RetrogeneDB ID: retro_nleu_1128

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397282.1:30180072..30180384(+)
• Located in intron of: ENSNLEG00000014203

Retrocopy information

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

Parental gene information

• Parental gene symbol: ERH
• Ensembl ID: ENSNLEG00000001514
• Aliases: None
• Description: Enhancer of rudimentary homolog [Source:UniProtKB/TrEMBL;Acc:G1QLG4]

Sequence

>retro_nleu_1128
ATGTCTCACACCATTTTGCTGGTACAGACTACCAAGAGGCCAGAAGGCAGAACTTATGCTGACTACGAATCTGTGAATGA
ATGCATGGAAGGCGTTTGTAAAATGTATGAAGACATGTGAAAAGAATGAATCCCAACAGTCCCTCTATCACATATGACAT
CAGTCAGTTGTTTGATTTCATCAATGATCTGGCAGACCTCAGCTGCCTGGTTTACCGAGCTGATACCCAGACATACCAGC
CTTATAAAAAAAGACTGGATTAAAGAGAAGATCTACATGCTTCTTCGTCGGCAGGCTCAACAGGCTAATAAA

Alignment

ORF - retro_nleu_1128 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.51 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MSHTILLVQPTKRPEGRTYADYESVNECMEGVCKMYEE-HLKRMNPNSPSITYDISQLFDFIDDLADLSC
          MSHTILLVQ.TKRPEGRTYADYESVNECMEGVCKMYE..H.KRMNPNSPSITYDISQLFDFI.DLADLSC
Retrocopy MSHTILLVQTTKRPEGRTYADYESVNECMEGVCKMYED<HVKRMNPNSPSITYDISQLFDFINDLADLSC

Parental  LVYRADTQTYQPY-NKDWIKEKIYVLLRRQAQQAGK
          LVYRADTQTYQPY..KDWIKEKIY.LLRRQAQQA.K
Retrocopy LVYRADTQTYQPY>KKDWIKEKIYMLLRRQAQQANK

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_1128 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 23 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000014940	2 retrocopies	retro_cjac_209, retro_cjac_846,
Equus caballus	ENSECAG00000019178	1 retrocopy	retro_ecab_45,
Gorilla gorilla	ENSGGOG00000004751	2 retrocopies	retro_ggor_2424, retro_ggor_2553,
Microcebus murinus	ENSMICG00000009623	1 retrocopy	retro_mmur_74,
Myotis lucifugus	ENSMLUG00000011879	1 retrocopy	retro_mluc_142,
Nomascus leucogenys	ENSNLEG00000001514	2 retrocopies	retro_nleu_1128 , retro_nleu_1604,
Oryctolagus cuniculus	ENSOCUG00000004636	1 retrocopy	retro_ocun_42,
Pan troglodytes	ENSPTRG00000006482	2 retrocopies	retro_ptro_2433, retro_ptro_2577,
Sorex araneus	ENSSARG00000005558	11 retrocopies	retro_sara_114, retro_sara_127, retro_sara_151, retro_sara_221, retro_sara_251, retro_sara_295, retro_sara_298, retro_sara_490, retro_sara_56, retro_sara_58, retro_sara_66,