RetrogeneDB ID: retro_mmul_198

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 2:151754772..151755567(+)
• Located in intron of: ENSMMUG00000000932

Retrocopy information

• Ensembl ID: ENSMMUG00000031508
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSMMUG00000021855
• Aliases: None
• Description: None

Sequence

>retro_mmul_198
ATGTTCGTTCCCTGCGGGGAATCGGCCCCCGACCTTGCCGGCTTCACCCTCCTAATGCCAGCAGTATCTGTTGGAAATGT
TGGCCAGCTTGCAATGGATCTGATTATTTCTACACTGAGTATGTCTAAGATTGGTTACTTCTATACCGATTGTCTTGTGC
CTATGGTTGGAAACAATCCATATGCGACTGCGGAAGGAAATTCAACAGAACTTAGTATAAATGCTGAAGTATATTCATTG
CCTTCAAGAAAGCTGGTGGCTCTTCAGTTAAGATCCATTTTTATTAAGTATAAATCAAAGCCGTTCTGTGAAAAACTGCT
TTCCTGGGTGAAAAGCAGCGGCTATGCCAGAGTCATTGTTCTTTCGAGCAGCCATTCATATCAGCGCAATGACCTGCAGC
TTCACAGTACTCCCTTCCGGTACCTACTCACACCTTCCATGCAAAGAAGTGTTCAAAATAAAATAAAGAGCCTTAACTGG
CAAGAAATGGAAAAAAGCCGGTGCATTCCAGAAATAGATGATTCCGAGTTTTGTATCCGCATTCCGGGGGGAGGAATCAC
AAAAACGCTCTATGATGAAAGCTGTTCTAAAGAAATCCAAATGGTAGTTCTGCTGAAATTTATTTCAGAAGGGGACAACA
TGCCAGATGCATTAGGTCTCGTTGAGTACCTTAATGAGTGGCTTCAGATAATCAAACCACTTAGCGATGACCCCACAGCA
TCTACCTCACGGTGGAAAATACCAAGTTCTTGGAGATTACTCTTTGGCAGTGGTCTTCCCCCAGCACTTTTTTGA

Alignment

ORF - retro_mmul_198 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.29 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MFVPCGESAPDLAGFTLLMPAVSVGNVGQLAMDLIISTLNMSKIGYFYTDCLVPMVGNNPYATAEGNSTE
          MFVPCGESAPDLAGFTLLMPAVSVGNVGQLAMDLIISTL.MSKIGYFYTDCLVPMVGNNPYATAEGNSTE
Retrocopy MFVPCGESAPDLAGFTLLMPAVSVGNVGQLAMDLIISTLSMSKIGYFYTDCLVPMVGNNPYATAEGNSTE

Parental  LSINAEGINFSIYKLYIILFSQWCAKYKSKPFCEKLLSWVKSSGCARVIVLSSSHSYQRNDLQLRSTPFR
          LSINAE.......KL..........KYKSKPFCEKLLSWVKSSG.ARVIVLSSSHSYQRNDLQL.STPFR
Retrocopy LSINAEVYSLPSRKLVALQLRSIFIKYKSKPFCEKLLSWVKSSGYARVIVLSSSHSYQRNDLQLHSTPFR

Parental  YLLTPSMQRSVQNKIKSLNWQEMEKSRCIPEIDDSEFCIRIPGGGITKTLYDESCSKEIQMAVLLKFVSE
          YLLTPSMQRSVQNKIKSLNWQEMEKSRCIPEIDDSEFCIRIPGGGITKTLYDESCSKEIQM.VLLKF.SE
Retrocopy YLLTPSMQRSVQNKIKSLNWQEMEKSRCIPEIDDSEFCIRIPGGGITKTLYDESCSKEIQMVVLLKFISE

Parental  GDNIPDALGLVEYLNEWLQIIKPLSDDPTASTSRWKIPSSWRLLFGSGLPPALF
          GDN.PDALGLVEYLNEWLQIIKPLSDDPTASTSRWKIPSSWRLLFGSGLPPALF
Retrocopy GDNMPDALGLVEYLNEWLQIIKPLSDDPTASTSRWKIPSSWRLLFGSGLPPALF

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	0.78 RPM	6.61 RPM
SRP007412_brain_prefrontal_cortex	0.71 RPM	8.01 RPM
SRP007412_cerebellum	1.23 RPM	7.75 RPM
SRP007412_heart	0.94 RPM	6.65 RPM
SRP007412_kidney	2.58 RPM	8.33 RPM
SRP007412_liver	0.59 RPM	7.20 RPM
SRP007412_testis	2.53 RPM	24.58 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_198 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_198 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_198 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000018855	1 retrocopy	retro_cfam_424,
Choloepus hoffmanni	ENSCHOG00000010042	1 retrocopy	retro_chof_1738,
Myotis lucifugus	ENSMLUG00000017744	1 retrocopy	retro_mluc_2496,
Macaca mulatta	ENSMMUG00000021855	1 retrocopy	retro_mmul_198 ,
Nomascus leucogenys	ENSNLEG00000009063	1 retrocopy	retro_nleu_1753,
Oryctolagus cuniculus	ENSOCUG00000005086	1 retrocopy	retro_ocun_1448,
Sus scrofa	ENSSSCG00000021827	2 retrocopies	retro_sscr_1008, retro_sscr_763,