RetrogeneDB ID: retro_mmul_1435

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 2:66053785..66054967(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMMUG00000002098
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: RNPC3
• Ensembl ID: ENSMMUG00000018039
• Aliases: None
• Description: None

Sequence

>retro_mmul_1435
TCTGATGACCCTGTCAAAGATGATAAAGAAAAGAAAGAACTTGGTTATTTAACAGTAGAAAATGGAATTGCACCAAACCA
TGGGCTGACTTTTCCTAATTCATGCCTCAAATATATGTATTCACCACCTTCCAGCACAATCCTAGCAAACAGAGTAAATG
CTTTGGCAAGCATGCCTAAGTTCTATGTACAGGTCCTTCATCTTATGAATAAAATGAATTTGCCCACACCTTTTAGACCA
ATTACTGTGCGACCTCCCATGTATGAAGACCATATGCCATTGCATGCACCTCTTCCACCCACATCTCCTCAGCCACCTGA
GGAACCTCCTTGGCCAGACGATGATGAGGAATTATCTAGTGAAGAATTAGAATATGAAAGCAGTGATGATGAGGACTGAC
AGAGAATGAACAAACCAATGGAACTAGCAAATCTTCAGCTCAAAAGACCCAAAACAATAAAGCAGCACCATGTGAAAAAA
AAAGAGAAAATTAAAGGATATGTTGAGCACACTTTTGTGTCCTTCACACAGCAGTTTACATCCAGTGCTGTTACCTTCAG
ATGTATTTGACCAACCACAACCTGTAGGTAATAAAAGAATTGAATTCCATATATCTACCGACATGCCAGCTGCATTTAAG
AAAGATTTAGAGAAGAAACAAAATTGTGAGAAAAAAACTATGATTTACCTGCTACTGAAGTTGATGCATCCAATATAGGA
TTTGGAAAAATCTTTCCCAAACCTAATTGGAACATCACAGAGGAGATTAAAGAAGACTCTGATGAAATGCCATCAGAATG
TGTTTCTAGAAGGGAACTGGAAAAGGACAGAATTTCTAGAGAAGAAATGGAAACACTTTCAGTTTTCAGGAGTTATGAAC
CTGGTGAACAAAAATGTAGAATTTATGTAAAGAATTTAGCTAGACATGTTCAAGAAAAGGACCTTAAGTATATTTTTGGA
AGATATGTTGACTTTTCATCAGAAACACAGTGGATCACGTTTGATATACGTTTGATGAAAGAAGGTCGTATGAAAGGACA
AGCTTTCACTGCACTTCCTAAGGAAAAAGCAGCAGCAAAAGCCTTAAAGGAAGCTAATGGATATGTGCTTTTTGGAAAAC
CCATGGTGGTTCAATTTGCTCGATCTGCTAGGCCAAAACAAGATCCTAAGGAAGGAAAAAGA

Alignment

ORF - retro_mmul_1435 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.63 %
• Parental protein coverage: 73.18 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  SETPSQKKKKKKKKKNINILNVFF--YRLTFPLNSCLKYMYPPPSSTILANIVNALASVPKFYVQVLHLM
          S..P....K.KK........N.......LTFP.NSCLKYMY.PPSSTILAN.VNALAS.PKFYVQVLHLM
Retrocopy SDDPVKDDKEKKELGYLTVENGIAPNHGLTFP-NSCLKYMYSPPSSTILANRVNALASMPKFYVQVLHLM

Parental  NKMNLPTPFGPITARPPMYEDYMPLHAPLPPTSPQPPEEPPLPDEDEELSSEESEYESTDDEDRQRMNKL
          NKMNLPTPF.PIT.RPPMYED.MPLHAPLPPTSPQPPEEPP.PD.DEELSSEE.EYES.DDED.QRMNK.
Retrocopy NKMNLPTPFRPITVRPPMYEDHMPLHAPLPPTSPQPPEEPPWPDDDEELSSEELEYESSDDED*QRMNKP

Parental  MELANLQPKRPKTIKQRHVRKK-RKIRDMLNTPLCPSHSSLHPVLLPSDVFDQPQPVGNKRIEFHISTDM
          MELANLQ.KRPKTIKQ.HV....RK..DML.T.LCPSHSSLHPVLLPSDVFDQPQPVGNKRIEFHISTDM
Retrocopy MELANLQLKRPKTIKQHHVXXX>RKLKDMLSTLLCPSHSSLHPVLLPSDVFDQPQPVGNKRIEFHISTDM

Parental  PAAFKKDLEKEQNCE-EKNHDLPATEVDASNIGFGKIFPKPNLDITEEIKEDSDEMPSECISRRELEKGR
          PAAFKKDLEK.QNCE.EKN.DLPATEVDASNIGFGKIFPKPN..ITEEIKEDSDEMPSEC.SRRELEK.R
Retrocopy PAAFKKDLEKKQNCE<EKNYDLPATEVDASNIGFGKIFPKPNWNITEEIKEDSDEMPSECVSRRELEKDR

Parental  ISREEMETLSVFRSYEPGEPNCRIYVKNLAKHVQEKDLKYIFGRYVDFSSETQRIMFDIRLMKEGRMKGQ
          ISREEMETLSVFRSYEPGE..CRIYVKNLA.HVQEKDLKYIFGRYVDFSSETQ.I.FDIRLMKEGRMKGQ
Retrocopy ISREEMETLSVFRSYEPGEQKCRIYVKNLARHVQEKDLKYIFGRYVDFSSETQWITFDIRLMKEGRMKGQ

Parental  AFIGLPNEKAATKALKEANGYVLFGKPMVVQFARSARPKQDPKEGKR
          AF..LP.EKAA.KALKEANGYVLFGKPMVVQFARSARPKQDPKEGKR
Retrocopy AFTALPKEKAAAKALKEANGYVLFGKPMVVQFARSARPKQDPKEGKR

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	1.34 RPM	30.37 RPM
SRP007412_brain_prefrontal_cortex	0.08 RPM	17.14 RPM
SRP007412_cerebellum	1.68 RPM	52.89 RPM
SRP007412_heart	0.29 RPM	9.01 RPM
SRP007412_kidney	1.41 RPM	22.77 RPM
SRP007412_liver	0.12 RPM	7.05 RPM
SRP007412_testis	0.45 RPM	4.64 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_1435 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_1435 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_1435 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2800
Pan troglodytes	retro_ptro_1897
Pongo abelii	retro_pabe_2224
Callithrix jacchus	retro_cjac_1397

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000035686	1 retrocopy	retro_cjac_1397,
Homo sapiens	ENSG00000185946	1 retrocopy	retro_hsap_2800,
Macaca mulatta	ENSMMUG00000018039	1 retrocopy	retro_mmul_1435 ,
Nomascus leucogenys	ENSNLEG00000012013	1 retrocopy	retro_nleu_1539,
Nomascus leucogenys	ENSNLEG00000015566	1 retrocopy	retro_nleu_1538,
Pongo abelii	ENSPPYG00000001102	1 retrocopy	retro_pabe_2224,
Pan troglodytes	ENSPTRG00000033902	1 retrocopy	retro_ptro_1897,