RetrogeneDB ID: retro_mmus_562

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 10:56656193..56656886(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000045048
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Stard6
• Ensembl ID: ENSMUSG00000079608
• Aliases: Stard6, 1700011K09Rik, 4833424I06Rik, 4933429L05Rik, AI644424
• Description: StAR-related lipid transfer (START) domain containing 6 [Source:MGI Symbol;Acc:MGI:2156774]

Sequence

>retro_mmus_562
ATGGACTATAAGGCAATTGCCCAACAAACTGCTGAACAAGTTTTAGCTTACAATCAAGACCTATCTGGCTGGAAACTCAT
TAAATCTTCAAAAAAGGTAACTGTTTCCAGCAAGACCTCTAGAATATTCCACGGAAACCTATACCGCGTTGAAGGAATAA
TCCCAGAATCAGCAGCTCATCTCTCTGACTTCCTCTTCAAACATGATCACAGAGTCTCATGGGACAAATCATTGAAAGGG
TTCAATGTGATACACAAGATTGATTCGGACACACTCATATGCCACACCATTACACAAAGTTTTGCCATGGGCTCAATTTC
CCCTAGAGACTTTATCGACTTAGTACACATCAAGCACTATGAAAGGAACGTGGACATTATCAGTACTAAAAGTGTGGACT
TCCCAGGATATGCTCCAACTTCGACTTATATCCGTGGCTTTAATCATCCCTCTGGCTATGTGTGTTCACCTCTGAAGGAA
AACCCAGCCTATTCCAAGCTAGTGATTTTTGTCCAGACAGAGATGAAAGGAAAATTGCCTGCATCGGTAATTGAAAAGTC
TATGCCTTCCAACTTAGTAAGCTTCCTCCTCAATGTGAAAGATGGCGTAAAGACGTACAGAATTCCACCCATACGTGCCC
GGCACAGTTCGCACTCCTCTGTGCACAAAAAGAAAGAAGGACATTCTGCCATT

Alignment

ORF - retro_mmus_562 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 100. %
• Parental protein coverage: 99.14 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MDYKAIAQQTAEQVLAYNQDLSGWKLIKSSKKVTVSSKTSRIFHGNLYRVEGIIPESAAHLSDFLFKHDH
          MDYKAIAQQTAEQVLAYNQDLSGWKLIKSSKKVTVSSKTSRIFHGNLYRVEGIIPESAAHLSDFLFKHDH
Retrocopy MDYKAIAQQTAEQVLAYNQDLSGWKLIKSSKKVTVSSKTSRIFHGNLYRVEGIIPESAAHLSDFLFKHDH

Parental  RVSWDKSLKGFNVIHKIDSDTLICHTITQSFAMGSISPRDFIDLVHIKHYERNVDIISTKSVDFPGYAPT
          RVSWDKSLKGFNVIHKIDSDTLICHTITQSFAMGSISPRDFIDLVHIKHYERNVDIISTKSVDFPGYAPT
Retrocopy RVSWDKSLKGFNVIHKIDSDTLICHTITQSFAMGSISPRDFIDLVHIKHYERNVDIISTKSVDFPGYAPT

Parental  STYIRGFNHPSGYVCSPLKENPAYSKLVIFVQTEMKGKLPASVIEKSMPSNLVSFLLNVKDGVKTYRIPP
          STYIRGFNHPSGYVCSPLKENPAYSKLVIFVQTEMKGKLPASVIEKSMPSNLVSFLLNVKDGVKTYRIPP
Retrocopy STYIRGFNHPSGYVCSPLKENPAYSKLVIFVQTEMKGKLPASVIEKSMPSNLVSFLLNVKDGVKTYRIPP

Parental  IRARHSSHSSVHKKKEGHSAI
          IRARHSSHSSVHKKKEGHSAI
Retrocopy IRARHSSHSSVHKKKEGHSAI

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	0.42 RPM
SRP007412_cerebellum	0.00 RPM	0.22 RPM
SRP007412_heart	0.00 RPM	0.28 RPM
SRP007412_kidney	0.00 RPM	0.17 RPM
SRP007412_liver	0.00 RPM	0.05 RPM
SRP007412_testis	1.83 RPM	107.62 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_562 was not detected

EST

1 EST(s) were mapped to retro_mmus_562 retrocopy

EST ID	Start	End	Identity	Match	Mis-match	Score
BF318858	56656182	56656547	99.8	364	1	363

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_3868	1047 libraries	21 libraries	0 libraries	3 libraries	1 library

The graphical summary, for retro_mmus_562 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_562 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_562 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
Mus musculus	ENSMUSG00000079608	1 retrocopy	retro_mmus_562 ,
Ictidomys tridecemlineatus	ENSSTOG00000004409	1 retrocopy	retro_itri_924,