RetrogeneDB ID: retro_mmus_256

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 3:85871666..85872164(-)
• Located in intron of: ENSMUSG00000074513

Retrocopy information

• Ensembl ID: ENSMUSG00000031286
• Aliases: Glt28d2, 4732486J07Rik, Glt28d1l
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: Alg13
• Ensembl ID: ENSMUSG00000041718
• Aliases: Alg13, 2810046O15Rik, 4833435D08Rik, Glt28d1, MDS031, OTTMUSG00000018917
• Description: asparagine-linked glycosylation 13 [Source:MGI Symbol;Acc:MGI:1914824]

Sequence

>retro_mmus_256
ATGAAGAGAGTGTTTGTGACCGTCGGGACCACCAGTTTCGACGACCTCATCGCTCGAGTGGTTGCCCACGATAGCGTTCA
GATCCTCAAGAATCTGGGTTACAACCAACTTGTCCTCCAAATTGGTAGAGGCACTGTGGTGCCTGAGCCATTCAGTACTG
AGTCATTCACTCTGGATGTTTACAGATATAAGGACTCTTTGAAAGAAGACCTTCAGCAAGCCGACCTTGTCATTAGCCAT
GCAGGTGCAGGAAGCTGTTTGGAGAGTCTGGAGAAAGGCAAACCACTTGTGGTAGTTGTGAATGAAAAGTTAATGAACAA
TCATCAGTTTGAACTGGCAAAGCAGTTGCACAAAGAAGGCCATCTCTTCTACTGTACCTGCAGCATGCTTCCTGAGCTGT
TACAGTCAATGGATTTATCAACATTGAAATGTTATCCTCCTGGACAGCCAGAGAAATTTTCTGCATTTTTGGATAAAGTT
GTTGGATTACAAAAATAA

Alignment

ORF - retro_mmus_256 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.12 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MKRAFVTVGTTSFDELVARVVANDCVQILESLGYNHLVLQVGRGTVVPKPFRTESFTLDVYRYKDSLKED
          MKR.FVTVGTTSFD.L.ARVVA.D.VQIL..LGYN.LVLQ.GRGTVVP.PF.TESFTLDVYRYKDSLKED
Retrocopy MKRVFVTVGTTSFDDLIARVVAHDSVQILKNLGYNQLVLQIGRGTVVPEPFSTESFTLDVYRYKDSLKED

Parental  LQQADLVISHAGAGSCLESLEKGKPLVVVVNEKLMNNHQFELAKQLHKEGHLFYCTCSTLPGLLQSMDLS
          LQQADLVISHAGAGSCLESLEKGKPLVVVVNEKLMNNHQFELAKQLHKEGHLFYCTCS.LP.LLQSMDLS
Retrocopy LQQADLVISHAGAGSCLESLEKGKPLVVVVNEKLMNNHQFELAKQLHKEGHLFYCTCSMLPELLQSMDLS

Parental  TLKCYPPGQPEKFSAFLDKVVGLQK
          TLKCYPPGQPEKFSAFLDKVVGLQK
Retrocopy TLKCYPPGQPEKFSAFLDKVVGLQK

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	7.87 RPM
SRP007412_cerebellum	0.13 RPM	9.34 RPM
SRP007412_heart	0.37 RPM	3.64 RPM
SRP007412_kidney	0.46 RPM	4.85 RPM
SRP007412_liver	0.33 RPM	4.42 RPM
SRP007412_testis	0.18 RPM	33.34 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_256 was not detected

EST

No EST(s) were mapped for retro_mmus_256 retrocopy.

TSS

No TSS is located nearby retro_mmus_256 retrocopy 5' end.

Lab

retro_mmus_256 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_256 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Echinops telfairi	ENSETEG00000005613	1 retrocopy	retro_etel_1023,
Monodelphis domestica	ENSMODG00000005175	1 retrocopy	retro_mdom_1156,
Mus musculus	ENSMUSG00000041718	1 retrocopy	retro_mmus_256 ,
Oryctolagus cuniculus	ENSOCUG00000000232	2 retrocopies	retro_ocun_1459, retro_ocun_477,
Otolemur garnettii	ENSOGAG00000031713	2 retrocopies	retro_ogar_2864, retro_ogar_3363,
Tupaia belangeri	ENSTBEG00000010726	2 retrocopies	retro_tbel_117, retro_tbel_6,