RetrogeneDB ID: retro_pabe_1060

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 13:76660710..76663060(-)
• 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_1060
AGAGGTGTGGCAGCACTACCTGAGAGTACGAGAGCAGATTCGAATCCTTATGGTTTTCCATGGGAACCGGTGGTATGTGC
AGCTGTTGTTGGATTGTTTGTTGTTCTCCTTTTTTTGTGGAGAAGTTTTAGATCGGTTAGGAGTCGGCTTTATGTGGGAA
GAGAGAAAAAACTTGGTGAAACGCTTTCTGGACTAATTGAAGAAAAATGTAAACTACTTGAAAAATTTAGCCTTATTCAA
AAAGAGTATGAAGGCTATGAAGTAGAGTCATCTTTAGAGGATGCCAGCTTTGAGAAGGCGGTAGCAGAAGCACGAAGTTT
GGAGGCAACCTGTGAAAAGCTGAACAGGTCCAATTCTGAACTTGAGGATGAAATCCTCTGTCTAGAAAAAGAGTTAAAAG
AAGAGAAATCTAAACATTCTCAACAGGATGAATTGATGGCAGATATTTCAAAAAGGATACAATCTCTAGAAGATGAGTCA
AAATCCCTCAAATCACAGATAGCTGAAGCCAAAATCATCTGCAAGATTTTTCAAACGAATGAAGAACGATGGGCGATAGC
AATAAAAGATGCTTTGAGTGAAAATTCTCAACTTCAGGAAAGCCAGAAACAGCTTTTGCAAGAAGCTGAAGTATGGAAAG
AACAAGTGAGTGAACTTAATAAACAGCAAATAACATTTGAAGACTCCAAAGTACATGCAGGACAAGTTCTAAATGATAAA
GAAAATCATATCAAGACTCTGACTGGACACTTGCTAAAGATGAAAGATCAGGCTGCTATGCTTGAAGAAGACACAACGGA
TGATGATAACTTGGAATTAGAAGTGAACAGTCAATCAGAAAACGGTGCTTACTTAGATGATCCTCCAAAAGGAGCTTTGA
AGAAACTGATTCATGCTGCTAAGTTAAATTTTTCTTTAAAAATCTTAGAAGGAGAAAGAAACCACATTATTATTCAGTTA
TCTGAAGTGGACAAAACAAAGGAAGAGCTTACAGAGCATATTAAAAATCTTCAGACTCAACAAGCATCTTTGCAGTCAGA
AAACATATATTTTGAAAGTGAGAAACAGAAGCTTCAACAGAAACTTAAAATAATGACTGAATTATATCAAGAAAATGAAA
TGACACTCCACAGGAAATTGACAATAGAGGAAAATTACCGGATAGAAGAAAAAGAGAAGCCTTCTAAAGTGGAAGAAAAG
ATGAGCCATGCCACTGAAGAGCTGGAGACCTATAGAAAGCTAGCCAAAGATCTTGAAGAAGAATTGGAGAGAACTGTTCA
TTTTTATCAAAAGCAGGTTATTTCCTATGAGAAAAAAGGACATGATAATTGGTTGGCAGCTTGGACTGCTGAAAGAAACC
TCAATGATTTAAGGAAAGAAAATGCTCACAACAAACAAAAATTAACTGAAACAGAGTTTAAATTTGAACTTTTAGAAAAA
GATCCTAATGCACTTGATGTTTCAAACCCAGCATCTGGCAGAGAGCATTCCCCATATGGTCCCTCACCATTGGGTCAGCC
TTCATCTGAAACGAGAGCTTTCCTCTCTCCTCAAACTTTGTTGGAGGGTCCACTCAGACTCTCACCTGTGCTTCCAGTGG
GAGGAGGAAGAAGCCCAAGCAGCCCAGGGAATCCTCTGGACCATAAGATTACCAATGAAAGAGGAGAACCAAGCTGTGAT
AGGTTAACTGATCCTCACAGGGCTCCTTCTGACACTGGGTCCCTGTCATCTCCATGGGAACAGGACCGTAGGATGATGTT
TCCTCCACCAGGACAATCATATCCTGATTCAGCTCTTCCTCCACAAAGGGAAGACAGATTTTATTCTAATTCTGATAGAC
TGTCTGGACCAGCAGAACTCAGAAGTTTTAATATGCCTTCTTTGGATAAAATGGATGGGTCAATGCCTTCAGAAATGGAA
TCCACTAGAAATGATGCCAAAGATGATCCTGGTAGTTTAAGTGTGCCTGATTCATCTCTCCCTGCTGAAAATGAAGCAAC
TGGCCCTGGCTTTATTCCTCCACCTCTTGCTCCAATCAGCGGTCCGTTGTTTCCAGTGGATACAAGGGGCCCGTTCATGA
GAAGAGGACCTCCTTTCCCCCAACCTCCTCCAGGAACCATGTTTGGAGCTTCACGAGGTTATTTTCCACCAAGGGATTTC
CCAGGTCCACCACATGCTCCATTTGCAATGAGAAACATCTGTCCACCGAGGGGTTTACCTCCTTACTTTCATCCAAGACC
TGGATTTTACCCCAACCCCACATTCTGAAGGTAGAAGCGAGTTCCCTTCGTGGTTGATTCTGCCTTCAAAGGAGCCTGCT
ACTTAACATCCAGAACCACAACAAGAAACC

Alignment

ORF - retro_pabe_1060 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.17 %
• Parental protein coverage: 58.59 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  RVVAALPEGMRPDSNPYGFPWELVICAAVVGFFAVLFFSWRSFRSVSNQCYTKRIPVFSEKQTLLLENKI
          R.VAALPE..R.DSNPYGFPWE.V.CAAVVG.F.VL.F.WRSFRSV....Y..R.....E....L.E.K.
Retrocopy RGVAALPESTRADSNPYGFPWEPVVCAAVVGLFVVLLFLWRSFRSVRSRLYVGREKKLGETLSGLIEEKC

Parental  RRVFTCDVALFQYEGYEVESSLKNASFEKEATEAQSLEATCEKLNRSNSELEDEILCLEKELKEEKSKHS
          ............YEGYEVESSL..ASFEK...EA.SLEATCEKLNRSNSELEDEILCLEKELKEEKSKHS
Retrocopy KLLEKFSLIQKEYEGYEVESSLEDASFEKAVAEARSLEATCEKLNRSNSELEDEILCLEKELKEEKSKHS

Parental  EQDELMADISKRIQSLEDESKSLKSQVAEAKMTFKIFQMNEERLKIAIKDALNENSELQESQKQLLQDAE
          .QDELMADISKRIQSLEDESKSLKSQ.AEAK...KIFQ.NEER..IAIKDAL.ENS.LQESQKQLLQ.AE
Retrocopy QQDELMADISKRIQSLEDESKSLKSQIAEAKIICKIFQTNEERWAIAIKDALSENSQLQESQKQLLQEAE

Parental  VWKEQVSELNKQKVTFEDSKVHAEQVLNDKENHIKTLTERLLKMKDWAAMLGEDITDDDNLELEMNSESE
          VWKEQVSELNKQ..TFEDSKVHA.QVLNDKENHIKTLT..LLKMKD.AAML.ED.TDDDNLELE.NS.SE
Retrocopy VWKEQVSELNKQQITFEDSKVHAGQVLNDKENHIKTLTGHLLKMKDQAAMLEEDTTDDDNLELEVNSQSE

Parental  NGAYLDNPPKGALKKLIHAAKLNASLKTLEGERNQIYIQLSEVDKTKEELTEHIKNLQTEQASLQSENTH
          NGAYLD.PPKGALKKLIHAAKLN.SLK.LEGERN.I.IQLSEVDKTKEELTEHIKNLQT.QASLQSEN..
Retrocopy NGAYLDDPPKGALKKLIHAAKLNFSLKILEGERNHIIIQLSEVDKTKEELTEHIKNLQTQQASLQSENIY

Parental  FENENQKLQQKLKVMTELYQENEMKLHRKLTVEENYRLEKEEKLSKVDEKISHATEELETYRKRAKDLEE
          FE.E.QKLQQKLK.MTELYQENEM.LHRKLT.EENYR.E..EK.SKV.EK.SHATEELETYRK.AKDLEE
Retrocopy FESEKQKLQQKLKIMTELYQENEMTLHRKLTIEENYRIEEKEKPSKVEEKMSHATEELETYRKLAKDLEE

Parental  ELERTIHSYQGQIISHEKKAHDNWLAARNAERNLNDLRKENAHNRQKLTETELKFELLEKDPYALDVPNT
          ELERT.H.YQ.Q.IS.EKK.HDNWLAA..AERNLNDLRKENAHN.QKLTETE.KFELLEKDP.ALDV.N.
Retrocopy ELERTVHFYQKQVISYEKKGHDNWLAAWTAERNLNDLRKENAHNKQKLTETEFKFELLEKDPNALDVSNP

Parental  AFGREHSPYGPSPLGWPSSETRAFLSPPTLLEGPLRLSPLLPGGGGRGSRGPGNPLDHQITNERGESSCD
          A.GREHSPYGPSPLG.PSSETRAFLSP.TLLEGPLRLSP.LP.GGGR....PGNPLDH.ITNERGE.SCD
Retrocopy ASGREHSPYGPSPLGQPSSETRAFLSPQTLLEGPLRLSPVLPVGGGRSPSSPGNPLDHKITNERGEPSCD

Parental  RLTNPHRAPSDTGSLSPPWEQDRRMMFPPPGQSYPDSALPPQRQDRFCSNSGRLSGPAELRSFNMPSLDK
          RLT.PHRAPSDTGSLS.PWEQDRRMMFPPPGQSYPDSALPPQR.DRF.SNS.RLSGPAELRSFNMPSLDK
Retrocopy RLTDPHRAPSDTGSLSSPWEQDRRMMFPPPGQSYPDSALPPQREDRFYSNSDRLSGPAELRSFNMPSLDK

Parental  MDGSMPSEMESSRNDTKDDLGNLNVPDSSLPTENEATGPGFVPPPLAPIRGPLFPVDTRGPFLRRGPPFP
          MDGSMPSEMES.RND.KDD.G.L.VPDSSLP.ENEATGPGF.PPPLAPI.GPLFPVDTRGPF.RRGPPFP
Retrocopy MDGSMPSEMESTRNDAKDDPGSLSVPDSSLPAENEATGPGFIPPPLAPISGPLFPVDTRGPFMRRGPPFP

Parental  PPPPGAVFGASRDYFPPRDFPGPPHAPFAMRNVYPPR-GFPPYLPPRPGFFPPP-PHSEGRSEFPSGLIP
          .PPPG..FGASR.YFPPRDFPGPPHAPFAMRN..PPR.GF...L.......P.P.PHSEGRSEFPS.LI.
Retrocopy QPPPGTMFGASRGYFPPRDFPGPPHAPFAMRNICPPR<GFTSLLSSKTWILPQP<PHSEGRSEFPSWLIL

Parental  PSNEPATEHPEPQQET
          PS.EPAT.HPEPQQET
Retrocopy PSKEPAT*HPEPQQET

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	5.20 RPM
SRP007412_cerebellum	0.00 RPM	8.88 RPM
SRP007412_heart	0.00 RPM	9.60 RPM
SRP007412_kidney	0.00 RPM	44.81 RPM
SRP007412_liver	0.00 RPM	43.09 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_1060 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_1060 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_1060 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pan troglodytes	retro_ptro_876

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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,