RetrogeneDB ID: retro_ptro_510

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 10:93447293..93447804(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RAB11A
• Ensembl ID: ENSPTRG00000007188
• Aliases: None
• Description: None

Sequence

>retro_ptro_510
TTTGCAACAAGAAGCATCCAGATTGATAGCAAAACAATAAAGGCACAGATGTGGGACAGAGCAGGGCAAGAGTAATACGA
AGCTATAACATAAGCTTATTATCATGAAGATATAGGTGCCTTATTGGTTTAAGACATTGCTAAACATCTCACATATGAAA
ATACAGAATGATTGCTGAAAGAACTGAGCGATCACACTGATAGTAACATTGTTGTCATGTTATCATGGACAAATAAGAGT
GATTTACATCATCTCAGGGAAGTTCCTAGAGTTGAAGGCAAGAGCTTTGGCAGAAAAAAATGATTTGTCATTCATTGAGA
CATCTGCTCTAGACTCTACAAATGTAGAAGCTACTTTTCAGACAATTCTAACAGAGATACCTCACATTGTTTCTCAGAAG
CAAATGTCAGACAGAGCCGAAAAAGACATGTCCCCAAGCAATAATGTGGTTCCTGTTCATGTTCCACCAATCACTGAAAA
CAAACCAAAGGTGCAGTGCTGTCAGAACATC

Alignment

ORF - retro_ptro_510 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.53 %
• Parental protein coverage: 78.24 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  FATRSIQVDGKTIKAQIWDTAGQERYRAITSAYYRGAVGALLVYDIAKHLTYENVERWLKELRDHADSNI
          FATRSIQ.D.KTIKAQ.WD.AGQE.Y.AIT.AYY....GALLV.DIAKHLTYEN.E..LKEL.DH.DSNI
Retrocopy FATRSIQIDSKTIKAQMWDRAGQE*YEAIT*AYYHEDIGALLV*DIAKHLTYENTE*LLKELSDHTDSNI

Parental  VIMLVG-NKSDLRHLRAVPTDE-ARAFAEKNGLSFIETSALDSTNVEAAFQTILTEIYRIVSQKQMSDRR
          V.ML...NKSDL.HLR.VP..E.ARA.AEKN.LSFIETSALDSTNVEA.FQTILTEI..IVSQKQMSDR.
Retrocopy VVMLSWTNKSDLHHLREVPRVE>ARALAEKNDLSFIETSALDSTNVEATFQTILTEIPHIVSQKQMSDRA

Parental  ENDMSPSNNVVPIHVPPTTENKPKVQCCQNI
          E.DMSPSNNVVP.HVPP.TENKPKVQCCQNI
Retrocopy EKDMSPSNNVVPVHVPPITENKPKVQCCQNI

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	79.38 RPM
SRP007412_cerebellum	0.00 RPM	59.69 RPM
SRP007412_heart	0.03 RPM	54.50 RPM
SRP007412_kidney	0.00 RPM	75.53 RPM
SRP007412_liver	0.00 RPM	39.51 RPM
SRP007412_testis	0.00 RPM	240.06 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_510 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_510 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_510 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 17 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000018959	1 retrocopy	retro_btau_1850,
Callithrix jacchus	ENSCJAG00000007333	1 retrocopy	retro_cjac_1050,
Echinops telfairi	ENSETEG00000004920	5 retrocopies	retro_etel_1150, retro_etel_2132, retro_etel_2214, retro_etel_694, retro_etel_837,
Homo sapiens	ENSG00000103769	1 retrocopy	retro_hsap_715,
Gorilla gorilla	ENSGGOG00000014252	2 retrocopies	retro_ggor_538, retro_ggor_605,
Myotis lucifugus	ENSMLUG00000008820	2 retrocopies	retro_mluc_1606, retro_mluc_2435,
Macaca mulatta	ENSMMUG00000008006	1 retrocopy	retro_mmul_2463,
Nomascus leucogenys	ENSNLEG00000012853	1 retrocopy	retro_nleu_467,
Petromyzon marinus	ENSPMAG00000009335	1 retrocopy	retro_pmar_25,
Pongo abelii	ENSPPYG00000006573	1 retrocopy	retro_pabe_618,
Pan troglodytes	ENSPTRG00000007188	1 retrocopy	retro_ptro_510 ,