RetrogeneDB ID: retro_ptro_2580

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 7:145136563..145138521(+)
• 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_2580
GCAGCAGAAGCACGAAGTTTGGAGGCAACCTGTGAAAAGCTGAACAGGTCCAATTCTGAACTTGAGGATGAAATCCTCTG
TCTAGAAAAAGACTTAAAAGAAGAGAAATCTAAACATTCTCAACAAGATGAATTGATGGCGGATATTTCAAAAAGGATAC
AGTCTCTAGAAGAGGAGTCAAAATCCCTCAAATCACAAATAGCTGAAGCCAAAATCATCTGCAAGATATTTAAAATGAGT
GAAGAACGACGGGCTATAGCAATAAAAGATGCTTTGAATGAAAATTCTCAACTTCAGGAAAGCCAGAAACAGCTTTTGCA
AGAAGCTGAGGTATGGAAAGAACAAGTGAGTGAACTTAATAAACAGAAAATAACATTTGAAGACTCCAAAGTACACGCAG
AACAAGTTCTAAATGATAAAGAAAATCACATCAAGACCCTGACTGGACACTTGCTAATGATGAACGATCAGGCTGCTGTG
CTTGAAGAAGACACAACGGATGATGATAACCTGGAATTAGAAGTAAACAGTCAATCGGAAATGGTGCTAACTTAGATGAT
CCTCCAAAAGGAGCTTTGAAGAAACTGATTCATGCTGCTAAGTTAAATGTTTCTTTAAAAAGCTTAGAAGGAGAAAGAAA
CTACATTATTATTCAGTTATCTGAAGTTGATAAAACAAAGGAAGAGCTTACAGAGTATATGAAAAATCTTCAGACTCAAC
AAGCATCTTTGCAGTCAGAAAACATACATTTTGAAAGTGAGAATCAGAAGCTTCAACAGAAACTTAAAATAATGACTGAA
TTCTATCAAGAAAATGAAATGAAACTCCACAGGAAATTGACAATAGAGGAAAATTACCGGATAGAGGAAGAAGAGAAACT
TTCTAAAGTGGAAGAAAAGATCAGCCATGCCACTGAAGAGCTGGAGACCTATAGAAAGCTAGCCAAAGATCTTGAAGAAG
AATTGGAGAGAACTGTTCATTTTTATCAAAAGCAGGTTATTTCCTACGAGAAAAGAGGACATGATAATTGGTTGGCAGCT
CGGACTGCTGAAAGAAACCTCAATGATTTAAGGAAAGAAAATGCTCACAACAAACAAAAATTAACTGAAACAGAGTTGAA
ATTTGAACTTTTAGAAAAAGATCCTAATGCACTTGATGTTTCAAATACAGCATTTGGCAGAGAGCATTCCCTGAATGGTC
CCGCACCATTGGGTCGGCCTTCATCTGCAAAGAGAGCTTTTCTCTCTCCTCAAACTTTGTTGGAGGATCCACTGGGACTC
TGACCTGTGCTTCCGGAGGGAGGAGGAAGAGGCCCAAGAGGCCCAGGGAATCCCCTGGACCATCAGATTACCAATGAAAG
AGGAGAACCAAGCTGTGATAGGTTAACCGATCCTCACAGGGCTCCTTCTGACACTGGGTCCCTGTCATCTCTGGTGGAAC
AGGACTGTCAGATGATGTTTCCTCCACCAGGACAATCATATCCTGATTCAGCTCTTCCTCCTCAAAGGGAAGACAGATTT
TATTCTAATTCTGAAAGACTGTCTGGACCAGCAGAACCCAGAAGTTTTAAAATGACTTCTTTGGATAAAATGGATGGGTC
AATGCCTTCAGAAATGGAATCCAGTAGAAATGATGCCAAAGATGATCTTGGTAATTTAAATGTGCCTGATTCATCTCTCC
CTGCTGAAAATGAAGCAACTGGCCCTGGCTTTATTCCTCCACCTCTTGCTCCAGTCAGAGGACCATTGTTTCCAGTGGAT
ACAAGGGGCCCGTTCATGAGAAGAGGATCTCCTTTCCCCCCACCTCCTTCAGGAACCATGTTTGGAGCTTCTCGAGGTTA
TTTTCCACCAAGGGATTTCCCAGGTCCACCACATGCTCCATTTGCAATGAGAAACATCTACCCACCAAGGGGTTTACCTC
CTTACCTTCATCCGAGACCTGGATTTTACCCCAACCCC

Alignment

ORF - retro_ptro_2580 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.02 %
• Parental protein coverage: 81.22 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  ATEAQSLEATCEKLNRSNSELEDEILCLEKELKEEKSKHSERDELMADISKRIQSLEDESKSLKSQVAEA
          A.EA.SLEATCEKLNRSNSELEDEILCLEK.LKEEKSKHS..DELMADISKRIQSLE.ESKSLKSQ.AEA
Retrocopy AAEARSLEATCEKLNRSNSELEDEILCLEKDLKEEKSKHSQQDELMADISKRIQSLEEESKSLKSQIAEA

Parental  KMTFKIFQMNEERLKIAIKDALNENSQLQESQKQLLQEAEVWKEQVSELNKQKVTFEDSEVHAEQVLNDK
          K...KIF.M.EER..IAIKDALNENSQLQESQKQLLQEAEVWKEQVSELNKQK.TFEDS.VHAEQVLNDK
Retrocopy KIICKIFKMSEERRAIAIKDALNENSQLQESQKQLLQEAEVWKEQVSELNKQKITFEDSKVHAEQVLNDK

Parental  ESHIKTLTERLLKMKDWAAMLGEDITDDDNLELEMNSESE-NGAYLDNPPKGALKKLIHAAKLNASLKTL
          E.HIKTLT..LL.M.D.AA.L.ED.TDDDNLELE.NS.SE.NGA.LD.PPKGALKKLIHAAKLN.SLK.L
Retrocopy ENHIKTLTGHLLMMNDQAAVLEEDTTDDDNLELEVNSQSE<NGANLDDPPKGALKKLIHAAKLNVSLKSL

Parental  EGERNQIYIQLSEVDKTKEELTEHIKNLQTEQASLQSENTHFENENQKLQQKLKVMTELYQENEMKLHRK
          EGERN.I.IQLSEVDKTKEELTE..KNLQT.QASLQSEN.HFE.ENQKLQQKLK.MTE.YQENEMKLHRK
Retrocopy EGERNYIIIQLSEVDKTKEELTEYMKNLQTQQASLQSENIHFESENQKLQQKLKIMTEFYQENEMKLHRK

Parental  LTVEENYRLEKEEKLSKVDEKISHATEELETYRKRAKDLEEELERTIHSYQGQIISHEKKAHDNWLAARN
          LT.EENYR.E.EEKLSKV.EKISHATEELETYRK.AKDLEEELERT.H.YQ.Q.IS.EK..HDNWLAAR.
Retrocopy LTIEENYRIEEEEKLSKVEEKISHATEELETYRKLAKDLEEELERTVHFYQKQVISYEKRGHDNWLAART

Parental  AERNLNDLRKENAHNRQKLTETELKFELLEKDPYALDVPNTAFGREHSPYGPSPLGWPSSETRAFLSPPT
          AERNLNDLRKENAHN.QKLTETELKFELLEKDP.ALDV.NTAFGREHS..GP.PLG.PSS..RAFLSP.T
Retrocopy AERNLNDLRKENAHNKQKLTETELKFELLEKDPNALDVSNTAFGREHSLNGPAPLGRPSSAKRAFLSPQT

Parental  LLEGPLRLSPLLPGGGGRGSRGPGNPLDHQITNERGESSCDRLTDPHRAPSDTGSLSPPWDQDRRMMFPP
          LLE.PL.L.P.LP.GGGRG.RGPGNPLDHQITNERGE.SCDRLTDPHRAPSDTGSLS....QD..MMFPP
Retrocopy LLEDPLGL*PVLPEGGGRGPRGPGNPLDHQITNERGEPSCDRLTDPHRAPSDTGSLSSLVEQDCQMMFPP

Parental  PGQSYPDSALPPQRQDRFCSNSGRLSGPAELRSFNMPSLDKMDGSMPSEMESSRNDTKDDLGNLNVPDSS
          PGQSYPDSALPPQR.DRF.SNS.RLSGPAE.RSF.M.SLDKMDGSMPSEMESSRND.KDDLGNLNVPDSS
Retrocopy PGQSYPDSALPPQREDRFYSNSERLSGPAEPRSFKMTSLDKMDGSMPSEMESSRNDAKDDLGNLNVPDSS

Parental  LPAENEATGPGFVPPPLAPIRGPLFPVDTRGAFLRRGPPFPPPPPGAMFGASRDYFPPRDFPGPPPAPFA
          LPAENEATGPGF.PPPLAP.RGPLFPVDTRG.F.RRG.PFPPPP.G.MFGASR.YFPPRDFPGPP.APFA
Retrocopy LPAENEATGPGFIPPPLAPVRGPLFPVDTRGPFMRRGSPFPPPPSGTMFGASRGYFPPRDFPGPPHAPFA

Parental  MRNVYPPRGFPPYLPPRPGFFPPP
          MRN.YPPRG.PPYL.PRPGF.P.P
Retrocopy MRNIYPPRGLPPYLHPRPGFYPNP

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	0.00 RPM	11.02 RPM
SRP007412_kidney	0.00 RPM	54.97 RPM
SRP007412_liver	0.00 RPM	36.20 RPM
SRP007412_testis	1.48 RPM	20.44 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_2580 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2580 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2580 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,