RetrogeneDB ID: retro_nleu_2338

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397345.1:5700029..5700661(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MLX
• Ensembl ID: ENSNLEG00000011638
• Aliases: None
• Description: None

Sequence

>retro_nleu_2338
AAGGTGGAGTATGTCTACAGCTACAAAAGCTCAGACCTGAAATATTTTATAGAAAGCACCCACAATGGGACGGTAGTGTC
TAGAGCTAATAGCATCGGTTCCACCAGTGCCTCTTCCATCCCCAACACAGATGAGGAGGACAGTGATTACCACCAAGAGT
CCTACAAGGACTGGTAGTGGTGAGCACACACTGAGGCTGAGCAGAAGAGGAAGGATGTCATCAAGAGAGGCTGTGATGAT
CTTCAGACCATCATCCCCACATGCCAGCAGCAGGACTCCTGTATTGGCTCCCGAAAGCTCAGCAAAGCCATCATTCTACA
AAAGACCATTGACTACACTCAGTTTTTGCACAAGGAGAAGAAAATGCAGGAGGAGGAGGTGTCCACACTATGCAAGGACC
TCACGACCCTAAAGATCCTGAAAGGGAACTATGAGCAGATTGTGAAGGCACACCAGGACAACCCCCGTGAGGGGAGGGCC
AGGCCTCTGACCAAGTCAAGGTCAGTGTGTTTCGAGGTATCATGGACTCCCCGTTGCAGTCCTTCAATGCCTTCATCTCT
GTGACCAACTGCCAGGAGCTGTCGGCCTGTGTCTTCAGCTAGATTGAGGAGCACTGCAAGCCACAAGCCATG

Alignment

ORF - retro_nleu_2338 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.74 %
• Parental protein coverage: 71.96 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  KVEYAYSDNSLDPGLFVESTRKGSVVSRANSIGSTSASSVPNTDDEDSDYHQEAYKESYKDRRRRAHTQA
          KVEY.YS..S.D...F.EST..G.VVSRANSIGSTSASS.PNTD.EDSDYHQ....ESYKD....AHT.A
Retrocopy KVEYVYSYKSSDLKYFIESTHNGTVVSRANSIGSTSASSIPNTDEEDSDYHQ----ESYKDW*W*AHTEA

Parental  EQKRRDAIKRGCEEASASYPPMARPCWGLGEGEQSQPYLL--AIDYIQFLHKEKKKQEEEVSTLRKDVTA
          EQKR.D.IKRGC.......P.........G....S....L...IDY.QFLHKEKK.QEEEVSTL.KD.T.
Retrocopy EQKRKDVIKRGCDDLQTIIPTCQQQDSCIGSRKLSKAIILQKTIDYTQFLHKEKKMQEEEVSTLCKDLTT

Parental  LKIMKVNYEQIVKAHQDNPHE-GEDQVSDQVKFNVFQGIMDSLFQSFNASISVASFQELSACVFSWIEEH
          LKI.K.NYEQIVKAHQDNP.E.GE.Q.SDQVK..VF.GIMDS..QSFNA.ISV...QELSACVFS.IEEH
Retrocopy LKILKGNYEQIVKAHQDNPRE<GEGQASDQVKVSVFRGIMDSPLQSFNAFISVTNCQELSACVFS*IEEH

Parental  CKPQTL
          CKPQ..
Retrocopy CKPQAM

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_2338 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 8 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000005011	1 retrocopy	retro_cjac_2774,
Homo sapiens	ENSG00000108788	1 retrocopy	retro_hsap_2216,
Gorilla gorilla	ENSGGOG00000010869	1 retrocopy	retro_ggor_1748,
Microcebus murinus	ENSMICG00000010258	1 retrocopy	retro_mmur_1373,
Monodelphis domestica	ENSMODG00000014918	2 retrocopies	retro_mdom_501, retro_mdom_539,
Nomascus leucogenys	ENSNLEG00000011638	1 retrocopy	retro_nleu_2338 ,
Pongo abelii	ENSPPYG00000008387	1 retrocopy	retro_pabe_2087,
Pan troglodytes	ENSPTRG00000009208	1 retrocopy	retro_ptro_1681,