RetrogeneDB ID: retro_ptro_2023

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 4:152797933..152798260(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: AKIRIN2
• Ensembl ID: ENSPTRG00000018409
• Aliases: None
• Description: Pan troglodytes akirin 2 (AKIRIN2), mRNA. [Source:RefSeq mRNA;Acc:NM_001251907]

Sequence

>retro_ptro_2023
CAGAAGAGAAGATACTCAGAAACGAGTTTCCAAGACACAGATCCGTGTTGTACTTCTGATGCACATGCATTTCTCCTCAG
TGGATCAGCTTCACCAGGAACTTCATCTGCAGCATCCTCACCATTAAAAAAAGAACAGCCCTTATTTACTCTATGGCAGG
TTGGGATGATCTGTGAACATTAGTTGAAAGAACATGAAGAGAAAGTTTGGGAAGAATATGAAGAATACTGAACACAAAAC
TTGCAGAACAATAATGATGCATCTGTGAAGTTTACGCATGATCAAATAATGTGACGATATGGAGAAGAGCCTGCTAGTTA
TGTTTCA

Alignment

ORF - retro_ptro_2023 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.96 %
• Parental protein coverage: 54.68 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  QKRRHLETSFQQTDPCCTSDAQPHAFLLSGPASPGTSSAASSPLKKEQPLFTLRQVGMICERLLKEREEK
          QKRR..ETSFQ.TDPCCTSDA..HAFLLSG.ASPGTSSAASSPLKKEQPLFTL.QVGMICE..LKE.EEK
Retrocopy QKRRYSETSFQDTDPCCTSDA--HAFLLSGSASPGTSSAASSPLKKEQPLFTLWQVGMICEH*LKEHEEK

Parental  VREEYEE-ILNTKLAEQ-YDAFVKFTHDQIMRRYGEQPASYVS
          V.EEYEE.ILNTKLAEQ..DA.VKFTHDQIM.RYGE.PASYVS
Retrocopy VWEEYEE<ILNTKLAEQ>NDASVKFTHDQIM*RYGEEPASYVS

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	30.99 RPM
SRP007412_cerebellum	0.00 RPM	30.44 RPM
SRP007412_heart	0.00 RPM	15.74 RPM
SRP007412_kidney	0.00 RPM	21.37 RPM
SRP007412_liver	0.03 RPM	21.44 RPM
SRP007412_testis	0.00 RPM	38.78 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_2023 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2023 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2023 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2991
Gorilla gorilla	retro_ggor_2071
Pongo abelii	retro_pabe_2477
Macaca mulatta	retro_mmul_1914

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 14 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	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,