RetrogeneDB ID: retro_ptro_1727

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 2B:195652251..195652728(-)
• Located in intron of: ENSPTRG00000012749

Retrocopy information

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

Parental gene information

• Parental gene symbol: RAB1A
• Ensembl ID: ENSPTRG00000011989
• Aliases: None
• Description: None

Sequence

>retro_ptro_1727
ATGTCCAGCATGAATCCCAAATTGATTATTTATTCAAATTACTTCTGATTGGCGACTCTGGGGTTGGAAAGTCTTGCCTC
CTTCTTAGGTTTGCAGATGATAACATATACAGAAAGCTACATCAGCACAATTGGTATGGATTTCAAAATAAGAACTATAG
AGTTAGACGGGAAAACAATCAAGCTTCAAATATGGAACACAGCAGAACAGGAAAGGTTTCGAACAGTCATCTCCAGTTAT
TACAGAGGAGCCAATGGTATCCTAGTGGTGTATGATGTGACAGATCAGGAGTCCTTCAATAATATTAAACAGTGACTGCA
GAAAATAGATCGTTATCCCAGTGAAAACATCAACAAATTGTTGGTAGGGAACAAGTGTGATCTGACCACAGAGAAAGTAG
TAGACTACACAACAGCCAAGGAATTTGCTGATTCCCTTGGAATTCTGTTTTTGGAAACTAGTGCTAGGAATGCAACA

Alignment

ORF - retro_ptro_1727 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.2 %
• Parental protein coverage: 77.56 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MSSMNP-EYDYLFKLLLIGDSGVGKSCLLLRFADD-TYTESYISTIGVDFKIRTIELDGKTIKLQIWDTA
          MSSMNP...DYLFKLLLIGDSGVGKSCLLLRFADD.TYTESYISTIG.DFKIRTIELDGKTIKLQIW.TA
Retrocopy MSSMNP<QIDYLFKLLLIGDSGVGKSCLLLRFADD>TYTESYISTIGMDFKIRTIELDGKTIKLQIWNTA

Parental  GQERFRTITSSYYRGAHGIIVVYDVTDQESFNNVKQWLQEIDRYASENVNKLLVGNKCDLTTKKVVDYTT
          .QERFRT..SSYYRGA.GI.VVYDVTDQESFNN.KQ.LQ.IDRY.SEN.NKLLVGNKCDLTT.KVVDYTT
Retrocopy EQERFRTVISSYYRGANGILVVYDVTDQESFNNIKQ*LQKIDRYPSENINKLLVGNKCDLTTEKVVDYTT

Parental  AKEFADSLGIPFLETSAKNAT
          AKEFADSLGI.FLETSA.NAT
Retrocopy AKEFADSLGILFLETSARNAT

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	0.02 RPM	91.25 RPM
SRP007412_cerebellum	0.11 RPM	94.03 RPM
SRP007412_heart	0.20 RPM	78.72 RPM
SRP007412_kidney	0.24 RPM	137.51 RPM
SRP007412_liver	0.23 RPM	133.52 RPM
SRP007412_testis	0.11 RPM	142.16 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_1727 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_1727 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_1727 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2362
Gorilla gorilla	retro_ggor_1792
Pongo abelii	retro_pabe_2135

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Echinops telfairi	ENSETEG00000002205	2 retrocopies	retro_etel_1687, retro_etel_413,
Homo sapiens	ENSG00000138069	2 retrocopies	retro_hsap_2362, retro_hsap_3626,
Macaca mulatta	ENSMMUG00000021721	1 retrocopy	retro_mmul_951,
Oryctolagus cuniculus	ENSOCUG00000017003	1 retrocopy	retro_ocun_800,
Pongo abelii	ENSPPYG00000012360	1 retrocopy	retro_pabe_2135,
Pan troglodytes	ENSPTRG00000001370	1 retrocopy	retro_ptro_681,
Pan troglodytes	ENSPTRG00000003915	1 retrocopy	retro_ptro_2892,
Pan troglodytes	ENSPTRG00000011989	1 retrocopy	retro_ptro_1727 ,
Rattus norvegicus	ENSRNOG00000004992	1 retrocopy	retro_rnor_110,
Ictidomys tridecemlineatus	ENSSTOG00000020693	1 retrocopy	retro_itri_1541,
Drosophila melanogaster	FBgn0016700	1 retrocopy	retro_dmel_36,