RetrogeneDB ID: retro_ptro_1290

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 18:27456464..27456812(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSPTRG00000009323
• Aliases: None
• Description: None

Sequence

>retro_ptro_1290
ATGGAGCCCCTGAACCAGCAAACGCACAAGCAGGTTCATGAGATACATTCTCACATGGGACACCTGGAGACGGCAGACAA
GCAGTCTGTGCACTTAGTAGAAGGTGAAATCCAAGCAAGCACAGACCAGATATTCAGCCATCTAGAACATCTGGAGATTT
TGTCCAGCAAGGAGCCCCCTAACAAAAGGCAGAATGCCAAACTTCGGGTTGACCAGTTTAAGTATGATGTTCAGCACCTG
CAGACTGCTCTCAGAAACTTCCAGCACTGGTGCTATGCAAGGGAGCAGCAGGAGGGACAGCAAGAAGAGCTTCTATCTCA
AACCTTCACCACTAACAATTCTCAATCG

Alignment

ORF - retro_ptro_1290 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.62 %
• Parental protein coverage: 50.22 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MEPLYQQTHKQVHEIQSCMGRLETADKQSVHIVENEIQASIDQIFSRLERLEILSSKEPPNKRQNAKLRV
          MEPL.QQTHKQVHEI.S.MG.LETADKQSVH.VE.EIQAS.DQIFS.LE.LEILSSKEPPNKRQNAKLRV
Retrocopy MEPLNQQTHKQVHEIHSHMGHLETADKQSVHLVEGEIQASTDQIFSHLEHLEILSSKEPPNKRQNAKLRV

Parental  DQLKYDVQHLQTALRNFQHRRHAREQQERQREELLSRTFTTNDSDT
          DQ.KYDVQHLQTALRNFQH...AREQQE.Q.EELLS.TFTTN.S..
Retrocopy DQFKYDVQHLQTALRNFQHWCYAREQQEGQQEELLSQTFTTNNSQS

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	12.10 RPM
SRP007412_cerebellum	0.07 RPM	11.69 RPM
SRP007412_heart	0.00 RPM	7.40 RPM
SRP007412_kidney	0.10 RPM	18.20 RPM
SRP007412_liver	0.29 RPM	13.62 RPM
SRP007412_testis	0.00 RPM	31.93 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_1290 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_1290 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_1290 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000013419	1 retrocopy	retro_cfam_1351,
Callithrix jacchus	ENSCJAG00000020030	1 retrocopy	retro_cjac_3180,
Felis catus	ENSFCAG00000028951	1 retrocopy	retro_fcat_678,
Myotis lucifugus	ENSMLUG00000002709	1 retrocopy	retro_mluc_752,
Pongo abelii	ENSPPYG00000008290	1 retrocopy	retro_pabe_1596,
Pan troglodytes	ENSPTRG00000009323	1 retrocopy	retro_ptro_1290 ,
Ictidomys tridecemlineatus	ENSSTOG00000016069	2 retrocopies	retro_itri_1790, retro_itri_270,
Vicugna pacos	ENSVPAG00000009295	1 retrocopy	retro_vpac_567,