RetrogeneDB ID: retro_pabe_3705

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: X:134930157..134933353(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSPPYG00000001815
• Aliases: None
• Description: None

Sequence

>retro_pabe_3705
GTGAGCTTGGGGCTGTAGGGGGCACTGGAGGTCCAGCTGACACTGGAGACGGTTATCCGGACACTGGAGAGAAGCGTCCT
GGGCCATGAGAAGGGCTTGGGCGCGCAGGACCTGGCCCAGGACACTCAGACCGTTATCCTACCTGCCCGCATCAGGGAGA
TTGTCACCCGCAACCTCTCCCGGCCTGAGAGCCCAGTCCCACTGCGGGCCACAAAGATAGCACTGCTGCTGTCGCTGCAG
AGAAAGAACCAGCTGCTGAAGCAGGAGCTGTCGCGCGCAGAGGACTTACTGGCCCAGAGCCACGCCAAGCGTGATGAGCT
CACCATTAAGCACAATGCGCTGGAGCAGGCTGTGCGTCTGGAGTCTGAGGAGCTGGAGATGCAGGAGCCCGGGGGCTGGT
ACAGCAGAGCGTGGAGTTGCGGAGGCAGCTGCAGGAGGAGCAGGCGTCCTACTGGCCGCAAGCTGCTGGCCTACCAGGAG
GGCCAACAGCGGCAGGCCCAGCTTGTGCAGCAGCTGCAGGCCAAGATTCTCCAGTACAAGAAGAGGTGCTCGGAGCTGGA
GCAGCAGCTGCTGGAGAGATCCGGAGAGCTTGAGCAGCAGCGACTGAGGGACACAGAGCACAGCCAAGACCTGGAGAGCG
CCCTCATTCGGCTGGAGGAGGAGGAGCAGAGGAGTGCCAGCCTGGTCCAGGTGAATGCCATGCTCCGAGAGCAGCTGGAC
CACGCAGGCTCGGCCAGCCAGACTCTGAGTGAGGACATACGAAAGGTGACCAGCGACTGGACACGCAGCCGCAAGGAGCT
GGAGCAGCGGGAGGCGGCATGGAGGCTCGAGGAGGAGTCCTTTAACGCCTACTTCAGCAACGAGCACAGTCGCCTGTTAC
TCCTCTGGAGGCAGGTGGGGGTCAGGTGACTGGTCAGCGAGGTGAAGATGTCCACCGAGAGGGACCTGCTGCAGCTGGGA
GGGGAGCTGGCCTGGACATCATGCGCTGTCCAGGAGGCGGGCCTGGTACTGAGCACGGGCCTGCCGCTGGCAGAGAGCGG
GGCTGAAGCGGCCCTGGAGAAGCAGGCCCTGCTGCAGGCCCAGCTGGAGGAGCAGCTGCGGGACAAGGTGCTCCGTGAGA
AGGACCTGGCCCAGCAGCAGATGCAAAGCGACCTGGACAAGGCCGACCTCAGTGCCAGAGTGACAGAGCTGGCCCTGGCA
GTGGAGCGTCTTCAGAAGCAGAATCTGTAGTAGGATTAGGTCAACAAGCCCCTCGGCAAGCCTGAGGCCCTGGAATCCCT
GCGGCTACAGGAGCAGGTGGCCCTGTAGACAGAGGATGGAGAGGGGCTGCAGCAGACCCTGAGGGACCTCGCACGGGCTG
TCCTGTTGGACACTGAGACGGCGTCCAGCTGAGCGGCTCCGAGCACACCACGGACGCGTCCGAAGGCAGCCTGCGGGGCT
CTCAGGCCAGCGGATCCCATCCCCACCGCAGTGCTCCTCACTGGGCAGCGGCCGTTCGCCCCGCCGAAGCCGGTGCCCGG
CTAGCTCAGACTCCTCCAGGTTAGCCCTGATCCACTCTGCCCTGCGCAAGCGACAGCTGCAAGTCCAGGACATGCATGGG
CACTATGAGGCAAACCAGGACCTGCTGGGCACCCTGTGGAAGCAGCTTAGCGACAGCGAGGTTGAGCGGCGGGCCCTAGA
GGAACAGTTCCAGCACCAGCAGGACAAGACCGATGGCGCCATGCAGGCCCACGAGGACGCCCAGCGCGAGGTACAGAGGC
TGCGGAACGCCAATGAGCTCCTGAGCAGGGAGAAGAGCAACCTGGCCCACAGTCTGCAGGTGGCCCAGCAACAGGCCAAG
GACCTTCTGAAGGAGCGTGAGAAGCTGCAGGCTGCCCAGGAGGAGCTGCGGCGCCAGCGGGACCGATAGGAGGAAAAGCA
GGAGGACGCTGTGCAGGATGGTGCACGGGTGCGCCAGGAGCTTGAGCGCAGCCATAAACAGCTAGAGCAGCTGGAAGGGA
AGCGCTCAGGCCTGGCCAAGGAGCTGGTGGAGGTGAGGGAGGCGCTGAGCTGCTCCACACTGCAGCGGGACATGCTGCAG
GCCGAGAAGGTCGAGGTGGCCGAGGCGCTGACCAAGGTTGAGGCTGGCCAGGTGAAACTCGAGCTCTCCGTGACCAAGCT
GAGGGCAGAGGGGGCCTCCCTGCAGGACTCCCTGTCCAAGCTGAGCGCCCTCAACGAGAGCCTCGCTCAGGATAAGTTGG
ATCTGAACCGCCTTGTCGCCCAGCTGGAGGAAGAAAAGGCAGCCCTGCAGGGCCGCCTGCGGCAGGCGGAGCAGGAAGCC
ACCGTGGCGCAGGAAGAGCAGGAGCGGCTGGAGGAGCTGCGGTTGGAGCAGGAGGTGGCGCGGCAGGGCCTGGAGGGCTC
CCTGCGAGTGGCAGAGGAGGTCCAGGAGGCGCTGGAGCAGCAGCTCCCCACGCTGCGCCATGAGCGCAGCCGGCTGCAGG
AGCAGCTACCCCAGCTCTCCCAGCAGCTGAGCGGGCGGGAGCAGGAGCCGGAGCAGGCTCGGCGGGAGGCACAGTGGCAG
GCAGAGGCGCCGGAGTCAGTGGTCCAGGAGAAGGAGGCGCTAGCCAAGGGGCGCACTGGCCTGGTCATGCAGCTGGCGGC
CGCGCAGCGTGAAGGCAGGACCCTGTCAGAGGAGGCCACACGCCTGCGCTTGGAGAAGGAAGCCCTGGAGAGCAGCCTGT
TTGAGGTGCAAGGGCACCTGGCTCAGCTCGAGGCCCGCTGGGATCAGCTGGAAGCCGATGGGCAGGCCCTGCTGTTGGCC
AAGGAGACCCTGACTGGGGAGCTGGCGGGCCTGCGGCAGCAAATAATAGCTACAAAGGAGAAAGCCAGCCTAGACAAGGA
GCTGATGGCCCAGAAGCTGGTGCAGGCTGAGCAGGAGGCCCAGGCCTCTCTGCGGGAGCAGCGGGCAGCCCATGAGGATG
ACTGGCAGTGAGTCCAGAGCGAAAAGGGGGCAGCATGGTGGGAGCTGGAAGCCGAGCGGGCCCAGCTGCAGAGTCAGCTG
CAGTGCGAGCAGGAGGAGCTGCTGGCCCGACTGGAGATCGAGAAGGAAGAGCTGAGCGAGGAGATCGCTGCCTTGCAGCA
GGAGCGCGACAAGAGCCTCCTCCTGGCCGAGAGCAAGAAGCAGCAGGCCTTGTCTCTGAAGGGGTCTGAAAAGACT

Alignment

ORF - retro_pabe_3705 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.22 %
• Parental protein coverage: 57.4 %
• Number of stop codons detected: 8
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  MSLGLAGAQEVELTLETVIQTLESSVLCQEKGLGAWDLAQDAQITSLPARIREIVTHNLSRPDSPVLLPA
          .SLGL.GA.EV.LTLETVI.TLE.SVL..EKGLGA.DLAQD.Q...LPARIREIVT.NLSRP.SPV.L.A
Retrocopy VSLGL*GALEVQLTLETVIRTLERSVLGHEKGLGAQDLAQDTQTVILPARIREIVTRNLSRPESPVPLRA

Parental  TEMASLLSLQEENQLLQQELSRVEDLLAQSRAERDELAIKYNAVSERLEQGLRLESGELETQEP-RGLVR
          T..A.LLSLQ..NQLL.QELSR.EDLLAQS.A.RDEL.IK.NA....LEQ..RLES.ELE.QEP.RGLV.
Retrocopy TKIALLLSLQRKNQLLKQELSRAEDLLAQSHAKRDELTIKHNA----LEQAVRLESEELEMQEP<RGLVQ

Parental  QSVELRRQLQEEQASY-RRKLQAYQEGQQRQAQLVQRLQGKILQYKKRCSELEQQLLERSGELEQQRLRD
          QSVELRRQLQEEQASY..RKL.AYQEGQQRQAQLVQ.LQ.KILQYKKRCSELEQQLLERSGELEQQRLRD
Retrocopy QSVELRRQLQEEQASY>GRKLLAYQEGQQRQAQLVQQLQAKILQYKKRCSELEQQLLERSGELEQQRLRD

Parental  TEHNQDLESALIRLEEEQQRSASLAQVNAMLREQLDQAGSANQALSEDIRK-TSDWTRSRKELEQREAAW
          TEH.QDLESALIRLEEE.QRSASL.QVNAMLREQLD.AGSA.Q.LSEDIRK.TSDWTRSRKELEQREAAW
Retrocopy TEHSQDLESALIRLEEEEQRSASLVQVNAMLREQLDHAGSASQTLSEDIRKVTSDWTRSRKELEQREAAW

Parental  RREEESFNAYFSNEHSRLLLLWRQVVGFRRLISEVKMFTERDLLQLGGELARTSRAVQEAGLGLSTGLRL
          R.EEESFNAYFSNEHSRLLLLWRQV.G.R.L.SEVKM.TERDLLQLGGELA.TS.AVQEAGL.LSTGL.L
Retrocopy RLEEESFNAYFSNEHSRLLLLWRQV-GVR*LVSEVKMSTERDLLQLGGELAWTSCAVQEAGLVLSTGLPL

Parental  AESRAEAALEKQALLQAQLEEQLRDKVLREKDLAQQQMQSDLDKADLSARVTELTLAVERLQKQNLEKDQ
          AES.AEAALEKQALLQAQLEEQLRDKVLREKDLAQQQMQSDLDKADLSARVTEL.LAVERLQKQNL..D.
Retrocopy AESGAEAALEKQALLQAQLEEQLRDKVLREKDLAQQQMQSDLDKADLSARVTELALAVERLQKQNL**D*

Parental  VNKDLTEKLEALESLRLQEQAALETEDGEGLQQTLRDLAQAVLSDAES-GVQLSGSERTADASEGSLRG-
          VNK.L..K.EALESLRLQEQ.AL.TEDGEGLQQTLRDLA.AVL.D.E..GVQLSGSE.T.DASEGSLRG.
Retrocopy VNKPLG-KPEALESLRLQEQVAL*TEDGEGLQQTLRDLARAVLLDTET<GVQLSGSEHTTDASEGSLRG<

Parental  LSGQRTPSPPRRSSPGRGRSPRRGPSPACSDSSTLALIHSALHKRQLQVQDMRGRYEASQDLLGTLRKQL
          LSGQR.PSPP..SS.G.GRSPRR...PA.SDSS.LALIHSAL.KRQLQVQDM.G.YEA.QDLLGTL.KQL
Retrocopy LSGQRIPSPPQCSSLGSGRSPRRSRCPASSDSSRLALIHSALRKRQLQVQDMHGHYEANQDLLGTLWKQL

Parental  SDSESERRALEEQLQRLRDKTDGAMQAHEDAQREVQRLRSANELLSREKSNLAHSLQVAQQQAEELRQER
          SDSE.ERRALEEQ.Q...DKTDGAMQAHEDAQREVQRLR.ANELLSREKSNLAHSLQVAQQQA..L..ER
Retrocopy SDSEVERRALEEQFQHQQDKTDGAMQAHEDAQREVQRLRNANELLSREKSNLAHSLQVAQQQAKDLLKER

Parental  EKLQAAQEELRRQWDRLEEEQEDAVQDGARVRRELERSHRQLEQLEGKRSVLAKELVEVREALSHATLQR
          EKLQAAQEELRRQ.DR.EE.QEDAVQDGARVR.ELERSH.QLEQLEGKRS.LAKELVEVREALS..TLQR
Retrocopy EKLQAAQEELRRQRDR*EEKQEDAVQDGARVRQELERSHKQLEQLEGKRSGLAKELVEVREALSCSTLQR

Parental  DMLQAEKAEVSEALTKAEAGRVELELSMTKLRAEEASLQDSLSKLSALNESLAQDKLDLNRLVAQLEAEK
          DMLQAEK.EV.EALTK.EAG.V.LELS.TKLRAE.ASLQDSLSKLSALNESLAQDKLDLNRLVAQLE.EK
Retrocopy DMLQAEKVEVAEALTKVEAGQVKLELSVTKLRAEGASLQDSLSKLSALNESLAQDKLDLNRLVAQLEEEK

Parental  AALQGRQRQAEQEATVAREEQERLEELRLEQEVARQGLEGSLRVAEQAQEALEQQLPTLRHERSRLQEQL
          AALQGR.RQAEQEATVA.EEQERLEELRLEQEVARQGLEGSLRVAE..QEALEQQLPTLRHERSRLQEQL
Retrocopy AALQGRLRQAEQEATVAQEEQERLEELRLEQEVARQGLEGSLRVAEEVQEALEQQLPTLRHERSRLQEQL

Parental  AQLSRQLSGREQELEQARREAQWQVEALERAAREKEALAKERAGLAVQLAAAEREGRTLSEEATRLRLEK
          .QLS.QLSGREQE.EQARREAQWQ.EA.E....EKEALAK.R.GL..QLAAA.REGRTLSEEATRLRLEK
Retrocopy PQLSQQLSGREQEPEQARREAQWQAEAPESVVQEKEALAKGRTGLVMQLAAAQREGRTLSEEATRLRLEK

Parental  EALEGSLFEVQRQLAQLEARREQLEAEGQALLLAKETLTGELAGLRQQIIATQEKASLDKELMAQKLVQA
          EALE.SLFEVQ..LAQLEAR..QLEA.GQALLLAKETLTGELAGLRQQIIAT.EKASLDKELMAQKLVQA
Retrocopy EALESSLFEVQGHLAQLEARWDQLEADGQALLLAKETLTGELAGLRQQIIATKEKASLDKELMAQKLVQA

Parental  EREAQASLREQRAAHEEDLQRLQREKEAAWRELEAERAQLQSQLQREQEELLARLEAEKEELSEEIAALQ
          E.EAQASLREQRAAHE.D.Q..Q.EK.AAW.ELEAERAQLQSQLQ.EQEELLARLE.EKEELSEEIAALQ
Retrocopy EQEAQASLREQRAAHEDDWQ*VQSEKGAAWWELEAERAQLQSQLQCEQEELLARLEIEKEELSEEIAALQ

Parental  QERDEGLLLAESEKQQALSLKESEKT
          QERD..LLLAES.KQQALSLK.SEKT
Retrocopy QERDKSLLLAESKKQQALSLKGSEKT

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	11.00 RPM
SRP007412_cerebellum	0.49 RPM	16.29 RPM
SRP007412_heart	0.06 RPM	1.96 RPM
SRP007412_kidney	0.07 RPM	12.30 RPM
SRP007412_liver	0.00 RPM	3.37 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_3705 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_3705 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_3705 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Pongo abelii	ENSPPYG00000001815	1 retrocopy	retro_pabe_3705 ,