RetrogeneDB ID: retro_pabe_29

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 10:129871489..129873532(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSPPYG00000002767
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: CTAGE5
• Ensembl ID: ENSPPYG00000005768
• Aliases: None
• Description: CTAGE family, member 5 [Source:HGNC Symbol;Acc:7057]

Sequence

>retro_pabe_29
ATGAGACTGGATTCGAATCCTCATGGTTTTCCATGGAAATTGGTGATATGTGCAGCTGTTGCTGCATTTTTTGCTGTTCT
CCTTTTTCTGTGGAGAAGTTTTAGATCGGTTAGGAGTCGGCTTTATGTGGGAAGAGAGAAAAAGCTTGCTATAATGCTTT
CTGGACTAATTGAAGAAAAATGTAAACTACTTGAAAAATTTAGCCTTGTTCAAAAAGAGTATGAAGACTATGAAGTGGTG
TCATCTTTAGAGGATGCCAGCTTTGAGAAGGCGGCAACAGAAGCACAAAGTTTGGAGGCAATCTGTGAAAAGCTGAACAG
GTCCAATTCTGAACTTGAGCATGAAATACTCTGTCTAGAAAAAGAGTTAAAAGAAGAGAAATCTAAACATTCTCAACAAA
ATGAATTGATGGCGGATATTTCAAAAAGGATACAGCCTCTAGCAGATGAGTCAAAATCCCTCAAATCACAAGTAACTGAA
GCCAAAATGATCTTCAAGAGATTTCAAATGACTGAAAAACAACTGAAGATAGCAATAAAAGACGCTTTGAATGAAAATTC
TCAACTTCAGGAAAGCCAGAAACAGCTTTTGCAAGAAGCTGAAGTATGGAACGAACAAGTGAGTGAACTTAATAAACAGA
AAATAACATTTGAAGACTCCAAAGTACATGCAGAACAAGTTCTAAATGATAAAGAAAATCACATCAAGACTCTGACTGAA
CGCTTGCTAAAGATGAAAGATTGGACTGCTAGGCTTAGAGAAGACGTAACGGATGATGATAACTTAGAAGTGAACAGTGA
ATCAGAAGATGGTGCTTACTTAGATGATCCTCCAAAAGGAGCTTTGAAGAAACTGATTCATGCTGCTAAGTTAAATGCTT
CTTTAAAAACCTTAGAAGGAGAAAGAAACCAAATTTATATCCAGTTATCTGAAATTGATAAAACAAAGGAAGAGCTTACA
GAGCATATTAAAAATCTTCAGACTGAACAAGCATCTTTGCAGTCAGAAAACACACATTCAGAAAGTGAGAATCAGAAGCT
TCAACAGAAACTTAAAGTAATGACTGAATTCTATCAAGAAAATGAAATGAAACTCTACAGGAAATTAACAGTAGAGGAAA
ATAACCAGTTAGAGAAAGAAGAGAAACTTTCCGAGGTAGACAAAAAGATCAGCCATGCCACCAAAGAGCTGGAGACCTAC
AGACAGCAAGCCAAAGATCTTGAAGAAGAATTGGAGAGAACTATTCATTATTATCAACGGCAGATTATTTCCCATGAGAA
AAAAGCGCATCATAATTGGTTGGCAGCTTGGACTGCTGAAAGAAACCTCAATGATTTAAGGAAAGAAAATGCTCACAACA
GACAAAAATTAACTGAAACAGAGTTTAAATTTGAACTTTTAGAGAAAGATCCTTATGCACTCGATGTTCCAAATACAGCA
TTTGGCAGAGAGCATTCCCCATATGGTTCCTCATCATTGGGTCGGCCTTCATCTGAAACGAGAGCTTTTCTCTCTCCCGC
AACTCTGTTGGAGGGTCCACTCAGACTCTCACCTTTGCCTCCAGTGGGAGAAGGAAGAGGCTCAAGAGGCCCAGAAAATC
CTCTGGACCATCAGATTACCAAGGAAAGAGGAGAATCAAGCTGTGAGAGGTTAACCGATCCTCACAGGTCTCCTTCTGAC
ACTGGGCCCCTGTCACCTCCGAGGGAACAAGACCGTAGGATGATGTTTCCTCCACCAGGGCAATCATATCTTGATTCAGC
TCTTCCTCCACAAAGGCAAGACAGATTTTATTCTAACTCTGGTAGACTGTCTGGACCAGCAGAACTCAGAAGTTTTAATA
TGCCTCCTTTGGATAAAATGGATAGGTCAATGCCTTCAGAAATGGAATCCAGTAGAAATGATACCAAAGATGATCTTGGC
AATTTAAATATCCCTGATTCATCTCTCCCTGCTGAAAATGAAGCAACTGGCCCTGGCTTTGTTCCTCCACCTCTTGCCCC
AGTCAGAGGTCCATTGTTTCCAGTGGATACAAGGGCCCCGTTC

Alignment

ORF - retro_pabe_29 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.19 %
• Parental protein coverage: 51.05 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MRPDSNPYGFPWELVICAAVVGFFAVLFFSWRSFRSVSNQCYTKRIPVFSEKQTLLLENKIRRVFTCDVA
          MR.DSNP.GFPW.LVICAAV..FFAVL.F.WRSFRSV....Y..R..........L.E.K..........
Retrocopy MRLDSNPHGFPWKLVICAAVAAFFAVLLFLWRSFRSVRSRLYVGREKKLAIMLSGLIEEKCKLLEKFSLV

Parental  LFQYEGYEVESSLKNASFEKEATEAQSLEATCEKLNRSNSELEDEILCLEKELKEEKSKHSEQDELMADI
          ...YE.YEV.SSL..ASFEK.ATEAQSLEA.CEKLNRSNSELE.EILCLEKELKEEKSKHS.Q.ELMADI
Retrocopy QKEYEDYEVVSSLEDASFEKAATEAQSLEAICEKLNRSNSELEHEILCLEKELKEEKSKHSQQNELMADI

Parental  SKRIQSLEDESKSLKSQVAEAKMTFKIFQMNEERLKIAIKDALNENSELQESQKQLLQDAEVWKEQVSEL
          SKRIQ.L.DESKSLKSQV.EAKM.FK.FQM.E..LKIAIKDALNENS.LQESQKQLLQ.AEVW.EQVSEL
Retrocopy SKRIQPLADESKSLKSQVTEAKMIFKRFQMTEKQLKIAIKDALNENSQLQESQKQLLQEAEVWNEQVSEL

Parental  NKQKVTFEDSKVHAEQVLNDKENHIKTLTERLLKMKDWAAMLGEDITDDDNLELEMNSESENGAYLDNPP
          NKQK.TFEDSKVHAEQVLNDKENHIKTLTERLLKMKDW.A.L.ED.TDDDNLE...NSESE.GAYLD.PP
Retrocopy NKQKITFEDSKVHAEQVLNDKENHIKTLTERLLKMKDWTARLREDVTDDDNLEV--NSESEDGAYLDDPP

Parental  KGALKKLIHAAKLNASLKTLEGERNQIYIQLSEVDKTKEELTEHIKNLQTEQASLQSENTHFENENQKLQ
          KGALKKLIHAAKLNASLKTLEGERNQIYIQLSE.DKTKEELTEHIKNLQTEQASLQSENTH.E.ENQKLQ
Retrocopy KGALKKLIHAAKLNASLKTLEGERNQIYIQLSEIDKTKEELTEHIKNLQTEQASLQSENTHSESENQKLQ

Parental  QKLKVMTELYQENEMKLHRKLTVEENYRLEKEEKLSKVDEKISHATEELETYRKRAKDLEEELERTIHSY
          QKLKVMTE.YQENEMKL.RKLTVEEN..LEKEEKLS.VD.KISHAT.ELETYR..AKDLEEELERTIH.Y
Retrocopy QKLKVMTEFYQENEMKLYRKLTVEENNQLEKEEKLSEVDKKISHATKELETYRQQAKDLEEELERTIHYY

Parental  QGQIISHEKKAHDNWLAARNAERNLNDLRKENAHNRQKLTETELKFELLEKDPYALDVPNTAFGREHSPY
          Q.QIISHEKKAH.NWLAA..AERNLNDLRKENAHNRQKLTETE.KFELLEKDPYALDVPNTAFGREHSPY
Retrocopy QRQIISHEKKAHHNWLAAWTAERNLNDLRKENAHNRQKLTETEFKFELLEKDPYALDVPNTAFGREHSPY

Parental  GPSPLGWPSSETRAFLSPPTLLEGPLRLSPLLPGGGGRGSRGPGNPLDHQITNERGESSCDRLTNPHRAP
          G.S.LG.PSSETRAFLSP.TLLEGPLRLSPL.P.G.GRGSRGP.NPLDHQIT.ERGESSC.RLT.PHR.P
Retrocopy GSSSLGRPSSETRAFLSPATLLEGPLRLSPLPPVGEGRGSRGPENPLDHQITKERGESSCERLTDPHRSP

Parental  SDTGSLSPPWEQDRRMMFPPPGQSYPDSALPPQRQDRFCSNSGRLSGPAELRSFNMPSLDKMDGSMPSEM
          SDTG.LSPP.EQDRRMMFPPPGQSY.DSALPPQRQDRF.SNSGRLSGPAELRSFNMP.LDKMD.SMPSEM
Retrocopy SDTGPLSPPREQDRRMMFPPPGQSYLDSALPPQRQDRFYSNSGRLSGPAELRSFNMPPLDKMDRSMPSEM

Parental  ESSRNDTKDDLGNLNVPDSSLPTENEATGPGFVPPPLAPIRGPLFPVDTRGPF
          ESSRNDTKDDLGNLN.PDSSLP.ENEATGPGFVPPPLAP.RGPLFPVDTR.PF
Retrocopy ESSRNDTKDDLGNLNIPDSSLPAENEATGPGFVPPPLAPVRGPLFPVDTRAPF

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	0.06 RPM	5.20 RPM
SRP007412_cerebellum	0.00 RPM	8.88 RPM
SRP007412_heart	0.03 RPM	9.60 RPM
SRP007412_kidney	0.17 RPM	44.81 RPM
SRP007412_liver	0.03 RPM	43.09 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_29 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_29 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_29 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_640
Pan troglodytes	retro_ptro_466

---

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,