RetrogeneDB ID: retro_nleu_457

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397265.1:3116379..3117628(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: KRT5
• Ensembl ID: ENSNLEG00000017746
• Aliases: None
• Description: None

Sequence

>retro_nleu_457
GGCAGCAGCTTCTGGGGTGGCCTGGGCAGAGGCTGTGATGGGGCCAGCAGTATGGGAGGCATCACAGCTGTCACAGTCAA
CCAGAGCCTGCTGAGCCCCCTTAACCTGCAGGTGGACCCCAACATCCAGGCCATGTGCACCCAGGAGAAGGAGCAGATCA
AGACCCTCAACAACAAGTTTGCCTCCTTCATTGACAAGGTATGGTTGCTGGAGCAGCAGAACAAGATGCTGGAGACCAAG
TGGAGCGTTCTGCAGCAGCAGAAGATGACTCTGAGTAACATGGACAGCATGTTAGAGAGCTACATCAACAACCTTCAGCG
GCAGTTGGAGACTCTGGGTCAGGAGAAGCTGAAGCTGGAGGAAGAGGCTGGCAGCATGCAGGGGCTAGTGGAGGGCTTCA
AGAACAAATATAAGGGTAAGATCAATAAGCATACAGAGATGGAGAATGAATTTGTCCTCATCAAGGAGGTTGTAGATGAC
GCTTACATGAACAAGGTAGAGCTGGAGTCTTGCCTGGAAGGGCTGACTGATGAGATCAACTTCCTCAGGCAGCTGTATGA
AGAGGAGATCCGGGAGCTGTCCCAGATCTTGGACACATCTGTGGTTCTGTCCATGGACAACAGATGCTCCCTGGACATGG
ACAGCATCATTGCCGAGGTCAAGGCCCAGTATGAAGAGATCGCCAACGCAGCCAGGCCAAGGCTGAGAGCATGTACCAGA
TCAAATATGAGGAGCTGCAGACGCTTGCTGGGAAGCACGGGGATGACCTGTGTCATACAAATATGGAGATCTCTGAGATG
AACTGGAACATCAGCTGGCTCCAGGCTGAGATAGAGGGCCTCAAAGGCCAGAGGGCTTCCCTGGAGGCCGCCATCACAGA
TGCTGAGCAGCATGGGGAGCTGGCTGTTAAGAATGCCAACATCAAGCTGTATGAGCTGGGGCCCACCCTGCAGTGGGCCG
AGCAGGACATGGTGCAGCAGCTGCATGAGTGCCAGGAGCTGATGAAATCCAGCTGGCTCTGGACATTGAGATTGCCACCT
ACAGGAAGCTGCTGGAGGGCATGGAGAGCTGGCTGGAGTTGGGGATGCAGCACATGCAGAACATGAGTATCCATATGAAG
ACCACTGGTGGCTATGCAGGTGGGCTGAGCTCAGCCTATGGGGACCTCACAAGCCCCAGCCTCAGCTATGGCCTGGGCTC
CAGCTTTGGCTCTGGCACAGGCTCCATCTCCTTCAGTTGCACCAGCTCC

Alignment

ORF - retro_nleu_457 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 55.76 %
• Parental protein coverage: 71.04 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  GAGFGGGFGGPGFPVCPPGGIQEVTVNQSLLTPLNLQIDPSIQRVRTEEREQIKTLNNKFASFIDKVRFL
          G..F.GG.G.........GGI..VTVNQSLL.PLNLQ.DP.IQ...T.E.EQIKTLNNKFASFIDKV..L
Retrocopy GSSFWGGLGRGCDGASSMGGITAVTVNQSLLSPLNLQVDPNIQAMCTQEKEQIKTLNNKFASFIDKVWLL

Parental  EQQNKVLDTKWTLLQEQGTKTVRQNLEPLFEQYINNLRRQLDSIVGERGRLDSELRNMQDLVEDFKNKYE
          EQQNK.L.TKW..LQ.Q..K....N.....E.YINNL.RQL.....E...L..E...MQ.LVE.FKNKY.
Retrocopy EQQNKMLETKWSVLQQQ--KMTLSNMDSMLESYINNLQRQLETLGQEKLKLEEEAGSMQGLVEGFKNKYK

Parental  DEINKRTTAENEFVMLKKDVDAAYMNKVELEAKVDALMDEINFMKMFFDAELSQMQTHVSDTSVVLSMDN
          ..INK.T..ENEFV..K..VD.AYMNKVELE.....L.DEINF.......E.........DTSVVLSMDN
Retrocopy GKINKHTEMENEFVLIKEVVDDAYMNKVELESCLEGLTDEINFLRQLYEEEIREL-SQILDTSVVLSMDN

Parental  NRNLDLDSIIAEVKAQYEEIAN-RSRTEAESWYQTKYEELQQTAGRHGDDLRNTKHEISEMNRMIQRLRA
          ...LD.DSIIAEVKAQYEEIAN.RS...AES.YQ.KYEELQ..AG.HGDDL..T..EISEMN..I..L.A
Retrocopy RCSLDMDSIIAEVKAQYEEIAN<RSQAKAESMYQIKYEELQTLAGKHGDDLCHTNMEISEMNWNISWLQA

Parental  EIDNVKKQCANLQNAIADAEQRGELALKDARNKLAELEEALQKAKQDMARLLREYQELMNT-KLALDVEI
          EI...K.Q.A.L..AI.DAEQ.GELA.K.A..KL.EL...LQ.A.QDM...L.E.QELM....LALD.EI
Retrocopy EIEGLKGQRASLEAAITDAEQHGELAVKNANIKLYELGPTLQWAEQDMVQQLHECQELMKS<QLALDIEI

Parental  ATYRKLLEGEECRLSGEGVGPVNISVVTSSVSSGYGGGSGYSSGLGGGLGGGLGGGLGGGLGGG-GSGSY
          ATYRKLLEG.E..L...G...............GY.G..G.SS..G......L..GLG...G.G.GS.S.
Retrocopy ATYRKLLEGMESWLE-LGMQHMQNMSIHMKTTGGYAG--GLSSAYGDLTSPSLSYGLGSSFGSGTGSISF

Parental  YSSSS
          ...SS
Retrocopy SCTSS

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_457 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 12 parental genes, and 30 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000011913	4 retrocopies	retro_chof_1848, retro_chof_2381, retro_chof_2385, retro_chof_778,
Erinaceus europaeus	ENSEEUG00000009412	1 retrocopy	retro_eeur_521,
Echinops telfairi	ENSETEG00000007907	1 retrocopy	retro_etel_1586,
Nomascus leucogenys	ENSNLEG00000017733	8 retrocopies	retro_nleu_1913, retro_nleu_225, retro_nleu_2285, retro_nleu_2421, retro_nleu_2485, retro_nleu_2727, retro_nleu_2787, retro_nleu_672,
Nomascus leucogenys	ENSNLEG00000017740	1 retrocopy	retro_nleu_1808,
Nomascus leucogenys	ENSNLEG00000017746	5 retrocopies	retro_nleu_2270, retro_nleu_2596, retro_nleu_354, retro_nleu_457 , retro_nleu_852,
Nomascus leucogenys	ENSNLEG00000017748	2 retrocopies	retro_nleu_2823, retro_nleu_3100,
Nomascus leucogenys	ENSNLEG00000017753	1 retrocopy	retro_nleu_1726,
Nomascus leucogenys	ENSNLEG00000017758	2 retrocopies	retro_nleu_593, retro_nleu_726,
Nomascus leucogenys	ENSNLEG00000026579	1 retrocopy	retro_nleu_311,
Pongo abelii	ENSPPYG00000004548	1 retrocopy	retro_pabe_1103,
Vicugna pacos	ENSVPAG00000011707	3 retrocopies	retro_vpac_334, retro_vpac_551, retro_vpac_555,