RetrogeneDB ID: retro_mmus_110

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 13:18030741..18031593(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000075053
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: Vdac3
• Ensembl ID: ENSMUSG00000008892
• Aliases: None
• Description: voltage-dependent anion channel 3 [Source:MGI Symbol;Acc:MGI:106922]

Sequence

>retro_mmus_110
ATGTGTAACACACCAACTTACTGCGACCTAGGAAAGGCTGCCAAGGATGTCTTTAACAAAGGGTATGGGTTTGGCATGGT
CAAGATAGATCTGAAAACCAAGTCTTGTAGTGGAGTGGAATTTTCTACTTCAGGTCATGCTTATACTGATACAGGGAAAG
CATCAGGCAACCTAGAGACCAAATATAAGGTCTGCAACTATGGGCTCACCTTCACCCAAAAGTGGAATACAGACAACACT
CTTGGGACAGAAATCTCTTGGGAGAATAAGTTGGCTGAAGGGTTGAAACTGACTCTTGATACCATATTTGTACCAAACAC
AGGAAAGAAGAGTGGGAAATTAAAGGCCTCCTATAGACGGGATTGTTTTAGTCTCGGCAGTAATGTTGATATAGATTTTT
CTGAACCGACCATCTATGGCTGGGCTGTGTTGGCCTTTGAAGGTGGGCTTGCTGGCTATCAGATGAGTTTTGACACAGCC
AAATCCAAACTGTCTCAGAATAATTTCGCTCTTGGTTACAAGGCTGCAGACTTCCAGCTGCATACTCACGTGAATGATGG
CACTGAGTTTGGAGGCTCAATCTACCAGAAAGTTAACGAGAGGATTGAAACGTCAATAAACCTGGCATGGACAGCTGGCA
GCAACAACACTCGTTTTGGCATCGCTGCTAAATATAAGCTGGATTGTAGAACTTCTCTATCTGCCAAAGTAAACAATGCC
AGTTTAATTGGACTGGGTTATACGCAGACCCTCCGACCAGGAGTCAAACTGACCCTGTCAGCTTTAATAGATGGAAAGAA
CTTCAATGCAGGAGGCCACAAGGTTGGATTGGGATTTGAACTGGAGGCTTAG

Alignment

ORF - retro_mmus_110 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 99.29 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MCNTPTYCDLGKAAKDVFNKGYGFGMVKIDLKTKSCSGVEFSTSGHAYTDTGKASGNLETKYKVCNYGLT
          MCNTPTYCDLGKAAKDVFNKGYGFGMVKIDLKTKSCSGVEFSTSGHAYTDTGKASGNLETKYKVCNYGLT
Retrocopy MCNTPTYCDLGKAAKDVFNKGYGFGMVKIDLKTKSCSGVEFSTSGHAYTDTGKASGNLETKYKVCNYGLT

Parental  FTQKWNTDNTLGTEISWENKLAEGLKLTLDTIFVPNTGKKSGKLKASYRRDCFSLGSNVDIDFSGPTIYG
          FTQKWNTDNTLGTEISWENKLAEGLKLTLDTIFVPNTGKKSGKLKASYRRDCFSLGSNVDIDFS.PTIYG
Retrocopy FTQKWNTDNTLGTEISWENKLAEGLKLTLDTIFVPNTGKKSGKLKASYRRDCFSLGSNVDIDFSEPTIYG

Parental  WAVLAFEGWLAGYQMSFDTAKSKLSQNNFALGYKAADFQLHTHVNDGTEFGGSIYQKVNERIETSINLAW
          WAVLAFEG.LAGYQMSFDTAKSKLSQNNFALGYKAADFQLHTHVNDGTEFGGSIYQKVNERIETSINLAW
Retrocopy WAVLAFEGGLAGYQMSFDTAKSKLSQNNFALGYKAADFQLHTHVNDGTEFGGSIYQKVNERIETSINLAW

Parental  TAGSNNTRFGIAAKYKLDCRTSLSAKVNNASLIGLGYTQTLRPGVKLTLSALIDGKNFNAGGHKVGLGFE
          TAGSNNTRFGIAAKYKLDCRTSLSAKVNNASLIGLGYTQTLRPGVKLTLSALIDGKNFNAGGHKVGLGFE
Retrocopy TAGSNNTRFGIAAKYKLDCRTSLSAKVNNASLIGLGYTQTLRPGVKLTLSALIDGKNFNAGGHKVGLGFE

Parental  LEA
          LEA
Retrocopy LEA

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	0.58 RPM	34.13 RPM
SRP007412_cerebellum	0.96 RPM	27.05 RPM
SRP007412_heart	0.84 RPM	65.06 RPM
SRP007412_kidney	1.46 RPM	33.86 RPM
SRP007412_liver	0.44 RPM	18.19 RPM
SRP007412_testis	2.88 RPM	65.45 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_mmus_110 was not detected

EST

No EST(s) were mapped for retro_mmus_110 retrocopy.

TSS

TSS No.	TSS Name	TSS expression level (Expr) in TPM range:
		no expression	0 < Expr ≤ 1	1 < Expr ≤ 5	5 < Expr ≤ 10	Expr > 10
TSS #1	TSS_27321	328 libraries	491 libraries	245 libraries	8 libraries	0 libraries

The graphical summary, for retro_mmus_110 TSS expression levels > 0 TPM .
TSS expression levels were studied across 1072 TSS-CAGE libraries, based on FANTOM5 data.
The expression values were visualized using beanplot. If you have any doubts, how to read it, read more in Kampstra P (2008)

Lab

retro_mmus_110 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_110 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 26 parental genes, and 60 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000005095	1 retrocopy	retro_amel_729,
Bos taurus	ENSBTAG00000014068	4 retrocopies	retro_btau_1537, retro_btau_1607, retro_btau_365, retro_btau_685,
Canis familiaris	ENSCAFG00000005502	5 retrocopies	retro_cfam_1513, retro_cfam_2146, retro_cfam_258, retro_cfam_665, retro_cfam_713,
Choloepus hoffmanni	ENSCHOG00000007369	1 retrocopy	retro_chof_16,
Dasypus novemcinctus	ENSDNOG00000013885	1 retrocopy	retro_dnov_1753,
Equus caballus	ENSECAG00000000438	1 retrocopy	retro_ecab_799,
Echinops telfairi	ENSETEG00000002652	2 retrocopies	retro_etel_1456, retro_etel_1487,
Felis catus	ENSFCAG00000010075	2 retrocopies	retro_fcat_1985, retro_fcat_599,
Homo sapiens	ENSG00000078668	1 retrocopy	retro_hsap_1375,
Gallus gallus	ENSGALG00000003755	1 retrocopy	retro_ggal_11,
Gorilla gorilla	ENSGGOG00000001932	2 retrocopies	retro_ggor_1071, retro_ggor_3043,
Microcebus murinus	ENSMICG00000010235	1 retrocopy	retro_mmur_1361,
Monodelphis domestica	ENSMODG00000015526	5 retrocopies	retro_mdom_1130, retro_mdom_1331, retro_mdom_1869, retro_mdom_420, retro_mdom_669,
Mus musculus	ENSMUSG00000008892	2 retrocopies	retro_mmus_110 , retro_mmus_1505,
Mus musculus	ENSMUSG00000020402	3 retrocopies	retro_mmus_2013, retro_mmus_3079, retro_mmus_3124,
Mus musculus	ENSMUSG00000021771	1 retrocopy	retro_mmus_2667,
Nomascus leucogenys	ENSNLEG00000012890	1 retrocopy	retro_nleu_2593,
Otolemur garnettii	ENSOGAG00000016163	4 retrocopies	retro_ogar_2770, retro_ogar_2870, retro_ogar_589, retro_ogar_995,
Pongo abelii	ENSPPYG00000018554	8 retrocopies	retro_pabe_1145, retro_pabe_1960, retro_pabe_2304, retro_pabe_3163, retro_pabe_3665, retro_pabe_3791, retro_pabe_819, retro_pabe_971,
Pan troglodytes	ENSPTRG00000020205	2 retrocopies	retro_ptro_2548, retro_ptro_945,
Pteropus vampyrus	ENSPVAG00000014822	2 retrocopies	retro_pvam_637, retro_pvam_907,
Rattus norvegicus	ENSRNOG00000019277	1 retrocopy	retro_rnor_1596,
Sarcophilus harrisii	ENSSHAG00000017953	1 retrocopy	retro_shar_658,
Tupaia belangeri	ENSTBEG00000007420	4 retrocopies	retro_tbel_1801, retro_tbel_2150, retro_tbel_2261, retro_tbel_884,
Tarsius syrichta	ENSTSYG00000007112	1 retrocopy	retro_tsyr_918,
Tursiops truncatus	ENSTTRG00000009681	3 retrocopies	retro_ttru_1201, retro_ttru_1254, retro_ttru_634,