RetrogeneDB ID: retro_mmus_2458

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 4:48627883..48628117(-)
• Located in intron of: ENSMUSG00000028347

Retrocopy information

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

Parental gene information

• Parental gene symbol: Glipr2
• Ensembl ID: ENSMUSG00000028480
• Aliases: Glipr2, 5730414A08Rik, C77180, GAPR-1
• Description: GLI pathogenesis-related 2 [Source:MGI Symbol;Acc:MGI:1917770]

Sequence

>retro_mmus_2458
CACAGGGTTTCCCCTCTGAAGCTTTGCCAGAAGCTCAGTTAGGAAGCAGAGCAGGATTTGGAGGTCCCTGCCAACACAAG
AATCCTCAAGCACGGCCCAGAGTCCAGTTGTGGCCAGTGTTGGGAAAACCTTGCATAGGCACCCTGCACTCAGGCAAGAA
AGGAAGTGGCTGACCGGTGACACAGGGAGATCAAGAACGACCACTCCCAGGAGCCTGGCTTCTGAGACGGGACA

Alignment

ORF - retro_mmus_2458 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 60.26 %
• Parental protein coverage: 50.65 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  HGVPPLKLCKKLNREAQQYSEALASTRILKHSPESSRGQCGENLAWASYDQTGKDVADRWYSEIKSYNFQ
          H.V.PLKLC.KL..EA.Q..E..A.TRILKH.PESS.GQC.ENLA.A...Q..K.VADR...EIK....Q
Retrocopy HRVSPLKLCQKLS*EAEQDLEVPANTRILKHGPESSCGQCWENLA*APCTQARKEVADR*HREIKNDHSQ

Parental  QPGFTSGT
          .PGF..GT
Retrocopy EPGF*DGT

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	0.02 RPM	2.45 RPM
SRP007412_cerebellum	0.00 RPM	3.91 RPM
SRP007412_heart	0.00 RPM	3.39 RPM
SRP007412_kidney	0.00 RPM	3.33 RPM
SRP007412_liver	0.00 RPM	1.01 RPM
SRP007412_testis	0.00 RPM	1.88 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_2458 was not detected

EST

No EST(s) were mapped for retro_mmus_2458 retrocopy.

TSS

No TSS is located nearby retro_mmus_2458 retrocopy 5' end.

Lab

retro_mmus_2458 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_2458 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Rattus norvegicus	retro_rnor_2217

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000030686	1 retrocopy	retro_cfam_428,
Dasypus novemcinctus	ENSDNOG00000008950	1 retrocopy	retro_dnov_2040,
Dipodomys ordii	ENSDORG00000012831	1 retrocopy	retro_dord_342,
Felis catus	ENSFCAG00000012762	2 retrocopies	retro_fcat_115, retro_fcat_1587,
Microcebus murinus	ENSMICG00000017673	1 retrocopy	retro_mmur_1525,
Myotis lucifugus	ENSMLUG00000011791	2 retrocopies	retro_mluc_1145, retro_mluc_475,
Mus musculus	ENSMUSG00000028480	1 retrocopy	retro_mmus_2458 ,
Rattus norvegicus	ENSRNOG00000014838	1 retrocopy	retro_rnor_2217,
Tupaia belangeri	ENSTBEG00000009276	2 retrocopies	retro_tbel_1646, retro_tbel_4682,