RetrogeneDB ID: retro_nleu_2622

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397382.1:1151666..1152904(-)
• Located in intron of: ENSNLEG00000005353

Retrocopy information

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

Parental gene information

• Parental gene symbol: IPMK
• Ensembl ID: ENSNLEG00000012319
• Aliases: None
• Description: None

Sequence

>retro_nleu_2622
ATGGCAAGAGAGCCACTATCCCCGCTCCGGGTCGAGGCGCCGGGTCCCCCAGAAATGCGGACCCCACCGGCGATCGAGGC
CACCCCTGAGGGCACCCCGCAGCCGGCAGGCGGCAGACCCCGCCTCCTCAACGGCTGCGCCCATCTCGCATCAGGTGGCC
GGGCACATGTATGGGAAGGACAAAATTGGTATGCTGCAACATCCAGATGGCACAGTTTTGAAACAGTTACAACCACCTCC
AAGGGGCCCAAGAGAGCTGGAATTCTATAATATGGTTTATGCTGCTGACTGTACCGAGGGTGTTCTTCTAGTGCTACGAA
AATATTTGCCAAAATATTATGGCATCTGGCTACCTCCCACTGCCCCAAACGATTTACACCTAAAACTGGAAGATGTGACC
CATAAACTTAATAAGCCCTGTATAAAGGATGTAAAGATAGGGCAAAAAAGCTATGACCCTTTTTGCCTCATCTGAGAAGA
TTCAGCAACAGGTCAGCAAGGACCCATTAATGGAAAAGATTGGGTTCTTGGTGCTTGGCCTGAGGGTTTATCTCGTTTAT
TCCCATAGCTGTGAGACACAAACCAACATTATGGAAGAAGCTTAACAGAAGAAGCTACAAAGGATGGAGTCTCCGAATTT
TTTCATAATGGGTACTGCTTAAGAAAAGACGCTGTTGCTGCCATTATTCAGAAGACAGAAAATTCTGCAGTGGTTTGAAA
ACCAGAAGCAGCTTAACTTTTACGCAAGTTCATTACTGTTTGTTTAGGAAGGTTCATCTCAGCCAATCACCACAAAACTG
AATGACAGAAATTTGGCAGAAAAGTTTTTGTCCAAAGGACAACTGTCAGACACAGAGGTACTAGAGTGCAATAATAACTT
TCATGTATTAAGTTCCACAGTGAATAGGAAAATAGAGGTTTCAGTAGGCAAAAGCTTGTCCAAGATGTATGCTTGTCACA
GGAAAATGTAGACAAAAAAGCATCACTGTCAGACTTCATTGAAAGTTGAAAATCTGGAGCAAGACAATGGGTAGAAAAGC
ATGTCACAGGAACATTTAAATGGAAATGTACTTTCACAACCGGAAAAAGTTTTCTACCATCTTCCCACTGGTTGCCAAGA
GACTGCTGAAATGTGCATGATAGATTTTGCTCATATGTTCCTTAGCAACACAGTAGATGAGGGACATGTTTATGGGCTAA
AGCATTTAATGTCTGTACTTCGAAGTATTGTAGACAAT

Alignment

ORF - retro_nleu_2622 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.81 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 3
• Number of frameshifts detected: 6

Retrocopy - Parental Gene Alignment:

Parental  MAREPLSPLRVEAPGPPEMRTPPAIE-SPEGTPQPAGGRLRFLNGCVPLSHQVAGHMY-GKDK-VGILQH
          MAREPLSPLRVEAPGPPEMRTPPAIE..PEGTPQPAGGR.R.LNGC..L......H...G..K..G.LQH
Retrocopy MAREPLSPLRVEAPGPPEMRTPPAIEATPEGTPQPAGGRPRLLNGCAHLASGGRAHVW<GRTK<IGMLQH

Parental  PDGTVLKQLQPPPRGPRELEFYNMVYAADCFDGVLLELRKYLPKYYGIWSPPTAPNDLYLKLEDVTHKFN
          PDGTVLKQLQPPPRGPRELEFYNMVYAADC..GVLL.LRKYLPKYYGIW.PPTAPNDL.LKLEDVTHK.N
Retrocopy PDGTVLKQLQPPPRGPRELEFYNMVYAADCTEGVLLVLRKYLPKYYGIWLPPTAPNDLHLKLEDVTHKLN

Parental  KPCIMDVKIGQKSYDP-FASSEKIQQQVNKYPLMEEIGFLVLGMRVYHVHSDSYETQ-NQHYGRSLTKET
          KPCI.DVKIGQKSYDP.FASSEKIQQQV.K.PLME.IGFLVLG.RVY.V.S.S.ETQ.NQHYGRSLT.E.
Retrocopy KPCIKDVKIGQKSYDP>FASSEKIQQQVSKDPLMEKIGFLVLGLRVYLVYSHSCETQ<NQHYGRSLTEEA

Parental  IKDGVSRFFHNGYCLRKDAVAASIQKIE-KILQWFENQKQLNF-YASSLLFVYEGSSQPTTTKLNDRTLA
          .KDGVS.FFHNGYCLRKDAVAA.IQK.E.K..........L.F.YASSLLFV.EGSSQP.TTKLNDR.LA
Retrocopy TKDGVSEFFHNGYCLRKDAVAAIIQKTE<KFCSGLKTRSSLTF<YASSLLFV*EGSSQPITTKLNDRNLA

Parental  EKFLSKGQLSDTELLEYNNNFHVLSSTANGKIEASVGKSLSKMYARHRKMYTKKHHSQTSLKVENLEQGN
          EKFLSKGQLSDTE.LE.NNNFHVLSST.N.KIE.SVGKSLSKMYA.HRKM.TKKHH.QTSLKVENLEQ.N
Retrocopy EKFLSKGQLSDTEVLECNNNFHVLSSTVNRKIEVSVGKSLSKMYACHRKM*TKKHHCQTSLKVENLEQDN

Parental  GWKSMSQEHLNGNVLSQLEKVFYHLPTGCQEIAEVEVRMIDFAHVFPSNTIDEGYVYGLKHLISVLRSIL
          G.KSMSQEHLNGNVLSQ.EKVFYHLPTGCQE.A..E..MIDFAH.F.SNT.DEG.VYGLKHL.SVLRSI.
Retrocopy G*KSMSQEHLNGNVLSQPEKVFYHLPTGCQETA--EMCMIDFAHMFLSNTVDEGHVYGLKHLMSVLRSIV

Parental  DN
          DN
Retrocopy DN

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_2622 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.

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Anas platyrhynchos	ENSAPLG00000011011	1 retrocopy	retro_apla_14,
Cavia porcellus	ENSCPOG00000000222	1 retrocopy	retro_cpor_369,
Erinaceus europaeus	ENSEEUG00000009958	1 retrocopy	retro_eeur_110,
Homo sapiens	ENSG00000151151	2 retrocopies	retro_hsap_1244, retro_hsap_2032,
Gorilla gorilla	ENSGGOG00000008790	1 retrocopy	retro_ggor_1464,
Myotis lucifugus	ENSMLUG00000015030	1 retrocopy	retro_mluc_518,
Nomascus leucogenys	ENSNLEG00000012319	2 retrocopies	retro_nleu_2419, retro_nleu_2622 ,
Pongo abelii	ENSPPYG00000002433	3 retrocopies	retro_pabe_1035, retro_pabe_1086, retro_pabe_1689,
Pan troglodytes	ENSPTRG00000002516	2 retrocopies	retro_ptro_1351, retro_ptro_855,