RetrogeneDB ID: retro_nleu_2848

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397451.1:1667608..1668100(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: EIF3J
• Ensembl ID: ENSNLEG00000005568
• Aliases: None
• Description: None

Sequence

>retro_nleu_2848
CAGGAAGAAATTAAAAAGGGGTTAGAAGAACCTGAAGAACTCCAGGTGCTAACACCAGAGGAACAATTAACAGATAAACC
GCAGCTGGAGAAATCACAGGAAGAGTCAGACATGGAATTAGCAAAGGCAACTTTTGGTGTTAAGACTACTGTATGTGGAA
TGGATGCTATAAACCCATCTTCAAGGAACGACCTTACAGAGTTTGGAAAGTTACTAAAAGATAAAATTACACAAAATAAA
AAGTCACTATATTATGCCAGTTTTTTGGAAGTCTTACTTGGAGATGTGTGTATTTCATTGGAAACTGATGACTTGAAAAA
TGTTCCCAACACATTGTGCTTTGAAGTGAAAAACAGAAGCAAGCAAAGCCAAGCCAAAAAGAAGAACAAAGGTGTGGTTC
CTGGAGGGAGATTAAAAGCCACCATGACAAATGATCTGGTAGATTATGGTGGTGATGATGTAGGGTATGCACAAGACTAT
GAAAACGTCATG

Alignment

ORF - retro_nleu_2848 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.46 %
• Parental protein coverage: 64.48 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  QEEIKKRLEEPEEPKVLTPEEQLADKLRLKKLQEESDLELAKETFGVNNTVYGIDAMNPSSRDDFTEFGK
          QEEIKK.LEEPEE..VLTPEEQL.DK..L.K.QEESD.ELAK.TFGV..TV.G.DA.NPSSR.D.TEFGK
Retrocopy QEEIKKGLEEPEELQVLTPEEQLTDKPQLEKSQEESDMELAKATFGVKTTVCGMDAINPSSRNDLTEFGK

Parental  LLKDKITQYEKSLYYASFLEVLVRDVCISLEIDDLKKITNSLTVLCSEKQKQEKQSKAKKKKKGVVPGGG
          LLKDKITQ..KSLYYASFLEVL..DVCISLE.DDLK...N.L...C.E.....KQS.AKKK.KGVVPGG.
Retrocopy LLKDKITQNKKSLYYASFLEVLLGDVCISLETDDLKNVPNTL---CFEVKNRSKQSQAKKKNKGVVPGGR

Parental  LKATMKDDLADYGGYDGGYVQDYEDFM
          LKATM..DL.DYGG.D.GY.QDYE..M
Retrocopy LKATMTNDLVDYGGDDVGYAQDYENVM

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_2848 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 15 parental genes, and 24 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000002412	1 retrocopy	retro_cjac_589,
Cavia porcellus	ENSCPOG00000012396	3 retrocopies	retro_cpor_1357, retro_cpor_1358, retro_cpor_500,
Dipodomys ordii	ENSDORG00000008339	7 retrocopies	retro_dord_208, retro_dord_364, retro_dord_451, retro_dord_470, retro_dord_633, retro_dord_738, retro_dord_746,
Equus caballus	ENSECAG00000008716	1 retrocopy	retro_ecab_635,
Echinops telfairi	ENSETEG00000005052	1 retrocopy	retro_etel_1376,
Homo sapiens	ENSG00000104131	1 retrocopy	retro_hsap_4189,
Gorilla gorilla	ENSGGOG00000000548	2 retrocopies	retro_ggor_1687, retro_ggor_41,
Macropus eugenii	ENSMEUG00000010372	1 retrocopy	retro_meug_256,
Microcebus murinus	ENSMICG00000005006	1 retrocopy	retro_mmur_100,
Monodelphis domestica	ENSMODG00000017696	1 retrocopy	retro_mdom_141,
Mus musculus	ENSMUSG00000027236	1 retrocopy	retro_mmus_18,
Nomascus leucogenys	ENSNLEG00000005568	1 retrocopy	retro_nleu_2848 ,
Oryctolagus cuniculus	ENSOCUG00000005376	1 retrocopy	retro_ocun_1350,
Otolemur garnettii	ENSOGAG00000004694	1 retrocopy	retro_ogar_1227,
Pongo abelii	ENSPPYG00000006431	1 retrocopy	retro_pabe_3429,