RetrogeneDB ID: retro_nleu_2601

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397380.1:1058898..1059891(+)
• Located in intron of: ENSNLEG00000000311

Retrocopy information

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

Parental gene information

• Parental gene symbol: EIF4B
• Ensembl ID: ENSNLEG00000017727
• Aliases: None
• Description: None

Sequence

>retro_nleu_2601
ATGGCTGCCTCAGCAAAAGAGAAGAATAAGAAGGGGAAGACTATCTCCCTAACAGACTTTCTGGCTGAGGATGGGGGACT
GGTGGAGGAAGCAGCTATGTATCCAAACCAGTCAGCTGGGCTGATGAAACGGATGACCTGGAAGGAGATGTTTCAACTTG
GCACAGTAATAATGACGATGTGTATAGGGCGCCCCCAGTTGACCGTTCCATCCTTCCCACTGCTCCACGGACTGCTAGGG
AACCCATTATCGACTGGAGCCGTCTTCCCAAATCGCCACCCTACACTGCTTTTCTAGGGAACCTACCCTATGATGTGACA
GAAGAGTCAATGAGAATTCTTTAGAGGATTAAATATCAGTACAGTGCGTTTACCACGTGAACCCAGCAATCCAGAGAGGT
TGAAAGGTTCTGGTTATGCTGAATTTGATGACCCGGATTCCATGTTCAGTGCCCTGAGTCTCAATAAAGAATCTCTAGGT
AACAGGAGAATTCGAGTGGACGCTGCTGATCAAGCACAGGGTAAAGACAGGGACGATCGTTCTTTTGGCCATGAGAGAAA
TCGGGATTTTGACAAAACAGATACAGACTGGAGGGCTCGTCCTGCCACAGACAGCTTGGATGACTACTCGCCTAGAAGAG
GTGATGATTGTTTTGGAGACAAGTGTCAAGATTGTTATGATTCAGACCGGTATCGCGATGGGTATCGGGAGGGGTATCAG
GATGGCCCACGCTGGGATATGGATCGATATGGCGGCCAGGATTGCTATGATGACCCAGGCAGCAGACACTATGATAGAGG
CTATGAATCCCAGATAGGCAATGGCAGAAGAGCATTTGGTAGTGGGTACCACAGGGATAATGACTACAGAGGAGGCAGGG
ACCGCTCTGAAGACCGATACAACAGACGGGATGATCGGTCGTGGAGCTCCAGAGATGATTACACTTGGGATGATTATAGG
TGTGACGATAGAGGTCCCCCGCAAAGACCCAAA

Alignment

ORF - retro_nleu_2601 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.39 %
• Parental protein coverage: 53.76 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MAASAKKKNKKGKTISLTDFLAEDGG-TGGGSTYVSKPVSWADETDDLEGDVSTTWHSNDDDVYRAPPID
          MAASAK.KNKKGKTISLTDFLAEDGG.TGGGS.YVSKPVSWADETDDLEGDVST.WHSN.DDVYRAPP.D
Retrocopy MAASAKEKNKKGKTISLTDFLAEDGG<TGGGSSYVSKPVSWADETDDLEGDVST-WHSNNDDVYRAPPVD

Parental  RSILPTAPRAAREPNIDRSRLPKSPPYTAFL-GNLPYDVTEESIKEFFRGLNISAVRLPREPSNPERLKG
          RSILPTAPR.AREP.ID.SRLPKSPPYTAFL.G..P......S..EFFRGLNIS.VRLPREPSNPERLKG
Retrocopy RSILPTAPRTAREPIIDWSRLPKSPPYTAFL>GTYPM-M*QKSQ*EFFRGLNISTVRLPREPSNPERLKG

Parental  FGYAEFEDLDSLLSALSLNEESLGNRRIRVDVADQAQDKDRDDRSFGRDRNRDSDKTDTDWRARPATDSF
          .GYAEF.D.DS..SALSLN.ESLGNRRIRVD.ADQAQ.KDRDDRSFG..RNRD.DKTDTDWRARPATDS.
Retrocopy SGYAEFDDPDSMFSALSLNKESLGNRRIRVDAADQAQGKDRDDRSFGHERNRDFDKTDTDWRARPATDSL

Parental  DDYPPRRGDDSFGDKYRDRYDSDRYRDGYRDG----PRRDMDRYGGRDRYDDRGSRDYDRGYDSRIGSGR
          DDY.PRRGDD.FGDK..D.YDSDRYRDGYR.G....PR.DMDRYGG.D.YDD.GSR.YDRGY.S.IG.GR
Retrocopy DDYSPRRGDDCFGDKCQDCYDSDRYRDGYREGYQDGPRWDMDRYGGQDCYDDPGSRHYDRGYESQIGNGR

Parental  RAFGSGYRRDDDYRGGGDRYEDRYDRRDDRSWSSRDDYSRDDYRRDDRGPPQRPK
          RAFGSGY.RD.DYRGG.DR.EDRY.RRDDRSWSSRDDY..DDYR.DDRGPPQRPK
Retrocopy RAFGSGYHRDNDYRGGRDRSEDRYNRRDDRSWSSRDDYTWDDYRCDDRGPPQRPK

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_2601 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 13 parental genes, and 41 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000018176	2 retrocopies	retro_cjac_1717, retro_cjac_2001,
Cavia porcellus	ENSCPOG00000005595	3 retrocopies	retro_cpor_278, retro_cpor_752, retro_cpor_937,
Homo sapiens	ENSG00000063046	7 retrocopies	retro_hsap_1686, retro_hsap_2639, retro_hsap_2698, retro_hsap_3767, retro_hsap_4196, retro_hsap_4848, retro_hsap_4891,
Gorilla gorilla	ENSGGOG00000013695	5 retrocopies	retro_ggor_1233, retro_ggor_1263, retro_ggor_1882, retro_ggor_1883, retro_ggor_3024,
Loxodonta africana	ENSLAFG00000009534	1 retrocopy	retro_lafr_294,
Macropus eugenii	ENSMEUG00000012341	2 retrocopies	retro_meug_1054, retro_meug_585,
Macaca mulatta	ENSMMUG00000001062	5 retrocopies	retro_mmul_1428, retro_mmul_2384, retro_mmul_2589, retro_mmul_731, retro_mmul_783,
Mus musculus	ENSMUSG00000058655	1 retrocopy	retro_mmus_3686,
Nomascus leucogenys	ENSNLEG00000017727	3 retrocopies	retro_nleu_2371, retro_nleu_2601 , retro_nleu_721,
Pongo abelii	ENSPPYG00000025848	7 retrocopies	retro_pabe_1388, retro_pabe_1560, retro_pabe_2283, retro_pabe_260, retro_pabe_3532, retro_pabe_3768, retro_pabe_506,
Rattus norvegicus	ENSRNOG00000010103	2 retrocopies	retro_rnor_2467, retro_rnor_2972,
Ictidomys tridecemlineatus	ENSSTOG00000006800	1 retrocopy	retro_itri_604,
Tupaia belangeri	ENSTBEG00000005423	2 retrocopies	retro_tbel_2363, retro_tbel_4167,