RetrogeneDB ID: retro_mmus_3314

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 9:8153760..8154122(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Dstn
• Ensembl ID: ENSMUSG00000015932
• Aliases: Dstn, 2610043P17Rik, ADF, AU042046, Dsn, corn1, sid23p
• Description: destrin [Source:MGI Symbol;Acc:MGI:1929270]

Sequence

>retro_mmus_3314
AGTGCTCCACACCAGAAGAAATCAAGAAAGAAGGCTGTCATTTTCTGTCTCAGTGCAGACAAAAAGTGCACAGTCATTGA
AGAAGGTAAAGAGATCTTGGTGGGAGATGTTAGTGTCACCATAACTGATCCTTTCTAGCATTTTGTTGGAATGCTTCCTG
AAAAAGATTGTCGCTACGCTTTGTATGACGCCAGCTTTGAAACCAAGGAGTCCAAGAAAGAAGAGCTGATGTTCTCTTCT
TGTGGGCACCAGAACTAACACCTCTAAAAAGTAAAATGATCTATGCAAGCTTGAAGAATGCCATCGAAAAGAAATTTCCA
GGTATAAAGCATGAGTATCAAGCAAATGGGCCAGAAGCCCTC

Alignment

ORF - retro_mmus_3314 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.87 %
• Parental protein coverage: 72.73 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  STPEEIKKRKKAVIFCLSADKKCIVVEEGKEILVGDVGATITDPFKHFVGMLPEKDCRYALYDASFET-K
          S.P...K.RKKAVIFCLSADKKC.V.EEGKEILVGDV..TITDPF.HFVGMLPEKDCRYALYDASFET..
Retrocopy SAPHQKKSRKKAVIFCLSADKKCTVIEEGKEILVGDVSVTITDPF*HFVGMLPEKDCRYALYDASFETKE

Parental  ESRKEEL-MFFLWAPEQAPLKSKMIYASSKDAIKKKFPGIKHEYQANGPEDL
          ....E.....FLWAPE..PLKSKMIYAS.K.AI.KKFPGIKHEYQANGPE.L
Retrocopy SKKEELM<VLFLWAPELTPLKSKMIYASLKNAIEKKFPGIKHEYQANGPEAL

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	0.05 RPM	89.71 RPM
SRP007412_cerebellum	0.00 RPM	62.74 RPM
SRP007412_heart	0.00 RPM	67.09 RPM
SRP007412_kidney	0.00 RPM	124.24 RPM
SRP007412_liver	0.00 RPM	92.33 RPM
SRP007412_testis	0.05 RPM	19.07 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_3314 was not detected

EST

No EST(s) were mapped for retro_mmus_3314 retrocopy.

TSS

No TSS is located nearby retro_mmus_3314 retrocopy 5' end.

Lab

retro_mmus_3314 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_3314 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 22 parental genes, and 40 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000015434	1 retrocopy	retro_btau_880,
Choloepus hoffmanni	ENSCHOG00000003110	5 retrocopies	retro_chof_1308, retro_chof_1656, retro_chof_1758, retro_chof_2297, retro_chof_72,
Cavia porcellus	ENSCPOG00000005573	2 retrocopies	retro_cpor_700, retro_cpor_812,
Dasypus novemcinctus	ENSDNOG00000000934	1 retrocopy	retro_dnov_24,
Erinaceus europaeus	ENSEEUG00000011893	1 retrocopy	retro_eeur_529,
Homo sapiens	ENSG00000125868	1 retrocopy	retro_hsap_952,
Gorilla gorilla	ENSGGOG00000009007	1 retrocopy	retro_ggor_768,
Microcebus murinus	ENSMICG00000013687	1 retrocopy	retro_mmur_765,
Macaca mulatta	ENSMMUG00000013786	1 retrocopy	retro_mmul_782,
Mus musculus	ENSMUSG00000015932	1 retrocopy	retro_mmus_3314 ,
Mus musculus	ENSMUSG00000056201	6 retrocopies	retro_mmus_1729, retro_mmus_2103, retro_mmus_3127, retro_mmus_3556, retro_mmus_719, retro_mmus_970,
Mus musculus	ENSMUSG00000062929	1 retrocopy	retro_mmus_660,
Nomascus leucogenys	ENSNLEG00000009679	1 retrocopy	retro_nleu_2458,
Oryctolagus cuniculus	ENSOCUG00000027456	1 retrocopy	retro_ocun_1891,
Ochotona princeps	ENSOPRG00000000976	2 retrocopies	retro_opri_1078, retro_opri_696,
Pongo abelii	ENSPPYG00000010727	1 retrocopy	retro_pabe_812,
Pan troglodytes	ENSPTRG00000013275	1 retrocopy	retro_ptro_659,
Pteropus vampyrus	ENSPVAG00000000420	1 retrocopy	retro_pvam_1275,
Rattus norvegicus	ENSRNOG00000005924	1 retrocopy	retro_rnor_1710,
Sus scrofa	ENSSSCG00000007085	1 retrocopy	retro_sscr_954,
Tupaia belangeri	ENSTBEG00000017634	8 retrocopies	retro_tbel_1206, retro_tbel_1977, retro_tbel_2425, retro_tbel_2880, retro_tbel_2881, retro_tbel_4020, retro_tbel_679, retro_tbel_851,
Tursiops truncatus	ENSTTRG00000007291	1 retrocopy	retro_ttru_1503,