RetrogeneDB ID: retro_pabe_3499

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 9:98435330..98435562(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSPPYG00000029876
• Aliases: None
• Description: None

Sequence

>retro_pabe_3499
ATGACCCGCACTATGAAACCACTGGGAAATAGCTTTAAAGGAGTTTTAGTAGCTGAACTTGGCATTTGGGGATCATATTT
TGTGTTTAATAAGATGAACACAAGCCAAGATTTCAGGCAAACAATGAGTAAGAAATTTCCCTTCATTTTGGAAGTTTATT
ACAAATCCATTGAGCAGTCTAGAGTGTGTGGAATCGGAGGGCAAGGATCAAGAAAAATGGTTGAACAGAAAA

Alignment

ORF - retro_pabe_3499 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.25 %
• Parental protein coverage: 98.75 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MARTLEPLAKKIFKGVLVAELVGVFGAYFLFSKMHTSQDFRQTMSKKYPFILEVYYKSTEKSGMYGI-RE
          M.RT..PL....FKGVLVAEL.G..G.YF.F.KM.TSQDFRQTMSKK.PFILEVYYKS.E.S...GI...
Retrocopy MTRTMKPLGNS-FKGVLVAEL-GIWGSYFVFNKMNTSQDFRQTMSKKFPFILEVYYKSIEQSRVCGI>EG

Parental  LDQKTWLNSK
          .DQ..WLN.K
Retrocopy KDQEKWLNRK

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	16.70 RPM
SRP007412_cerebellum	0.00 RPM	24.32 RPM
SRP007412_heart	0.00 RPM	20.68 RPM
SRP007412_kidney	0.00 RPM	22.47 RPM
SRP007412_liver	0.00 RPM	15.45 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_3499 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_3499 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_3499 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_4294
Pan troglodytes	retro_ptro_2911
Gorilla gorilla	retro_ggor_2869

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 26 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000017579	1 retrocopy	retro_amel_629,
Choloepus hoffmanni	ENSCHOG00000013008	2 retrocopies	retro_chof_328, retro_chof_49,
Felis catus	ENSFCAG00000023228	2 retrocopies	retro_fcat_1289, retro_fcat_1750,
Homo sapiens	ENSG00000218739	2 retrocopies	retro_hsap_2312, retro_hsap_4294,
Gorilla gorilla	ENSGGOG00000025368	2 retrocopies	retro_ggor_1755, retro_ggor_2869,
Mus musculus	ENSMUSG00000062691	2 retrocopies	retro_mmus_426, retro_mmus_509,
Pongo abelii	ENSPPYG00000029876	2 retrocopies	retro_pabe_2045, retro_pabe_3499 ,
Pan troglodytes	ENSPTRG00000033858	2 retrocopies	retro_ptro_1687, retro_ptro_2911,
Rattus norvegicus	ENSRNOG00000040303	2 retrocopies	retro_rnor_1144, retro_rnor_973,
Sus scrofa	ENSSSCG00000020689	2 retrocopies	retro_sscr_328, retro_sscr_434,
Tursiops truncatus	ENSTTRG00000006884	7 retrocopies	retro_ttru_1069, retro_ttru_1866, retro_ttru_1946, retro_ttru_274, retro_ttru_526, retro_ttru_57, retro_ttru_832,