RetrogeneDB ID: retro_nleu_2663

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397391.1:2331621..2332746(-)
• Located in intron of: ENSNLEG00000002714

Retrocopy information

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

Parental gene information

• Parental gene symbol: TMEM183A
• Ensembl ID: ENSNLEG00000018106
• Aliases: None
• Description: None

Sequence

>retro_nleu_2663
ATGGCCCTGGGGCCCGGCCCGCTAGGCAGGCCTCGCCCAGATATGGTCGCCATGCCCAAGAGAGGAAAGTGACTCAAGTT
CTGGGCCCACGACGCCTGCTCGGGCCGAGTGACCGTGGCGGATTATGCCAACTCGGATCCGGCGGTCGTGAGGTCTGGAC
AAGTCAAGAAAGCCACAGCCAACGCTGTTCAGCAGGAAGTAAAATCTCTTTGTGGCTTGGAAGCCTCTCAGGTTCCTACA
GAGGAAGCTCTTTCTGGGGCTGGTGAGCCCTGTGACATCATCGAAAGCAGTGATGAGATGGATGCCCAGAAGGAAAGCAT
TCATGAGAGAACTGTCTCCAGAAAAAAGAAAAGCAAGAGACACAAAGAACTGCACAGGGCTGGAGGAGAAGAGTATCCCA
TGGATATTTGGCTATTGCTGGCCTCCTATATCCGTCCTGAGGACATTGTGAATTTTTCCCTGATTTGTAAGAATGCCTGG
ACTGTCACTTGCAGTGCTGCCTTTTGGACCAGGTTGTACCGAAGGCACTACACGCTGGATGCTTCCCTGCCTTTGCGTCT
GCGACCAGAGTCAATGGAGAAGCTGCACTGTCTCCGGGCTTGTGTGATCCGATCTCTGTACCATATGTATGAGCCATTTG
CTGCTCGAATCTTCAAGAATCCAGCCATTCCAGAAAGCACCCCCAGCACATTAAAGAATTCCAAATGCTTACTTTTCTGG
TGCAGAAAGATTGTTGGGAACAGACAGGAACCAATGTGGGAATTCAACTTCAAGTTCAAAAAAACAGTCCCCTAGGTTAA
AGAGCAAGTGTACAGGAGGATTGCAGCCTCCCGTTCAGTACGAAGATGTTCATACCAATCCAGACCAGGACTGCTGCCTA
CTGCAGGTCACCACCCTCAATTTCATCTTTATTCCGATTGTCATGGGAATGATATTTACTCTGTTTACTATCAATGTGAG
CACAGACATGTGGCATCATCGAGTGAGACTGGTGTTCCAAGATTCCCCTGTCCATGGTGGTCGGAAACTGCGCAGTGAAC
AGGGTGTGCAAGTCATCCTGGACCCAGTGCACGCGTTCGGCTCTTTGACTGGTGGCATCCTCAGTACCCATTCTCCCTGA
GAGCA

Alignment

ORF - retro_nleu_2663 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.97 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MARGPGPLGRPRPDTVAMPKRGKRLKFRAHDACSGRVTVADYANSDPAVVRSGRVKKAVANAVQQEVKSL
          MA.GPGPLGRPRPD.VAMPKRGK.LKF.AHDACSGRVTVADYANSDPAVVRSG.VKKA.ANAVQQEVKSL
Retrocopy MALGPGPLGRPRPDMVAMPKRGK*LKFWAHDACSGRVTVADYANSDPAVVRSGQVKKATANAVQQEVKSL

Parental  CGLEASQVPAEEALSGAGEPCDIIDSSDEMDAQEESIHERTVSRKKKSKRHKEELDGAGGEEYPMDIWLL
          CGLEASQVP.EEALSGAGEPCDII.SSDEMDAQ.ESIHERTVSRKKKSKRHKE.L..AGGEEYPMDIWLL
Retrocopy CGLEASQVPTEEALSGAGEPCDIIESSDEMDAQKESIHERTVSRKKKSKRHKE-LHRAGGEEYPMDIWLL

Parental  LASYIRPEDIVNFSLICKNAWTVTCTAAFWTRLYRRHYTLDASLPLRLRPESMEKLRCLRACVIRSLYHM
          LASYIRPEDIVNFSLICKNAWTVTC.AAFWTRLYRRHYTLDASLPLRLRPESMEKL.CLRACVIRSLYHM
Retrocopy LASYIRPEDIVNFSLICKNAWTVTCSAAFWTRLYRRHYTLDASLPLRLRPESMEKLHCLRACVIRSLYHM

Parental  YEPFAARISKNPAIPESTPSTLKNSKCLLFWCRKIVGNRQEPMWEFNFKFKK-QSPRLKSKCTGGLQPPV
          YEPFAARI.KNPAIPESTPSTLKNSKCLLFWCRKIVGNRQEPMWEFNFKFKK.QSPRLKSKCTGGLQPPV
Retrocopy YEPFAARIFKNPAIPESTPSTLKNSKCLLFWCRKIVGNRQEPMWEFNFKFKK>QSPRLKSKCTGGLQPPV

Parental  QYEDVHTNPDQDCCLLQVTTLNFIFIPIVMGMIFTLFTINVSTDMRHHRVRLVFQDSPVHGGRKLRSEQG
          QYEDVHTNPDQDCCLLQVTTLNFIFIPIVMGMIFTLFTINVSTDM.HHRVRLVFQDSPVHGGRKLRSEQG
Retrocopy QYEDVHTNPDQDCCLLQVTTLNFIFIPIVMGMIFTLFTINVSTDMWHHRVRLVFQDSPVHGGRKLRSEQG

Parental  VQVILDPVHS-VRLFDWWHPQYPFSLRA
          VQVILDPVH..VRLFDWWHPQYPFSLRA
Retrocopy VQVILDPVHA<VRLFDWWHPQYPFSLRA

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_2663 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 14 parental genes, and 21 retrocopies.

Species	Parental gene accession	Retrocopies number
Echinops telfairi	ENSETEG00000008318	1 retrocopy	retro_etel_1835,
Felis catus	ENSFCAG00000013106	1 retrocopy	retro_fcat_3,
Homo sapiens	ENSG00000163444	3 retrocopies	retro_hsap_2808, retro_hsap_2863, retro_hsap_3157,
Gorilla gorilla	ENSGGOG00000009834	2 retrocopies	retro_ggor_1358, retro_ggor_2533,
Loxodonta africana	ENSLAFG00000018443	1 retrocopy	retro_lafr_149,
Macaca mulatta	ENSMMUG00000000801	1 retrocopy	retro_mmul_1532,
Nomascus leucogenys	ENSNLEG00000018106	2 retrocopies	retro_nleu_2541, retro_nleu_2663 ,
Otolemur garnettii	ENSOGAG00000000911	1 retrocopy	retro_ogar_3209,
Pongo abelii	ENSPPYG00000000340	2 retrocopies	retro_pabe_1333, retro_pabe_2627,
Pan troglodytes	ENSPTRG00000001864	2 retrocopies	retro_ptro_1902, retro_ptro_2278,
Rattus norvegicus	ENSRNOG00000003594	2 retrocopies	retro_rnor_1954, retro_rnor_2386,
Sus scrofa	ENSSSCG00000015473	1 retrocopy	retro_sscr_879,
Ictidomys tridecemlineatus	ENSSTOG00000012466	1 retrocopy	retro_itri_421,
Tarsius syrichta	ENSTSYG00000007009	1 retrocopy	retro_tsyr_717,