RetrogeneDB ID: retro_mmus_88

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 3:34005016..34005463(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000044434
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: Carhsp1
• Ensembl ID: ENSMUSG00000008393
• Aliases: Carhsp1, 1200011K09Rik, Crhsp-24, D16Ertd465e
• Description: calcium regulated heat stable protein 1 [Source:MGI Symbol;Acc:MGI:1196368]

Sequence

>retro_mmus_88
ATGTCATCTGAGCCTCCTCCACCGCCGCTGCAGCCCCCCACGCATCAGACTTCTGTAGGGCTATTGGATACTCCTCGCAC
CCGGGATCGCTCTCCATCCCCCCTGCGGGGCAATGTGGTCCCTAGCCCTCTGCCTACCCGCCGGACAAGGACCTTCTCAG
CGACAGTGCGGGCTTCGCAGGGCCCCGTCTACAAAGGAGTCTGTAAATGCTTCTGCCGGTCCAAGGGCCACGGCTTCATC
ACCCCAGGTGATGGTGGTCCTGACATCTTCCTGCACATCTCTGATGTGGAAGGGGAGTATGTTCCGGTGGAAGGCGACGA
AGTCACCTATAAGATGTGCTCTATCCCGCCCAAGAACGAGAAGCTGCAGGCTGTAGAGGTGGTCATCACCCACCTGGCAC
CAGGGACCAAGCATGAGACCTGGTCTGGGCACGTCATCAGCAACTAG

Alignment

ORF - retro_mmus_88 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 99.32 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MSSEPPPPPLQPPTHQTSVGLLDTPRTRDRSPSPLRGNVVPSPLPTRRTRTFSATVRASQGPVYKGVCKC
          MSSEPPPPPLQPPTHQTSVGLLDTPRTRDRSPSPLRGNVVPSPLPTRRTRTFSATVRASQGPVYKGVCKC
Retrocopy MSSEPPPPPLQPPTHQTSVGLLDTPRTRDRSPSPLRGNVVPSPLPTRRTRTFSATVRASQGPVYKGVCKC

Parental  FCRSKGHGFITPADGGPDIFLHISDVEGEYVPVEGDEVTYKMCSIPPKNEKLQAVEVVITHLAPGTKHET
          FCRSKGHGFITP.DGGPDIFLHISDVEGEYVPVEGDEVTYKMCSIPPKNEKLQAVEVVITHLAPGTKHET
Retrocopy FCRSKGHGFITPGDGGPDIFLHISDVEGEYVPVEGDEVTYKMCSIPPKNEKLQAVEVVITHLAPGTKHET

Parental  WSGHVISN
          WSGHVISN
Retrocopy WSGHVISN

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	0.30 RPM	35.96 RPM
SRP007412_cerebellum	0.69 RPM	27.44 RPM
SRP007412_heart	0.03 RPM	18.74 RPM
SRP007412_kidney	0.60 RPM	27.80 RPM
SRP007412_liver	0.96 RPM	49.32 RPM
SRP007412_testis	9.79 RPM	42.49 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_mmus_88 was not detected

EST

No EST(s) were mapped for retro_mmus_88 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_94433	73 libraries	19 libraries	306 libraries	327 libraries	347 libraries

The graphical summary, for retro_mmus_88 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_88 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_88 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000017286	1 retrocopy	retro_cjac_194,
Macropus eugenii	ENSMEUG00000016403	1 retrocopy	retro_meug_1949,
Monodelphis domestica	ENSMODG00000005721	1 retrocopy	retro_mdom_12,
Mus musculus	ENSMUSG00000008393	1 retrocopy	retro_mmus_88 ,
Rattus norvegicus	ENSRNOG00000002610	1 retrocopy	retro_rnor_1025,