RetrogeneDB ID: retro_mmus_3240

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 8:127040347..127040700(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Gabarapl2
• Ensembl ID: ENSMUSG00000031950
• Aliases: None
• Description: gamma-aminobutyric acid (GABA) A receptor-associated protein-like 2 [Source:MGI Symbol;Acc:MGI:1890602]

Sequence

>retro_mmus_3240
ATGAAGTGAATGTTTAAGGAGGACCGCTCGCTGGAACACAGATACGTGGAATCCCGCGAAGATTCAGAATGAAGTACATC
GACCAGGTTCCGGTGATCGTGGAAAAAGTCTTTGGCTCTCAGATTGTTGACATTGGCAAAAGGAAGTACTTGGTCCCATC
CGACATCACTGTGGCTCAGTTCATGTGGATCATCAGAGAAAGAATCCAGCTTCCTTCTGAGGAGGTCATCTTCCTGTTTG
TGGACAAGACAGTCCCACAGTCCAGCCTAACTAGAGGACAGCTTTATGAGAAGGAAAAACATGAAGATGGATTCTTGTAT
GTGGCCTACAGCAGAGAGATCACTTTTGGCTTC

Alignment

ORF - retro_mmus_3240 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.71 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MKWMFKEDHSLEHRCVES-AKI-RAKYPDRVPVIVEKVSGSQIVDIDKRKYLVPSDITVAQFMWIIRKRI
          MK.MFKED.SLEHR.VES.AKI.R.KY.D.VPVIVEKV.GSQIVDI.KRKYLVPSDITVAQFMWIIR.RI
Retrocopy MK*MFKEDRSLEHRYVES>AKI>RMKYIDQVPVIVEKVFGSQIVDIGKRKYLVPSDITVAQFMWIIRERI

Parental  QLPSEKAIFLFVDKTVPQSSLTMGQLYEKEKDEDGFLYVAYSGENTFGF
          QLPSE..IFLFVDKTVPQSSLT.GQLYEKEK.EDGFLYVAYS.E.TFGF
Retrocopy QLPSEEVIFLFVDKTVPQSSLTRGQLYEKEKHEDGFLYVAYSREITFGF

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	29.88 RPM
SRP007412_cerebellum	0.00 RPM	32.09 RPM
SRP007412_heart	0.00 RPM	11.49 RPM
SRP007412_kidney	0.00 RPM	17.94 RPM
SRP007412_liver	0.00 RPM	9.99 RPM
SRP007412_testis	0.00 RPM	5.49 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_3240 was not detected

EST

No EST(s) were mapped for retro_mmus_3240 retrocopy.

TSS

No TSS is located nearby retro_mmus_3240 retrocopy 5' end.

Lab

retro_mmus_3240 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_3240 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000005453	2 retrocopies	retro_amel_1054, retro_amel_1238,
Canis familiaris	ENSCAFG00000031455	1 retrocopy	retro_cfam_639,
Callithrix jacchus	ENSCJAG00000014253	1 retrocopy	retro_cjac_146,
Dasypus novemcinctus	ENSDNOG00000002240	2 retrocopies	retro_dnov_1755, retro_dnov_2332,
Microcebus murinus	ENSMICG00000011981	1 retrocopy	retro_mmur_1473,
Mustela putorius furo	ENSMPUG00000009894	1 retrocopy	retro_mputfur_993,
Mus musculus	ENSMUSG00000018567	1 retrocopy	retro_mmus_3107,
Mus musculus	ENSMUSG00000031812	4 retrocopies	retro_mmus_1271, retro_mmus_2384, retro_mmus_2619, retro_mmus_846,
Mus musculus	ENSMUSG00000031950	5 retrocopies	retro_mmus_2637, retro_mmus_2655, retro_mmus_3240 , retro_mmus_456, retro_mmus_506,
Rattus norvegicus	ENSRNOG00000019425	1 retrocopy	retro_rnor_57,