RetrogeneDB ID: retro_mmus_1918

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 2:52619753..52620182(+)
• Located in intron of: ENSMUSG00000017412

Retrocopy information

• Ensembl ID: ENSMUSG00000025201
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Bloc1s2a
• Ensembl ID: ENSMUSG00000057506
• Aliases: Bloc1s2, 2410089B13Rik, BLOS2, Bloc1s2a
• Description: biogenesis of lysosome-related organelles complex-1, subunit 2A [Source:MGI Symbol;Acc:MGI:1920939]

Sequence

>retro_mmus_1918
ATGGCGGCGGCTGCGGAGGGCGTCCCGGCGACGCGACGGGAGGAGCAGCCACCTCGAGATGATGCTGCGGTGGAGACAGC
CGAGGAAGCAAAGGAGCCTGCCGAAGCTGACATCAATGAGCTCTGCAGGGACATGTTCTCCAAAATGGCCACATATTTGA
CTGGGGAACTGACAGCCACCAGTGAAGACTACAAACTCCTGGAAAATATGAATAAGCTAACAAGCTTGAAGTACCTTGAA
ATGAAAGATATTGCTATCAACATCAGCAGAAACCTGAAGGACTTAAACCAGAAATATGCTGAACTACAGCCATATCTGGA
CCAGATCAACATGATTGAGGAGCAGGTGGCAGCTCTGGAGCAGGCAGCCTACAAGCTCGATGCTTATTCAAAAAAACTGG
AAGCCAAGTACAAGAAGTTGGAGAAGCGA

Alignment

ORF - retro_mmus_1918 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

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

Retrocopy - Parental Gene Alignment:

Parental  MAAAAEGVPATRREEQPPRDDAAVETAEEAKEPAEADINELCRDMFSKMATYLTGELTATSEDYKLLENM
          MAAAAEGVPATRREEQPPRDDAAVETAEEAKEPAEADINELCRDMFSKMATYLTGELTATSEDYKLLENM
Retrocopy MAAAAEGVPATRREEQPPRDDAAVETAEEAKEPAEADINELCRDMFSKMATYLTGELTATSEDYKLLENM

Parental  NKLTSLKYLEMKDIAINISRNLKDLNQKYAELQPYLDQINMIEEQVAALEQAAYKLDAYSKKLEAKYKKL
          NKLTSLKYLEMKDIAINISRNLKDLNQKYAELQPYLDQINMIEEQVAALEQAAYKLDAYSKKLEAKYKKL
Retrocopy NKLTSLKYLEMKDIAINISRNLKDLNQKYAELQPYLDQINMIEEQVAALEQAAYKLDAYSKKLEAKYKKL

Parental  EKR
          EKR
Retrocopy EKR

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	0.12 RPM	6.03 RPM
SRP007412_cerebellum	0.04 RPM	5.17 RPM
SRP007412_heart	0.06 RPM	3.30 RPM
SRP007412_kidney	0.00 RPM	4.04 RPM
SRP007412_liver	0.00 RPM	3.11 RPM
SRP007412_testis	0.09 RPM	8.92 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_1918 was not detected

EST

No EST(s) were mapped for retro_mmus_1918 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_87539	421 libraries	318 libraries	329 libraries	4 libraries	0 libraries

The graphical summary, for retro_mmus_1918 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_1918 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_1918 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 65 retrocopies.

Species	Parental gene accession	Retrocopies number
Echinops telfairi	ENSETEG00000007299	1 retrocopy	retro_etel_861,
Macropus eugenii	ENSMEUG00000003630	57 retrocopies	retro_meug_1051, retro_meug_1098, retro_meug_1099, retro_meug_114, retro_meug_1152, retro_meug_1157, retro_meug_1175, retro_meug_1248, retro_meug_1276, retro_meug_1324, retro_meug_1353, retro_meug_1382, retro_meug_1405, retro_meug_1502, retro_meug_153, retro_meug_1592, retro_meug_1629, retro_meug_1687, retro_meug_1707, retro_meug_1715, retro_meug_1756, retro_meug_1785, retro_meug_1834, retro_meug_1844, retro_meug_1892, retro_meug_1925, retro_meug_1937, retro_meug_1955, retro_meug_1978, retro_meug_2007, retro_meug_2012, retro_meug_2083, retro_meug_2145, retro_meug_2177, retro_meug_2188, retro_meug_225, retro_meug_243, retro_meug_250, retro_meug_259, retro_meug_317, retro_meug_329, retro_meug_339, retro_meug_391, retro_meug_394, retro_meug_617, retro_meug_711, retro_meug_725, retro_meug_827, retro_meug_839, retro_meug_841, retro_meug_871, retro_meug_922, retro_meug_931, retro_meug_955, retro_meug_967, retro_meug_975, retro_meug_984,
Mus musculus	ENSMUSG00000057506	2 retrocopies	retro_mmus_1918 , retro_mmus_363,
Otolemur garnettii	ENSOGAG00000001395	4 retrocopies	retro_ogar_2024, retro_ogar_3475, retro_ogar_671, retro_ogar_696,
Tupaia belangeri	ENSTBEG00000016889	1 retrocopy	retro_tbel_4051,