RetrogeneDB ID: retro_ptro_299

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 1:52565304..52565908(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TRA2A
• Ensembl ID: ENSPTRG00000018988
• Aliases: None
• Description: None

Sequence

>retro_ptro_299
AGGAGACGAAGTAGCTCATATACACCAGAATACTGGCAGTGAAGGAGCCGAAATCATTCTCCAATGTCTAACCAGAGAAG
ACACACTGGCAGAAGGGCAAATCCAGATCCCAACACTTGCCTTAGAGTGTTTGGCCTTAGTTTGTACACAACAGACAGAG
ATCTTCATGAAATATGTTCTTGATATGGACCTTTGAATGGTGTCAATGTGGTTTACAATCAGCAAACTGGGCGATCTCAA
GGATTTGCTTTTGTACATTTTGAGGGAATAGATGACTCAAAGGAGGCTATGGTAAGGGCAAACAGAAAGGAGCTGGATGA
TAGAAGAAATTCGGGTGGATTATTCTATTACCAAGAGAATGCGCACACCTACACCAGGCATCTATATGGGCAGAACAACT
CATAGTGGTGGTGGCGGAGGTGGTGGCAAAGGCGGCAGTGGAGGTGGTCACAGACGTCGAGATTCTTACTATGATAGAGG
ATATGATCGTGGATATGACAGATATGAAGACTATGATTACCGGTACAGAAGATGATCACCTTCTCCTTATTATAGTCGAT
ACAGATCACAATCAAGATCTCATTCCTGCAGCCCAAGACACTAT

Alignment

ORF - retro_ptro_299 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.77 %
• Parental protein coverage: 71.63 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  RSRSRSYTPEYRRRRSRSHSPMSNRRRHTGSRANPDPNTCLGVFGLSLYTTERDLREVFSRYGPLSGVNV
          R.RS.SYTPEY...RSR.HSPMSN.RRHTG.RANPDPNTCL.VFGLSLYTT.RDL.E..S.YGPL.GVNV
Retrocopy RRRSSSYTPEYWQ*RSRNHSPMSNQRRHTGRRANPDPNTCLRVFGLSLYTTDRDLHEICS*YGPLNGVNV

Parental  VYDQRTGRSRGFAFVYFERIDDSKEAMERANGMELDGRR-IRVDYSITKRAHTPTPGIYMGRPTHSGGGG
          VY.Q.TGRS.GFAFV.FE.IDDSKEAM.RAN..ELD.RR.IRVDYSITKR..TPTPGIYMGR.THS.GGG
Retrocopy VYNQQTGRSQGFAFVHFEGIDDSKEAMVRANRKELDDRR>IRVDYSITKRMRTPTPGIYMGRTTHS-GGG

Parental  GGGGGGGGGGGGRRRDSYYDRGYDRGYDRYEDYDYRYRRRSPSPYYSRYRSRSRSRSYSPRRY
          GGGG.GG.GGG.RRRDSYYDRGYDRGYDRYEDYDYRYRR.SPSPYYSRYRS.SRS.S.SPR.Y
Retrocopy GGGGKGGSGGGHRRRDSYYDRGYDRGYDRYEDYDYRYRR*SPSPYYSRYRSQSRSHSCSPRHY

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	33.98 RPM
SRP007412_cerebellum	0.11 RPM	43.41 RPM
SRP007412_heart	0.00 RPM	23.58 RPM
SRP007412_kidney	0.03 RPM	41.92 RPM
SRP007412_liver	0.03 RPM	20.72 RPM
SRP007412_testis	0.00 RPM	54.48 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_299 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_299 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_299 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_386

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000001130	1 retrocopy	retro_chof_974,
Callithrix jacchus	ENSCJAG00000001509	1 retrocopy	retro_cjac_1759,
Echinops telfairi	ENSETEG00000007250	2 retrocopies	retro_etel_323, retro_etel_692,
Homo sapiens	ENSG00000164548	1 retrocopy	retro_hsap_386,
Gorilla gorilla	ENSGGOG00000009053	1 retrocopy	retro_ggor_391,
Mustela putorius furo	ENSMPUG00000013480	1 retrocopy	retro_mputfur_1442,
Nomascus leucogenys	ENSNLEG00000014794	1 retrocopy	retro_nleu_1481,
Otolemur garnettii	ENSOGAG00000009733	3 retrocopies	retro_ogar_1966, retro_ogar_2558, retro_ogar_3027,
Pongo abelii	ENSPPYG00000017728	1 retrocopy	retro_pabe_324,
Pan troglodytes	ENSPTRG00000018988	1 retrocopy	retro_ptro_299 ,
Pan troglodytes	ENSPTRG00000021864	1 retrocopy	retro_ptro_222,
Sorex araneus	ENSSARG00000012900	1 retrocopy	retro_sara_467,