RetrogeneDB ID: retro_mmus_377

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 1:156524230..156525403(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000096493
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Csnk2a1
• Ensembl ID: ENSMUSG00000074698
• Aliases: Csnk2a1, Csnk2a1-rs4
• Description: casein kinase 2, alpha 1 polypeptide [Source:MGI Symbol;Acc:MGI:88543]

Sequence

>retro_mmus_377
ATGTCGGGACCCGTGCCAAGCAGGGCCAGAGTTTACACAGATGTTAACACACACAGACCCCGAGAGTACTGGGATTATGA
ATCACATGTGGTGGAATGGGGGAATCAAGATGACTACCAGCTTGTTCGAAAATTAGGTAGGGGCAAATACAGTGAAGTGT
TTGAAGCCATCAACATCACAAATAATGAAAAAGTTGTTGTTAAAATTCTCAAGCCAGTAAAAAAGAAGAAAATTAAGCGT
GAAATAAAGATTTTGGAGAATTTGAGAGGTGGGCCCAACATCATCACACTTGCAGACATTGTAAAAGACCCTGTGTCACG
AACCCCTGCCTTGGTTTTTGAACATGTAAACAACACAGACTTCAAGCAATTGTACCAGACGTTAACAGACTATGACATTC
GATTTTACATGTATGAAATTCTGAAAGCCCTGGATTATTGTCACAGCATGGGGATTATGCACAGAGATGTGAAACCCCAT
AATGTCATGATTGATCATGAGCACAGAAAGCTTCGGCTAATAGACTGGGGTTTAGCTGAGTTTTACCATCCAGGCCAAGA
GTATAATGTCCGAGTTGCTTCTCGATATTTCAAAGGTCCAGAGCTACTTGTAGATTATCAGATGTACGATTATAGTTTGG
ATATGTGGAGCTTGGGTTGTATGCTGGCCAGTATGATCTTCCGGAAGGAGCCATTTTTCCATGGACATGACAATTATGAT
CAGTTGGTGAGGATAGCCAAGGTTCTGGGAACAGAAGATTTATATGACTATATTGACAAGTACAACATTGAATTAGATCC
ACGTTTCAACGATATCTTGGGCAGACACTCCCGTAAGCGATGGGAACGCTTTGTCCACAGTGAAAACCAGCATCTTGTCA
GCCCTGAGGCCTTGGATTTTCTGGACAAGCTGCTTCGATATGACCACCAGTCACGGCTCACTGCAAGAGAGGCCATGGAG
CACCCTTACTTCTACACTGTTGTGAAGGACCAGGCTCGAATGAGTTCCACTAGCATGGCAGGGGGCAGCACACCTGTCAG
CAGCGCCAATATGATGTCAGGGATTTCTTCAGTGCCAACTCCTTCACCCCTTGGACCTCTGGCAGGCTCACCAGTGATTG
CCGCTGCCAACTCACTTGGGATACCTGTTCCAGCTGCTGCTGGCGCTCAGCAG

Alignment

ORF - retro_mmus_377 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

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

Retrocopy - Parental Gene Alignment:

Parental  MSGPVPSRARVYTDVNTHRPREYWDYESHVVEWGNQDDYQLVRKLGRGKYSEVFEAINITNNEKVVVKIL
          MSGPVPSRARVYTDVNTHRPREYWDYESHVVEWGNQDDYQLVRKLGRGKYSEVFEAINITNNEKVVVKIL
Retrocopy MSGPVPSRARVYTDVNTHRPREYWDYESHVVEWGNQDDYQLVRKLGRGKYSEVFEAINITNNEKVVVKIL

Parental  KPVKKKKIKREIKILENLRGGPNIITLADIVKDPVSRTPALVFEHVNNTDFKQLYQTLTDYDIRFYMYEI
          KPVKKKKIKREIKILENLRGGPNIITLADIVKDPVSRTPALVFEHVNNTDFKQLYQTLTDYDIRFYMYEI
Retrocopy KPVKKKKIKREIKILENLRGGPNIITLADIVKDPVSRTPALVFEHVNNTDFKQLYQTLTDYDIRFYMYEI

Parental  LKALDYCHSMGIMHRDVKPHNVMIDHEHRKLRLIDWGLAEFYHPGQEYNVRVASRYFKGPELLVDYQMYD
          LKALDYCHSMGIMHRDVKPHNVMIDHEHRKLRLIDWGLAEFYHPGQEYNVRVASRYFKGPELLVDYQMYD
Retrocopy LKALDYCHSMGIMHRDVKPHNVMIDHEHRKLRLIDWGLAEFYHPGQEYNVRVASRYFKGPELLVDYQMYD

Parental  YSLDMWSLGCMLASMIFRKEPFFHGHDNYDQLVRIAKVLGTEDLYDYIDKYNIELDPRFNDILGRHSRKR
          YSLDMWSLGCMLASMIFRKEPFFHGHDNYDQLVRIAKVLGTEDLYDYIDKYNIELDPRFNDILGRHSRKR
Retrocopy YSLDMWSLGCMLASMIFRKEPFFHGHDNYDQLVRIAKVLGTEDLYDYIDKYNIELDPRFNDILGRHSRKR

Parental  WERFVHSENQHLVSPEALDFLDKLLRYDHQSRLTAREAMEHPYFYTVVKDQARMSSTSMAGGSTPVSSAN
          WERFVHSENQHLVSPEALDFLDKLLRYDHQSRLTAREAMEHPYFYTVVKDQARMSSTSMAGGSTPVSSAN
Retrocopy WERFVHSENQHLVSPEALDFLDKLLRYDHQSRLTAREAMEHPYFYTVVKDQARMSSTSMAGGSTPVSSAN

Parental  MMSGISSVPTPSPLGPLAGSPVIAAANSLGIPVPAAAGAQQ
          MMSGISSVPTPSPLGPLAGSPVIAAANSLGIPVPAAAGAQQ
Retrocopy MMSGISSVPTPSPLGPLAGSPVIAAANSLGIPVPAAAGAQQ

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	0.23 RPM	57.75 RPM
SRP007412_cerebellum	0.09 RPM	55.71 RPM
SRP007412_heart	0.25 RPM	64.19 RPM
SRP007412_kidney	0.21 RPM	63.31 RPM
SRP007412_liver	0.22 RPM	54.15 RPM
SRP007412_testis	0.09 RPM	12.67 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_mmus_377 was not detected

EST

4 EST(s) were mapped to retro_mmus_377 retrocopy

EST ID	Start	End	Identity	Match	Mis-match	Score
AA444207	156524486	156524977	99.2	487	3	482
CF163713	156524267	156524754	99.8	486	1	485
CK335741	156524442	156524913	100	471	0	471
DT902631	156524299	156524454	97.5	151	4	147

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_70767	257 libraries	478 libraries	335 libraries	0 libraries	2 libraries

The graphical summary, for retro_mmus_377 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_377 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_377 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000006946	1 retrocopy	retro_cfam_1408,
Homo sapiens	ENSG00000101266	1 retrocopy	retro_hsap_53,
Mus musculus	ENSMUSG00000074698	3 retrocopies	retro_mmus_1177, retro_mmus_2364, retro_mmus_377 ,
Otolemur garnettii	ENSOGAG00000002709	1 retrocopy	retro_ogar_820,