RetrogeneDB ID: retro_mmus_1718

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 18:46870821..46871103(+)
• Located in intron of: ENSMUSG00000024481

Retrocopy information

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

Parental gene information

• Parental gene symbol: Arf1
• Ensembl ID: ENSMUSG00000048076
• Aliases: None
• Description: ADP-ribosylation factor 1 [Source:MGI Symbol;Acc:MGI:99431]

Sequence

>retro_mmus_1718
ATGGGGAATATATTTGAAAACCTCTTCAGTGGCCAATTTGGCAAAGTAGAAGTGTGCATTCTCACGGTAGGCCTGGATGC
GGCAGGGAAGACAATTCTATATAAACTGAAGCTAGGTAATAGTGACCACAATTTCTACCGTTGGTTTCAACATGGCGACA
GTTGAGAACAAGAATATCAGCTTCTTTGTGTGGGTTGCGGGCATCCAGGACAAGATCCGCTGCTTCTTCCAGAATACTCA
GGCTTGATCTTCATGATGGATGGCAATGACAAAGAGCGTGTG

Alignment

ORF - retro_mmus_1718 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.69 %
• Parental protein coverage: 55.25 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MGNIFANLFKGLFGKKEMRILMVGLDAAGKTTILYKLKLGE-IVTTIPTIGFNVETVEYKNISFTVWDVG
          MGNIF.NLF.G.FGK.E..IL.VGLDAAGKT.ILYKLKLG....T.I.T.GFN..TVE.KNISF.VW..G
Retrocopy MGNIFENLFSGQFGKVEVCILTVGLDAAGKT-ILYKLKLGN>VTT-ISTVGFNMATVENKNISFFVWVAG

Parental  GQDKIRPLWRHYFQNTQ-GLIFVVDSNDRERV
          .QDKIR........NTQ.GLIF..D.ND.ERV
Retrocopy IQDKIRCFFQ----NTQ<GLIFMMDGNDKERV

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	206.71 RPM
SRP007412_cerebellum	0.00 RPM	147.63 RPM
SRP007412_heart	0.03 RPM	168.82 RPM
SRP007412_kidney	0.00 RPM	178.19 RPM
SRP007412_liver	0.00 RPM	159.78 RPM
SRP007412_testis	0.14 RPM	109.77 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_mmus_1718 was not detected

EST

No EST(s) were mapped for retro_mmus_1718 retrocopy.

TSS

No TSS is located nearby retro_mmus_1718 retrocopy 5' end.

Lab

retro_mmus_1718 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_1718 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Rattus norvegicus	retro_rnor_1348

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Parental genes homology:

Parental genes homology involve 17 parental genes, and 48 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000016671	10 retrocopies	retro_cjac_1295, retro_cjac_1691, retro_cjac_1719, retro_cjac_2189, retro_cjac_2896, retro_cjac_300, retro_cjac_3181, retro_cjac_3311, retro_cjac_3335, retro_cjac_390,
Cavia porcellus	ENSCPOG00000021174	1 retrocopy	retro_cpor_1310,
Ciona savignyi	ENSCSAVG00000007011	1 retrocopy	retro_csav_2,
Felis catus	ENSFCAG00000029374	1 retrocopy	retro_fcat_1829,
Homo sapiens	ENSG00000143761	3 retrocopies	retro_hsap_1008, retro_hsap_1160, retro_hsap_3763,
Gallus gallus	ENSGALG00000005393	1 retrocopy	retro_ggal_7,
Gorilla gorilla	ENSGGOG00000011263	5 retrocopies	retro_ggor_161, retro_ggor_2531, retro_ggor_3071, retro_ggor_801, retro_ggor_906,
Latimeria chalumnae	ENSLACG00000019009	1 retrocopy	retro_lcha_10,
Myotis lucifugus	ENSMLUG00000007020	6 retrocopies	retro_mluc_1631, retro_mluc_242, retro_mluc_2605, retro_mluc_428, retro_mluc_511, retro_mluc_876,
Mus musculus	ENSMUSG00000048076	1 retrocopy	retro_mmus_1718 ,
Mus musculus	ENSMUSG00000051853	1 retrocopy	retro_mmus_147,
Mus musculus	ENSMUSG00000062421	1 retrocopy	retro_mmus_2056,
Oryctolagus cuniculus	ENSOCUG00000023645	2 retrocopies	retro_ocun_1137, retro_ocun_247,
Pan troglodytes	ENSPTRG00000002066	2 retrocopies	retro_ptro_112, retro_ptro_5,
Tupaia belangeri	ENSTBEG00000009218	9 retrocopies	retro_tbel_1943, retro_tbel_2224, retro_tbel_2310, retro_tbel_2358, retro_tbel_2662, retro_tbel_2770, retro_tbel_3103, retro_tbel_4217, retro_tbel_4624,
Tetraodon nigroviridis	ENSTNIG00000011685	1 retrocopy	retro_tnig_19,
Tursiops truncatus	ENSTTRG00000014186	2 retrocopies	retro_ttru_1679, retro_ttru_347,