RetrogeneDB ID: retro_pabe_2477

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 4:155457211..155457520(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: AKIRIN2
• Ensembl ID: ENSPPYG00000016831
• Aliases: None
• Description: akirin 2 [Source:HGNC Symbol;Acc:21407]

Sequence

>retro_pabe_2477
GAAACGAGTTTCCAAGACACAGATCCATGTTGTACTTCTGATGCACATGCATTTCTCCTCAGTGGATCAGCTTCACCAGG
AACTTCATCTGCAGCATCCTCACCATTAAAAAAAGAACAGCCCTTATTTACTTTATGGCAGGTTGGGATGATCTGTGAAC
ATTTGTTGAAAGAACATGAAGAGAAAGTTTGGGAAGAATATGAAGAATATTGAACACAAAACTTGCAGAACAATAATGAT
GCGTCTGTGAAGTTTACGCATGATCAAATAATGTGACAATATGGAGAACAGCCTGCTAGTTATGTTTCA

Alignment

ORF - retro_pabe_2477 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.92 %
• Parental protein coverage: 51.72 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  ETSFQQTDPCCTSDAQPHAFLLSGPASPGTSSAASSPLKKEQPLFTLRQVGMICERLLKEREEKVREEYE
          ETSFQ.TDPCCTSDA..HAFLLSG.ASPGTSSAASSPLKKEQPLFTL.QVGMICE.LLKE.EEKV.EEYE
Retrocopy ETSFQDTDPCCTSDA--HAFLLSGSASPGTSSAASSPLKKEQPLFTLWQVGMICEHLLKEHEEKVWEEYE

Parental  E-ILNTKLAEQ-YDAFVKFTHDQIMRRYGEQPASYVS
          E.ILNTKLAEQ..DA.VKFTHDQIM..YGEQPASYVS
Retrocopy E<ILNTKLAEQ>NDASVKFTHDQIM*QYGEQPASYVS

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	26.71 RPM
SRP007412_cerebellum	0.00 RPM	22.37 RPM
SRP007412_heart	0.00 RPM	9.93 RPM
SRP007412_kidney	0.03 RPM	14.35 RPM
SRP007412_liver	0.00 RPM	16.19 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_2477 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_2477 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_2477 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2991
Pan troglodytes	retro_ptro_2023
Gorilla gorilla	retro_ggor_2071
Macaca mulatta	retro_mmul_1914

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Parental genes homology:

Parental genes homology involve 14 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000003082	1 retrocopy	retro_cfam_1014,
Choloepus hoffmanni	ENSCHOG00000012160	1 retrocopy	retro_chof_413,
Callithrix jacchus	ENSCJAG00000000769	1 retrocopy	retro_cjac_2231,
Dasypus novemcinctus	ENSDNOG00000000549	1 retrocopy	retro_dnov_1788,
Homo sapiens	ENSG00000135334	1 retrocopy	retro_hsap_2991,
Gorilla gorilla	ENSGGOG00000002448	1 retrocopy	retro_ggor_2071,
Macaca mulatta	ENSMMUG00000002824	1 retrocopy	retro_mmul_1914,
Pongo abelii	ENSPPYG00000001511	2 retrocopies	retro_pabe_3137, retro_pabe_3646,
Pongo abelii	ENSPPYG00000016831	1 retrocopy	retro_pabe_2477 ,
Pan troglodytes	ENSPTRG00000018409	1 retrocopy	retro_ptro_2023,
Rattus norvegicus	ENSRNOG00000008288	1 retrocopy	retro_rnor_1499,
Sorex araneus	ENSSARG00000006084	1 retrocopy	retro_sara_701,
Sarcophilus harrisii	ENSSHAG00000011555	2 retrocopies	retro_shar_363, retro_shar_579,
Sus scrofa	ENSSSCG00000004307	1 retrocopy	retro_sscr_897,