RetrogeneDB ID: retro_pabe_2119

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 2b:57664524..57666874(-)
• 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_2119
AGAGTTGTGGCAGCACTACCTGAGAGTATGAGACAAGATTCGAATCCTTACGGTTTTCCATGGGAACTGGTGGTATGTGC
AGCTGTTGTTGGATTTTTTGTTGTTCTCCTTTTTTTGTGGAGAAGTTTTAGATCGGTTAGGAGTCGGCTTTATGTGGGAA
GAGAGAAAAAACTTGGTGAAACGCTTTCTGGACTAATTGAAGAAAAATGTAAACTACTTGAAAAATTTAGCCTTATTCAA
AAAGAGTATGAAGGCTATGAAGTAGAGTCATCTTTAGAGGATGCCAGCTTTGAGAAGGCGGCAGCAGAAGCACGAAGTTT
GGAGGAAACCTGTGAAAAACTGAACAGGTCCAATTCTGAACTTGAGGATGAAATCCTCTGTCTAGAAATAGAGTTAAAAG
AAGAGAAATCTAAACATTCTCAACAAGATGAATTGATGGCAGATATTTCAAAAAGGATACAATCTCTAGAAGATGAGTCA
AAATCCCTCAAATTACAAATAGCTGAAGCCAAAATCATCTGCAAGATTTTTCAAATGCCTGAAGAACGATGGGCGATAGC
AATAAAAGATGCTTTGAGTGAAAATTCTCAACTTCAGGAAAGCCAGAAACAGCTTTTGCAAGAAGCTGAAGTATGGAAAG
AACAAGTGAGTGAACTTAATAAACAGAAAATAACATTTGAAGACTCCAAAGTACACGCAGAACAAGTTCTAAATGATAAA
GAAAATCACATCAAGACTCTGACTGGACACTTGCTAAAGCTGAAAGATCAGGCTGCTATGCTTGAAGAAGACACAACGGA
TGATGATAACTTGGAATTAGAAGTGAACAGTCAGTCGGAAAATGGTGCTTACTCAGATGATCCTCCAAAAGGAGCTTTGA
AGAAACTGATTCATGCTGCTAAGTTAAATGTTTCTTTAAAAACCTTAGAAGGAGAAAGAAACCACATTATTATTCAGTTA
TCTGAAGTAGACAAAACAAAGGAAGAGCTTACAGAGCATATTAAAAATCTTCAGACTCAACAAGCATCTTTGCAGTCAGA
AAACATATATTTTGAAAGTGAGAATCAGAAGCTTCAACTGAAACTTAAAATAATGACTGAATTATATCAAGAAAATGAAA
TGACACTCCACAGGAAATTGACAATAGAGGAAAACTACCAGATAGAGGAAGAAGAGGAACTTTCTAAAGTGGAAGAAAAG
ATCAGCCATGCCACTGAAGAGCTGGAGACCTATAGAAAGCTAGCCAAAGATCTTGAAGAAGAATTGGAGAGAACTGTTCA
TTTTTATCAAAAGCAGGTTATTTCCTATGAGAAAAAAGGACATGATAATTGGTTGGCAGCTCGGACTGCTGAAAGAAACC
TCAATGATTTAAGGAAAGAAAATGCTCACAACAAACAAAAATTAACTGAAACAGAGTTTAAATTTGAACTTTCAGAAAAA
GATCCTAATGCACTTGATGTTTCAAATACAGCATTTGGCAGAGAGCATTCCCCATATGGTCCCTCACCATTGGGTCGGCC
TTCATCTGAAATGAGAGCTTTTCTCTCTCCTCAAACTTTGTTGGAGGATCCACTCAGACTCTCACCTGTGCTTCCAGGGG
GAGGAGGAAGAAGCCCAAGTGGCCCAGGGAATCCTCTGGACCATCAGATTACCAATAAAAGAGGAGAGCCAAGCTGTGAT
AGGTCAACTGAGGCTCACAGGACTCCTTCTGACACTGGGTCCCTGTCATCTCTGTGGGAACAGGACCGTAGGATGATGTT
TCCTCCACCAGGACAATCATATCCTGATTCAGCTCTTCCTCCACAAAGGGAAGACAGATTTTATTCTAATTCTGATAGAC
TGACTGGACCAGCAGAACTCAGAAGTTTTAATACGCCTTCTTTGGATAAAATGAATGGGTCAATGCCTTCAGAAATGGAA
TCCACTAGAAATGATGCCAAAGATGATCCTGGTAGTTTAAATATGCCTGATTCATCTCTCCCTGCTGAAAATGAAGCAAC
TGGCCCTGGCTTTATTCCTCCACCTCTTGCTCCAATCAGTGGTCCATTGTTTCCAGTGGATACAAGGGGCCCGTTCATGA
GAAGAGGACCTCCTTTCCCCCCACCTCCTCCAGGAACCATGTTTGGAGCTTCACGAGGTTATTTTCTACCAAGGGATTTC
CCAGGTCCACCACATGCTCCATTTGCAATGAGAAACATCTATCCACCGAGGGGTTTACCTCCTTACTTTCATCCAAGACC
TAGATTTTACCCCAACCCCACATTCTGAAGGTAGAAGCGAGTTCCCTTCAGGGTTGATTCTGCCTTCAAAGGAGCCTGCT
ACTGAACATCCAGAACCACAGCAAGAAACC

Alignment

ORF - retro_pabe_2119 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.42 %
• Parental protein coverage: 58.59 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  RVVAALPEGMRPDSNPYGFPWELVICAAVVGFFAVLFFSWRSFRSVSNQCYTKRIPVFSEKQTLLLENKI
          RVVAALPE.MR.DSNPYGFPWELV.CAAVVGFF.VL.F.WRSFRSV....Y..R.....E....L.E.K.
Retrocopy RVVAALPESMRQDSNPYGFPWELVVCAAVVGFFVVLLFLWRSFRSVRSRLYVGREKKLGETLSGLIEEKC

Parental  RRVFTCDVALFQYEGYEVESSLKNASFEKEATEAQSLEATCEKLNRSNSELEDEILCLEKELKEEKSKHS
          ............YEGYEVESSL..ASFEK.A.EA.SLE.TCEKLNRSNSELEDEILCLE.ELKEEKSKHS
Retrocopy KLLEKFSLIQKEYEGYEVESSLEDASFEKAAAEARSLEETCEKLNRSNSELEDEILCLEIELKEEKSKHS

Parental  EQDELMADISKRIQSLEDESKSLKSQVAEAKMTFKIFQMNEERLKIAIKDALNENSELQESQKQLLQDAE
          .QDELMADISKRIQSLEDESKSLK.Q.AEAK...KIFQM.EER..IAIKDAL.ENS.LQESQKQLLQ.AE
Retrocopy QQDELMADISKRIQSLEDESKSLKLQIAEAKIICKIFQMPEERWAIAIKDALSENSQLQESQKQLLQEAE

Parental  VWKEQVSELNKQKVTFEDSKVHAEQVLNDKENHIKTLTERLLKMKDWAAMLGEDITDDDNLELEMNSESE
          VWKEQVSELNKQK.TFEDSKVHAEQVLNDKENHIKTLT..LLK.KD.AAML.ED.TDDDNLELE.NS.SE
Retrocopy VWKEQVSELNKQKITFEDSKVHAEQVLNDKENHIKTLTGHLLKLKDQAAMLEEDTTDDDNLELEVNSQSE

Parental  NGAYLDNPPKGALKKLIHAAKLNASLKTLEGERNQIYIQLSEVDKTKEELTEHIKNLQTEQASLQSENTH
          NGAY.D.PPKGALKKLIHAAKLN.SLKTLEGERN.I.IQLSEVDKTKEELTEHIKNLQT.QASLQSEN..
Retrocopy NGAYSDDPPKGALKKLIHAAKLNVSLKTLEGERNHIIIQLSEVDKTKEELTEHIKNLQTQQASLQSENIY

Parental  FENENQKLQQKLKVMTELYQENEMKLHRKLTVEENYRLEKEEKLSKVDEKISHATEELETYRKRAKDLEE
          FE.ENQKLQ.KLK.MTELYQENEM.LHRKLT.EENY..E.EE.LSKV.EKISHATEELETYRK.AKDLEE
Retrocopy FESENQKLQLKLKIMTELYQENEMTLHRKLTIEENYQIEEEEELSKVEEKISHATEELETYRKLAKDLEE

Parental  ELERTIHSYQGQIISHEKKAHDNWLAARNAERNLNDLRKENAHNRQKLTETELKFELLEKDPYALDVPNT
          ELERT.H.YQ.Q.IS.EKK.HDNWLAAR.AERNLNDLRKENAHN.QKLTETE.KFEL.EKDP.ALDV.NT
Retrocopy ELERTVHFYQKQVISYEKKGHDNWLAARTAERNLNDLRKENAHNKQKLTETEFKFELSEKDPNALDVSNT

Parental  AFGREHSPYGPSPLGWPSSETRAFLSPPTLLEGPLRLSPLLPGGGGRGSRGPGNPLDHQITNERGESSCD
          AFGREHSPYGPSPLG.PSSE.RAFLSP.TLLE.PLRLSP.LPGGGGR...GPGNPLDHQITN.RGE.SCD
Retrocopy AFGREHSPYGPSPLGRPSSEMRAFLSPQTLLEDPLRLSPVLPGGGGRSPSGPGNPLDHQITNKRGEPSCD

Parental  RLTNPHRAPSDTGSLSPPWEQDRRMMFPPPGQSYPDSALPPQRQDRFCSNSGRLSGPAELRSFNMPSLDK
          R.T..HR.PSDTGSLS..WEQDRRMMFPPPGQSYPDSALPPQR.DRF.SNS.RL.GPAELRSFN.PSLDK
Retrocopy RSTEAHRTPSDTGSLSSLWEQDRRMMFPPPGQSYPDSALPPQREDRFYSNSDRLTGPAELRSFNTPSLDK

Parental  MDGSMPSEMESSRNDTKDDLGNLNVPDSSLPTENEATGPGFVPPPLAPIRGPLFPVDTRGPFLRRGPPFP
          M.GSMPSEMES.RND.KDD.G.LN.PDSSLP.ENEATGPGF.PPPLAPI.GPLFPVDTRGPF.RRGPPFP
Retrocopy MNGSMPSEMESTRNDAKDDPGSLNMPDSSLPAENEATGPGFIPPPLAPISGPLFPVDTRGPFMRRGPPFP

Parental  PPPPGAVFGASRDYFPPRDFPGPPHAPFAMRNVYPPR-GFPPYLPPRPGFFPPP-PHSEGRSEFPSGLIP
          PPPPG..FGASR.YF.PRDFPGPPHAPFAMRN.YPPR.GF...L.......P.P.PHSEGRSEFPSGLI.
Retrocopy PPPPGTMFGASRGYFLPRDFPGPPHAPFAMRNIYPPR<GFTSLLSSKT*ILPQP<PHSEGRSEFPSGLIL

Parental  PSNEPATEHPEPQQET
          PS.EPATEHPEPQQET
Retrocopy PSKEPATEHPEPQQET

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	0.00 RPM	8.88 RPM
SRP007412_heart	0.06 RPM	9.60 RPM
SRP007412_kidney	0.00 RPM	44.81 RPM
SRP007412_liver	0.06 RPM	43.09 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_2119 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_2119 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_2119 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pan troglodytes	retro_ptro_1712

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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,