RetrogeneDB ID: retro_nleu_1097

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397281.1:24191528..24192340(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: HMGA1
• Ensembl ID: ENSNLEG00000008303
• Aliases: None
• Description: None

Sequence

>retro_nleu_1097
CAGCCTCTCGTGAGTCCCAGGACAGCGCTGGGAGGGAGTCAGAAGGAGCCCAGCGAAGTGCCAAAACCTAAGGGACCTCA
GGGCCGACCAAATGGAAGGAAAAACAAGGACGCTGCCAAGACCTGGAAAACCACCACAACTACAGGAAGGAAACCAAGGG
GCAGACCCAAAAAACTGGAGAAGGAGGAAGAGGAGGGCATCTCACTGGAGTCCTCGAAGGAGGAGCAGTGACCGTGCATG
CGTGTCGCCTGCTCCTCACTGGAGGAACAGCTTCCTTTTGGGACTGGACAGCTTTGCTCCGCTCCCACCGCCCCCATCCC
TTCCCCAGGCCCACCATCACCAGCGCCTCCAGCCGCCACCCCTGTCTTCCACCTGCGACTTCACCACCACACTACACAAC
ACACCAACAACTTCAGGGCCCCCATGGGCTGAGTGGGGAGCAGTTTTCCCCTGGCCTCGGTTCTCAGCTCCCCCCGCCCA
CCCACACATACACATGTGCCCTCCTGGACAAGGCTAACGTTCCACTTAGCCACACCCGGCACCTACTGTGTCCCCACTCC
CTTAATGGTGGGGACATTGCTCTCTGGGCTTTTGGTTTGGGGGCGCCCTCTCCACTCCTCCATTGTTCCCTCTGGCGTCC
CACAGTGGGGCCTGGGAGGGTTCCCGTGGCCTTAAAAGGGGCCCAAGCCCCATCTCATCCTGGCCCACCCTACTCCACTG
CCCTGGCAGCAGCAGGTGTGGCCAATGGAGGGGGCTGCTGGCCCCCAGGATTCTACCAGCCAAACTGCCTTTGTCACCAC
GTGGGGCTCACA

Alignment

ORF - retro_nleu_1097 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.06 %
• Parental protein coverage: 82.1 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  QPLAS-KQEKDGTEKRGRGRPRKQPPVSPGTALVGSQKEPSEVPTPKRPRGRPKGSKNK-GEGGRGGHLA
          QPL.S..Q...G.E..G..R..K....S..T.....Q............R...KG...K.GEGGRGGHL.
Retrocopy QPLVS<SQDSAGRESEGAQRSAKT*GTSGPTKWKEKQGRCQDLENHHNYRKETKGQTQKTGEGGRGGHLT

Parental  GVLGGGAVT-RACRLLLTGGAASFWDWTALLRSHRPHPFPRPTITTASGRHPHLPPVPSPPHYTAHQPLQ
          GVL.GGAVT..ACRLLLTGG.ASFWDWTALLRSHRPHPFPRPTIT.AS.RHP.LPP..SPPHYT.HQ.LQ
Retrocopy GVLEGGAVTVHACRLLLTGGTASFWDWTALLRSHRPHPFPRPTITSASSRHPCLPPATSPPHYTTHQQLQ

Parental  GSHGLSGEQFSPGLSSQLPPPTHAYTHALLDKANIPLSRTLHLLRPHSLGGGDIALWAFGLG-PSLLLHC
          G.HGLSGEQFSPGL.SQLPPPTH.YT.ALLDKAN.PLS.T.HLL.PHSL.GGDIALWAFGLG.PS.LLHC
Retrocopy GPHGLSGEQFSPGLGSQLPPPTHTYTCALLDKANVPLSHTRHLLCPHSLNGGDIALWAFGLGAPSPLLHC

Parental  SLW-PIVGPGRVPLHKRG-QAPSHPGTPYSSALAAAGVANGGGCWPPGFPQPNCLCHHVGLT
          SLW.P.VGPGRVP....G.QAPSHPG.PYS.ALAAAGVANGGGCWPPGF.QPNCLCHHVGLT
Retrocopy SLWRPTVGPGRVPVALKGAQAPSHPGPPYSTALAAAGVANGGGCWPPGFYQPNCLCHHVGLT

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_1097 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 10 parental genes, and 24 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000001061	1 retrocopy	retro_amel_1637,
Callithrix jacchus	ENSCJAG00000015226	2 retrocopies	retro_cjac_1197, retro_cjac_3158,
Homo sapiens	ENSG00000137309	4 retrocopies	retro_hsap_1175, retro_hsap_2277, retro_hsap_4663, retro_hsap_695,
Myotis lucifugus	ENSMLUG00000010085	2 retrocopies	retro_mluc_1619, retro_mluc_2429,
Macaca mulatta	ENSMMUG00000019529	2 retrocopies	retro_mmul_1276, retro_mmul_2406,
Mus musculus	ENSMUSG00000046711	1 retrocopy	retro_mmus_188,
Nomascus leucogenys	ENSNLEG00000008303	1 retrocopy	retro_nleu_1097 ,
Pongo abelii	ENSPPYG00000029838	4 retrocopies	retro_pabe_1941, retro_pabe_2441, retro_pabe_3623, retro_pabe_960,
Pan troglodytes	ENSPTRG00000040884	6 retrocopies	retro_ptro_1611, retro_ptro_2053, retro_ptro_3098, retro_ptro_499, retro_ptro_789, retro_ptro_807,
Rattus norvegicus	ENSRNOG00000000488	1 retrocopy	retro_rnor_164,