RetrogeneDB ID: retro_ptro_466

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 10:129806835..129808934(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSPTRG00000003059
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

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

Sequence

>retro_ptro_466
TATGAAGTAGCGTCATCGTTAGAGGATGCCAGCTTTGAGAAGGCGGCAGCAGAAGCACGAAGTTTGGAGGCAACCTGTGA
AAAGTTGAACAGGTCCAATTCTGAACTTGAGCATGAAATTCTCTGTCTAGAAAAAGAGTTAAAAGAAGAGAAATCTAAAC
ATTCTCAACAAAATGAATTGATGGCGGATATTTCAAAAACGATACAGCCTCTAGCAGATGAGTCAGAATCCCTCAAATCA
CAAGTAGCTGAAGCCAAAATGATCTTCAAGAGATTTAAAATGACTGAGAAACAACTGAAGATAGCAATAAAAGATGCTTT
GAATGAAAACTCTCACCTTCAGGAAAGCCAGAAACAGCTTTTGCAAGAAGCTGAAGTATGGAACGAACAAGTGAGTGAAC
TTAATAAACAGAAAATAACATGTGAAGACTCCAAAGTACATGCAGAACAAGTTCTAAATGATAAAGAAAATCACATCAAG
ACTCTGACTGAACGTTTGCTAAAGATGAAAGATTGGGCTGCTAGGCTTAGAGAAGACCTAACGGATGATGATAACTTAGA
ATTAGAAGTGAACAGTGAATCAGAAGATGATGCTCACTTAGATGATCCTCCAAAAGGAGCTCTGAAGAAACTGATTCATG
CTACTAAGTTAAATGCTTCTTTAAAAACCTTAGAAGGAGAAAGAAACCAAATTTATATCCAGTTATCTGAAATTGATAAA
ACAAAGGAAGAGCTTACAGAGCATATTAAAAATCTTCGGACTGAACAAGCATCTTTGCAGTCAGAAAACACACATTTTGA
AAGTGAGAATCAGAAGCTTCAACAGAAACTTAAAGTAATGACTGAATTATATCAAGAAAATGAAATGAAACTCTACAGGA
AATTAACAGTAGAGGAAAATAGCCGGTTAGAGAAAGAAGAGAAACTTTCTAAGGTAGACAAAAAGATCAGCCATGCCACT
AAAGAGCTGGAGACCTACAGACAGCAAGCCAAAGATCTTGAAGAAGAATTGGAGAGAACTATTCATTATTATCAACGGCA
GATTATTTCCCATGAGAAAAAAGCACATCATAATTGGTTGGCAGCTTGGACTGCTGAAAGAAACCTCAATGATTTAAGGA
AAGAAAATGCTCACAACAGACAAAAATTAACTGAAACAGAGTTTAAATTTGAACTTTTAGAAAAAGATCCTTATGTACTT
GATGTTCCAAATACAGAATTTGGCAGAGAGCATTCCCCATATGGTTCCTCATCATTGGGTCGGCCTTCATCTGAAACGAG
AGCTTTTCTCTCTCCCGCAACTCTGTTGGAGGGTCCACTCAGACTCTCACCTTTGCCTCCAGGGGGGGAAGGAAGAGGCT
CAAGAGGCCCAGGGAATCCTCTGGACCATCAGATTACCAAGGAAAGAGGAGAATCAAGCTGTGAGAGGTTAACCGATCCT
CACAGGTCTCCTTCTGACACTGGGTCCCTGTCACTTCCGAGGGAACAGGACCGTAGGATGATGTTTCCTCCACCAGGGCA
ATCATATCTTGATTCAGCTCTTCCTCCACAAAGGCAAGACAGATTTTATTCTAACTCTGGTAGACTGTCTGGACCAGCAG
AACTCAGAAGTTTTAATATGCCTCCTTTGGATAAAATGGATGGGTCAATGCCTTCAGAAATGGAATCCAGTAGAAATGAC
ACCAAAGATGATCTTGGTAATTTAAATATCCCTGATTCATCTCTCCCTGCTGAAAATGAAGCAACTGGCCCTGGCTTTGT
TCCTCCACCTCTTGCCCCAATCAGAGGTCCACTGTTTCCAGTGGATACAAGGGGCCCGTTCATGAGAAGAGGACCTGCTT
TCCCCCCACCTCCTCCAGGAACCAGGTTTGGAGCTTCTCGAGATTATTTTCCACCAAGGGATTTCCCAGGTCCACCACAT
GCTCCATTTGCAATGAGAAATGTCTATCCACCGAGGGGTTTTACTCCTTACCTTCCCCTCAAGACCTGGATTTTTCCCCC
CACCCCCACATTCTGAAGGTAGAAGTGAGTTCCCTTCAGGGGCTGATTCCGCCTTCAAATGAGCCTGCTACGGAACATCC
AAAACCGCAGCAAGATACC

Alignment

ORF - retro_ptro_466 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.73 %
• Parental protein coverage: 86.94 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  YEVESSLKDASFEKEATEAQSLEATCEKLNRSNSELEDEILCLEKELKEEKSKHSERDELMADISKRIQS
          YEV.SSL.DASFEK.A.EA.SLEATCEKLNRSNSELE.EILCLEKELKEEKSKHS...ELMADISK.IQ.
Retrocopy YEVASSLEDASFEKAAAEARSLEATCEKLNRSNSELEHEILCLEKELKEEKSKHSQQNELMADISKTIQP

Parental  LEDESKSLKSQVAEAKMTFKIFQMNEERLKIAIKDALNENSQLQESQKQLLQEAEVWKEQVSELNKQKVT
          L.DES.SLKSQVAEAKM.FK.F.M.E..LKIAIKDALNENS.LQESQKQLLQEAEVW.EQVSELNKQK.T
Retrocopy LADESESLKSQVAEAKMIFKRFKMTEKQLKIAIKDALNENSHLQESQKQLLQEAEVWNEQVSELNKQKIT

Parental  FEDSEVHAEQVLNDKESHIKTLTERLLKMKDWAAMLGEDITDDDNLELEMNSESENGAYLDNPPKGALKK
          .EDS.VHAEQVLNDKE.HIKTLTERLLKMKDWAA.L.ED.TDDDNLELE.NSESE..A.LD.PPKGALKK
Retrocopy CEDSKVHAEQVLNDKENHIKTLTERLLKMKDWAARLREDLTDDDNLELEVNSESEDDAHLDDPPKGALKK

Parental  LIHAAKLNASLKTLEGERNQIYIQLSEVDKTKEELTEHIKNLQTEQASLQSENTHFENENQKLQQKLKVM
          LIHA.KLNASLKTLEGERNQIYIQLSE.DKTKEELTEHIKNL.TEQASLQSENTHFE.ENQKLQQKLKVM
Retrocopy LIHATKLNASLKTLEGERNQIYIQLSEIDKTKEELTEHIKNLRTEQASLQSENTHFESENQKLQQKLKVM

Parental  TELYQENEMKLHRKLTVEENYRLEKEEKLSKVDEKISHATEELETYRKRAKDLEEELERTIHSYQGQIIS
          TELYQENEMKL.RKLTVEEN.RLEKEEKLSKVD.KISHAT.ELETYR..AKDLEEELERTIH.YQ.QIIS
Retrocopy TELYQENEMKLYRKLTVEENSRLEKEEKLSKVDKKISHATKELETYRQQAKDLEEELERTIHYYQRQIIS

Parental  HEKKAHDNWLAARNAERNLNDLRKENAHNRQKLTETELKFELLEKDPYALDVPNTAFGREHSPYGPSPLG
          HEKKAH.NWLAA..AERNLNDLRKENAHNRQKLTETE.KFELLEKDPY.LDVPNT.FGREHSPYG.S.LG
Retrocopy HEKKAHHNWLAAWTAERNLNDLRKENAHNRQKLTETEFKFELLEKDPYVLDVPNTEFGREHSPYGSSSLG

Parental  WPSSETRAFLSPPTLLEGPLRLSPLLPGGGGRGSRGPGNPLDHQITNERGESSCDRLTDPHRAPSDTGSL
          .PSSETRAFLSP.TLLEGPLRLSPL.PGG.GRGSRGPGNPLDHQIT.ERGESSC.RLTDPHR.PSDTGSL
Retrocopy RPSSETRAFLSPATLLEGPLRLSPLPPGGEGRGSRGPGNPLDHQITKERGESSCERLTDPHRSPSDTGSL

Parental  SPPWDQDRRMMFPPPGQSYPDSALPPQRQDRFCSNSGRLSGPAELRSFNMPSLDKMDGSMPSEMESSRND
          S.P..QDRRMMFPPPGQSY.DSALPPQRQDRF.SNSGRLSGPAELRSFNMP.LDKMDGSMPSEMESSRND
Retrocopy SLPREQDRRMMFPPPGQSYLDSALPPQRQDRFYSNSGRLSGPAELRSFNMPPLDKMDGSMPSEMESSRND

Parental  TKDDLGNLNVPDSSLPAENEATGPGFVPPPLAPIRGPLFPVDTRGAFLRRGPPFPPPPPGAMFGASRDYF
          TKDDLGNLN.PDSSLPAENEATGPGFVPPPLAPIRGPLFPVDTRG.F.RRGP.FPPPPPG..FGASRDYF
Retrocopy TKDDLGNLNIPDSSLPAENEATGPGFVPPPLAPIRGPLFPVDTRGPFMRRGPAFPPPPPGTRFGASRDYF

Parental  PPRDFPGPPPAPFAMRNVYPPRGFPPYL-PPRPGFFPPPPHSEGRSEFPS-GLIPPSNEPATEHPEPQQE
          PPRDFPGPP.APFAMRNVYPPRGF.PYL.P.RPGFFPPPPHSEGRSEFPS.GLIPPSNEPATEHP.PQQ.
Retrocopy PPRDFPGPPHAPFAMRNVYPPRGFTPYL>PSRPGFFPPPPHSEGRSEFPS>GLIPPSNEPATEHPKPQQD

Parental  T
          T
Retrocopy T

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	0.09 RPM	10.90 RPM
SRP007412_cerebellum	0.22 RPM	9.86 RPM
SRP007412_heart	0.09 RPM	11.02 RPM
SRP007412_kidney	0.65 RPM	54.97 RPM
SRP007412_liver	0.20 RPM	36.20 RPM
SRP007412_testis	5.27 RPM	20.44 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_466 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_466 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_466 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_640
Pongo abelii	retro_pabe_29

---

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,