RetrogeneDB ID: retro_nleu_1197

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397284.1:7010079..7010504(-)
• Located in intron of: ENSNLEG00000002768

Retrocopy information

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

Parental gene information

• Parental gene symbol: GMFB
• Ensembl ID: ENSNLEG00000012717
• Aliases: None
• Description: None

Sequence

>retro_nleu_1197
ATGAGTGGGTCTTTGGTGGTTTTGATGTTGCTGAAGATTTAGTGGAAAAGCTGAGAAAGTCTCGTTTTCACAAAGAAATG
AACAATGTTGCTATTATAATGAAGACTGACAAGGATAAACGCCTGGTGGTACTGGATGAGGAGCGTGAGGGTATTTCACC
AGATGAACTTAGAGATGAACTTCCTGAACGACAACCTCGTTTCATTGTGTATAGCTATAAATATCAACATAATGGATGGG
AGAGTTCCATATCCTCTGTGCTTTATTTTCTCCAGTCCTGTTGGATGTAAGCCTGAACAACGATGATATATGCTGGGAGT
AAGAATAAGCTAGTCCAGACAGCTGAACTAACCAAAATATTTGAAATAAGAAATACGGAAGAACTGACTGAAGAATGGTT
ACATGAGAAACTTGGATTTTTCCAC

Alignment

ORF - retro_nleu_1197 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.9 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MSESLVVC-DVAEDLVEKLRKFRFRKETNNAAIIMKIDKDKRLVVLDEELEGISPDELKDELPERQPRFI
          MS.SLVV..DVAEDLVEKLRK.RF.KE.NN.AIIMK.DKDKRLVVLDEE.EGISPDEL.DELPERQPRFI
Retrocopy MSGSLVVL<DVAEDLVEKLRKSRFHKEMNNVAIIMKTDKDKRLVVLDEEREGISPDELRDELPERQPRFI

Parental  VYSYKYQHD-DGRVSYPLCFIFSSPVGCKPEQQ-MMYAGSKNKLVQTAELTKVFEIRNTEDLTEEWLREK
          VYSYKYQH..DGRV.YPLCFIFSSPVGCKPEQ..M.YAGSKNKLVQTAELTK.FEIRNTE.LTEEWL.EK
Retrocopy VYSYKYQHN>DGRVPYPLCFIFSSPVGCKPEQR<MIYAGSKNKLVQTAELTKIFEIRNTEELTEEWLHEK

Parental  LGFFH
          LGFFH
Retrocopy LGFFH

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_1197 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	ENSCJAG00000007312	1 retrocopy	retro_cjac_736,
Cavia porcellus	ENSCPOG00000004207	1 retrocopy	retro_cpor_240,
Homo sapiens	ENSG00000197045	1 retrocopy	retro_hsap_2818,
Loxodonta africana	ENSLAFG00000004659	1 retrocopy	retro_lafr_493,
Macaca mulatta	ENSMMUG00000012326	1 retrocopy	retro_mmul_1498,
Nomascus leucogenys	ENSNLEG00000012717	1 retrocopy	retro_nleu_1197 ,
Oryctolagus cuniculus	ENSOCUG00000004488	2 retrocopies	retro_ocun_1849, retro_ocun_1881,
Pongo abelii	ENSPPYG00000005830	1 retrocopy	retro_pabe_2209,