RetrogeneDB ID: retro_ptro_90

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 12:122363170..122363506(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSPTRG00000040582
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: MRPL53
• Ensembl ID: ENSPTRG00000033835
• Aliases: None
• Description: None

Sequence

>retro_ptro_90
ATGGCAGCTGCCTTGGCTCGGCTTGGTCTGCGGCCTGTCAAACAGGTTCGGGTTCAGTTCTGTCTCTTCGAGAAAAACGT
GGAATCGACGAGGACCTTCCTGCAGGCGGTGAGCAGTGAGAAGGTCCGCTCCACTAATCTCAACTGCTCAGTGATTGCGG
ACGTGAGGCATGACGGCTCCGAGCCCTGCGTGGACGTGCTGTTCGGAGACGGGCATCGCCTGATTATGCGCGGCGCTCAT
CTCACCGCTCTGGAAATGCTCACCGCCTTCGCCTCCCACATCCGGGCCAGGGACGCGGCGGGCAGCGGGGACAAGCCGGG
TGCTGATACTGGTCGC

Alignment

ORF - retro_ptro_90 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 99.11 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAAALARLGLRPVKQVRVQFCPFEKNVESTRTFLQAVSSEKVRSTNLNCSVIADVRHDGSEPCVDVLFGD
          MAAALARLGLRPVKQVRVQFC.FEKNVESTRTFLQAVSSEKVRSTNLNCSVIADVRHDGSEPCVDVLFGD
Retrocopy MAAALARLGLRPVKQVRVQFCLFEKNVESTRTFLQAVSSEKVRSTNLNCSVIADVRHDGSEPCVDVLFGD

Parental  GHRLIMRGAHLTALEMLTAFASHIRARDAAGSGDKPGADTGR
          GHRLIMRGAHLTALEMLTAFASHIRARDAAGSGDKPGADTGR
Retrocopy GHRLIMRGAHLTALEMLTAFASHIRARDAAGSGDKPGADTGR

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	0.43 RPM	11.40 RPM
SRP007412_cerebellum	0.04 RPM	4.45 RPM
SRP007412_heart	0.06 RPM	5.33 RPM
SRP007412_kidney	0.13 RPM	13.97 RPM
SRP007412_liver	0.10 RPM	5.04 RPM
SRP007412_testis	0.00 RPM	3.06 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_90 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_90 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_90 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 5 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000016599	3 retrocopies	retro_btau_1132, retro_btau_1528, retro_btau_799,
Nomascus leucogenys	ENSNLEG00000000672	1 retrocopy	retro_nleu_44,
Oryctolagus cuniculus	ENSOCUG00000015342	1 retrocopy	retro_ocun_372,
Pan troglodytes	ENSPTRG00000033835	1 retrocopy	retro_ptro_90 ,
Tarsius syrichta	ENSTSYG00000002278	2 retrocopies	retro_tsyr_1300, retro_tsyr_1840,