RetrogeneDB ID: retro_mmus_1098

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 13:47010072..47010945(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000051606
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Coro1c
• Ensembl ID: ENSMUSG00000004530
• Aliases: Coro1c, AL022675, AW455561, AW548837
• Description: coronin, actin binding protein 1C [Source:MGI Symbol;Acc:MGI:1345964]

Sequence

>retro_mmus_1098
ATGCGGCGAGTGGTGCGGCAGAGCAAGTTCCGGCATGTCTTTGGACAGGCGGTGAAGAATGATCAGTGCTATGATGACAT
CCGCGTCTCCCGAGTCACCTGGGACAGTTCCTTTTGCGCCATCAACCCCAGATTCGTGGCCATCATCATAGAAGCAAGTA
GGGGAGGGGCCTTCCTGATGCTCCCTCTGCACAAGACGGGACAAATTGACAAATCCTACCCTACAGTGTGTGGCCACACA
GGACCAGTGCTGGACATAGACTGGTGTCCACATAACGATCAGGTTATCGCCAGCGGCTCAGAGGCCTGCATTGTTATGGT
TTGGCAGATCCCAGAAAATGGACTGACCCTTTCCCTGACTGAGCCTGTGGTGATTCTAGAAGGCCACTCAAAAAGAGTTG
GCATCGTGGCCTGGCACCCGACGGCCCACATTGTGCTTCTCAGTGCAGGCTGTGATAATGTCATTATCATCTGGAACGTG
GGGACAGGGGAAGCCCTCATCAACTTGGATGATATGCATTCAGACATGATTTACAACGAGAGCTGGAGCTGTAACGGTAG
TCTCATCTGCACAGCATCCAAAGACAAGAAAATGAGAGTCATTGACCCCAGGAAACAGGAGATGGCGGTGGAGAAGGAGA
AAGCACACGAAGGAGCCAGGCCTATGCGTGCCATCTTCCTGGCGGACGGCAACGTATTCACTACTGGCTTTAGCCGCATG
AGCGAGCGGCAGTTGACGCTCTGGAACCCAAAAAAACATGCAGAAACCAATGCTCTCCATGAAATGGACACTAGCAATGG
AGTGCTGCTCTCCTTCTACGACCCAGACACCAGCATCATCTACTTATGTGGGAAGGGTGACAGCAGTGTCCGC

Alignment

ORF - retro_mmus_1098 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.1 %
• Parental protein coverage: 61.39 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MRRVVRQSKFRHVFGQAVKNDQCYDDIRVSRVTWDSSFCAVNPRFVAIIIEASGGGAFLVLPLHKTGRID
          MRRVVRQSKFRHVFGQAVKNDQCYDDIRVSRVTWDSSFCA.NPRFVAIIIEAS.GGAFL.LPLHKTG.ID
Retrocopy MRRVVRQSKFRHVFGQAVKNDQCYDDIRVSRVTWDSSFCAINPRFVAIIIEASRGGAFLMLPLHKTGQID

Parental  KSYPTVCGHTGPVLDIDWCPHNDQVIASGSEDCTVMVWQIPENGLTLSLTEPVVILEGHSKRVGIVAWHP
          KSYPTVCGHTGPVLDIDWCPHNDQVIASGSE.C.VMVWQIPENGLTLSLTEPVVILEGHSKRVGIVAWHP
Retrocopy KSYPTVCGHTGPVLDIDWCPHNDQVIASGSEACIVMVWQIPENGLTLSLTEPVVILEGHSKRVGIVAWHP

Parental  TARNVLLSAGCDNAIIIWNVGTGEALINLDDMHSDMIYNVSWSRNGSLICTASKDKKVRVIDPRKQEIVA
          TA..VLLSAGCDN.IIIWNVGTGEALINLDDMHSDMIYN.SWS.NGSLICTASKDKK.RVIDPRKQE...
Retrocopy TAHIVLLSAGCDNVIIIWNVGTGEALINLDDMHSDMIYNESWSCNGSLICTASKDKKMRVIDPRKQEMAV

Parental  EKEKAHEGARPMRAIFLADGNVFTTGFSRMSERQLALWNPKNMQEPIALHEMDTSNGVLLPFYDPDTSII
          EKEKAHEGARPMRAIFLADGNVFTTGFSRMSERQL.LWNPK...E..ALHEMDTSNGVLL.FYDPDTSII
Retrocopy EKEKAHEGARPMRAIFLADGNVFTTGFSRMSERQLTLWNPKKHAETNALHEMDTSNGVLLSFYDPDTSII

Parental  YLCGKGDSSIR
          YLCGKGDSS.R
Retrocopy YLCGKGDSSVR

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	0.21 RPM	62.12 RPM
SRP007412_cerebellum	0.26 RPM	71.78 RPM
SRP007412_heart	2.52 RPM	35.05 RPM
SRP007412_kidney	0.42 RPM	48.49 RPM
SRP007412_liver	0.03 RPM	20.21 RPM
SRP007412_testis	1.19 RPM	17.93 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_1098 was not detected

EST

No EST(s) were mapped for retro_mmus_1098 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_29330	607 libraries	433 libraries	32 libraries	0 libraries	0 libraries
TSS #2	TSS_29331	499 libraries	434 libraries	136 libraries	3 libraries	0 libraries

The graphical summary, for retro_mmus_1098 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_1098 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_1098 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Mustela putorius furo	ENSMPUG00000003421	1 retrocopy	retro_mputfur_419,
Mus musculus	ENSMUSG00000004530	1 retrocopy	retro_mmus_1098 ,