RetrogeneDB ID: retro_mmus_2097

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 2:144365097..144365651(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000082313
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Calcoco2
• Ensembl ID: ENSMUSG00000006056
• Aliases: Calcoco2, 2410154J16Rik, C77254, Ndp52, Ndp52l1
• Description: calcium binding and coiled-coil domain 2 [Source:MGI Symbol;Acc:MGI:1343177]

Sequence

>retro_mmus_2097
ATGGACCAGTGCCCCATACCTACCTTGCTGGAACATGGCAACTTCTCTCAGGTCCTGTTTAACAATGTGGAGAAGTTCTA
TGTTCCTAAAGGAGATATCACGTGAGATATACCCTCACTGAAAAGTTCATCCCTCGACCCAAGGACTGGATCGGCATCTT
TAAAGTAGGGTGGAAGACCACTCAGGAGTATTATACCTTCATGTGGGCTCCCTTGCCAAAAGACCAAAACAAGGATTCAG
CCACACAGCAGGAAATCCAATTCAAAGCTTATTACCTTCCCAAGGATGTGGAGTGCTACCAGTTCTGCTATGTGGATGAA
GATGGTTTGGTCCGGGGAACAAGTGTCCCTTTCCAGTTCTGTCCAGACCCTGACGAGGACATAATTGTTGTTATCAATAT
GGAAAAGGTAGAAGAGATGGAACTGCTCAGTGAGGAGCTTTACCAAGAAAACCAGGAGCTGAAAGACAAGTACACTGACC
TCCATGAGCAGCTACAGAGGAAGCAGGTGGCACTGGAAGCAACACAGAGGGTCAATAAGACCTTAGAACAGGAA

Alignment

ORF - retro_mmus_2097 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.94 %
• Parental protein coverage: 59.68 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MDQCPIPTLLEHGNFSQVLFNNVEKFYAPRGDIM-CYYTLTEKFIPRRKDWIGIFKVGWKTTQEYYTFMW
          MDQCPIPTLLEHGNFSQVLFNNVEKFY.P.GDI....YTLTEKFIPR.KDWIGIFKVGWKTTQEYYTFMW
Retrocopy MDQCPIPTLLEHGNFSQVLFNNVEKFYVPKGDIT<VRYTLTEKFIPRPKDWIGIFKVGWKTTQEYYTFMW

Parental  APLPKDQNKDSATQQEIQFKAYYLPKDVERYQFCYVDEDGLVRGTSVPFQFCPDPDEDIMVVINKEKVEE
          APLPKDQNKDSATQQEIQFKAYYLPKDVE.YQFCYVDEDGLVRGTSVPFQFCPDPDEDI.VVIN.EKVEE
Retrocopy APLPKDQNKDSATQQEIQFKAYYLPKDVECYQFCYVDEDGLVRGTSVPFQFCPDPDEDIIVVINMEKVEE

Parental  MEQLSEELYQQNQELKDKYADLHEQLQRKQVALEATQRVNKTLEHK
          ME.LSEELYQ.NQELKDKY.DLHEQLQRKQVALEATQRVNKTLE..
Retrocopy MELLSEELYQENQELKDKYTDLHEQLQRKQVALEATQRVNKTLEQE

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	0.02 RPM
SRP007412_cerebellum	0.00 RPM	0.00 RPM
SRP007412_heart	0.00 RPM	0.00 RPM
SRP007412_kidney	0.02 RPM	0.00 RPM
SRP007412_liver	0.00 RPM	0.00 RPM
SRP007412_testis	0.05 RPM	0.14 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_mmus_2097 was not detected

EST

No EST(s) were mapped for retro_mmus_2097 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_81091	1041 libraries	15 libraries	16 libraries	0 libraries	0 libraries

The graphical summary, for retro_mmus_2097 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_2097 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_2097 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 4 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Mus musculus	ENSMUSG00000006056	3 retrocopies	retro_mmus_1016, retro_mmus_1108, retro_mmus_2097 ,
Otolemur garnettii	ENSOGAG00000011709	1 retrocopy	retro_ogar_3090,
Rattus norvegicus	ENSRNOG00000031074	1 retrocopy	retro_rnor_1194,
Ictidomys tridecemlineatus	ENSSTOG00000013395	1 retrocopy	retro_itri_1120,