RetrogeneDB ID: retro_mmus_2069

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 2:103819002..103819476(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000081010
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Trappc6b
• Ensembl ID: ENSMUSG00000020993
• Aliases: Trappc6b, 5830498C14Rik, C79212
• Description: trafficking protein particle complex 6B [Source:MGI Symbol;Acc:MGI:1925482]

Sequence

>retro_mmus_2069
ATGGCGGACGAGGCGTTGTTTTTGCTTCTCCATAACGAGATGGTGTCCGGAGTTTACAAGTCCGCTGAACAGGGGGAAGT
GGAAAATGGAAGGTGTATTACTAAGCTGGAGAACACGGGGTTCCGAGTGGGACAAGGATTGATAGAAAGGTTTACGAAAG
ACACTGAAAGGTTCAAGGTTGAATTAGACATCATGAAGTTCATCTGTAAAGATTTTTGGACTACAGTATTCAAGAAACAG
ATCGACAATCTAAGGACAAATCATCAGGGCATATATGTACTTCAGGACAACAAATTTCGACTACTCATTCAGCTGTCTGC
AGGAAAACAGTATTTAGAACATGCGTCCAAGTATCTAGCACTTACATGTGGCTTAATCAGAGGGCGCTTGTCAAACTTGG
GAATAAAAAGTATTGTAACAGCTGAAGTCTCTTCAATGCCTGCCTGCAAATTTCAGGTGATGATACAGAAGCTA

Alignment

ORF - retro_mmus_2069 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.57 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MADEALFLLLHNEMVSGVYKSAEQGEVENGRCVTKLESMGFRVGQGLIERFTKDTARFKDELDIMKFICK
          MADEALFLLLHNEMVSGVYKSAEQGEVENGRC.TKLE..GFRVGQGLIERFTKDT.RFK.ELDIMKFICK
Retrocopy MADEALFLLLHNEMVSGVYKSAEQGEVENGRCITKLENTGFRVGQGLIERFTKDTERFKVELDIMKFICK

Parental  DFWTTVFKKQIDNLRTNHQGIYVLQDNKFRLLIQLSAGKQYLEHASKYLAFTCGLIRGGLSNLGIKSIVT
          DFWTTVFKKQIDNLRTNHQGIYVLQDNKFRLLIQLSAGKQYLEHASKYLA.TCGLIRG.LSNLGIKSIVT
Retrocopy DFWTTVFKKQIDNLRTNHQGIYVLQDNKFRLLIQLSAGKQYLEHASKYLALTCGLIRGRLSNLGIKSIVT

Parental  AEVSSMPACKFQVMIQKL
          AEVSSMPACKFQVMIQKL
Retrocopy AEVSSMPACKFQVMIQKL

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	0.07 RPM	46.28 RPM
SRP007412_cerebellum	0.00 RPM	38.91 RPM
SRP007412_heart	0.03 RPM	29.64 RPM
SRP007412_kidney	0.08 RPM	47.14 RPM
SRP007412_liver	0.05 RPM	22.72 RPM
SRP007412_testis	0.18 RPM	28.04 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_2069 was not detected

EST

No EST(s) were mapped for retro_mmus_2069 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_78321	814 libraries	228 libraries	30 libraries	0 libraries	0 libraries
TSS #2	TSS_78322	1020 libraries	48 libraries	4 libraries	0 libraries	0 libraries

The graphical summary, for retro_mmus_2069 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_2069 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_2069 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Echinops telfairi	ENSETEG00000013828	1 retrocopy	retro_etel_1104,
Myotis lucifugus	ENSMLUG00000002627	2 retrocopies	retro_mluc_1179, retro_mluc_663,
Mus musculus	ENSMUSG00000020993	2 retrocopies	retro_mmus_1734, retro_mmus_2069 ,
Oryctolagus cuniculus	ENSOCUG00000002171	1 retrocopy	retro_ocun_813,
Sarcophilus harrisii	ENSSHAG00000001400	1 retrocopy	retro_shar_235,
Ictidomys tridecemlineatus	ENSSTOG00000002897	2 retrocopies	retro_itri_476, retro_itri_795,
Tupaia belangeri	ENSTBEG00000003331	1 retrocopy	retro_tbel_4529,