RetrogeneDB ID: retro_pabe_1588

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 18:34036673..34039034(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

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_1588
GTCCTGGAGTTGCTACGCAGGGTTGTGGCAGCACTGACTGAAGGTATGAGACCCGATTCTCATCCTTATGGTTTTCCATG
GGAATTGGTGATACGTGCAGCTGTTGTTGGATTTTTTGCTGTTCTCTTCCTGTGGAGAAGTTTTAGATCAGTTACAAGTC
GGCTTTATGTGAGAAGAGAGAAAAAGTTTGCTGTGGCGCTTTCTGGACTAATTGAAGAAAAATGTAAACTACTTGAAAAA
TTTAGCCTTGTTCAAAAAGAGTATGAAGGCTATGAAGTAGAGTCATCTTTAAAGGATGCCAGCTTTGAGAAGGAGGCAAC
AGAAGCACAAAGTTTGGAGGCAACCTGCGAAAAGCTGAACAGGTTCAATTCTGAACTTGAGTATGAAATACTCTGTCTAG
AAAAAGAGTTAAAAGAAGAGAAATCTAAACATTCTGAACAAAATGAATTGATGGCGGATATTTCCAAAAGGATACAGTCG
CTAGAAGATGAGTCAAAATCCCTCAAATCACAAGTAGCTGAAGCCAAAATGACCTTCAAGAGATTTCAAGTAAATGAAGA
ACAACTGGAGATAGAAATACAAGATGCTTTGAATGAGAATTCTCAACTTCAGGAAAGCCAGAAACAGCTTTTGCAAGAAG
CTGAAGTATGGAAAGAACAAGTGAGTGAACTGATTAAACAGAAAAGAACATTTGAAGACTCCAAAGTGCATGCAGAACAA
GTTCTAAATGATAAAGAAAATCACATCAAGACTCTGACTAAACGCTTGCTAAAGATGAAAGATGGGGTTGCTATGCTTGA
AGAAGATGTAATGGATGATAACTTGGAATTAGAAATGAACAGTGAATCGGAAGATGGTGCTTACTTAGATAATCCTCCAA
AAGGAGCTTTGAGGAAACTGATTCATACTGCTAAGTTAAATGCTTCTTTAAAAACCTTAGAAGGAGAAAGAAACCAAATT
TATATTCAATTATCTGAAGTTGATAAAACAAAGGAAGAGCTTACAGAGCATATTAAAAATCTTCAGACTGAACAAGCATC
TTTGCAGTCAGAAAACACACATTTTGAAAGTGAGAATCAGAAGCTTCAGCAGAAACTTAAAGTAATGACCGAATTATATC
AAGAAAATGAAATGAAACTCCACAGGAAATTAATAGTAGAGGGGAAATGCCGGTTAGAGAAAGAAGAGAAACTTTCTAAA
GTAGACAAAATGATCAGCCATGCCACTGAAGAGCTGGAGACCTACCGAAAGCGAGCCAAAGATCTTAAAGAATTTGAGAG
AACTATTCATTTTTATCAAAAGAAGATGATTCTCCATGAGAAAAAAGCACGTGATAATTGGTCGGCAGCTTGGACTGCTG
AAAGAAAACTCAATGATTTAAGGAAAGAAAATGCTCACAACAGACAAAAATTAACTGAAATAGAGTTTAAAATAAAACTT
TTAGAAAAAGATCCGTATGGACTTGATGTTCCAAATACAGCATTTGGCAGACAGCATTCCCCATATGGTCCCTCACCATT
AGGTCGACCTTCATCTGAAACGAAAACTTCTCTCTATCCTCCAACTTTGTTGGAGGGTCCTCTCAGACTCTCACCTTTGC
TTCCAGGGGGAGGAGGAAAAGGCTCCAGAGGCCCAGGGAATCCTCTGGACCATCAGATTACCAATGAAAGAGGAGAATCA
AGCTGTGATAAGTTAACTGATCCTCACAGGGCTCCTTCTGACACTGGGCCCCTGTCACCTTCGTGGGAACAGGACTGTAG
GATGATGTTTCCTTCACCAGGACAATCATATCCTGATTCAGCTCTTCCTCCACAAAGGCAAGACAGATTTTATTCTAATT
GTGCTAGACTCTCTGGACCAGCAGAACTCAAAAGTTTTAATATGCCTTCTTTGGATAAAATGGATGGGTCAATGCCTTCG
GAAATGGAATCCAGTAGAAATGATACCAAAGATAATCTTGGTAATTTAAAGGTGCCTGATTCATCTCTCCCCACTGAAAA
TGAAGCAACTGGCCCTGGCTTTGTTCCTCCACCTCTTGCTCCAATTAGAGGTTCATTGTTTCCAGTAGATACAAGGGGCC
CGTTGATGAGAAGAGGACTTCCTTTACCCCCACCTCCTCCAGGAACCATGTTTAGAGCTTCTCCAGATTATTTTCCACCA
AGGAATGTCCCAGGTCCACCACGTGCTCCATTTGCAATAAGAAATATCTATCTACCGAGAGGTTTTCCTCCTTACCGTCC
CCCAAGACCTGGATTTACCCCCCCAACCCCCACATTCTGAAGGTAGAATGAGTTTCCATCAGGGTTGAGTCCGACTTCAA
ATGAGCCTGCTGCTGAACATCCAGAACGACAGCAAGAAACC

Alignment

ORF - retro_pabe_1588 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.83 %
• Parental protein coverage: 59.04 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  IVILTERVVAALPEGMRPDSNPYGFPWELVICAAVVGFFAVLFFSWRSFRSVSNQCYTKRIPVFSEKQTL
          ...L..RVVAAL.EGMRPDS.PYGFPWELVI.AAVVGFFAVLF..WRSFRSV....Y..R...F......
Retrocopy VLELLRRVVAALTEGMRPDSHPYGFPWELVIRAAVVGFFAVLFL-WRSFRSVTSRLYVRREKKFAVALSG

Parental  LLENKIRRVFTCDVALFQYEGYEVESSLKNASFEKEATEAQSLEATCEKLNRSNSELEDEILCLEKELKE
          L.E.K.............YEGYEVESSLK.ASFEKEATEAQSLEATCEKLNR.NSELE.EILCLEKELKE
Retrocopy LIEEKCKLLEKFSLVQKEYEGYEVESSLKDASFEKEATEAQSLEATCEKLNRFNSELEYEILCLEKELKE

Parental  EKSKHSEQDELMADISKRIQSLEDESKSLKSQVAEAKMTFKIFQMNEERLKIAIKDALNENSELQESQKQ
          EKSKHSEQ.ELMADISKRIQSLEDESKSLKSQVAEAKMTFK.FQ.NEE.L.I.I.DALNENS.LQESQKQ
Retrocopy EKSKHSEQNELMADISKRIQSLEDESKSLKSQVAEAKMTFKRFQVNEEQLEIEIQDALNENSQLQESQKQ

Parental  LLQDAEVWKEQVSELNKQKVTFEDSKVHAEQVLNDKENHIKTLTERLLKMKDWAAMLGEDITDDDNLELE
          LLQ.AEVWKEQVSEL.KQK.TFEDSKVHAEQVLNDKENHIKTLT.RLLKMKD..AML.ED..DD.NLELE
Retrocopy LLQEAEVWKEQVSELIKQKRTFEDSKVHAEQVLNDKENHIKTLTKRLLKMKDGVAMLEEDVMDD-NLELE

Parental  MNSESENGAYLDNPPKGALKKLIHAAKLNASLKTLEGERNQIYIQLSEVDKTKEELTEHIKNLQTEQASL
          MNSESE.GAYLDNPPKGAL.KLIH.AKLNASLKTLEGERNQIYIQLSEVDKTKEELTEHIKNLQTEQASL
Retrocopy MNSESEDGAYLDNPPKGALRKLIHTAKLNASLKTLEGERNQIYIQLSEVDKTKEELTEHIKNLQTEQASL

Parental  QSENTHFENENQKLQQKLKVMTELYQENEMKLHRKLTVEENYRLEKEEKLSKVDEKISHATEELETYRKR
          QSENTHFE.ENQKLQQKLKVMTELYQENEMKLHRKL.VE...RLEKEEKLSKVD..ISHATEELETYRKR
Retrocopy QSENTHFESENQKLQQKLKVMTELYQENEMKLHRKLIVEGKCRLEKEEKLSKVDKMISHATEELETYRKR

Parental  AKDLEEELERTIHSYQGQIISHEKKAHDNWLAARNAERNLNDLRKENAHNRQKLTETELKFELLEKDPYA
          AKDL.E..ERTIH.YQ...I.HEKKA.DNW.AA..AER.LNDLRKENAHNRQKLTE.E.K..LLEKDPY.
Retrocopy AKDLKE-FERTIHFYQKKMILHEKKARDNWSAAWTAERKLNDLRKENAHNRQKLTEIEFKIKLLEKDPYG

Parental  LDVPNTAFGREHSPYGPSPLGWPSSETRAFLSPPTLLEGPLRLSPLLPGGGGRGSRGPGNPLDHQITNER
          LDVPNTAFGR.HSPYGPSPLG.PSSET...L.PPTLLEGPLRLSPLLPGGGG.GSRGPGNPLDHQITNER
Retrocopy LDVPNTAFGRQHSPYGPSPLGRPSSETKTSLYPPTLLEGPLRLSPLLPGGGGKGSRGPGNPLDHQITNER

Parental  GESSCDRLTNPHRAPSDTGSLSPPWEQDRRMMFPPPGQSYPDSALPPQRQDRFCSNSGRLSGPAELRSFN
          GESSCD.LT.PHRAPSDTG.LSP.WEQD.RMMFP.PGQSYPDSALPPQRQDRF.SN..RLSGPAEL.SFN
Retrocopy GESSCDKLTDPHRAPSDTGPLSPSWEQDCRMMFPSPGQSYPDSALPPQRQDRFYSNCARLSGPAELKSFN

Parental  MPSLDKMDGSMPSEMESSRNDTKDDLGNLNVPDSSLPTENEATGPGFVPPPLAPIRGPLFPVDTRGPFLR
          MPSLDKMDGSMPSEMESSRNDTKD.LGNL.VPDSSLPTENEATGPGFVPPPLAPIRG.LFPVDTRGP..R
Retrocopy MPSLDKMDGSMPSEMESSRNDTKDNLGNLKVPDSSLPTENEATGPGFVPPPLAPIRGSLFPVDTRGPLMR

Parental  RGPPFPPPPPGAVFGASRDYFPPRDFPGPPHAPFAMRNVYPPRGFPPYLPPRPGF-FPPPPHSEGR-SEF
          RG.P.PPPPPG..F.AS.DYFPPR..PGPP.APFA.RN.Y.PRGFPPY.PPRPGF......HSEGR..EF
Retrocopy RGLPLPPPPPGTMFRASPDYFPPRNVPGPPRAPFAIRNIYLPRGFPPYRPPRPGF>XXXXXHSEGR<NEF

Parental  PSGLIPPSNEPATEHPEPQQET
          PSGL.P.SNEPA.EHPE.QQET
Retrocopy PSGLSPTSNEPAAEHPERQQET

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	0.22 RPM	5.20 RPM
SRP007412_cerebellum	0.12 RPM	8.88 RPM
SRP007412_heart	0.24 RPM	9.60 RPM
SRP007412_kidney	0.73 RPM	44.81 RPM
SRP007412_liver	0.86 RPM	43.09 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_1588 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_1588 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_1588 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_78
Pan troglodytes	retro_ptro_1286

---

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,