RetrogeneDB ID: retro_pabe_712

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 11:75582330..75584044(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ORC3
• Ensembl ID: ENSPPYG00000016830
• Aliases: ORC3, ORC3L
• Description: origin recognition complex, subunit 3 [Source:HGNC Symbol;Acc:8489]

Sequence

>retro_pabe_712
ATGGCCACCTCCTCAGTGTCTAAGGGCTGCTTTGTTTTTAAGCCAAACTCCAAAAACAGAAAGATCTCTGTGCCAATGGA
AGACTATTTTAACAAAGGGAAAAATGAGCCTAAGGACAGTAAGCTTCAATTTGGAACTTAGTTGATATGGCAGCAAATGA
AATCTGAAAATGAGCCACTACAAGAGGAATTAAATAAAAACTTGTTTGACAATCTAACTGAATTTGTGCAAAAATCTCAT
TCTGGATTCCGGAAGGATTCAAGAGACTTGGGCTGTCAAACAAAACTCAGAGAAATTCCAACTGCTGCTCTTGTTCTTGG
TGTGAAAGTCACAGATCATGATTTAACATTCAGAAGTCTAACAGAGGCCCTTCAGAATAAAGTCACACCATATGTAGTCT
CATCGCAAGCTAAAGACTGTCCAGATATGAAACACTTTTTGCAAAAGTTGATCTCACAATTAATGAACTGCTGTGTAGAT
CTAAAATCCAAAGAGGGGGAAAGCATTCAGGTCACCCAGAGAAATACACGTTATTTAATGGATTCACTTTCCAGTTGGTA
CATGACTGTCACACAGAAGACAGACCCAAAAATGCCAAGCAAAAAGAGGACTACTTCTAGCCAATGGCAGTCTCTTCCTG
TTTTGGCTGCCTTAAAGGATATGGAAAGCTTTGCCACAAAAGTACTGCAAGACTTCATAATTATCAGCAGTCAACATCTG
CATGAATTTCCACTAATATTCATTTTTGGAATCGCCACTTCTATTATCAACCACTGATTGTTTCCTCATGCAGTATCATC
TCTATTGTGCATAGAACTGTTCCAATTTTTGTCTTGCAAGGAGCATCTGACTATGGTACTCAATAAGCTACTTCTTACAA
CTCAGTTTCCCTTTAAAATAAGTGAAAAAATATTGCAGGTTCTGACCAACATCTTTTTGTATCGTGATTTCTCAATTCAA
AACTTTATAAAAGGCTTCAACTTTCTCTATTAGGGCATTTCTGTTCCCAGCCCTTAAGTGTCCTGTGCTGTAATCTTCCA
GAAGACAAAAGAAGAATAAATTTCTTATCAAATAATCAATGTGAAAACATCTGATGTCTTCCATCTTTTAGGAGATACGT
GGAAAAGCAAGCTTCAGAAAAGCAAGTTGTGCTCTTGACCAGTGAGAGATGTTTGAAGGAGGAAACACAATTATTACTAG
AAAACCTGCATGTTTATCACATGAATTACTTTCTGGCTTTGAGATGTGTTCATAAGTTCACCTCTTCTCTTCCCAAATAT
CCACTAGGTCGACAGATCAGAGAGCTGTACCGCACATGTTTAGAAAAGAACATCCGGAATTCAGAGGAATATGCATCAGT
CTTGCAGCTGCTGAAGATGTTGGCAAAGGATGAACTGATGACCATACTTGAGAAATGTTTCAAGGTTTTTAAATCTTCTT
GTGAAAAGCACCTTGGCAGCACAGCTAAGAGAATACAGGAGTTCCTGGCCTAGTTTCAGAGCCTTGATGAAACCAAAGAG
GTAGAAGATGCTTCTGGTTCATAGCCAAAGGGGCTTCAGAAGACAGACCTCTATCATCTTCAGAAGTCTTTACTGGAAAT
GCAGGAGTTAAGCAGAAGTAAAAAGCAAACCAAATTTGAAGTACTCAGAGAAAAGGTTGTGAACTTCATGACTGTCTAGT
GAGAGAATACCTTCTGCCTCCTGAGACACAGCCT

Alignment

ORF - retro_pabe_712 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.15 %
• Parental protein coverage: 80.73 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MATSSMSKGCFVFKPNSKKRKISLPIDDYFKKGKNEPEDSKLRFETYQLIWQQMKSENERLQEELNKNLF
          MATSS.SKGCFVFKPNSK.RKIS.P..DYF.KGKNEP.DSKL.F.T..LIWQQMKSENE.LQEELNKNLF
Retrocopy MATSSVSKGCFVFKPNSKNRKISVPMEDYFNKGKNEPKDSKLQFGT*-LIWQQMKSENEPLQEELNKNLF

Parental  DSLIEFLQKSHSGFQKNSRDLGGQIKLREIPTAALVLGVNVTDHDLTFRSLTEALQNNVTPYVISLQAKD
          D.L.EF.QKSHSGF.K.SRDLG.Q.KLREIPTAALVLGV.VTDHDLTFRSLTEALQN.VTPYV.S.QAKD
Retrocopy DNLTEFVQKSHSGFRKDSRDLGCQTKLREIPTAALVLGVKVTDHDLTFRSLTEALQNKVTPYVVSSQAKD

Parental  CPDMKHFLQKLVSQLMDCCVDIKSKEEESVQVTQRKTHYSMDSLSSWYMTVTQKTDPKMLSKKRTTSSQW
          CPDMKHFLQKL.SQLM.CCVD.KSKE.ES.QVTQR.T.Y.MDSLSSWYMTVTQKTDPKM.SKKRTTSSQW
Retrocopy CPDMKHFLQKLISQLMNCCVDLKSKEGESIQVTQRNTRYLMDSLSSWYMTVTQKTDPKMPSKKRTTSSQW

Parental  QSPPVVVILKDMESFATKVLQDFIIISSQHLHEFPLILIFGIATSPIIIHRLLPHAVSSLLCIELFQSLS
          QS.PV...LKDMESFATKVLQDFIIISSQHLHEFPLI.IFGIATS.II.H.L.PHAVSSLLCIELFQ.LS
Retrocopy QSLPVLAALKDMESFATKVLQDFIIISSQHLHEFPLIFIFGIATS-IINH*LFPHAVSSLLCIELFQFLS

Parental  CKEHLTTVLDKLLLTTQFPFKINEKVLQVLTNIFLYHDFSIQNFIKG-LQLSLLEHFYSQPLSVLCCNLP
          CKEHLT.VL.KLLLTTQFPFKI.EK.LQVLTNIFLY.DFSIQNFIKG.LQLSLL.HF.SQPLSVLCCNLP
Retrocopy CKEHLTMVLNKLLLTTQFPFKISEKILQVLTNIFLYRDFSIQNFIKG<LQLSLLGHFCSQPLSVLCCNLP

Parental  EAKRRINFLSNNQCENIRRLPSFRRHVEKQASEKQVALLTNERCLKEETQLLLENLHIYHMNYFLVLRCL
          E.KRRINFLSNNQCENI..LPSFRR.VEKQASEKQV.LLT.ERCLKEETQLLLENLH.YHMNYFL.LRC.
Retrocopy EDKRRINFLSNNQCENI*CLPSFRRYVEKQASEKQVVLLTSERCLKEETQLLLENLHVYHMNYFLALRCV

Parental  HKFTSSLPKYPLGRQIRELYCTCLEKNIWDSEEYASVLQLLRMLAKDELMTILEKCFKVFKSYCENHLGS
          HKFTSSLPKYPLGRQIRELY.TCLEKNI..SEEYASVLQLL.MLAKDELMTILEKCFKVFKS.CE.HLGS
Retrocopy HKFTSSLPKYPLGRQIRELYRTCLEKNIRNSEEYASVLQLLKMLAKDELMTILEKCFKVFKSSCEKHLGS

Parental  TAKRIEEFLAQFQSLDETKEEEDASGSQPKGLQKTDLYHLQKSLLEMKELRRSKKQTKFEVLRENVVNFI
          TAKRI.EFLA.FQSLDETKE.EDASGS.PKGLQKTDLYHLQKSLLEM.EL.RSKKQTKFEVLRE.VVNF.
Retrocopy TAKRIQEFLA*FQSLDETKEVEDASGS*PKGLQKTDLYHLQKSLLEMQELSRSKKQTKFEVLREKVVNFM

Parental  -DCLVREYLLPPETQP
          .DCLVREYLLPPETQP
Retrocopy <DCLVREYLLPPETQP

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	6.30 RPM
SRP007412_cerebellum	0.00 RPM	13.86 RPM
SRP007412_heart	0.00 RPM	5.12 RPM
SRP007412_kidney	0.00 RPM	5.40 RPM
SRP007412_liver	0.03 RPM	4.41 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_712 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_712 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_712 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_798
Pan troglodytes	retro_ptro_555

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000000730	1 retrocopy	retro_cjac_913,
Homo sapiens	ENSG00000135336	1 retrocopy	retro_hsap_798,
Macaca mulatta	ENSMMUG00000002821	1 retrocopy	retro_mmul_1075,
Nomascus leucogenys	ENSNLEG00000012990	1 retrocopy	retro_nleu_413,
Pongo abelii	ENSPPYG00000016830	1 retrocopy	retro_pabe_712 ,
Pan troglodytes	ENSPTRG00000018408	1 retrocopy	retro_ptro_555,