RetrogeneDB ID: retro_nleu_2398

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397352.1:879231..879828(+)
• Located in intron of: ENSNLEG00000000878

Retrocopy information

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

Parental gene information

• Parental gene symbol: RPL13A
• Ensembl ID: ENSNLEG00000005211
• Aliases: None
• Description: None

Sequence

>retro_nleu_2398
CAGGTCCTGGTACTTGACGACGGAGGCCATCTCCTGGGCCCCCCTGGCGGCCATCGTGGCTAACTAGGTACTGCTAGGCT
GGAAGGTGGTGGTCGTACGCTGCGAGGGCATCAACATTTCTGGCAATTTCTACAGAAACAAGTTGAAGTACCTGGCTTTC
CCCCGCAAGCGGATGAACACCAACCCTTCGCGAGGTCCCTACCACCTCCTGGCCCCCAGCCGCATCTTCTGGCACTCGTG
CGAGGCTTGCTGCCCCACGAGACCAAGTGAGGCCAGGCCGCTCTGGACCGCCTCAAGGTGTTTGACGGCATCCCACCTCC
CTATGACAAGAAAAAGCCAATGGTGGTTCCTGATGCCTTCAAGGTCGTGCGTCTGAAGCTTACAAGAAAGTTTGCCTATC
TGGAGCGCCTGGCTCACGATGGTGGCTGGAAGTACCAGGCAGTGACAGCCACCCTGGAGGAGAAGAGGAAGGAGAAGGCC
AAGATCCACTACCGGAAGAAAAAACAGCTCATGAGGCTACGGAAACGGGCCAAGAAGAACGTGGAGAAGAAAACTGACAA
ATACACAGAGGTCCTCAAGACCCACGGACTCCTGGTC

Alignment

ORF - retro_nleu_2398 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.57 %
• Parental protein coverage: 98.49 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  QVLVLDGRGHLLGR-LAAIVAKQVLLGRKVVVVRCEGINISGNFYRNKLKYLAFLRKRMNTNPSRGPYHF
          QVLVLD..GHLLG..LAAIVA..VLLG.KVVVVRCEGINISGNFYRNKLKYLAF.RKRMNTNPSRGPYH.
Retrocopy QVLVLDDGGHLLGP>LAAIVAN*VLLGWKVVVVRCEGINISGNFYRNKLKYLAFPRKRMNTNPSRGPYHL

Parental  RAPSRIFWRT-VRGMLPHKTKRGQAALDRLKVFDGIPPPYDKR--MVVPAALKVVRLKPTR-FAYLGRLA
          .APSRIFW...VRG.LPH.TK.GQAALDRLKVFDGIPPPYDK...MVVP.A.KVVRLK.TR.FAYL.RLA
Retrocopy LAPSRIFWHS<VRGLLPHETK*GQAALDRLKVFDGIPPPYDKKKPMVVPDAFKVVRLKLTRKFAYLERLA

Parental  HEVGWKYQAVTATLEEKRKEKAKIHYRKKKQLMRLRKQAEKNVEKKIDKYTEVLKTHGLLV
          H..GWKYQAVTATLEEKRKEKAKIHYRKKKQLMRLRK.A.KNVEKK.DKYTEVLKTHGLLV
Retrocopy HDGGWKYQAVTATLEEKRKEKAKIHYRKKKQLMRLRKRAKKNVEKKTDKYTEVLKTHGLLV

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_2398 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 96 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000005296	3 retrocopies	retro_btau_1251, retro_btau_719, retro_btau_789,
Callithrix jacchus	ENSCJAG00000000072	16 retrocopies	retro_cjac_1130, retro_cjac_1706, retro_cjac_182, retro_cjac_197, retro_cjac_1997, retro_cjac_2170, retro_cjac_2322, retro_cjac_2467, retro_cjac_2468, retro_cjac_2665, retro_cjac_2699, retro_cjac_2755, retro_cjac_3009, retro_cjac_664, retro_cjac_941, retro_cjac_972,
Echinops telfairi	ENSETEG00000017076	2 retrocopies	retro_etel_46, retro_etel_853,
Loxodonta africana	ENSLAFG00000016213	3 retrocopies	retro_lafr_1160, retro_lafr_576, retro_lafr_810,
Microcebus murinus	ENSMICG00000009318	6 retrocopies	retro_mmur_240, retro_mmur_283, retro_mmur_311, retro_mmur_359, retro_mmur_65, retro_mmur_736,
Macaca mulatta	ENSMMUG00000007551	14 retrocopies	retro_mmul_1100, retro_mmul_1256, retro_mmul_1638, retro_mmul_1756, retro_mmul_2179, retro_mmul_2249, retro_mmul_2352, retro_mmul_2399, retro_mmul_296, retro_mmul_500, retro_mmul_520, retro_mmul_547, retro_mmul_837, retro_mmul_924,
Mus musculus	ENSMUSG00000074129	3 retrocopies	retro_mmus_1129, retro_mmus_1334, retro_mmus_20,
Nomascus leucogenys	ENSNLEG00000005211	23 retrocopies	retro_nleu_1173, retro_nleu_1429, retro_nleu_1568, retro_nleu_159, retro_nleu_1823, retro_nleu_1873, retro_nleu_1892, retro_nleu_1897, retro_nleu_2047, retro_nleu_228, retro_nleu_2398 , retro_nleu_2415, retro_nleu_2463, retro_nleu_2614, retro_nleu_2789, retro_nleu_2928, retro_nleu_330, retro_nleu_392, retro_nleu_441, retro_nleu_475, retro_nleu_513, retro_nleu_744, retro_nleu_760,
Otolemur garnettii	ENSOGAG00000004625	7 retrocopies	retro_ogar_1496, retro_ogar_211, retro_ogar_2254, retro_ogar_3148, retro_ogar_54, retro_ogar_596, retro_ogar_612,
Pongo abelii	ENSPPYG00000010251	1 retrocopy	retro_pabe_148,
Pan troglodytes	ENSPTRG00000011298	1 retrocopy	retro_ptro_31,
Pteropus vampyrus	ENSPVAG00000010958	3 retrocopies	retro_pvam_129, retro_pvam_625, retro_pvam_771,
Rattus norvegicus	ENSRNOG00000020618	10 retrocopies	retro_rnor_1073, retro_rnor_1112, retro_rnor_1212, retro_rnor_1292, retro_rnor_1357, retro_rnor_1742, retro_rnor_564, retro_rnor_593, retro_rnor_665, retro_rnor_988,
Sus scrofa	ENSSSCG00000003166	4 retrocopies	retro_sscr_290, retro_sscr_300, retro_sscr_392, retro_sscr_743,