RetrogeneDB ID: retro_nleu_1911

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397315.1:1737208..1737908(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: VTA1
• Ensembl ID: ENSNLEG00000015053
• Aliases: None
• Description: None

Sequence

>retro_nleu_1911
ATGTTCATAATTGCTCTACTGTCTCCACTTCCTCCCCAGTTTAAGAGCATACAGCATCATATGAGAACAGCTCAGGAGCA
TGACAAGCAGGACCCCGCGGTGCTCTATTACTGTTGTTTCTATGCAATGCAAACCATAATGAAAACTGATAGTAAAACTC
CTGAGAGTTGTACATTTTTATCAAAGCTAATGGGTCAGTTAGAAATGCTTATGAAGCAGTTTGGTGATAATGAAGCTATT
AGGCAAGAAAATACTTAGTCCTGCTCATTTGGAGAATTATGCTTAGAAAATGTTTGTATAATCAGACAATGGTCATGCTG
GGTGATTTCACAAGATGATCAAGCTCTTTTTAAACTCCACAGTTTTAAATAGATGTCATAATAATATTAGGACAACTCAT
TGATGAAAATGTGAAACACAGAAAGTATGTAAGATGAAAGGCAAAATATATTCATATTTGTTTAAAGAATGGGGAGCTGC
CTCAACTAGTATCTGCTGGAATTGAAGAAGATAACAATATTGCAGAAAATGAAAATGCTGAAGCAACCTATCTGTCCACT
ATGCCATGTCAGCCACCATTTTCAATTTACGACCCAAGCCACATGCATAAAGGAAATATACTAGAATACAGATTCCTCCC
AGTGCACACACTCCAGCTAATACATCAGTAGAAATGCATCACAATGCAGATGTAACAAAT

Alignment

ORF - retro_nleu_1911 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 63.6 %
• Parental protein coverage: 76.87 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MAALAPLPPLPAQFKSIQHHLRTAQEHDKRDPVVAYYCRLYAMQTGMKIDSKTPECRKFLSKLMDQLEAL
          M...A.L.PLP.QFKSIQHH.RTAQEHDK.DP.V.YYC..YAMQT.MK.DSKTPE...FLSKLM.QLE.L
Retrocopy MFIIALLSPLPPQFKSIQHHMRTAQEHDKQDPAVLYYCCFYAMQTIMKTDSKTPESCTFLSKLMGQLEML

Parental  KKQLGDNEAITQE-IVGCAHLENYALKMFLYADNEDRAGRFHKNMIKSFYTASLL-IDVITVFGELTDEN
          .KQ.GDNEAI.QE.I...AHLENYA.KMF...DN...AG.FHK.MIK.F.....L.IDVI...G.L.DEN
Retrocopy MKQFGDNEAIRQE>ILSPAHLENYA*KMFV*SDN-GHAG*FHK-MIKLFLNSTVL>IDVIIILGQLIDEN

Parental  VKHRKYARWKATYIHNCLKNGETPQAGPVGIEEDNDVEENEDAGAASLPTQPTQPSSSSTYDPSNMPSGS
          VKHRKY.R.KA.YIH.CLKNGE.PQ....GIEEDN...ENE.A.A..L.T.P.QP...S.YDPS.M..G.
Retrocopy VKHRKYVR*KAKYIHICLKNGELPQLVSAGIEEDNNIAENENAEATYLSTMPCQP-PFSIYDPSHMHKGN

Parental  -YTGIQIPPGAHAPANTPAEVPHSTGVAS
          .YT.IQIPP.AH.PANT..E..H...V..
Retrocopy <YTRIQIPPSAHTPANTSVEMHHNADVTN

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_1911 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 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000009844	1 retrocopy	retro_hsap_4088,
Gorilla gorilla	ENSGGOG00000015524	1 retrocopy	retro_ggor_2742,
Microcebus murinus	ENSMICG00000004420	2 retrocopies	retro_mmur_1290, retro_mmur_290,
Macaca mulatta	ENSMMUG00000023012	1 retrocopy	retro_mmul_751,
Nomascus leucogenys	ENSNLEG00000015053	1 retrocopy	retro_nleu_1911 ,
Oryctolagus cuniculus	ENSOCUG00000002554	10 retrocopies	retro_ocun_1543, retro_ocun_1689, retro_ocun_1790, retro_ocun_1810, retro_ocun_1821, retro_ocun_1832, retro_ocun_1848, retro_ocun_1853, retro_ocun_1864, retro_ocun_965,
Pan troglodytes	ENSPTRG00000018662	1 retrocopy	retro_ptro_2773,
Rattus norvegicus	ENSRNOG00000011540	1 retrocopy	retro_rnor_799,
Tursiops truncatus	ENSTTRG00000014998	1 retrocopy	retro_ttru_1825,