RetrogeneDB ID: retro_ptro_555

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 11:77808922..77810636(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ORC3
• Ensembl ID: ENSPTRG00000018408
• Aliases: ORC3, ORC3L
• Description: None

Sequence

>retro_ptro_555
ATGGCCACCTCCTCAGTGTCTAAGGGCTGCTTTGTTTTTAAGCCAAACTCCAAAAAGAGAAAGATCTCTGTGCCAATGGA
GGACTATTTTAACAGAGGGAAAAATGAGCCTAAGGACAGTAAGCTTCAATTTGGAACTTAGTTGATATGGCAGCAAATGA
AATCTGAAAATGAGCCACTACAAGAGGAATTAAATAAAAACTTGTTTGACAATCTAACTGAATTTCTGCAAAAATCTCAT
TCTGGATTCCAGAAGAATTCAAGAGACTTGGGCTGTCAAACAAAACTCAGAGAAATTCCAACTGCTGCTCTTGTTCTTGG
TGTGAAAGTTACAGATCATGATTTAACATTCAGAAGTCTAACAGAGGCCCTTCAGAATAAAGTCACACCATATGTAGTCT
CATCGCAAGCTAAAGACTGTCCAGATATGAAACGTTTTTTGCAAAAGTTGGTCTCATAATTAATGAACTGCTGTGTACAT
CTAAAATCCAAAGAGGGGGAAAGCGTTCAGGTCACCCAGAGAAATACACATTATTTAATGGATTCACTTTCCAGTTGGTA
CATGACTGTCACACAGAAGACAGATCCAAAAATGCCAAGCAAAAAGAGGACTACTTCTAGCCAATGGCAGTCTCCTCCTG
TTTTGGCTACCTTAAAGGATATGGAAAGCTTTGCCACAAAAGTACTGCAAGATTTCATAATTATCAGCAGTCAACATCTG
CATGAATTTCCACTAATACTCATTGTGGGAATCGCCACATCTATTATCAACCACCGATTGTTTCCTCATGCAGTATCATC
TCTGTTGTGCATAGAACTGTTCCAATTTTTGTCTTGCAAGGAGCATCTGACTATGGTACTCAATAAGCTACTTCTTACAA
CTCAGTTTCCCTTTAAAATAAATGAAAAAGTATTGCAGGTTCTGACCAACATCTTTTTGTATCATGATTTCTCGATTCAA
AACTTTATAAAAGGCTTCAACTTTCTTTATTAGAGCATTTCTGTTCCCAGCCCTTAAGTGTCCTGTGCTGTAATCTTCCA
TAAGTCAAAAGAAGAATAAATTTTTTATCAAATAATCAATGTGAAAACATCTGACGTCTTCCATCTTTTAGGAGATATGT
GGAAAAGCAAGCTTCAGAAAAGCAAGTTGTGCTCTTGACCAGTGAGAGATGTTTGAAGGAGGAAACACAATTATTACTAG
AAAACCTGCATGTTTATCATATGAATTACTTTCTGGTTTTGAGATGTGTTCATAAGTTCACCTCTTCTCTTCCCAAGTAT
CCACTAGGTCGACAGATCAGAGAGTTGTACCGCACATGTTTAGAAAAGAACATCCGGAATTCAGAGGAGTATGCATCAGT
CTTGCAGCTGCTGAAGATGTTGGCAAAGGATGAACTGATGACCATACTTGAGAAATGTTTCGAGGTTTTTATATCTTCTT
GTGAAAAGCACCTTGGCAGCACAGCTAAGAGAATACAGGAATTCCTGGCCCAGTTTCAGAGCTTCGATGAAACCAAAGAG
GTAGAAGATGCTTCTGGTTCATAGCCAAAGGGGCTTCAGAAGGCAGACCTCTATCATCTTCAGAAGTCTTTACTGGAAAT
GAAGGAGTTAAGCAGAAGTAAAAAGCAAACCAAATTTGAAGTACTCAGAGAAAAGGCTGTGAACTTCATGACTGTCTAGT
GAGAGAATACCTTCTGCCTCCTGAGACACAGCCT

Alignment

ORF - retro_ptro_555 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.19 %
• Parental protein coverage: 80.73 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MATSSMSKGCFVFKPSSKKRKISLPIEDYFNKGKNEPEDSKLRFETYQLIWQQMKSENERLQEELNKNLF
          MATSS.SKGCFVFKP.SKKRKIS.P.EDYFN.GKNEP.DSKL.F.T..LIWQQMKSENE.LQEELNKNLF
Retrocopy MATSSVSKGCFVFKPNSKKRKISVPMEDYFNRGKNEPKDSKLQFGT*-LIWQQMKSENEPLQEELNKNLF

Parental  GNLIEFLQKSHSGFQKNSRDLGGQIKLREIPTAALVLGVNVTDHDLTFRSLTEALQNNVTPYVVSLQAKD
          .NL.EFLQKSHSGFQKNSRDLG.Q.KLREIPTAALVLGV.VTDHDLTFRSLTEALQN.VTPYVVS.QAKD
Retrocopy DNLTEFLQKSHSGFQKNSRDLGCQTKLREIPTAALVLGVKVTDHDLTFRSLTEALQNKVTPYVVSSQAKD

Parental  CPDMKHFLQKLISQLMDCCVDIKSKEEESVHVTQRKTHYSMDSLSSWYMTVTQKTDPKMLSKKRTTSSQW
          CPDMK.FLQKL.S.LM.CCV..KSKE.ESV.VTQR.THY.MDSLSSWYMTVTQKTDPKM.SKKRTTSSQW
Retrocopy CPDMKRFLQKLVS*LMNCCVHLKSKEGESVQVTQRNTHYLMDSLSSWYMTVTQKTDPKMPSKKRTTSSQW

Parental  QSPPVVVILKDMESFATKVLQDFIIISSQHLHEFPLILIFGIATSPIIIHRLLPHAVSSLLCIELFQSLS
          QSPPV...LKDMESFATKVLQDFIIISSQHLHEFPLILI.GIATS.II.HRL.PHAVSSLLCIELFQ.LS
Retrocopy QSPPVLATLKDMESFATKVLQDFIIISSQHLHEFPLILIVGIATS-IINHRLFPHAVSSLLCIELFQFLS

Parental  CKEHLTTVLDKLLLTTQFPFKINEKVLQVLTNIFLYHDFSVQNFIKG-LQLSLLEHFYSQPLSVLCCNLP
          CKEHLT.VL.KLLLTTQFPFKINEKVLQVLTNIFLYHDFS.QNFIKG.LQLSLLEHF.SQPLSVLCCNLP
Retrocopy CKEHLTMVLNKLLLTTQFPFKINEKVLQVLTNIFLYHDFSIQNFIKG<LQLSLLEHFCSQPLSVLCCNLP

Parental  EAKRRINFLSNNQCENIRRLPSFRRYVEKQASEKQVALLTNERYLKEETQLLLENLHVYHMNYFLVLRCL
          ..KRRINFLSNNQCENI.RLPSFRRYVEKQASEKQV.LLT.ER.LKEETQLLLENLHVYHMNYFLVLRC.
Retrocopy *VKRRINFLSNNQCENI*RLPSFRRYVEKQASEKQVVLLTSERCLKEETQLLLENLHVYHMNYFLVLRCV

Parental  HKFTSSLPKYPLGRQIRELYCTCLEKNIWDSEEYASVLQLLRMLAKDELMTILEKCFKVFKSYCENHLGS
          HKFTSSLPKYPLGRQIRELY.TCLEKNI..SEEYASVLQLL.MLAKDELMTILEKCF.VF.S.CE.HLGS
Retrocopy HKFTSSLPKYPLGRQIRELYRTCLEKNIRNSEEYASVLQLLKMLAKDELMTILEKCFEVFISSCEKHLGS

Parental  TAKRIEEFLAQFQSLDETEEEEDASGSQPKGLQKTDLYHLQKSLLEMKELRRSKKQTKFEVLRENVVNFI
          TAKRI.EFLAQFQS.DET.E.EDASGS.PKGLQK.DLYHLQKSLLEMKEL.RSKKQTKFEVLRE..VNF.
Retrocopy TAKRIQEFLAQFQSFDETKEVEDASGS*PKGLQKADLYHLQKSLLEMKELSRSKKQTKFEVLREKAVNFM

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	0.02 RPM	13.96 RPM
SRP007412_cerebellum	0.00 RPM	18.14 RPM
SRP007412_heart	0.00 RPM	8.39 RPM
SRP007412_kidney	0.00 RPM	12.84 RPM
SRP007412_liver	0.00 RPM	7.23 RPM
SRP007412_testis	0.00 RPM	30.56 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_555 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_555 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_555 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_798
Pongo abelii	retro_pabe_712

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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 ,