RetrogeneDB ID: retro_nleu_2140

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397331.1:4264611..4265342(-)
• Located in intron of: ENSNLEG00000001119

Retrocopy information

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

Parental gene information

• Parental gene symbol: SUCLA2
• Ensembl ID: ENSNLEG00000002948
• Aliases: None
• Description: succinate-CoA ligase, ADP-forming, beta subunit [Source:HGNC Symbol;Acc:11448]

Sequence

>retro_nleu_2140
GGTTCAAAAGATGTTGAGATGAAGGCGCAGGTTTTAGCTGATGGTAGAGGAAAAGGAACATTTGAAAGTGGCCTCAAAGG
AGGAGTGAAGATAGTTTTCTCTCTAGAAGAAGCAAAAGCTGTTTCCTCAGAAATGATTGGGAAAAAGTTGTTTACCAAGC
AAATGGGAGAAAAGGGCGGAATATGCAACCAAGTATTGAAGCGAAAATACCCTAGGGGAGAAGACTACTTTGCAATAGGG
ATGGAAAGGTCATTTCAAGGTCCTGTATTAATAGGAAGTTCACATGGTGGTGTCAACATTGCAGATGTTGCTGCTGAGAC
TCCTGATGCAATTAAAGAACCTGTTGATATTGTAGAAGGCATCAAAAAGGAACAAGCTCTCCGGCTTGAACAGAAGATGG
AATTTCCACCTAATATTGTGGATTCTGCAGCAGAAAACATGATCAAGCTTTACAGCCTTTTTCTGAAATATGATGCAACC
ATGATAAGAAATAAATCCAATGGTGAAGATTCAGATGGAGCTGTGCTGTGATGGATGCAAAGATCAATTTTGACTCTAAT
TCAGCCTATCGCCAAAAGAAAATCTTTGATCTACAGGACTGAACCCAGGAAGATGAAAGTGACAAAGATGCTGCTAAGGC
AGATCTCAACTACATTGGCCTGAAAGGAAATACAGACTGTCTAGTAAACGGTGCTGGTTTGGCCATGGCCTCAATGGATA
TAATAAAACTT

Alignment

ORF - retro_nleu_2140 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.4 %
• Parental protein coverage: 66.04 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  GSKDVVIKAQVLAGGRGKGTFESGLKGGVKIVFSPEEAKAVSSQMIGKKLFTKQTGEKGRICNQVLVCER
          GSKDV..KAQVLA.GRGKGTFESGLKGGVKIVFS.EEAKAVSS.MIGKKLFTKQ.GEKG.ICNQVL...R
Retrocopy GSKDVEMKAQVLADGRGKGTFESGLKGGVKIVFSLEEAKAVSSEMIGKKLFTKQMGEKGGICNQVL--KR

Parental  KYPRREYYFAIAMERSFQGPVLIGSSHGGVNIEDVAAETPEAIIKEPIDIEEGIKKEQALQLAQKMGFPP
          KYPR.E.YFAI.MERSFQGPVLIGSSHGGVNI.DVAAETP.AI.KEP.DI.EGIKKEQAL.L.QKM.FPP
Retrocopy KYPRGEDYFAIGMERSFQGPVLIGSSHGGVNIADVAAETPDAI-KEPVDIVEGIKKEQALRLEQKMEFPP

Parental  NIVESAAENMVKLYSLFLKYDATMI-EINPMV-EDSDGAVL-CMDAKINFDSNSAYRQKKIFDLQDWTQE
          NIV.SAAENM.KLYSLFLKYDATMI.EINPMV.EDSDGAVL..MDAKINFDSNSAYRQKKIFDLQD.TQE
Retrocopy NIVDSAAENMIKLYSLFLKYDATMI>EINPMV<EDSDGAVL<VMDAKINFDSNSAYRQKKIFDLQD*TQE

Parental  DERDKDAAKANLNYIGLDGNIGCLVNGAGLAMATMDIIKL
          DE.DKDAAKA.LNYIGL.GN..CLVNGAGLAMA.MDIIKL
Retrocopy DESDKDAAKADLNYIGLKGNTDCLVNGAGLAMASMDIIKL

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_2140 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 12 parental genes, and 23 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000014610	2 retrocopies	retro_acar_26, retro_acar_52,
Callithrix jacchus	ENSCJAG00000009278	2 retrocopies	retro_cjac_1233, retro_cjac_2379,
Cavia porcellus	ENSCPOG00000014961	1 retrocopy	retro_cpor_1113,
Homo sapiens	ENSG00000136143	3 retrocopies	retro_hsap_2236, retro_hsap_2281, retro_hsap_3445,
Gorilla gorilla	ENSGGOG00000008224	3 retrocopies	retro_ggor_1668, retro_ggor_1694, retro_ggor_2327,
Macaca mulatta	ENSMMUG00000007539	1 retrocopy	retro_mmul_1231,
Mustela putorius furo	ENSMPUG00000001488	1 retrocopy	retro_mputfur_768,
Nomascus leucogenys	ENSNLEG00000002948	3 retrocopies	retro_nleu_1963, retro_nleu_2140 , retro_nleu_2302,
Nomascus leucogenys	ENSNLEG00000007553	1 retrocopy	retro_nleu_915,
Otolemur garnettii	ENSOGAG00000007452	1 retrocopy	retro_ogar_2196,
Pongo abelii	ENSPPYG00000005352	2 retrocopies	retro_pabe_1939, retro_pabe_2852,
Pan troglodytes	ENSPTRG00000005859	3 retrocopies	retro_ptro_1581, retro_ptro_1615, retro_ptro_2337,