RetrogeneDB ID: retro_mmul_962

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 12:72148798..72149398(-)
• Located in intron of: ENSMMUG00000017524

Retrocopy information

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

Parental gene information

• Parental gene symbol: MYL6B
• Ensembl ID: ENSMMUG00000005214
• Aliases: MYL6B, MYL6
• Description: None

Sequence

>retro_mmul_962
CCTCCCAAGGATATTCTGGGGAGGAACCAGCAGGGCTCTCCATCTCCAAAGCAGCTGCCAAGCCAGCAGCAGCATGAGCC
CCTCCAGCCAAGACCAAAGCTGAGCCAGCTACCCCATCCCCAGGCCCCTGAGAAAATCCAGGAGCCCCCAGTCGATCTCT
CCAAAGTGATGATCAAGTTTAACAAAGACCACCTGGAGGAGTTCAAGGCGGCCTTCAAGCTGTTTAACTGAGTGGGGGCT
GGCAAGATCCTGTACAGCCAGTTTGGGGACATGATGCGGGCCCTGGGCCAAAACCCCACCAATGCCAAGGTGCTCAAGTT
CCTTGAGAACCCCAAGAGTGATGAGCTGAAGTCCCAGCATGTGGACTTCGAGACTTTCCTACCCATGCTCCAGGTGACAG
CCAAGAACCGGAACCAAGGCACGTATGAGGACTACTTGGAGGGGCTTCATGTGTTTGACAAGGAGGGGAATAGCAAAGTC
TCGGGAGCAGAGCTCAGACAAGTCCTCATCACCCTGGGAGAGAAGATGGCTGAGGAGGAGATGGAGACTGTTCTGGCAGG
ACATGAGGACAGCATCAACGAGGAGGCCTTCCTGAAACAC

Alignment

ORF - retro_mmul_962 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.17 %
• Parental protein coverage: 97.13 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  PKKDV-PVKKPAGPSISKPAAKPAAAAGAP-PAKSKAEPAVPQAPQKTQEPPIDLSKVVIEFNKDQLEEF
          P.KD......PAG.SISK.AAKPAAA...P.P.........PQAP.K.QEPP.DLSKV.I.FNKD.LEEF
Retrocopy PPKDI<SGEEPAGLSISKAAAKPAAA*APP>PRPKLSQLPHPQAPEKIQEPPVDLSKVMIKFNKDHLEEF

Parental  KEAFELFDRVGDGKILYSQCGDVMRALGQNPTNAEVLKVLGNPKSDELKSRRVDFETFLPMLQAVAKNRD
          K.AF.LF..VG.GKILYSQ.GD.MRALGQNPTNA.VLK.L.NPKSDELKS..VDFETFLPMLQ..AKNR.
Retrocopy KAAFKLFN*VGAGKILYSQFGDMMRALGQNPTNAKVLKFLENPKSDELKSQHVDFETFLPMLQVTAKNRN

Parental  QGTYEDYLEGLRVFDKEGDGKVMGAELRHVLTTLGEKMTEEEVETVLAGHEDSNGCINYEAFLKH
          QGTYEDYLEGL.VFDKEG..KV.GAELR.VL.TLGEKM.EEE.ETVLAGHEDS...IN.EAFLKH
Retrocopy QGTYEDYLEGLHVFDKEGNSKVSGAELRQVLITLGEKMAEEEMETVLAGHEDS---INEEAFLKH

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	0.11 RPM	30.03 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	66.40 RPM
SRP007412_cerebellum	0.06 RPM	21.96 RPM
SRP007412_heart	0.00 RPM	18.25 RPM
SRP007412_kidney	0.12 RPM	12.21 RPM
SRP007412_liver	0.00 RPM	5.34 RPM
SRP007412_testis	0.04 RPM	21.56 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_962 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_962 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_962 has 5 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2383
Pan troglodytes	retro_ptro_1741
Gorilla gorilla	retro_ggor_1808
Pongo abelii	retro_pabe_2150
Callithrix jacchus	retro_cjac_2848

---

Parental genes homology:

Parental genes homology involve 15 parental genes, and 28 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000000110	1 retrocopy	retro_cfam_1894,
Callithrix jacchus	ENSCJAG00000011620	3 retrocopies	retro_cjac_113, retro_cjac_2566, retro_cjac_2848,
Dasypus novemcinctus	ENSDNOG00000007592	1 retrocopy	retro_dnov_2073,
Homo sapiens	ENSG00000196465	1 retrocopy	retro_hsap_2383,
Gorilla gorilla	ENSGGOG00000003277	2 retrocopies	retro_ggor_1808, retro_ggor_2233,
Loxodonta africana	ENSLAFG00000012658	1 retrocopy	retro_lafr_734,
Macaca mulatta	ENSMMUG00000005214	1 retrocopy	retro_mmul_962 ,
Macaca mulatta	ENSMMUG00000031838	6 retrocopies	retro_mmul_1633, retro_mmul_1663, retro_mmul_211, retro_mmul_2221, retro_mmul_2410, retro_mmul_96,
Nomascus leucogenys	ENSNLEG00000026948	1 retrocopy	retro_nleu_369,
Oryctolagus cuniculus	ENSOCUG00000017368	1 retrocopy	retro_ocun_374,
Otolemur garnettii	ENSOGAG00000001521	3 retrocopies	retro_ogar_1918, retro_ogar_3179, retro_ogar_680,
Procavia capensis	ENSPCAG00000005927	2 retrocopies	retro_pcap_223, retro_pcap_242,
Pongo abelii	ENSPPYG00000004646	1 retrocopy	retro_pabe_2150,
Pan troglodytes	ENSPTRG00000023043	2 retrocopies	retro_ptro_1741, retro_ptro_2579,
Rattus norvegicus	ENSRNOG00000028837	2 retrocopies	retro_rnor_1432, retro_rnor_216,