RetrogeneDB ID: retro_ptro_115

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 10:46271881..46272436(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSPTRG00000042112
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: RHEBL1
• Ensembl ID: ENSPTRG00000004897
• Aliases: None
• Description: None

Sequence

>retro_ptro_115
ATGCCGCAGTCCAAGTCTCGGAAGATCGCGATCCTGGGCTACCGGTCTGTGGGGAAATCCTCATTGACGATTCAATTTGT
TGAAGGCCAATTTGTGGACTCCTACGATCCAACCATAGAAAACACTTTTACAAAGTTGATCACAGTAAATGGACAAGAAT
ATCATCTTCAACTTGTAGACACAGCCGGGCAAGATGAATATTCTATCTTTCCTCAGACATACTCCATAGATATTAATGGC
TATATTCTTGTGTATTCTGTTACATCAATCAAAAGTTTTGAAGTGATTAAAGTTATCCATGGCAAATTGTTGGATATGGT
GGGGAAAGTACAAATACCTATTATGTTGGTTGGGAATAAGAAAGACCTGCATATGGAAAGGGTGATCAGTTATGAAGAAG
GGAAAGCTTTGGCAGAATCTTGGAATGCAGCTTTTTTGGAATCTTCTGCTAAAGAAAATCAGACTGCTGTTGATGTTTTT
CGAGGGATAATTTTGGAGGCAGAAAAAATGGACGGGGCAGCTTCACAAGGCAAGTCTTCATGCTCGGTAATGTGA

Alignment

ORF - retro_ptro_115 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 53.98 %
• Parental protein coverage: 96.17 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MPLVRYRKVVILGYRSVGKTSLAHQFVEGEFSEGYDPTVENTYSKIVTLGKDEFHLHLVDTAGQDEYSIL
          MP....RK..ILGYRSVGK.SL..QFVEG.F...YDPT.ENT..K..T....E.HL.LVDTAGQDEYSI.
Retrocopy MPQSKSRKIAILGYRSVGKSSLTIQFVEGQFVDSYDPTIENTFTKLITVNGQEYHLQLVDTAGQDEYSIF

Parental  PYSFIIGVHGYVLVYSVTSLHSFQVIESLYQKLHEGHGKTRVPVVLVGNKADLSPEREVQAVEGKKLAES
          P....I...GY.LVYSVTS..SF.VI.....KL....GK...P..LVGNK.DL..ER.....EGK.LAES
Retrocopy PQTYSIDINGYILVYSVTSIKSFEVIKVIHGKLLDMVGKVQIPIMLVGNKKDLHMERVISYEEGKALAES

Parental  WGATFMESSARENQLTQGIFTKVIQEIARVENSYGQ
          W.A.F.ESSA.ENQ.....F...I.E.........Q
Retrocopy WNAAFLESSAKENQTAVDVFRGIILEAEKMDGAASQ

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	23.40 RPM	3.41 RPM
SRP007412_cerebellum	21.51 RPM	1.11 RPM
SRP007412_heart	22.30 RPM	0.23 RPM
SRP007412_kidney	16.19 RPM	0.81 RPM
SRP007412_liver	22.75 RPM	0.95 RPM
SRP007412_testis	17.39 RPM	0.63 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_115 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_115 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_115 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_568
Homo sapiens	retro_hsap_570

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000002998	1 retrocopy	retro_cpor_1328,
Erinaceus europaeus	ENSEEUG00000008514	2 retrocopies	retro_eeur_338, retro_eeur_528,
Oryctolagus cuniculus	ENSOCUG00000016881	1 retrocopy	retro_ocun_1802,
Otolemur garnettii	ENSOGAG00000013477	1 retrocopy	retro_ogar_2338,
Pan troglodytes	ENSPTRG00000004897	1 retrocopy	retro_ptro_115 ,
Rattus norvegicus	ENSRNOG00000021571	1 retrocopy	retro_rnor_2059,