RetrogeneDB ID: retro_pabe_2865

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 6:52596897..52597500(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: DKFZP468F1219
• Ensembl ID: ENSPPYG00000013892
• Aliases: None
• Description: mitochondrial carnitine/acylcarnitine carrier protein [Source:RefSeq peptide;Acc:NP_001126542]

Sequence

>retro_pabe_2865
CAGAAACACCTAGAGGATGTTCTCAGCTATCCCCAGCTGTTTGCAGCTGGGATGTTATCTGGTACATTCACCACAGGCAT
CATGACACCTGGAGAACCCATCAAGTGCTTGTTACACTTTCAGCCTTCTTCAGGGGAAACCAAGTACACTGGAACCTTGG
ACTGTGCAAAGAAGTTGTACCAGGAGTTTCAGATCCAAGGCATCTACAAAGGGACCGTGCTTACCCTTATGTGAGATGTT
CCAGCTAGCGAAACGTATTTCACGACATAAGAATGGCTAAAAAATATCTTCACTCTGGAAGGAAAGAGGGTCCATGAGCT
CAGTGTGCCTTGAATCCTGGTGGCTGGGTGCATTGCAGGGATCTTCAAGTGGGCTATGGCAGTCCCCCAAGATGTGCTCA
AGTCTCCCTTCCAGACTGCACCTCCTGGGAAATATCCTAATGGTTTTGGAGATGTGCTGAGGGAGCTGATCTGGGATGAA
GGAATCACATCCTTGTCTAAAGGGTCTGATGCAGTGATGACCCAAGCCCTCCCAGCCAATGCGGCCTGTTTCCTTGGCCT
TGAAGTTGCCATGAAGTTTCTTAATTGGGCCACCCCCGACTTG

Alignment

ORF - retro_pabe_2865 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.59 %
• Parental protein coverage: 66.78 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  QKHPEDVLSYPQLFAAGMLSGVFTTGIMTPGERIKCLLQIQASSGESKYTGTLDCAKKLYQEFGIRGIYK
          QKH.EDVLSYPQLFAAGMLSG.FTTGIMTPGE.IKCLL..Q.SSGE.KYTGTLDCAKKLYQEF.I.GIYK
Retrocopy QKHLEDVLSYPQLFAAGMLSGTFTTGIMTPGEPIKCLLHFQPSSGETKYTGTLDCAKKLYQEFQIQGIYK

Parental  GTVLTLMRDVPASGMYFMTYEWLKNVFTPEGKRVSELSAPRILVAGGIAGIFNWAVAIPPDVLKSRFQTA
          GTVLTLM.DVPAS..YF.T.EWLKN.FT.EGKRV.ELS.P.ILVAG.IAGIF.WA.A.P.DVLKS.FQTA
Retrocopy GTVLTLM*DVPASETYFTT*EWLKNIFTLEGKRVHELSVP*ILVAGCIAGIFKWAMAVPQDVLKSPFQTA

Parental  PPGKYPNGFRDVLRELIRDEGVTSLYKGFNAVMIRAFPANAACFLGFEVAMKFLNWAIPNL
          PPGKYPNGF.DVLRELI.DEG.TSL.KG..AVM..A.PANAACFLG.EVAMKFLNWA.P.L
Retrocopy PPGKYPNGFGDVLRELIWDEGITSLSKGSDAVMTQALPANAACFLGLEVAMKFLNWATPDL

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	10.01 RPM
SRP007412_cerebellum	0.00 RPM	6.32 RPM
SRP007412_heart	0.00 RPM	40.37 RPM
SRP007412_kidney	0.00 RPM	13.29 RPM
SRP007412_liver	0.00 RPM	40.33 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_2865 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_2865 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_2865 has 5 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3469
Pan troglodytes	retro_ptro_2352
Gorilla gorilla	retro_ggor_2341
Macaca mulatta	retro_mmul_1764
Callithrix jacchus	retro_cjac_2338

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000003285	1 retrocopy	retro_cjac_2338,
Homo sapiens	ENSG00000178537	1 retrocopy	retro_hsap_3469,
Gorilla gorilla	ENSGGOG00000028046	1 retrocopy	retro_ggor_2341,
Macaca mulatta	ENSMMUG00000015418	1 retrocopy	retro_mmul_1764,
Monodelphis domestica	ENSMODG00000013383	3 retrocopies	retro_mdom_1584, retro_mdom_229, retro_mdom_266,
Nomascus leucogenys	ENSNLEG00000006700	1 retrocopy	retro_nleu_342,
Pongo abelii	ENSPPYG00000013892	1 retrocopy	retro_pabe_2865 ,
Pan troglodytes	ENSPTRG00000014900	1 retrocopy	retro_ptro_2352,
Drosophila melanogaster	FBgn0031881	1 retrocopy	retro_dmel_15,