RetrogeneDB ID: retro_pabe_3022

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 6:162394509..162395067(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: YKT6
• Ensembl ID: ENSPPYG00000017595
• Aliases: None
• Description: YKT6 v-SNARE homolog (S. cerevisiae) [Source:HGNC Symbol;Acc:16959]

Sequence

>retro_pabe_3022
ATGAAGCTGTACAGCCTCAGTGTCCTCTACAAAGGCGAGGCCAAGGTAGTGCTGCTCAAAGCCAGGTACGACGATGTCTC
TTCCTTCAGCTTTTTCCAAAGATCCAGCGTTCAGGAATTCATGACTTTCACCAATCAACTGATTGTGGAGCATTCATCCA
AAAGCACTAGAGCTTCTGTCGAAGAGCAAGACTGTCTGTGGCACGTCTTTGTCCGGAATGACAGTCTTGCAGGTGACAAT
AAATGCCCATCCCGGGTGGCCTTTACCTTGCTGGAGAAAGTACTAGATGAATTCTCCAAGCAAGTCAACAGGATAGACTG
GCCAGTAGGATCCCCTGCTACAATCCACTCTGCAGCCCTGGATGGTCACCTCAGTAGATACCAGAACCCATGAGATGTTG
CCACCATGACTAACGTGCAGGCCGAACCAGACGAGACCCAAATCATTATGCACAATACCATGGAGTCTTTGTTAGAGCAA
GGTGAGAAGCTAGGTGGCTTAGTGTCCAAATCCGAGGTGCTGGGAACACAGTCTAAAGCCTTCTACAAAACTGCCCGG

Alignment

ORF - retro_pabe_3022 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.21 %
• Parental protein coverage: 95.45 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MKLYSLSVLYKGEAKVVLLKAAYD-VSSFSFFQRSSVQEFMTFTSQLIVERSSKGTRASVKEQDYLCHVY
          MKLYSLSVLYKGEAKVVLLKA.YD.VSSFSFFQRSSVQEFMTFT.QLIVE.SSK.TRASV.EQD.L.HV.
Retrocopy MKLYSLSVLYKGEAKVVLLKARYDDVSSFSFFQRSSVQEFMTFTNQLIVEHSSKSTRASVEEQDCLWHVF

Parental  VRNDSLAGVVIADNEYPSRVAFTLLEKVLDEFSKQVDRIDWPVGSPATIHYPALDGHLSRYQNPREADPM
          VRNDSLAG....DN..PSRVAFTLLEKVLDEFSKQV.RIDWPVGSPATIH..ALDGHLSRYQNP.....M
Retrocopy VRNDSLAG----DNKCPSRVAFTLLEKVLDEFSKQVNRIDWPVGSPATIHSAALDGHLSRYQNP*DVATM

Parental  TKVQAELDETKIILHNTMESLLERGEKLDDLVSKSEVLGTQSKAFYKTAR
          T.VQAE.DET.II.HNTMESLLE.GEKL..LVSKSEVLGTQSKAFYKTAR
Retrocopy TNVQAEPDETQIIMHNTMESLLEQGEKLGGLVSKSEVLGTQSKAFYKTAR

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP007412_brain_prefrontal_cortex	0.00 RPM	72.76 RPM
SRP007412_cerebellum	0.00 RPM	46.09 RPM
SRP007412_heart	0.00 RPM	20.38 RPM
SRP007412_kidney	0.00 RPM	68.78 RPM
SRP007412_liver	0.00 RPM	18.42 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_3022 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_3022 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_3022 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3687
Pan troglodytes	retro_ptro_2500
Gorilla gorilla	retro_ggor_2493

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Parental genes homology:

Parental genes homology involve 19 parental genes, and 22 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000017618	1 retrocopy	retro_amel_967,
Bos taurus	ENSBTAG00000000274	1 retrocopy	retro_btau_601,
Canis familiaris	ENSCAFG00000002903	1 retrocopy	retro_cfam_740,
Choloepus hoffmanni	ENSCHOG00000011207	1 retrocopy	retro_chof_657,
Callithrix jacchus	ENSCJAG00000008053	2 retrocopies	retro_cjac_2394, retro_cjac_2492,
Dasypus novemcinctus	ENSDNOG00000015173	1 retrocopy	retro_dnov_1364,
Dipodomys ordii	ENSDORG00000016393	1 retrocopy	retro_dord_621,
Erinaceus europaeus	ENSEEUG00000001247	1 retrocopy	retro_eeur_267,
Felis catus	ENSFCAG00000014362	1 retrocopy	retro_fcat_1327,
Gorilla gorilla	ENSGGOG00000027036	1 retrocopy	retro_ggor_2493,
Macropus eugenii	ENSMEUG00000014769	1 retrocopy	retro_meug_2068,
Mustela putorius furo	ENSMPUG00000018200	2 retrocopies	retro_mputfur_141, retro_mputfur_165,
Mus musculus	ENSMUSG00000002741	1 retrocopy	retro_mmus_825,
Nomascus leucogenys	ENSNLEG00000003689	1 retrocopy	retro_nleu_2275,
Oryctolagus cuniculus	ENSOCUG00000002981	1 retrocopy	retro_ocun_15,
Pongo abelii	ENSPPYG00000017595	1 retrocopy	retro_pabe_3022 ,
Pan troglodytes	ENSPTRG00000019141	1 retrocopy	retro_ptro_2500,
Sus scrofa	ENSSSCG00000016750	1 retrocopy	retro_sscr_1063,
Tursiops truncatus	ENSTTRG00000006052	2 retrocopies	retro_ttru_1320, retro_ttru_417,