RetrogeneDB ID: retro_mmus_3107

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 8:15437864..15438149(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Gabarap
• Ensembl ID: ENSMUSG00000018567
• Aliases: None
• Description: gamma-aminobutyric acid receptor associated protein [Source:MGI Symbol;Acc:MGI:1861742]

Sequence

>retro_mmus_3107
ATGAAGTTCCAGTGCAAAGAAGAGCATCCATTTGAGAAGTGCTGCTCTGAGGGTGAGAAAATCCAAAAGAAATCCCCAGA
CTGGGTCCCAGTGATAGTTGAAAAAGTTCCCAAAGCTCAGATAGGAGTCCTGGACAAAAAGGAATACCTGGTGCCTTCTG
ATCTTATGGTTGGTCAATTCTACTTCTTGATCCGGAAGGGAATCCATCTTCCTGCTGAAGATTCCTTGTTTTTATTCGGC
AACAATGTCATTCCATCCACCAGTGCCACCATGGGTCAGCTGTAC

Alignment

ORF - retro_mmus_3107 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.05 %
• Parental protein coverage: 81.2 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MKFVYKEEHPFEKRRSEGEKIRKKYPDRVPVIVEKAPKARIGDLDKKKYLVPSDLTVGQFYFLIRKRIHL
          MKF..KEEHPFEK..SEGEKI.KK.PD.VPVIVEK.PKA.IG.LDKK.YLVPSDL.VGQFYFLIRK.IHL
Retrocopy MKFQCKEEHPFEKCCSEGEKIQKKSPDWVPVIVEKVPKAQIGVLDKKEYLVPSDLMVGQFYFLIRKGIHL

Parental  RAEDALFFFVNNVIPPTSATMGQLY
          .AED.LF.F.NNVIP.TSATMGQLY
Retrocopy PAEDSLFLFGNNVIPSTSATMGQLY

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	82.75 RPM
SRP007412_cerebellum	0.00 RPM	74.81 RPM
SRP007412_heart	0.00 RPM	127.76 RPM
SRP007412_kidney	0.00 RPM	172.73 RPM
SRP007412_liver	0.00 RPM	129.61 RPM
SRP007412_testis	0.05 RPM	178.15 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_mmus_3107 was not detected

EST

No EST(s) were mapped for retro_mmus_3107 retrocopy.

TSS

No TSS is located nearby retro_mmus_3107 retrocopy 5' end.

Lab

retro_mmus_3107 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_3107 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 15 parental genes, and 25 retrocopies.

Species	Parental gene accession	Retrocopies number
Ciona intestinalis	ENSCING00000012473	1 retrocopy	retro_cint_25,
Callithrix jacchus	ENSCJAG00000016655	2 retrocopies	retro_cjac_2851, retro_cjac_3820,
Gorilla gorilla	ENSGGOG00000013770	1 retrocopy	retro_ggor_821,
Loxodonta africana	ENSLAFG00000000744	1 retrocopy	retro_lafr_61,
Macaca mulatta	ENSMMUG00000010545	1 retrocopy	retro_mmul_155,
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,
Nomascus leucogenys	ENSNLEG00000008049	2 retrocopies	retro_nleu_1670, retro_nleu_4,
Oryctolagus cuniculus	ENSOCUG00000006997	1 retrocopy	retro_ocun_311,
Pongo abelii	ENSPPYG00000007901	1 retrocopy	retro_pabe_122,
Pan troglodytes	ENSPTRG00000034115	1 retrocopy	retro_ptro_60,
Rattus norvegicus	ENSRNOG00000017417	2 retrocopies	retro_rnor_1818, retro_rnor_2093,
Sus scrofa	ENSSSCG00000017936	1 retrocopy	retro_sscr_163,
Drosophila melanogaster	FBgn0052672	1 retrocopy	retro_dmel_23,