RetrogeneDB ID: retro_nleu_413

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397264.1:10095958..10097675(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ORC3
• Ensembl ID: ENSNLEG00000012990
• Aliases: None
• Description: None

Sequence

>retro_nleu_413
ATGGCCACCTCCTCAGTGTCTAAGGGCTGCTTTGCTTTTAAGCCAGACTCCAAAAAGAGAAAGATCTCTGTGCCAATGGA
GGACTATTTTAACAAAGGGAAAAATGAGCCTGAGGACAGTAAGCTTCAATTTGGAACTTAGTTGATACGGCAGCAAATGA
AATCTGAAAATGAGCCACTACAAGAGGAATTAAATAAAAACTTGTTTGACAATCTAATTGAATTTCTGCAAAAATCTCAT
TCTGGATTCCAGAAGAATTCAAGAGACTTGGGCTGTCAAACAAAACTCAGAGAAATTCCAACTGCTGCTCTTGTTCTTGG
TGTGAAAGTCACAGATCACGATTTAACATTCAGAAGTCTAACAGAGGCCCTTCAGAATAAAGTCACACCATATGTAGTCT
CATCGCAAGCTAAAGACTGTCCAGATATGAAACATTTTTTTGCAAAAGTTGGTCTCACAATTAATGAACTGTTGTGTAGA
TCCAAAATCCAAAGAGGGGGCAAGCGTTCAGGTCACCCAGAGAAATACACATTATTTAATGGATTCACTTTCCAGTTGGT
ACATGACTGTTACACAGAAGACAGACCCAAAAATGCCAAGCAAAAAGAGGACTACTTCTAGCCAATGGCCGTCTCCTCCT
GTTTTGGCTACCTTAAAGGATATGGAAAGCTTTGCCACAAAAGTACTGCAAGACTTCATAATTATCAGCAGTCAACATCT
GCATGAATTTCCACTAATACTCATTTCTGGAATCACCACATCTATTATCAACCACCGATTGTTTCCTCATGCAGTATCAT
CTCTATTGTGCATAGAACTGTTCCAGTTTTTGTCTTGCAAGGAGCATCTGACTATGGTACTCAATAAGCTACTTCTTACA
ACTCAGTTTCCCTTTAAAATAAGTGGAAAAGTATTGCAGGTTCTGACCAACATCTTTTTGTATCATGATTTCTCAATTCA
AAACTTTATAAAAGGCTTCAACTTTCTCTGTTAGAGCATTTCTGTTCCCAGCCCTTAAGTGTCATGTGCTATAATCTTCC
AGAAGCCAAAAGAAGAATAAATTTTTTATCAGATAATCAATGTGAAAACATCTGACATCTTCCATCTTTCAGGCGATACG
TGGAAAAGCAAGCTTCAGAAAAGCAAGTTGCGCTCTTGACCAGTGAAAGATGTTCGCAGGAGGAAACACAATTATTACTA
GAAAACCTGCATGTTTATCATATGAATTACTTTCTAGTTTTAAGATGTGTTCATAAGTTCACCTCTTCTCTTCCCAAGTA
TCCACTAGGTCGACAGATCAGAGAGTTGTACCGCACATGTTTAGAAAAGAACATACAGAATTCAGAGGAGTATGCGTCAG
TCTTGCAGCTGCTGAAGATGTTGGCAAAGGATGAACTGATGACCATACTTGAGAAATGTTTCAAGGTTTTTAAATCTTCT
TGTGAAAAGCACCTTGGCAGCACAGCTAAGAGAATACAGGAGTTCCTGGCCCAGTTTCAGAGCCTCGATGAAACCAAAGA
GGAAGAAGATGCTTCTGGTTCACAGCCAAAGGGGCTTCAGAAGACAGACGTCTATCATCTTCAGAGGACTTTACTGGAAA
TGAAGGAGTTAAGCAGAAGTAAGAAGGAAACCAAATTTGAAGTACTCAGAGAAGAGAGGTTGTGAACTTCATGACTGTCT
AGGGAGAGAATACCTTCTGCCTCCTGAGACACAGCCT

Alignment

ORF - retro_nleu_413 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.02 %
• Parental protein coverage: 80.76 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MATSSMSKGCFVFKPNSKKRKISLPVEDYFNKGKNEHEDSKLRFETYQLIWQQMKSENERLQEELNKNLF
          MATSS.SKGCF.FKP.SKKRKIS.P.EDYFNKGKNE.EDSKL.F.T..LI.QQMKSENE.LQEELNKNLF
Retrocopy MATSSVSKGCFAFKPDSKKRKISVPMEDYFNKGKNEPEDSKLQFGT*-LIRQQMKSENEPLQEELNKNLF

Parental  DSLIEFLQKSHCGFQKNSRDLGGQIKLREIPTAALVLGVNVTDHDLTFRSLTEALQNNVTPYVVSLQAKD
          D.LIEFLQKSH.GFQKNSRDLG.Q.KLREIPTAALVLGV.VTDHDLTFRSLTEALQN.VTPYVVS.QAKD
Retrocopy DNLIEFLQKSHSGFQKNSRDLGCQTKLREIPTAALVLGVKVTDHDLTFRSLTEALQNKVTPYVVSSQAKD

Parental  CPDIKHF-LQKLVSQLMDCCVDIKSKEEESVQVTQRKTHYSMDSLSSWYMTVTQKTDPKMQSKKRTTSSQ
          CPD.KHF.LQKLVSQLM.CCVD.KSKE..SVQVTQR.THY.MDSLSSWYMTVTQKTDPKM.SKKRTTSSQ
Retrocopy CPDMKHF>LQKLVSQLMNCCVDPKSKEGASVQVTQRNTHYLMDSLSSWYMTVTQKTDPKMPSKKRTTSSQ

Parental  WQSPPVVVILKDMESFATKVLQDFIIISSQHLHEFPLILIFGIATSPIIIHRLLPHAVSSLLCIELFQSL
          W.SPPV...LKDMESFATKVLQDFIIISSQHLHEFPLILI.GI.TS.II.HRL.PHAVSSLLCIELFQ.L
Retrocopy WPSPPVLATLKDMESFATKVLQDFIIISSQHLHEFPLILISGITTS-IINHRLFPHAVSSLLCIELFQFL

Parental  SCKEHLTTVLDKLLLTTQFPFKINEKVLQVLTNIFLYHDFSIQNFIKG-LQLSLLEHFYSQPLSVLCCNL
          SCKEHLT.VL.KLLLTTQFPFKI..KVLQVLTNIFLYHDFSIQNFIKG.LQLSLLEHF.SQPLSV.C.NL
Retrocopy SCKEHLTMVLNKLLLTTQFPFKISGKVLQVLTNIFLYHDFSIQNFIKG<LQLSLLEHFCSQPLSVMCYNL

Parental  PEAKRRINFLSNNQCENIRRLPSFRRYVEKQASEKQVALLTDERCLKEETQLLLENLHVYHMNYFLVLRC
          PEAKRRINFLS.NQCENI..LPSFRRYVEKQASEKQVALLT.ERC..EETQLLLENLHVYHMNYFLVLRC
Retrocopy PEAKRRINFLSDNQCENI*HLPSFRRYVEKQASEKQVALLTSERCSQEETQLLLENLHVYHMNYFLVLRC

Parental  LHKFTSSLPKYPLGRQVRELYCTCLEKNIWDSEEYASVLQLLRMLAKDELMTILEKCFKVFKSYCENHLG
          .HKFTSSLPKYPLGRQ.RELY.TCLEKNI..SEEYASVLQLL.MLAKDELMTILEKCFKVFKS.CE.HLG
Retrocopy VHKFTSSLPKYPLGRQIRELYRTCLEKNIQNSEEYASVLQLLKMLAKDELMTILEKCFKVFKSSCEKHLG

Parental  STAKRIEEFLAQFQSLDAETKEEEDASGSQPKGLQKTDLYHLQKSLLEMKELRRSKKQTKFEVLRENVV-
          STAKRI.EFLAQFQSLD.ETKEEEDASGSQPKGLQKTD.YHLQ..LLEMKEL.RSKK.TKFEVLRE....
Retrocopy STAKRIQEFLAQFQSLD-ETKEEEDASGSQPKGLQKTDVYHLQRTLLEMKELSRSKKETKFEVLREERL>

Parental  NFIDCLVREYLLPPETQP
          ...DCL.REYLLPPETQP
Retrocopy ELHDCLGREYLLPPETQP

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Nomascus leucogenys was not studied using RNA-Seq expression data.

ChIP-Seq

Nomascus leucogenys was not studied using ChIP-Seq data.

EST

Nomascus leucogenys was not studied using EST data.

TSS

Nomascus leucogenys was not studied using FANTOM5 data.

Lab

retro_nleu_413 was not experimentally validated.

Homology

Retrocopy orthology:

Nomascus leucogenys does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

---

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,