RetrogeneDB ID: retro_mmus_2667

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 5:91760695..91761577(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Vdac2
• Ensembl ID: ENSMUSG00000021771
• Aliases: Vdac2, Vdac6, mVDAC2, mVDAC6
• Description: voltage-dependent anion channel 2 [Source:MGI Symbol;Acc:MGI:106915]

Sequence

>retro_mmus_2667
GCTGAGTGCTGTGTACCGGTATGCCCACGGCTGATGTGTATCCCTCCACTGTATGCTGACCTCGGCAATGTTGCCAGAGA
CATTCTTCAACAAAGGATTTGGCTTTGGGTTGGTGAAGCTGGATGTGAAGACGAGGTCATGCAGCAGTGTGGAATTTTCA
ACGTCTGGCTCATCTAATACAGACACTGGTAAAGTTAGCGGGACCTTGGAGACCAAGTACAAATGGTGTGAGTATGGTCT
GACTTTCACAGAGAAATGGAACACGGATAACAGTCTGAGGACAGAGATTGCAATTCAAGACCAGATTTGTCAAGGTTTGA
AACTGACTTCTGACACCACCTTTTCACCGAACACAGGAAAGAAAAGTGGTAAAATCAAGTCTGCTTACAAGAGGGAGTGT
ATAAACCTTGGCTGTGATGTTGACTTTGATTTTGCTGGACCTGCCATCCATGGATCAGCTGTCTTTGGTTACGAGGGCTG
GCTTGCTGGGTACCAAATGACTTTGTCAGTGCCAAGTCAAAGCTGACAAGGAGTAACTTTGCAGTCGGCTACAGGACTGG
GGACTTCCAGCTACACACAAATGTAAATAATGGGACAGAATTTGGAGGATCAATTTATCAGATAGTATGTGAAGATTTTG
ACACTTCAGTAAACCTTGTTTGGACATCAGGTACCAACTGCACTCGTTTTGGCATTGCAGCTAAATACCGGTTGGATCCT
ACTGCCTCTATCTCTGCAAAGGTCAACAACTCTAGTTTAATTGGAGTGGGCTATACTCAGACTCTGAGGCCTGGTGTGAA
GCTTACACTATCTGCTCTGGTAGACGGGAAGAGCTTTAATGCTGGAGGCCACAAACTTGGGCTTGCCTTGGAATTGGAGG
CT

Alignment

ORF - retro_mmus_2667 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.59 %
• Parental protein coverage: 99.66 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  AECCVPVCPRPMCIPPPYADLGKAARDI-FNKGFGFGLVKLDVKTKSCSGVEFSTSGSSNTDTGKVSGTL
          AECCVPVCPR.MCIPP.YADLG..ARDI.FNKGFGFGLVKLDVKT.SCS.VEFSTSGSSNTDTGKVSGTL
Retrocopy AECCVPVCPRLMCIPPLYADLGNVARDI>FNKGFGFGLVKLDVKTRSCSSVEFSTSGSSNTDTGKVSGTL

Parental  ETKYKWCEYGLTFTEKWNTDNTLGTEIAIEDQICQGLKLTFDTTFSPNTGKKSGKIKSAYKRECINLGCD
          ETKYKWCEYGLTFTEKWNTDN.L.TEIAI.DQICQGLKLT.DTTFSPNTGKKSGKIKSAYKRECINLGCD
Retrocopy ETKYKWCEYGLTFTEKWNTDNSLRTEIAIQDQICQGLKLTSDTTFSPNTGKKSGKIKSAYKRECINLGCD

Parental  VDFDFAGPAIHGSAVFGYEGWLAGYQMT-FDSAKSKLTRSNFAVGYRTGDFQLHTNVNNGTEFGGSIYQK
          VDFDFAGPAIHGSAVFGYEGWLAGYQMT.F.SAKSKLTRSNFAVGYRTGDFQLHTNVNNGTEFGGSIYQ.
Retrocopy VDFDFAGPAIHGSAVFGYEGWLAGYQMT<FVSAKSKLTRSNFAVGYRTGDFQLHTNVNNGTEFGGSIYQI

Parental  VCEDFDTSVNLAWTSGTNCTRFGIAAKYQLDPTASISAKVNNSSLIGVGYTQTLRPGVKLTLSALVDGKS
          VCEDFDTSVNL.WTSGTNCTRFGIAAKY.LDPTASISAKVNNSSLIGVGYTQTLRPGVKLTLSALVDGKS
Retrocopy VCEDFDTSVNLVWTSGTNCTRFGIAAKYRLDPTASISAKVNNSSLIGVGYTQTLRPGVKLTLSALVDGKS

Parental  FNAGGHKLGLALELEA
          FNAGGHKLGLALELEA
Retrocopy FNAGGHKLGLALELEA

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	0.37 RPM	118.05 RPM
SRP007412_cerebellum	0.04 RPM	134.17 RPM
SRP007412_heart	0.78 RPM	277.59 RPM
SRP007412_kidney	0.42 RPM	208.82 RPM
SRP007412_liver	0.08 RPM	78.24 RPM
SRP007412_testis	0.73 RPM	347.71 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_mmus_2667 was not detected

EST

No EST(s) were mapped for retro_mmus_2667 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_116424	337 libraries	521 libraries	207 libraries	7 libraries	0 libraries
TSS #2	TSS_116425	709 libraries	241 libraries	122 libraries	0 libraries	0 libraries

The graphical summary, for retro_mmus_2667 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_2667 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_2667 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 18 parental genes, and 32 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000012975	2 retrocopies	retro_btau_1252, retro_btau_1389,
Canis familiaris	ENSCAFG00000015398	1 retrocopy	retro_cfam_376,
Callithrix jacchus	ENSCJAG00000001145	1 retrocopy	retro_cjac_2385,
Felis catus	ENSFCAG00000026943	3 retrocopies	retro_fcat_1385, retro_fcat_804, retro_fcat_815,
Homo sapiens	ENSG00000165637	1 retrocopy	retro_hsap_2114,
Gorilla gorilla	ENSGGOG00000005861	5 retrocopies	retro_ggor_1677, retro_ggor_1949, retro_ggor_2934, retro_ggor_3036, retro_ggor_425,
Macropus eugenii	ENSMEUG00000012995	1 retrocopy	retro_meug_30,
Myotis lucifugus	ENSMLUG00000007500	2 retrocopies	retro_mluc_1710, retro_mluc_2252,
Mustela putorius furo	ENSMPUG00000003268	1 retrocopy	retro_mputfur_354,
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 ,
Otolemur garnettii	ENSOGAG00000030039	1 retrocopy	retro_ogar_2116,
Rattus norvegicus	ENSRNOG00000013505	1 retrocopy	retro_rnor_2652,
Sarcophilus harrisii	ENSSHAG00000012048	1 retrocopy	retro_shar_325,
Tupaia belangeri	ENSTBEG00000001946	4 retrocopies	retro_tbel_1504, retro_tbel_1541, retro_tbel_1885, retro_tbel_4597,
Tarsius syrichta	ENSTSYG00000004764	1 retrocopy	retro_tsyr_14,
Vicugna pacos	ENSVPAG00000008068	1 retrocopy	retro_vpac_156,