RetrogeneDB ID: retro_nleu_342

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397263.1:6150156..6150751(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SLC25A20
• Ensembl ID: ENSNLEG00000006700
• Aliases: None
• Description: None

Sequence

>retro_nleu_342
ATAGCCTACCAGCCAAAGCCCATCAGCCCGCTCAAGAACCTGCTGGCCAGCAGCTTTAGTGGCACGTGCCTGGTGTTCAT
GGGGCACCCTCTGGACACTGTCAAGGTCCGACTGCAGACACAGCCACGGAGTTTGCCTAGACAGCCTCCCATATACTGTG
GGACCTTTGACTCTCTCCCAAAGACTCTTAGAAGGGGCATCACAGGGCTGTATCAGGGAATGGCTGCCCTTATCATCGGT
GTCACCCCCATGTTTGCTGTGTGCTTCTCTGGGTTTGGTTTGAGGAAGCAACTATGACAGAAACACCCAGAGGATGTGCT
CGGCTATCCCCAGCTGTTTGCAGCTGGGATGTTATCTGGTACATTCACCACAGGCATTGTGACCCCTGGAGAACCCATCA
AGTGCTTGTTACACTTTCAGCCTTCTTCAGGGGAAACCAAGTACACTGGAACCTTGGACTGTGCAAAGAAGTTGTACCAG
GAGTTTCAGATTCCGAGGCATCTACAAAGGGACCGTGCTTACCCTTATGTGAGATGTTCCAGCTAGCGGAACTTATTTCA
TGACATATGAATGGCTCCAGAAGGAAAGCAGGCCC

Alignment

ORF - retro_nleu_342 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.5 %
• Parental protein coverage: 66.11 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MADQPKPISPLKNLLAGGFGGVCLVFVGHPLDTVKVRLQTQPPSLPGQPPMYSGTFDCFRKTLFREGITG
          .A.QPKPISPLKNLLA..F.G.CLVF.GHPLDTVKVRLQTQP.SLP.QPP.Y.GTFD...KTL.R.GITG
Retrocopy IAYQPKPISPLKNLLASSFSGTCLVFMGHPLDTVKVRLQTQPRSLPRQPPIYCGTFDSLPKTL-RRGITG

Parental  LYRGMAAPIIGVTPMFAVCFFGFGLGKKLQQKHPEDVLSYPQLFAAGMLSGVFTTGIMTPGERIKCLLQI
          LY.GMAA.IIGVTPMFAVCF.GFGL.K.L.QKHPEDVL.YPQLFAAGMLSG.FTTGI.TPGE.IKCLL..
Retrocopy LYQGMAALIIGVTPMFAVCFSGFGLRKQL*QKHPEDVLGYPQLFAAGMLSGTFTTGIVTPGEPIKCLLHF

Parental  QASSGESKYTGTLDCAKKLYQEFGI-RGIYKGTVLTLMRDVPASGMYFMTYEWLKNIFTP
          Q.SSGE.KYTGTLDCAKKLYQEF.I.RGIYKGTVLTLM.DVPASG.YFMTYEWL.....P
Retrocopy QPSSGETKYTGTLDCAKKLYQEFQI>RGIYKGTVLTLM*DVPASGTYFMTYEWLQKESRP

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_342 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 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000003285	1 retrocopy	retro_cjac_2338,
Homo sapiens	ENSG00000178537	1 retrocopy	retro_hsap_3469,
Gorilla gorilla	ENSGGOG00000028046	1 retrocopy	retro_ggor_2341,
Macaca mulatta	ENSMMUG00000015418	1 retrocopy	retro_mmul_1764,
Monodelphis domestica	ENSMODG00000013383	3 retrocopies	retro_mdom_1584, retro_mdom_229, retro_mdom_266,
Nomascus leucogenys	ENSNLEG00000006700	1 retrocopy	retro_nleu_342 ,
Pongo abelii	ENSPPYG00000013892	1 retrocopy	retro_pabe_2865,
Pan troglodytes	ENSPTRG00000014900	1 retrocopy	retro_ptro_2352,
Drosophila melanogaster	FBgn0031881	1 retrocopy	retro_dmel_15,