RetrogeneDB ID: retro_sara_300

Retrocopy location

• Organism: Shrew (Sorex araneus)
• Coordinates: scaffold_153738:4816..5246(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: VDAC2
• Ensembl ID: ENSSARG00000011194
• Aliases: None
• Description: voltage-dependent anion channel 2 [Source:HGNC Symbol;Acc:12672]

Sequence

>retro_sara_300
TTTTCTACTTCTGGTCATGCCTACAATGATATAGGGAAAGTGCGGGAAACCTAGACACCAAATACAAGGTCTGTAATTAT
GGACTTACCTTTGTCCAAAAATGGAACACAGACAATACACTTGGAACAGAAATCTCTTGAGAGAGTAAGTTGGCTGACGG
GTGGAAGCTGACTCTTGATACCATATTTGTACCAACAAAGGAAAGAAGAGTGGGAAATTGAAGGCCTCCTATAGACAGGA
TTGTTTCAGTCTTGGCAGTAGTGTTGACATAGATTTTTCTGGACCAACCATCTATGGCTGGGCTGTGTTGGCCTTTGAAG
GTAGGTTTGCTGGTTATCAAATGGGTTTTGCTACAGCAAAACCCAAACTGTGTCAGAGTAATTTTTCTCTGGGTTACAAG
GCTGCAGACTTCCAGCTGCATACTCATGTC

Alignment

ORF - retro_sara_300 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 59.59 %
• Parental protein coverage: 51.06 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  FSTSGSSNTDTGKV-TGTLETKYKWCEYGLTFTEKWNTDNTLGTEIAIEDQICQGLKLTFDTTFSP-NTG
          FSTSG....D.GKV..G.L.TKYK.C.YGLTF..KWNTDNTLGTEI..E.....G.KLT.DT.F.P.N.G
Retrocopy FSTSGHAYNDIGKV<AGNLDTKYKVCNYGLTFVQKWNTDNTLGTEIS*ESKLADGWKLTLDTIFVP<NKG

Parental  KKSGKIKSSYKRECINLGCDIDFDFAGPAIHGSAVFGYEGWLAGYQMTFDSAKSKLTRNNFAVGYRTGDF
          KKSGK.K.SY...C..LG...D.DF.GP.I.G.AV...EG..AGYQM.F..AK.KL...NF..GY...DF
Retrocopy KKSGKLKASYRQDCFSLGSSVDIDFSGPTIYGWAVLAFEGRFAGYQMGFATAKPKLCQSNFSLGYKAADF

Parental  QLHTNV
          QLHT.V
Retrocopy QLHTHV

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Sorex araneus was not studied using RNA-Seq expression data.

ChIP-Seq

Sorex araneus was not studied using ChIP-Seq data.

EST

Sorex araneus was not studied using EST data.

TSS

Sorex araneus was not studied using FANTOM5 data.

Lab

retro_sara_300 was not experimentally validated.

Homology

Retrocopy orthology:

Sorex araneus does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Macropus eugenii	ENSMEUG00000012995	1 retrocopy	retro_meug_30,
Rattus norvegicus	ENSRNOG00000013505	1 retrocopy	retro_rnor_2652,
Sorex araneus	ENSSARG00000008221	6 retrocopies	retro_sara_115, retro_sara_327, retro_sara_355, retro_sara_533, retro_sara_668, retro_sara_702,
Sorex araneus	ENSSARG00000011194	2 retrocopies	retro_sara_300 , retro_sara_59,
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,