RetrogeneDB ID: retro_mmus_630

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 10:28065665..28066020(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Slmo2
• Ensembl ID: ENSMUSG00000016257
• Aliases: Slmo2, 2310042G06Rik, AA407013
• Description: slowmo homolog 2 (Drosophila) [Source:MGI Symbol;Acc:MGI:1913640]

Sequence

>retro_mmus_630
ATGGGTTAAGCAAGAACCAACACATACTCTGCCAGAACCTTCTATAGTTGACCCCATAAAGACGAAAATGGAATCCACAC
CTATTAGTATTTCATTTACAAATATGGTTTCAATAGAGGAGAGAATTTCATGATTTTCATATAAACCACACCCTCGGGAC
CCAGGAAAACCTGTGTTGAATCAGGAAGACATCATCACTACAAATGGGGGCAGCCTCAAAAACCACCTTGAAGGACTCAT
GGCCCACACTGTTCCTTCAAAGGATAACAAAGGCTTTGAAGCAATGGGATGGGTGAGCCATTGGCTGAGGTTGAAGAATT
CTGTATCAACAAGAGGAAGCCTTAGGACACCCATG

Alignment

ORF - retro_mmus_630 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 52.46 %
• Parental protein coverage: 60.51 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  IGAARTKTY-VQEHSVVDPVTRTMELKSTNISFTNMVSVDERLT---YKPHLQDPEKTVLTQEALITVKG
          .G.ART.TY...E.S.VDP....ME.....ISFTNMVS..ER.....YKPH..DP.K.VL.QE..IT..G
Retrocopy MG*ARTNTY>LPEPSIVDPIKTKMESTPISISFTNMVSIEERIS*FSYKPHPRDPGKPVLNQEDIITTNG

Parental  VSLSSYLEGLMASTISSNASKGREAMEWVIHKLNAEIEELAASARGSIRTPM
          .SL...LEGLMA.T..S...KG.EAM.WV.H.L.........S.RGS.RTPM
Retrocopy GSLKNHLEGLMAHTVPSKDNKGFEAMGWVSHWLRL---KNSVSTRGSLRTPM

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	30.25 RPM
SRP007412_cerebellum	0.00 RPM	27.66 RPM
SRP007412_heart	0.00 RPM	46.07 RPM
SRP007412_kidney	0.00 RPM	37.86 RPM
SRP007412_liver	0.00 RPM	28.21 RPM
SRP007412_testis	0.00 RPM	21.82 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_630 was not detected

EST

No EST(s) were mapped for retro_mmus_630 retrocopy.

TSS

No TSS is located nearby retro_mmus_630 retrocopy 5' end.

Lab

retro_mmus_630 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_630 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Rattus norvegicus	retro_rnor_423

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 45 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000018905	4 retrocopies	retro_cjac_1286, retro_cjac_2921, retro_cjac_3171, retro_cjac_3236,
Dasypus novemcinctus	ENSDNOG00000014548	3 retrocopies	retro_dnov_1402, retro_dnov_2032, retro_dnov_2311,
Echinops telfairi	ENSETEG00000009651	3 retrocopies	retro_etel_1130, retro_etel_1262, retro_etel_632,
Loxodonta africana	ENSLAFG00000000300	1 retrocopy	retro_lafr_700,
Myotis lucifugus	ENSMLUG00000014907	2 retrocopies	retro_mluc_1887, retro_mluc_845,
Macaca mulatta	ENSMMUG00000007560	4 retrocopies	retro_mmul_1155, retro_mmul_1644, retro_mmul_2123, retro_mmul_539,
Monodelphis domestica	ENSMODG00000016608	5 retrocopies	retro_mdom_1596, retro_mdom_1619, retro_mdom_1620, retro_mdom_1655, retro_mdom_405,
Mus musculus	ENSMUSG00000016257	2 retrocopies	retro_mmus_2725, retro_mmus_630 ,
Mus musculus	ENSMUSG00000024530	1 retrocopy	retro_mmus_1332,
Oryctolagus cuniculus	ENSOCUG00000005621	8 retrocopies	retro_ocun_1944, retro_ocun_1954, retro_ocun_455, retro_ocun_486, retro_ocun_549, retro_ocun_619, retro_ocun_775, retro_ocun_926,
Ochotona princeps	ENSOPRG00000002550	8 retrocopies	retro_opri_1069, retro_opri_1090, retro_opri_141, retro_opri_216, retro_opri_45, retro_opri_663, retro_opri_683, retro_opri_770,
Rattus norvegicus	ENSRNOG00000046644	2 retrocopies	retro_rnor_422, retro_rnor_423,
Sorex araneus	ENSSARG00000004671	2 retrocopies	retro_sara_282, retro_sara_430,