RetrogeneDB ID: retro_mmus_3333

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 9:44374743..44375195(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000060467
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Myl6
• Ensembl ID: ENSMUSG00000090841
• Aliases: Myl6, ESMLC, LC17, LC17-GI, LC17-NM, LC17A, LC17B, MLC-3, MLC1SM, MLC3SM, MLC3nm, Myln
• Description: myosin, light polypeptide 6, alkali, smooth muscle and non-muscle [Source:MGI Symbol;Acc:MGI:109318]

Sequence

>retro_mmus_3333
ATGTGTGACTTCACGAGGACCAGACCGCAGAATTCAAGGAGGCTTTCCAGCTGTTTGACCGAACAGGTGATGGCAAGATC
CTGTACAACCAGTGTGGGGATGTGATGCGGGCCCTGGGCCAGAACCCTACCAACGCCGAGGTGCTCAAGGTCCTGGGAAA
CCCCAAGAGTGATGAGATGAATGTGAAGGTGCTGGACTTTGAGCACTTCCTGCCCATGCTGCAGACCGTGGCCAAGAACA
AGGACCAGGGAACCTACGAGGATTATGTTGAAGGCCTTCGTGTGTTTGACAAGGAAGGAAATGGCACCGTCATGGGTGCT
GAAATCTGTCATGTCCTAGTCACACTGGGCGAGAAGATGACAGAGGAAGAAGTAGAGATGCTAGTGGCGGGGCATGAGGA
CAGCAATGGTTGCATCAACTATGAAGAGCTTGTCCGGATGGTGCTGAATGGC

Alignment

ORF - retro_mmus_3333 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.03 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MCDFT-EDQTAEFKEAFQLFDRTGDGKILYSQCGDVMRALGQNPTNAEVLKVLGNPKSDEMNVKVLDFEH
          MCDFT.EDQTAEFKEAFQLFDRTGDGKILY.QCGDVMRALGQNPTNAEVLKVLGNPKSDEMNVKVLDFEH
Retrocopy MCDFT<EDQTAEFKEAFQLFDRTGDGKILYNQCGDVMRALGQNPTNAEVLKVLGNPKSDEMNVKVLDFEH

Parental  FLPMLQTVAKNKDQGTYEDYVEGLRVFDKEGNGTVMGAEIRHVLVTLGEKMTEEEVEMLVAGHEDSNGCI
          FLPMLQTVAKNKDQGTYEDYVEGLRVFDKEGNGTVMGAEI.HVLVTLGEKMTEEEVEMLVAGHEDSNGCI
Retrocopy FLPMLQTVAKNKDQGTYEDYVEGLRVFDKEGNGTVMGAEICHVLVTLGEKMTEEEVEMLVAGHEDSNGCI

Parental  NYEELVRMVLNG
          NYEELVRMVLNG
Retrocopy NYEELVRMVLNG

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	0.07 RPM	86.35 RPM
SRP007412_cerebellum	0.22 RPM	88.75 RPM
SRP007412_heart	0.09 RPM	73.25 RPM
SRP007412_kidney	0.54 RPM	113.42 RPM
SRP007412_liver	0.16 RPM	60.32 RPM
SRP007412_testis	0.05 RPM	23.83 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_mmus_3333 was not detected

EST

No EST(s) were mapped for retro_mmus_3333 retrocopy.

TSS

TSS No.	TSS Name	TSS expression level (Expr) in TPM range:
		no expression	0 < Expr ≤ 1	1 < Expr ≤ 5	5 < Expr ≤ 10	Expr > 10
TSS #1	TSS_150146	70 libraries	158 libraries	528 libraries	183 libraries	133 libraries

The graphical summary, for retro_mmus_3333 TSS expression levels > 0 TPM .
TSS expression levels were studied across 1072 TSS-CAGE libraries, based on FANTOM5 data.
The expression values were visualized using beanplot. If you have any doubts, how to read it, read more in Kampstra P (2008)

Lab

retro_mmus_3333 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_3333 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 30 retrocopies.

Species	Parental gene accession	Retrocopies number
Macropus eugenii	ENSMEUG00000001272	1 retrocopy	retro_meug_2172,
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	ENSMUSG00000061816	1 retrocopy	retro_mmus_973,
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,
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,