RetrogeneDB ID: retro_pabe_618

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 10:92653267..92653777(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RAB11A
• Ensembl ID: ENSPPYG00000006573
• Aliases: None
• Description: Ras-related protein Rab-11A [Source:UniProtKB/Swiss-Prot;Acc:Q5R9M7]

Sequence

>retro_pabe_618
TTTGCAACAAGGAGCATCCAGATTGATAGGAAAACAATAAAGGCACAGATGTGGGACAGAGCAGGGCAAGAGTAATACGA
AGCCATAACATAAGCTTATTATCATGGAGATGTAGGTGCCTTACTGGTTTAAGACATTGCTAAACATCTCACATATGAAA
ATACAGAATGATTGCTGAAAGAACTGAGCGATCACACTGATAGTAACATTGTCGTCATGTTATCATGGACAAATAAGAGT
GATTTACATCATCTCAGGGAAGTTCCTAGAGTTGAAGCAAGAGCTTTGGCAGAAAAAAATGGTTTGTCATTCATTGAGAC
ATCTGCTCTAGACTCTACAAATGTAGAAGCTACTTTTCAGACAATTCTAACAGAGATACCTCACATTGTTTCTCAGAAGC
ACATGTCAGACAGAGCCGAAAATGACATGTCCCCAAGCAATAATGTGGTTCCTGTTCATGTTCCACCAATCACTGAAAAC
AAACCAAAGGTGCAGTGCTGTCAGAACATC

Alignment

ORF - retro_pabe_618 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.76 %
• Parental protein coverage: 78.24 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  FATRSIQVDGKTIKAQIWDTAGQERYRAITSAYYRGAVGALLVYDIAKHLTYENVERWLKELRDHADSNI
          FATRSIQ.D.KTIKAQ.WD.AGQE.Y.AIT.AYY.G.VGALLV.DIAKHLTYEN.E..LKEL.DH.DSNI
Retrocopy FATRSIQIDRKTIKAQMWDRAGQE*YEAIT*AYYHGDVGALLV*DIAKHLTYENTE*LLKELSDHTDSNI

Parental  VIMLVG-NKSDLRHLRAVPTDEARAFAEKNGLSFIETSALDSTNVEAAFQTILTEIYRIVSQKQMSDRRE
          V.ML...NKSDL.HLR.VP..EARA.AEKNGLSFIETSALDSTNVEA.FQTILTEI..IVSQK.MSDR.E
Retrocopy VVMLSWTNKSDLHHLREVPRVEARALAEKNGLSFIETSALDSTNVEATFQTILTEIPHIVSQKHMSDRAE

Parental  NDMSPSNNVVPIHVPPTTENKPKVQCCQNI
          NDMSPSNNVVP.HVPP.TENKPKVQCCQNI
Retrocopy NDMSPSNNVVPVHVPPITENKPKVQCCQNI

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	55.51 RPM
SRP007412_cerebellum	0.00 RPM	65.18 RPM
SRP007412_heart	0.00 RPM	31.49 RPM
SRP007412_kidney	0.00 RPM	48.63 RPM
SRP007412_liver	0.03 RPM	36.17 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_618 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_618 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_618 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_715
Macaca mulatta	retro_mmul_2463

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 19 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	ENSPPYG00000000128	1 retrocopy	retro_pabe_3321,
Pongo abelii	ENSPPYG00000006573	1 retrocopy	retro_pabe_618 ,
Pongo abelii	ENSPPYG00000018056	1 retrocopy	retro_pabe_3574,
Pan troglodytes	ENSPTRG00000007188	1 retrocopy	retro_ptro_510,