RetrogeneDB ID: retro_pabe_2250

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 3:119458679..119458958(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: KIAA1143
• Ensembl ID: ENSPPYG00000013954
• Aliases: None
• Description: KIAA1143 [Source:HGNC Symbol;Acc:29198]

Sequence

>retro_pabe_2250
CCAGCCGAGCCAGCATTCCCGGCTCGCTTCAAGGAGTGGATTGGCTATAGGGAGGAGCCCACCGCAGAGACCAAGAGAAT
GCAGCCTCATCTCCCAGATGAAAATGGGGATCACAGTGACAAAGATGAAGAGCCTCACGTGATGGTTTTTAAAAAGGGAG
ACCTGTCAGTTGAAGAAGTCATGAAAAGTAAAGCAGAAGTAAAGGCTGCCAAAGCAGATAAAGAACCAGCTCCAACTGAG
GGAAGAATCATTTATCAAAAACCAGTGAAGCACCAGTCA

Alignment

ORF - retro_pabe_2250 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.72 %
• Parental protein coverage: 61.04 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  PAEPAFLARFKERVGYREGPTVETKRIQPQLPDEDGDHSDKEDEQPQVVVLKKGDLSVEEVMKIKAEIKA
          PAEPAF.ARFKE..GYRE.PT.ETKR.QP.LPDE.GDHSDK.DE.P.V.V.KKGDLSVEEVMK.KAE.KA
Retrocopy PAEPAFPARFKEWIGYREEPTAETKRMQPHLPDENGDHSDK-DEEPHVMVFKKGDLSVEEVMKSKAEVKA

Parental  AKADEEPAPADGRIIYRKPVKHPS
          AKAD.EPAP..GRIIY.KPVKH.S
Retrocopy AKADKEPAPTEGRIIYQKPVKHQS

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	19.02 RPM
SRP007412_cerebellum	0.00 RPM	28.82 RPM
SRP007412_heart	0.00 RPM	15.29 RPM
SRP007412_kidney	0.00 RPM	15.11 RPM
SRP007412_liver	0.00 RPM	9.73 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_2250 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_2250 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_2250 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2762
Pan troglodytes	retro_ptro_1869

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000014132	1 retrocopy	retro_cfam_2208,
Homo sapiens	ENSG00000163807	2 retrocopies	retro_hsap_1399, retro_hsap_2762,
Nomascus leucogenys	ENSNLEG00000005987	1 retrocopy	retro_nleu_666,
Oryctolagus cuniculus	ENSOCUG00000000929	2 retrocopies	retro_ocun_1601, retro_ocun_432,
Pongo abelii	ENSPPYG00000013954	1 retrocopy	retro_pabe_2250 ,
Pan troglodytes	ENSPTRG00000014824	1 retrocopy	retro_ptro_1869,
Pteropus vampyrus	ENSPVAG00000012438	2 retrocopies	retro_pvam_367, retro_pvam_458,
Sus scrofa	ENSSSCG00000011308	2 retrocopies	retro_sscr_844, retro_sscr_874,
Ictidomys tridecemlineatus	ENSSTOG00000010817	1 retrocopy	retro_itri_307,