RetrogeneDB ID: retro_mmus_3127

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 8:42246910..42247408(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000053038
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Cfl1
• Ensembl ID: ENSMUSG00000056201
• Aliases: None
• Description: cofilin 1, non-muscle [Source:MGI Symbol;Acc:MGI:101757]

Sequence

>retro_mmus_3127
ATGGCCTCTGGTGTGGCTGTCTCTGATGGTGTCATCAAGGTGTTCAATGACATGAAGGTTCGCAAGTCTTCAACACCAGA
AGAAGTGAAGAAACGCAAGAAGGCAGTGCTCTTTTGCCTGAGTGAGGACAAGAAGAACATCATCCTGGAGGAGGGCAAGG
AGATCCTGGTAGGAGATGTGGGGCATACTGTGGACGACCCCTACACCACTTTTGTCAAGATGCTGCCAGACAAGGACTGC
TGCTATGCACTCTATGATGCAACCTATGAGACCAAGGAGAGCAAGAAGGAGGACCTGGTGTTCATCTTCTGGGCCCCCGA
GAATGCACCCCTTAAGAGCAAAATGATCTATGCCAGCTCCAAGGATGCCATCAAGAAGAAGCTGACAGGAATCAAGCATG
AATTACAAGCTAACTGCTACGAGGAGGTCAAGGACCACTGCACCCTGGCAGAGAAACTAGGTGGCAGCGCGGTCATTTCC
CTGGAGGGCAAGCCTTTG

Alignment

ORF - retro_mmus_3127 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.19 %
• Parental protein coverage: 73.13 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MASGVAVSDGVIKVFNDMKVRKSSTPEEVKKRKKAVLFCLSEDKKNIILEEGKEILVGDVGQTVDDPYTT
          MASGVAVSDGVIKVFNDMKVRKSSTPEEVKKRKKAVLFCLSEDKKNIILEEGKEILVGDVG.TVDDPYTT
Retrocopy MASGVAVSDGVIKVFNDMKVRKSSTPEEVKKRKKAVLFCLSEDKKNIILEEGKEILVGDVGHTVDDPYTT

Parental  FVKMLPDKDCRYALYDATYETKESKKEDLVFIFWAPENAPLKSKMIYASSKDAIKKKLTGIKHELQANCY
          FVKMLPDKDC.YALYDATYETKESKKEDLVFIFWAPENAPLKSKMIYASSKDAIKKKLTGIKHELQANCY
Retrocopy FVKMLPDKDCCYALYDATYETKESKKEDLVFIFWAPENAPLKSKMIYASSKDAIKKKLTGIKHELQANCY

Parental  EEVKDRCTLAEKLGGSAVISLEGKPL
          EEVKD.CTLAEKLGGSAVISLEGKPL
Retrocopy EEVKDHCTLAEKLGGSAVISLEGKPL

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	0.70 RPM	385.58 RPM
SRP007412_cerebellum	0.43 RPM	286.45 RPM
SRP007412_heart	0.16 RPM	80.81 RPM
SRP007412_kidney	0.23 RPM	152.73 RPM
SRP007412_liver	0.30 RPM	115.90 RPM
SRP007412_testis	0.23 RPM	106.85 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_3127 was not detected

EST

No EST(s) were mapped for retro_mmus_3127 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_142262	59 libraries	40 libraries	628 libraries	270 libraries	75 libraries

The graphical summary, for retro_mmus_3127 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_3127 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_3127 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 45 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000024955	6 retrocopies	retro_cfam_1544, retro_cfam_366, retro_cfam_660, retro_cfam_67, retro_cfam_943, retro_cfam_964,
Callithrix jacchus	ENSCJAG00000001916	1 retrocopy	retro_cjac_347,
Felis catus	ENSFCAG00000013272	3 retrocopies	retro_fcat_1456, retro_fcat_303, retro_fcat_991,
Myotis lucifugus	ENSMLUG00000024685	6 retrocopies	retro_mluc_1905, retro_mluc_2114, retro_mluc_216, retro_mluc_2218, retro_mluc_455, retro_mluc_507,
Macaca mulatta	ENSMMUG00000019016	5 retrocopies	retro_mmul_316, retro_mmul_493, retro_mmul_556, retro_mmul_667, retro_mmul_705,
Mus musculus	ENSMUSG00000015932	1 retrocopy	retro_mmus_3314,
Mus musculus	ENSMUSG00000056201	6 retrocopies	retro_mmus_1729, retro_mmus_2103, retro_mmus_3127 , retro_mmus_3556, retro_mmus_719, retro_mmus_970,
Mus musculus	ENSMUSG00000062929	1 retrocopy	retro_mmus_660,
Oryctolagus cuniculus	ENSOCUG00000025604	4 retrocopies	retro_ocun_1123, retro_ocun_1390, retro_ocun_324, retro_ocun_478,
Otolemur garnettii	ENSOGAG00000016503	8 retrocopies	retro_ogar_1442, retro_ogar_1581, retro_ogar_1648, retro_ogar_2192, retro_ogar_302, retro_ogar_405, retro_ogar_453, retro_ogar_828,
Rattus norvegicus	ENSRNOG00000020660	2 retrocopies	retro_rnor_1354, retro_rnor_693,
Tupaia belangeri	ENSTBEG00000016751	2 retrocopies	retro_tbel_153, retro_tbel_3085,