RetrogeneDB ID: retro_mmus_1639

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 17:37713549..37713846(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000067189
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Scoc
• Ensembl ID: ENSMUSG00000063253
• Aliases: Scoc, 0610011C06Rik, 2810002J11Rik, AA415030, SCOCO
• Description: short coiled-coil protein [Source:MGI Symbol;Acc:MGI:1927654]

Sequence

>retro_mmus_1639
GACCATTCATTAAAGCGTTTGCGTTCGAGAGCTGAAAGTCTGCTACCCAAGATGATGAATGCTGACATGGACGCAGTTGA
TGCTGAAAATCAGGTGGAACTGGAAGAAAAGACTCGACTTATTAATCAGGTGTTGGAACTCCAACACACACTTGAAGATC
TTTCTGCAAGAGTAGATGCAGTTAAGGAAGAAAATCTGAAGCTAAAGTCGGAAAATCAAGTTCTCGGACAATATATAGAA
AACCTCATGTCTGCTTCTAGTGTTTTTCAAACAACTGATACAAAAAGCAAAAGGAAG

Alignment

ORF - retro_mmus_1639 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 97.98 %
• Parental protein coverage: 79.2 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  DHSLKSWRSRAESLLPKMMNADMDAVDAENQVELEEKTRLINQVLELQHTLEDLSARVDAVKEENLKLKS
          DHSLK..RSRAESLLPKMMNADMDAVDAENQVELEEKTRLINQVLELQHTLEDLSARVDAVKEENLKLKS
Retrocopy DHSLKRLRSRAESLLPKMMNADMDAVDAENQVELEEKTRLINQVLELQHTLEDLSARVDAVKEENLKLKS

Parental  ENQVLGQYIENLMSASSVFQTTDTKSKRK
          ENQVLGQYIENLMSASSVFQTTDTKSKRK
Retrocopy ENQVLGQYIENLMSASSVFQTTDTKSKRK

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	39.67 RPM
SRP007412_cerebellum	0.35 RPM	20.67 RPM
SRP007412_heart	0.00 RPM	7.63 RPM
SRP007412_kidney	0.10 RPM	22.85 RPM
SRP007412_liver	0.03 RPM	1.97 RPM
SRP007412_testis	0.00 RPM	2.01 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_1639 was not detected

EST

No EST(s) were mapped for retro_mmus_1639 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_53940	165 libraries	197 libraries	628 libraries	76 libraries	6 libraries

The graphical summary, for retro_mmus_1639 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_1639 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_1639 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 22 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000010957	2 retrocopies	retro_amel_176, retro_amel_725,
Callithrix jacchus	ENSCJAG00000003060	2 retrocopies	retro_cjac_713, retro_cjac_95,
Erinaceus europaeus	ENSEEUG00000011107	1 retrocopy	retro_eeur_19,
Macropus eugenii	ENSMEUG00000014534	2 retrocopies	retro_meug_1580, retro_meug_823,
Monodelphis domestica	ENSMODG00000025528	2 retrocopies	retro_mdom_1163, retro_mdom_1265,
Mus musculus	ENSMUSG00000063253	2 retrocopies	retro_mmus_1639 , retro_mmus_2306,
Oryctolagus cuniculus	ENSOCUG00000006591	3 retrocopies	retro_ocun_1400, retro_ocun_1657, retro_ocun_429,
Rattus norvegicus	ENSRNOG00000003853	1 retrocopy	retro_rnor_609,
Sarcophilus harrisii	ENSSHAG00000003474	1 retrocopy	retro_shar_572,
Tarsius syrichta	ENSTSYG00000011814	6 retrocopies	retro_tsyr_1232, retro_tsyr_1446, retro_tsyr_1566, retro_tsyr_2025, retro_tsyr_34, retro_tsyr_446,