RetrogeneDB ID: retro_mmus_2675

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 5:101035541..101035807(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: Ensa
• Ensembl ID: ENSMUSG00000038619
• Aliases: Ensa, 1700020C18Rik, 2610007F17Rik, AI451924
• Description: endosulfine alpha [Source:MGI Symbol;Acc:MGI:1891189]

Sequence

>retro_mmus_2675
AAGCAAGAGAACAGATCTCCCACACAGGAGACCGGTGATGAGAAGCAGGACACATAGGAGAAAGAAGATATTCTTCTGAA
AGCACTGATGAGGCAAAGGCAAAGACTGAAGATAAGGCCGATGCTGAACCCTGGAAGCTCTGACTTCCTCATGAAGAAAC
TCCAGAAAAGGCAGCAGTGCTTCACCTGGGGAATCACAGCATAGCCAAAGCCAAGGCAAAGAAAAGGCAACTTTAAAGCA
CAGGGCCAAACAAGAACTTGGTAACT

Alignment

ORF - retro_mmus_2675 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 50.55 %
• Parental protein coverage: 76.92 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  KQEEENPAEETGEEKQDTQEKEGILPEKAEEAKLKAKYPSLGQKPGGSDFLMKRLQKGQKYF-DSGDYNM
          KQE...P..ETG.EKQDT.EKE.IL...........K.......PG.SDFLMK.LQK.Q..F...G....
Retrocopy KQENRSPTQETGDEKQDT*EKEDILLKALMRQRQRLKIRPM-LNPGSSDFLMKKLQKRQQCF<HLGNHSI

Parental  AKAKMKNKQLPSAGADKNLVT
          AKAK.K..QL.S.G..KNLVT
Retrocopy AKAKAKKRQL*STGPNKNLVT

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	196.74 RPM
SRP007412_cerebellum	0.00 RPM	137.25 RPM
SRP007412_heart	0.00 RPM	94.48 RPM
SRP007412_kidney	0.00 RPM	73.82 RPM
SRP007412_liver	0.00 RPM	37.49 RPM
SRP007412_testis	0.00 RPM	53.06 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_2675 was not detected

EST

No EST(s) were mapped for retro_mmus_2675 retrocopy.

TSS

No TSS is located nearby retro_mmus_2675 retrocopy 5' end.

Lab

retro_mmus_2675 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_2675 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000143420	3 retrocopies	retro_hsap_1449, retro_hsap_2208, retro_hsap_2452,
Mus musculus	ENSMUSG00000038619	1 retrocopy	retro_mmus_2675 ,
Oryctolagus cuniculus	ENSOCUG00000003267	3 retrocopies	retro_ocun_296, retro_ocun_396, retro_ocun_722,
Otolemur garnettii	ENSOGAG00000005863	3 retrocopies	retro_ogar_1769, retro_ogar_1911, retro_ogar_2262,
Pongo abelii	ENSPPYG00000000893	2 retrocopies	retro_pabe_1803, retro_pabe_2081,
Rattus norvegicus	ENSRNOG00000048617	1 retrocopy	retro_rnor_1776,