RetrogeneDB ID: retro_pabe_1007

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 13:59212458..59214806(+)
• 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_1007
AGGGTTATGGCAGCACTGACTGAAGGCAGGAGACCAGATTCGAATCCTTATGGATTTCCATGGGAATTGGTGGTATGTGC
AGCTGTCATTGGATTTTTTGCTGTTCCCTTTTTCTTGTGGAGAAGTTTTAGATCGGTTAGGAGTCGGCTTTATGTGGGAA
GAGAGAAAAAGCTTGCTGTAGCACTTTCTGGACTAATTGAAGAAAAATGTAGACTACTTGAAAAATTTAGCCTTGTTCAA
AAAGAGTATGAAGGCTATGAAGTGGAGTCATCTTTAGAGGATGCCAGCTTTGAGAAGGAGACAACAGAAGCACAAAGTTT
GGAGGCAACCTGTGAAAAGCTGAACAGGTCCAATTCTGAACTGGAGCATGAAATACTCTGTCTAGAAAAGGAGTTAAAAG
AAAGGAAATCTAAACATTCTGAACAAGATGAGGTGATGGCGGATATTTCCAAAAGGATACAGTCTCTAGAAGATGAGTCA
AAATCCCTCAAATCCCAAGTAGCTGAAGCCAAAATGACCTTCAAGAGATTTCAAATGAATGAAGAACAAATGAAGATAGG
AATACAAGATGCTTTGAATGAAAATTCTCAACTTCAGGAAAGCCAGAAACAGCTTTTGCAAGAAGCTGAAGTATGGAAAG
AACAAGTGAGTGAACTTAATAAACAGAAAATAGCATTTGAAGACTCCAAAGTACATGCAGAACAAGTTCTAAATGATAAA
GAAAATCACATCAAGACTCTGACTGAACACTTGCTAAAGATCAAAGATCAGGCTGCTATGCTGGAAGAAGACATAACAGA
TGATAGTAACTTGGAATTAGAAATGAACAGTGAATCAGAAGATGGTGCTTACTTAGATAATCCTCCAAAAGGAGCTTTGA
AGAAACTGCTTCATGCTGCTAAGTTAAATGCTTCTTTAACAACCTTAGAAGGAGAAAGAAACCAAATTTATATTCAGTTA
TCTGAAGTTGATAAAACCAAGGAAGAGCTTAGAGAGCATATTAAAAATCTTCAGACGGAACAAGCATCTTTGCAGTTGGA
AAACACACATTTTGAAAGTGAGAATCAGAAGCTTCAACAGAAACTTAAGGTAATGACAGAATTATATCAAGAAAATGAAA
TGAAACTCTGCAGGAAATTAATAGTAGAAGAAAATAACCGGCTAGAGAAAGAGAAACTTTCTAAAGTAGATGAAATGATC
AGCCATACTGCTGAAGAGCTGGAGACCTGCAGAAATCGAGTCAGAGATCTTGAAGAAGAATTTGAGAGATCTATTCATTT
TTATCAAGGGAAGATTATATACCATGAGAAAAAAACACACAATAATTGTTTGGCCGCATGGACTGCTGAAAGAAACCTCA
ATGATTTAAGGAAAGAAAATGCTCACAATAGACAAAAATTAGCTGAAACAGAGTTTAAAATTAAACTTTTAGGAAAAGAT
CCTTATGCACTTGATATTCCAAATACAGCATTTGGCAGAGAGCTTTCCTCATATGGTCCCTCACCACTGGGTCGGCCTTC
ATCTGAAACGAGAGCTTTTCTCTATCCTCCAACTTTGTTGGAGGGTCCACTCAGACTCTCACCTTTGCTTCCAGGGGGAG
GAGGAAGAGGCCCAAGAGGCCCAGGGAATCCTCTGGACCATCAGACTACCAAAGAAAGAGGAGAATCAAGCTGTGATAGG
TTTACCTATCCTCACAGGGCTCCTTCTGACACTGGGTTCCTCTCACCTCCATGGGAACAGGACCGTAGGATGATGTCTCC
TCCACCAGGACAATCATATCCTGATTCATCTCTTCCTCCACAAAGGCAAGACAGATTTCATTCTAATTGTGCTAGACGCT
CTGGACCAGCAGAACTCAGAAGTTTTAATATGCCTTCTTTGGATAAAATGGATGGGTCAATGCCTTCAGAAATGGAATCC
AGTAGAAATGATACCAAAGATAATCTTGGTAATTTAAATGTGCCTGATTCATCTCTCCCCGCTGGAAATGAAGCGACTGG
CCCTGGCTTTGTCCCTCCACCTCTTGCTCCAATCAGAGGTCCATTGTTTCCGGTGGATATGAGGGGCCCGTTCATGAGAA
GAGGACCTCCTTTCCCTCCACCTCCTCCAGGAACCATGTTTGGAGCTTCTCCAGATTATTTTCCACCAAAGGATGTCCCA
GGTCCACCACGTGCTTCATTTGCAATGAGAAACGTCTATCCACCAAGGGGTTTTCCTCCTTACCTTCCCCCAAGACTTGG
ATTTCCCCCCTCACCCCCACATTCTGAAGATAGAGTGAGTTTCCTTCAGGGTTGAGTCTGCCTTCAAATGAGCCTGCTAC
TGAAGATCCAGAACCACAGCAAGAAACC

Alignment

ORF - retro_pabe_1007 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.95 %
• Parental protein coverage: 58.59 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  RVVAALPEGMRPDSNPYGFPWELVICAAVVGFFAVLFFSWRSFRSVSNQCYTKRIPVFSEKQTLLLENKI
          RV.AAL.EG.RPDSNPYGFPWELV.CAAV.GFFAV.FF.WRSFRSV....Y..R..........L.E.K.
Retrocopy RVMAALTEGRRPDSNPYGFPWELVVCAAVIGFFAVPFFLWRSFRSVRSRLYVGREKKLAVALSGLIEEKC

Parental  RRVFTCDVALFQYEGYEVESSLKNASFEKEATEAQSLEATCEKLNRSNSELEDEILCLEKELKEEKSKHS
          R...........YEGYEVESSL..ASFEKE.TEAQSLEATCEKLNRSNSELE.EILCLEKELKE.KSKHS
Retrocopy RLLEKFSLVQKEYEGYEVESSLEDASFEKETTEAQSLEATCEKLNRSNSELEHEILCLEKELKERKSKHS

Parental  EQDELMADISKRIQSLEDESKSLKSQVAEAKMTFKIFQMNEERLKIAIKDALNENSELQESQKQLLQDAE
          EQDE.MADISKRIQSLEDESKSLKSQVAEAKMTFK.FQMNEE..KI.I.DALNENS.LQESQKQLLQ.AE
Retrocopy EQDEVMADISKRIQSLEDESKSLKSQVAEAKMTFKRFQMNEEQMKIGIQDALNENSQLQESQKQLLQEAE

Parental  VWKEQVSELNKQKVTFEDSKVHAEQVLNDKENHIKTLTERLLKMKDWAAMLGEDITDDDNLELEMNSESE
          VWKEQVSELNKQK..FEDSKVHAEQVLNDKENHIKTLTE.LLK.KD.AAML.EDITDD.NLELEMNSESE
Retrocopy VWKEQVSELNKQKIAFEDSKVHAEQVLNDKENHIKTLTEHLLKIKDQAAMLEEDITDDSNLELEMNSESE

Parental  NGAYLDNPPKGALKKLIHAAKLNASLKTLEGERNQIYIQLSEVDKTKEELTEHIKNLQTEQASLQSENTH
          .GAYLDNPPKGALKKL.HAAKLNASL.TLEGERNQIYIQLSEVDKTKEEL.EHIKNLQTEQASLQ.ENTH
Retrocopy DGAYLDNPPKGALKKLLHAAKLNASLTTLEGERNQIYIQLSEVDKTKEELREHIKNLQTEQASLQLENTH

Parental  FENENQKLQQKLKVMTELYQENEMKLHRKLTVEENYRLEKEEKLSKVDEKISHATEELETYRKRAKDLEE
          FE.ENQKLQQKLKVMTELYQENEMKL.RKL.VEEN.RLEKE.KLSKVDE.ISH..EELET.R.R..DLEE
Retrocopy FESENQKLQQKLKVMTELYQENEMKLCRKLIVEENNRLEKE-KLSKVDEMISHTAEELETCRNRVRDLEE

Parental  ELERTIHSYQGQIISHEKKAHDNWLAARNAERNLNDLRKENAHNRQKLTETELKFELLEKDPYALDVPNT
          E.ER.IH.YQG.II.HEKK.H.N.LAA..AERNLNDLRKENAHNRQKL.ETE.K..LL.KDPYALD.PNT
Retrocopy EFERSIHFYQGKIIYHEKKTHNNCLAAWTAERNLNDLRKENAHNRQKLAETEFKIKLLGKDPYALDIPNT

Parental  AFGREHSPYGPSPLGWPSSETRAFLSPPTLLEGPLRLSPLLPGGGGRGSRGPGNPLDHQITNERGESSCD
          AFGRE.S.YGPSPLG.PSSETRAFL.PPTLLEGPLRLSPLLPGGGGRG.RGPGNPLDHQ.T.ERGESSCD
Retrocopy AFGRELSSYGPSPLGRPSSETRAFLYPPTLLEGPLRLSPLLPGGGGRGPRGPGNPLDHQTTKERGESSCD

Parental  RLTNPHRAPSDTGSLSPPWEQDRRMMFPPPGQSYPDSALPPQRQDRFCSNSGRLSGPAELRSFNMPSLDK
          R.T.PHRAPSDTG.LSPPWEQDRRMM.PPPGQSYPDS.LPPQRQDRF.SN..R.SGPAELRSFNMPSLDK
Retrocopy RFTYPHRAPSDTGFLSPPWEQDRRMMSPPPGQSYPDSSLPPQRQDRFHSNCARRSGPAELRSFNMPSLDK

Parental  MDGSMPSEMESSRNDTKDDLGNLNVPDSSLPTENEATGPGFVPPPLAPIRGPLFPVDTRGPFLRRGPPFP
          MDGSMPSEMESSRNDTKD.LGNLNVPDSSLP..NEATGPGFVPPPLAPIRGPLFPVD.RGPF.RRGPPFP
Retrocopy MDGSMPSEMESSRNDTKDNLGNLNVPDSSLPAGNEATGPGFVPPPLAPIRGPLFPVDMRGPFMRRGPPFP

Parental  PPPPGAVFGASRDYFPPRDFPGPPHAPFAMRNVYPPRGFPPYLPPRPGFFPPPPHSEGR-SEFPSGLIPP
          PPPPG..FGAS.DYFPP.D.PGPP.A.FAMRNVYPPRGFPPYLPPR.GF.P.PPHSE.R.SEFPSGL..P
Retrocopy PPPPGTMFGASPDYFPPKDVPGPPRASFAMRNVYPPRGFPPYLPPRLGFPPSPPHSEDR<SEFPSGLSLP

Parental  SNEPATEHPEPQQET
          SNEPATE.PEPQQET
Retrocopy SNEPATEDPEPQQET

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	0.03 RPM	9.60 RPM
SRP007412_kidney	0.03 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_1007 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_1007 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_1007 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pan troglodytes	retro_ptro_826

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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,