RetrogeneDB ID: retro_mmul_1633

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 3:111871624..111872077(+)
• Located in intron of: ENSMMUG00000020418

Retrocopy information

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

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_1633
ATGTGTGACTTCACCGAAGACCAGACCACAGAGTTCAAGGAGGCCTTCCAGCTGTTTGACCGAACAGGTGATGGCAAGAT
CCTGTACAGCCAGTGTGGGGACGTGATGAGGGCCCTGGGCCAGAACCCTACCAACGCCGAGGTGCTCAAGGTCCTGGGGA
ACCCCAAGAGTGATGAGAAGAACGTGAAGGTGCTGGACTTTGAGCACTTTCTGCCCATGCTGCAGACAGTGGCCAAGAAC
AAGGACCAGGGCACCTATGAGGATTATGTCGAAGGACTTCGGGTGTTTGACAAGGAAGGAAATGGCACTGTCATGGGTGC
TGAAATCCGGCATGTTCTTGTCACACTGGGTGAGAAGATGACAGAGGAAGAAGTAGAGATGCTGGTGGCAGGGCACGAGG
ACAGCAATGGTTGTATCAACTATGAAGCGTTTGTGAGGCATATCCTGTCGGGG

Alignment

ORF - retro_mmul_1633 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.68 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MCDFTEDQTAEFKEAFQLFDRTGDGKILYSQCGDVMRALGQNPTNAEVLKVLGNPKSDEMNVKVLDFEHF
          MCDFTEDQT.EFKEAFQLFDRTGDGKILYSQCGDVMRALGQNPTNAEVLKVLGNPKSDE.NVKVLDFEHF
Retrocopy MCDFTEDQTTEFKEAFQLFDRTGDGKILYSQCGDVMRALGQNPTNAEVLKVLGNPKSDEKNVKVLDFEHF

Parental  LPMLQTVAKNKDQGTYEDYVEGLRVFDKEGNGTVMGAEIRHVLVTLGEKMTEEEVEMLVAGHEDSNGCIN
          LPMLQTVAKNKDQGTYEDYVEGLRVFDKEGNGTVMGAEIRHVLVTLGEKMTEEEVEMLVAGHEDSNGCIN
Retrocopy LPMLQTVAKNKDQGTYEDYVEGLRVFDKEGNGTVMGAEIRHVLVTLGEKMTEEEVEMLVAGHEDSNGCIN

Parental  YEAFVRHILSG
          YEAFVRHILSG
Retrocopy YEAFVRHILSG

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	0.63 RPM	100.91 RPM
SRP007412_cerebellum	0.19 RPM	58.05 RPM
SRP007412_heart	0.53 RPM	265.63 RPM
SRP007412_kidney	0.23 RPM	173.24 RPM
SRP007412_liver	0.16 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_1633 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_1633 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_1633 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,