RetrogeneDB ID: retro_mmul_2221

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 7:45386620..45387071(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMMUG00000019021
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: MMU.2449
• Ensembl ID: ENSMMUG00000031838
• Aliases: None
• Description: myosin, light polypeptide 6, alkali, smooth muscle and non-muscle [Source:RefSeq peptide;Acc:NP_001180478]

Sequence

>retro_mmul_2221
ATGTGGGACTTCACCGAAGACCAGACCACAGAGTTCAAGGAGGCGTTCCAGCTGTTTGACCGAACAGGTGATGGCAAGAT
CCTGTACACCAGTGTGGGGACGTAATGAGGGCCCTGGGCCAGAATCCAACAACACCAAGGTGCTCAAGGTCCTGGGGAAC
CCCAAGAGTGATGAGATGAATGTGAAGGTGCTGGACTTTGAGCACTTTCTGCCCATGCTGCAGACAGTGGCCAAGAACAA
GGACCAGGGCACCTATGAGGATTATGTCGAAGGACTTCGGGTGTTTGACGAGGAAGGAAATGGCACTGTCATGGGTGCTG
AAATCCGGCATGTTCTTGTCACAGTGGGTGAGAAGATGACAGAGGTAGAAGTAGAGATGCTGGTGGCAGGGCACGAGGAC
AGCAATGGTTGTATCAACTATGAAGAGCTCGTCTGCGTGGTGCTGAATGGC

Alignment

ORF - retro_mmul_2221 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.54 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MCDFTEDQTAEFKEAFQLFDRTGDGKILYS-QCGDVMRALGQNPT-NAEVLKVLGNPKSDEMNVKVLDFE
          M.DFTEDQT.EFKEAFQLFDRTGDGKILY..QCGDVMRALGQNPT.N..VLKVLGNPKSDEMNVKVLDFE
Retrocopy MWDFTEDQTTEFKEAFQLFDRTGDGKILYT<QCGDVMRALGQNPT<NTKVLKVLGNPKSDEMNVKVLDFE

Parental  HFLPMLQTVAKNKDQGTYEDYVEGLRVFDKEGNGTVMGAEIRHVLVTLGEKMTEEEVEMLVAGHEDSNGC
          HFLPMLQTVAKNKDQGTYEDYVEGLRVFD.EGNGTVMGAEIRHVLVT.GEKMTE.EVEMLVAGHEDSNGC
Retrocopy HFLPMLQTVAKNKDQGTYEDYVEGLRVFDEEGNGTVMGAEIRHVLVTVGEKMTEVEVEMLVAGHEDSNGC

Parental  INYEAFVRHILSG
          INYE..V...L.G
Retrocopy INYEELVCVVLNG

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	57.37 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	100.91 RPM
SRP007412_cerebellum	0.00 RPM	58.05 RPM
SRP007412_heart	0.29 RPM	265.63 RPM
SRP007412_kidney	0.12 RPM	173.24 RPM
SRP007412_liver	0.08 RPM	100.82 RPM
SRP007412_testis	0.04 RPM	37.47 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_2221 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_2221 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_2221 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 14 parental genes, and 42 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000092841	2 retrocopies	retro_hsap_1786, retro_hsap_2533,
Macropus eugenii	ENSMEUG00000001272	1 retrocopy	retro_meug_2172,
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,
Mus musculus	ENSMUSG00000090841	7 retrocopies	retro_mmus_1281, retro_mmus_1504, retro_mmus_2328, retro_mmus_3231, retro_mmus_3333, retro_mmus_3358, retro_mmus_434,
Nomascus leucogenys	ENSNLEG00000000205	2 retrocopies	retro_nleu_2736, retro_nleu_779,
Oryctolagus cuniculus	ENSOCUG00000017371	1 retrocopy	retro_ocun_1300,
Otolemur garnettii	ENSOGAG00000034596	1 retrocopy	retro_ogar_2549,
Pongo abelii	ENSPPYG00000004647	3 retrocopies	retro_pabe_1467, retro_pabe_1864, retro_pabe_538,
Pan troglodytes	ENSPTRG00000005080	2 retrocopies	retro_ptro_1196, retro_ptro_1476,
Sarcophilus harrisii	ENSSHAG00000004472	6 retrocopies	retro_shar_137, retro_shar_318, retro_shar_452, retro_shar_510, retro_shar_719, retro_shar_765,
Sus scrofa	ENSSSCG00000025467	1 retrocopy	retro_sscr_829,
Ictidomys tridecemlineatus	ENSSTOG00000023318	1 retrocopy	retro_itri_1478,
Tupaia belangeri	ENSTBEG00000000485	8 retrocopies	retro_tbel_130, retro_tbel_1715, retro_tbel_2980, retro_tbel_332, retro_tbel_3515, retro_tbel_3545, retro_tbel_3707, retro_tbel_4075,