RetrogeneDB ID: retro_nleu_592

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397268.1:23562309..23563460(+)
• Located in intron of: ENSNLEG00000005150

Retrocopy information

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

Parental gene information

• Parental gene symbol: FAM20B
• Ensembl ID: ENSNLEG00000015580
• Aliases: None
• Description: None

Sequence

>retro_nleu_592
ATATGTCAACTGCCAAGCAGTGTTTCACCACTTGATCACCTGAGGGCTTTTCACCGAATGATGACTGGCTTGTGGATGGA
GCTGTCACCCAAGTTGGACCACACGTTGCAGTTTACCTAGGAGATTGCAGCCCAGTGGGTTGTTCCCCAGGAAGTGTACT
GTGAAGAGACACCAGAGCTGGGGGCAATCATGCATGCCATGGCCACCAAGCAAATTATTCAAGCTGATTTGGGTTATAAA
GGGACACAGCTGAAAGCCTTACTGATACTTGAAAGGGAACAGAAAGTTGTTTTCGAACCTAAGTAGTATAGCCGAGACCA
TGTAGTGGAAGGGAACCACATGCCGGTTATGATAGACACAATGCGGAGGTAGCAGCCTTTCACTTGGACAGGATTGTGGG
TGTCCCAGAGCCCTGTTGATGGTGGGCATATTTGTTCACCTTCAGACAGAGATCAAGCTTGTTACCATGGAGCAGCTGTT
GAGCCCGTTCCTAACTGTAGGAAACAATACTTGTTTTTATGGGAAGGGTTATTACTACTGAGAAACAGAACCAGCTTGTG
CTGATGGAGACACAATGGAAAAACCTGTCACACTTCGGCTTCCAGATGTGTGGCCTCTCCAGAAACACCAACAACCGTGG
GCCAGGACTTACCAAAAAGGCAAGTTGGCCAGGTGGGAGTATGATGAGAGCTACTATGAGGCTGTGAAGAAAACATCCCT
TTATGACTCTGGCCTGTGCCTCTTGGACACCATTAACACAGCTGTCTTTGATTACCTGATTGACAATGCTGACAGCCATT
ACTATAAGAACTTTCAAGATAATTAGGGCGCCAGTATGCTCATCCTTCTTGATAACGACAAAAGCTTTGGGAACCCCTTG
CTGGATGAAAGAAGCATTCTTTCCCCTCTCCATCAGTGTGGCATCACTCGGGTTTCTACCTGGAACAGACGGAACTACCT
AAAGAATGGTGTGCTGAAGTCTGCCTTAAAATCTGCCATGGCCCGTGACCCCTCTCCCCAGTGCTCTCTGATCCTCATCT
GGACACCATGGACCAGTGGCTCCTGAGTGTCCTGGCCACCGTGGAGCAGTGCACTGACCAGTGTGGGATGGACACTGTAT
GGTGGAAGACACGATGCCTTTCTCCCACTTG

Alignment

ORF - retro_nleu_592 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.89 %
• Parental protein coverage: 94.13 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  IDNLDTSAANREDQRAFHRMMTGLRVELAPKLDHTLQSPWEIAAQWVVPREVYPEETPELGAIMHAMATK
          I..L..S.......RAFHRMMTGL..EL.PKLDHTLQ...EIAAQWVVP.EVY.EETPELGAIMHAMATK
Retrocopy ICQLPSSVSPLDHLRAFHRMMTGLWMELSPKLDHTLQFT*EIAAQWVVPQEVYCEETPELGAIMHAMATK

Parental  KIIKADVGYKGTQLKALLILEGGQKVVFKPKRYSRDYVVEG-EPYAGYDRHNAEVAAFHLDRILGFR-RA
          .II.AD.GYKGTQLKALLILE..QKVVF.PK.YSRD.VVEG.EP.AGYDRHNAEVAAFHLDRI.G...RA
Retrocopy QIIQADLGYKGTQLKALLILEREQKVVFEPK*YSRDHVVEG<EPHAGYDRHNAEVAAFHLDRIVGVP<RA

Parental  PLVVGRFVNLRTEIKPVATEQLLSTFLTVGNNTCFYGKCYYCRETEPACADGDTMEGSVTLWLPDVWPLQ
          .L.VG.FV.L.TEIK.V..EQLLS.FLTVGNNTCFYGK.YY..ETEPACADGDTME..VTL.LPDVWPLQ
Retrocopy LLMVGIFVHLQTEIKLVTMEQLLSPFLTVGNNTCFYGKGYYY*ETEPACADGDTMEKPVTLRLPDVWPLQ

Parental  KHRHPWGRTYREGKLARWEYDESYCDAVKKTSPYDSGPRLLDIIDTAVFDYLIGNADRHHYESFQDDEGA
          KH..PW.RTY..GKLARWEYDESY..AVKKTS.YDSG..LLD.I.TAVFDYLI.NAD.H.Y..FQD..GA
Retrocopy KHQQPWARTYQKGKLARWEYDESYYEAVKKTSLYDSGLCLLDTINTAVFDYLIDNADSHYYKNFQDN*GA

Parental  SMLILLDNAKSFGNPSLDERSILAPLYQCCIIRVSTWNRLNYLKNGVLKSALKSAMAHD-PISPVLSDPH
          SMLILLDN.KSFGNP.LDERSIL.PL.QC.I.RVSTWNR.NYLKNGVLKSALKSAMA.D.P.SPVLSDPH
Retrocopy SMLILLDNDKSFGNPLLDERSILSPLHQCGITRVSTWNRRNYLKNGVLKSALKSAMARD<PLSPVLSDPH

Parental  LDAVDQRLLSVLATVKQCTDQFGMDTV-LVEDRMPLSHL
          LD..DQ.LLSVLATV.QCTDQ.GMDTV..VED.MP.SHL
Retrocopy LDTMDQWLLSVLATVEQCTDQCGMDTV<MVEDTMPFSHL

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_592 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 23 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000005236	6 retrocopies	retro_chof_1509, retro_chof_1926, retro_chof_2615, retro_chof_2629, retro_chof_799, retro_chof_868,
Dasypus novemcinctus	ENSDNOG00000006175	2 retrocopies	retro_dnov_1484, retro_dnov_2346,
Echinops telfairi	ENSETEG00000005651	1 retrocopy	retro_etel_1128,
Homo sapiens	ENSG00000116199	1 retrocopy	retro_hsap_2730,
Gorilla gorilla	ENSGGOG00000002484	1 retrocopy	retro_ggor_1899,
Macropus eugenii	ENSMEUG00000006654	1 retrocopy	retro_meug_414,
Macaca mulatta	ENSMMUG00000006260	1 retrocopy	retro_mmul_1533,
Nomascus leucogenys	ENSNLEG00000015580	1 retrocopy	retro_nleu_592 ,
Otolemur garnettii	ENSOGAG00000012751	1 retrocopy	retro_ogar_2800,
Pongo abelii	ENSPPYG00000000466	2 retrocopies	retro_pabe_2268, retro_pabe_2269,
Pan troglodytes	ENSPTRG00000001725	1 retrocopy	retro_ptro_1845,
Ictidomys tridecemlineatus	ENSSTOG00000005086	2 retrocopies	retro_itri_441, retro_itri_539,
Tarsius syrichta	ENSTSYG00000005482	3 retrocopies	retro_tsyr_2065, retro_tsyr_2124, retro_tsyr_89,