RetrogeneDB ID: retro_mmul_2463

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 9:93336846..93337356(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MMU.4075
• Ensembl ID: ENSMMUG00000008006
• Aliases: None
• Description: ras-related protein Rab-11A [Source:RefSeq peptide;Acc:NP_001248718]

Sequence

>retro_mmul_2463
TTTGCAACAAGAAGCATCCAGATTGATAGGGAAACAATAAAGGCACAGGTATGGGACAGAGCAGGGCAAGAGTAATACCA
AGCTATAACATAAGCATATTATCATAGAGATGTAGGTGCCTTATTGGGTTAAGACATTGCTAAACATCTCACATACGAAA
ATATAGAACGATTGCTGAAAGAACTGAGAGATCACACTGATAGTAACATTGTCGTCATGTTATCATGGACAAATAAGGGT
GATTTACGTCATCTCAGGGAAGTTCCTATAGTTGAAGCAAGAGCTTTGGCAGAAAAAAATGATTTGTCATTCAATGAGAC
ATCTGCTCTAGACTCTACAAATGTAGAAGCTACTTTTCAGACAATTCTAACAGAGATATCCCACATTGTTTCTCAGAAGC
AAGTATCAGACAGAGCGGAAAACGACATGTCCCCAAGCAGTAATGTGGTTCCTATTCATGTTCCACCAATCACTGAAAAC
AAACCAAAAGTGCAATGCTCTCAGAACATC

Alignment

ORF - retro_mmul_2463 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.41 %
• Parental protein coverage: 78.24 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  FATRSIQVDGKTIKAQIWDTAGQERYRAITSAYYRGAVGALLVYDIAKHLTYENVERWLKELRDHADSNI
          FATRSIQ.D..TIKAQ.WD.AGQE.Y.AIT.AYY...VGALL..DIAKHLTYEN.ER.LKELRDH.DSNI
Retrocopy FATRSIQIDRETIKAQVWDRAGQE*YQAIT*AYYHRDVGALLG*DIAKHLTYENIERLLKELRDHTDSNI

Parental  VIMLVG-NKSDLRHLRAVPTDEARAFAEKNGLSFIETSALDSTNVEAAFQTILTEIYRIVSQKQMSDRRE
          V.ML...NK.DLRHLR.VP..EARA.AEKN.LSF.ETSALDSTNVEA.FQTILTEI..IVSQKQ.SDR.E
Retrocopy VVMLSWTNKGDLRHLREVPIVEARALAEKNDLSFNETSALDSTNVEATFQTILTEISHIVSQKQVSDRAE

Parental  NDMSPSNNVVPIHVPPTTENKPKVQCCQNI
          NDMSPS.NVVPIHVPP.TENKPKVQC.QNI
Retrocopy NDMSPSSNVVPIHVPPITENKPKVQCSQNI

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	0.00 RPM	97.37 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	69.02 RPM
SRP007412_cerebellum	0.00 RPM	88.34 RPM
SRP007412_heart	0.00 RPM	50.64 RPM
SRP007412_kidney	0.00 RPM	88.26 RPM
SRP007412_liver	0.00 RPM	40.38 RPM
SRP007412_testis	0.00 RPM	114.81 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_2463 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_2463 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_2463 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_715
Pongo abelii	retro_pabe_618

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 18 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 ,
Macaca mulatta	ENSMMUG00000017720	1 retrocopy	retro_mmul_2336,
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,