGGAACAGGACCGTAGGATGATGTTTCCTCCACCAGGACAATC
ATATCCTGATTCAGCTCTTCCTCCACAAAGGGAAGACAGATTTTATTCTAATTCTGATAGACTGTCTGGACCAGCAGAAC
TCAGAAGTTTTAATATGCCTTGTTTGGATAAAATGGATGGGTCAATGCCTTCAGAAATGGAATCCACTAGAAATGATGCC
AAAGATGATCCTGGTCATTTAAATGTGCCTGATTCATCTCTCCCTGCTGAAAATGAAGCAACTGGCCCTGGCTTTATTCC
TCCACCTCTTGCTGCAATCAGTGGTCCATTGTTTCCAGTGGATACAAGGGGCCTGTTCACCAGAAGAGGACCTCCTTTCC
CCCAACCTCCTCCAGGAACCATGTTTGGAGCTTCACGAGGTTATTTTCTATCAAGGGATTTCCCAGGTCCACCACATGCT
CCATTTGCAATGAGAAACATCTATCCACCGAGGGGTTTACCTCCTTACTTTCATCCAAGACCTGGATTTTACCCCAACCC
CACATTCTGAAGGTAGAAGCAAGTTCCCTTGAGGGTTGATTCCACCTTCAAAGGAGCCTGCTACTGAACATCCAGAACCA
CAGCAAGAA

Alignment

ORF - retro_ptro_1712 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.57 %
• Parental protein coverage: 86.82 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  YEVESSLKDASFEKEATEAQSLEATCEKLNRSNSELEDEILCLEKELKEEKSKHSERDELMADISKRIQS
          YEV.SSL.DASFEK.A.EA.SLEATCEKLNRSNSELEDEILCLE.ELKEEKSKHS..DELMADISKRIQS
Retrocopy YEVQSSLEDASFEKAAAEARSLEATCEKLNRSNSELEDEILCLEIELKEEKSKHSQQDELMADISKRIQS

Parental  LEDESKSLKSQVAEAKMTFKIFQMNEERLKIAIKDALNENSQLQESQKQLLQEAEVWKEQVSELNKQKVT
          LEDESKSLKSQ.AEA....KI....EER..IAIKDAL.ENSQLQESQKQLLQEAEVWKEQVSELNKQK.T
Retrocopy LEDESKSLKSQIAEARIICKILPVTEERRAIAIKDALSENSQLQESQKQLLQEAEVWKEQVSELNKQKIT

Parental  FEDSEVHAEQVLNDKESHIKTLTERLLKMKDWAAMLGEDITDDDNLELEMNSESENGAYLDNPPKGALKK
          FEDS.V.AEQVLNDKE.H.KTLT..LLKMKD.AAML.ED.TDDDNLELE.NS.SENGAYLD.PPK.ALKK
Retrocopy FEDSKVYAEQVLNDKENHNKTLTGQLLKMKDQAAMLEEDTTDDDNLELEVNSQSENGAYLDDPPKRALKK

Parental  LIHAAKLNASLKTLEGERNQIYIQLSEVDKTKEELTEHIKNLQTEQASLQSENTHFENENQKLQQKLKVM
          LIHA.KLN.SLK.LEGERN.I.IQLSEVDKTKEELTEHIKNLQT.QASLQSEN..FE.ENQKLQQKLK.M
Retrocopy LIHATKLNVSLKALEGERNHIIIQLSEVDKTKEELTEHIKNLQTQQASLQSENIYFESENQKLQQKLKIM

Parental  TELYQENEMKLHRKLTVEENYRLEKEEKLSKVDEKISHATEELETYRKRAKDLEEELERTIHSYQGQIIS
          TELYQENEM.LHRKLT.EENYR.E.EEKLSKV.EKISH.TEELETYRK.AKDLEEELERT.H.YQ.Q.IS
Retrocopy TELYQENEMTLHRKLTIEENYRIEEEEKLSKVEEKISHVTEELETYRKLAKDLEEELERTVHFYQKQVIS

Parental  HEKKAHDNWLAARNAERNLNDLRKENAHNRQKLTETELKFELLEKDPYALDVPNTAFGREHSPYGPSPLG
          .EKK...NWLAAR.AERNLNDLRKENAHN.QKLTETE.KFELLEKDP.ALDV.NTAFGRE.SPYGPSPLG
Retrocopy YEKKGRNNWLAARTAERNLNDLRKENAHNKQKLTETEFKFELLEKDPNALDVSNTAFGRELSPYGPSPLG

Parental  WPSSETRAFLSPPTLLEGPLRLSPLLPGGGGRGSRGPGNPLDHQITNERGESSCDRLTDPHRAPSDTGSL
          .PSSETRAFLSP.TLLE.PLRLSP.LPGGGG..S..PGNPLDHQITN.RGE.SCDR.TD.HRAPSDTGSL
Retrocopy QPSSETRAFLSPQTLLEDPLRLSPVLPGGGGSPS-SPGNPLDHQITNKRGEPSCDRSTDAHRAPSDTGSL

Parental  SPPWDQDRRMMFPPPGQSYPDSALPPQRQDRFCSNSGRLSGPAELRSFNMPSLDKMDGSMPSEMESSRND
          S.PW.QDRRMMFPPPGQSYPDSALPPQR.DRF.SNS.RLSGPAELRSFNMP.LDKMDGSMPSEMES.RND
Retrocopy SSPWEQDRRMMFPPPGQSYPDSALPPQREDRFYSNSDRLSGPAELRSFNMPCLDKMDGSMPSEMESTRND

Parental  TKDDLGNLNVPDSSLPAENEATGPGFVPPPLAPIRGPLFPVDTRGAFLRRGPPFPPPPPGAMFGASRDYF
          .KDD.G.LNVPDSSLPAENEATGPGF.PPPLA.I.GPLFPVDTRG.F.RRGPPFP.PPPG.MFGASR.YF
Retrocopy AKDDPGHLNVPDSSLPAENEATGPGFIPPPLAAISGPLFPVDTRGLFTRRGPPFPQPPPGTMFGASRGYF

Parental  PPRDFPGPPPAPFAMRNVYPPR-GFPPYLPPRPGFFPPP-PHSEGRSEFPSGLIPPSNEPATEHPEPQQE
          ..RDFPGPP.APFAMRN.YPPR.GF...L.......P.P.PHSEGRS.FP.GLIPPS.EPATEHPEPQQE
Retrocopy LSRDFPGPPHAPFAMRNIYPPR<GFTSLLSSKTWILPQP<PHSEGRSKFP*GLIPPSKEPATEHPEPQQE

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	10.90 RPM
SRP007412_cerebellum	0.04 RPM	9.86 RPM
SRP007412_heart	0.00 RPM	11.02 RPM
SRP007412_kidney	0.00 RPM	54.97 RPM
SRP007412_liver	0.03 RPM	36.20 RPM
SRP007412_testis	0.95 RPM	20.44 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_1712 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_1712 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_1712 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pongo abelii	retro_pabe_2119

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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,