RetrogeneDB ID: retro_nleu_1471

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397295.1:5491646..5492072(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PLEKHB2
• Ensembl ID: ENSNLEG00000010698
• Aliases: None
• Description: None

Sequence

>retro_nleu_1471
CAGATTGTTTGCTCAGATGGGAAAGCAATTAGTCTTTGTGCAGAAAACACAGTGATTGCTTGGCCTGGAAATTTACACTC
CAAGATTCCGGGACAAACACAGCCTGTGTGGGCTCCACAGTCATGACTGATGAGACACTTGTGGTTTCCCCCCCTCCACC
ACACACAGCCTATGCTGCACCAGCCACTGAGGAATAGGGCTGTGAGCCATACAGTGGTGTGTGCCTGCCAGGAACTCAAA
TTGTCTATGCTGCTAATGGACAGGCATATGCTGTGCCCTACCAGTACTCGTATGCAGGACTTTATGGACAGCAGCCTGCT
AACCAAGTCATCATTCAGGACTGATATCGAGACAGTGACCTGGGCAGTGGGCATGTTGGCAGGAGTGGCCATGGTCATGG
CCTTAGGGTGTCTATTCTTGGTCTTC

Alignment

ORF - retro_nleu_1471 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.43 %
• Parental protein coverage: 65.32 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  QIVCRDGKTISLCAEST-DDCLAWKFTLQDSRTNTAYVGSAVMTDETSVVSSPPPYTAYAAPAPEQAYSY
          QIVC.DGK.ISLCAE.T..DCLAWKFTLQDS.TNTA.VGS.VMTDET.VVS.PPP.TAY.A.........
Retrocopy QIVCSDGKAISLCAENT<SDCLAWKFTLQDSGTNTACVGSTVMTDETLVVSPPPPHTAY-AAPATEE*GC

Parental  GPYGGAYPPGTQVVYAANGQAYAVPYQYPYAGLYGQQPVNQVIIRERYRDNDSDLALG-MLAGAATGMAL
          .PY.G...PGTQ.VYAANGQAYAVPYQY.YAGLYGQQP.NQVII...YR..DSDL..G.MLAG.A..MAL
Retrocopy EPYSGVCLPGTQIVYAANGQAYAVPYQYSYAGLYGQQPANQVIIQD*YR--DSDLGSG>MLAGVAMVMAL

Parental  GSLFWVF
          G.LF.VF
Retrocopy GCLFLVF

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_1471 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 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000000941	2 retrocopies	retro_btau_1134, retro_btau_1635,
Cavia porcellus	ENSCPOG00000026329	1 retrocopy	retro_cpor_985,
Equus caballus	ENSECAG00000017331	1 retrocopy	retro_ecab_1069,
Felis catus	ENSFCAG00000027063	1 retrocopy	retro_fcat_213,
Homo sapiens	ENSG00000115762	1 retrocopy	retro_hsap_1890,
Meleagris gallopavo	ENSMGAG00000001052	1 retrocopy	retro_mgal_17,
Monodelphis domestica	ENSMODG00000018634	1 retrocopy	retro_mdom_720,
Nomascus leucogenys	ENSNLEG00000010698	2 retrocopies	retro_nleu_1471 , retro_nleu_2016,
Oryctolagus cuniculus	ENSOCUG00000024282	1 retrocopy	retro_ocun_654,
Otolemur garnettii	ENSOGAG00000028408	2 retrocopies	retro_ogar_2771, retro_ogar_703,
Pongo abelii	ENSPPYG00000012740	1 retrocopy	retro_pabe_1570,
Ictidomys tridecemlineatus	ENSSTOG00000020509	1 retrocopy	retro_itri_56,