RetrogeneDB ID: retro_mmus_363

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 1:132284452..132284806(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000089808
• 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_363
GATGATGCTGCGGTGGAGACAGCCGAGGAAGCAAAGGAGCCTGCCGAAGCTGACATCAATGAGCTCTGCCGGGACATGTT
CTCCAAAATGGCCACATACTTGACTGGGGAACTGACAGCCACCAGTGAAGACTACAAACTCCTGGAAAATATGAATAAGC
TAACAAGCTTGAAGTACCTTGAGATGAAAGATATTGCTATCAACATCAGCAGAAACCTGAAGGACTTAAACCAGAAATAT
GCGGAACTACAGCCGTATCTTGACCAGATCAACATGATTGAGGACCAGGCAGCCTACAAGCTCGATGCTTATTCAAAAAA
ACTGGAAGCCAAGTACAGGAAGTTGGAGAAGCGA

Alignment

ORF - retro_mmus_363 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.29 %
• Parental protein coverage: 81.82 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  DDAAVETAEEAKEPAEADINELCRDMFSKMATYLTGELTATSEDYKLLENMNKLTSLKYLEMKDIAINIS
          DDAAVETAEEAKEPAEADINELCRDMFSKMATYLTGELTATSEDYKLLENMNKLTSLKYLEMKDIAINIS
Retrocopy DDAAVETAEEAKEPAEADINELCRDMFSKMATYLTGELTATSEDYKLLENMNKLTSLKYLEMKDIAINIS

Parental  RNLKDLNQKYAELQPYLDQINMIEEQVA-ALEQAAYKLDAYSKKLEAK
          RNLKDLNQKYAELQPYLDQINMIE.Q.A..L.....KL.A...KLE..
Retrocopy RNLKDLNQKYAELQPYLDQINMIEDQAAYKLDAYSKKLEAKYRKLEKR

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	6.03 RPM
SRP007412_cerebellum	0.04 RPM	5.17 RPM
SRP007412_heart	0.00 RPM	3.30 RPM
SRP007412_kidney	0.02 RPM	4.04 RPM
SRP007412_liver	0.03 RPM	3.11 RPM
SRP007412_testis	0.00 RPM	8.92 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_363 was not detected

EST

No EST(s) were mapped for retro_mmus_363 retrocopy.

TSS

No TSS is located nearby retro_mmus_363 retrocopy 5' end.

Lab

retro_mmus_363 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_363 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,