RetrogeneDB ID: retro_sara_117

Retrocopy location

• Organism: Shrew (Sorex araneus)
• Coordinates: GeneScaffold_3548:242783..243339(+)
• Located in intron of: ENSSARG00000000149

Retrocopy information

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

Parental gene information

• Parental gene symbol: CCDC28A
• Ensembl ID: ENSSARG00000002666
• Aliases: None
• Description: coiled-coil domain containing 28A [Source:HGNC Symbol;Acc:21098]

Sequence

>retro_sara_117
GAACCAATGGAGGAGCGGAGAGTGAAGCGGAGAAGTCCTAAGTCATTCAGCGCCCACTCGACTCAGGGGATCAGTGCCCC
AAAAAATGCCGTTGCAGTGAGTAAAAGCACCGGATTTTCAAATCCTGCATCACAGTCAACATCGCTGCGGCCAAAGTTAA
GAGAGTTATGAAAGAAACGACCAAGCCTCAGGGAGGGGAAGGGCAAGGCGCCCAGGCCACGCCCATCCAGCGCTCCTTCC
TCACCGGCGTCTCGGGTGTCCAGGAGATGAGAGGGGCCTCCTCAGCCTCTTGAATGACTCCCATTCTGGGAAACTGCAAG
CGTTCGGAAATGAATGTTCCATTGAGCAGATGGAGCATGTTCGGGGAATGCAGGAGAAATTGGCTCGCTGGAATTTGGAG
CTCTACGGGGAGTTAGAAGAACTTCCTGAGGATAAGAGAAAAGCAGCCCGTGACGCTAATCTGGACAGACTTCTGTCTGA
CCTCGAAGAACTGAGCTCGTCCATACAGAAACTGCATTGGGCCCACGCACGAGATGTTCCGAACACTTCTGCCGGC

Alignment

ORF - retro_sara_117 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.36 %
• Parental protein coverage: 66.67 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  KPMEERRVKRRSPKSFSAHSTQGVSAKKNAIPVSKSTGFSNPASQSTSQRPKL-KRVMKEKTKPQGGEGK
          .PMEERRVKRRSPKSFSAHSTQG.SA.KNA..VSKSTGFSNPASQSTS.RPKL.KRVMKE.TKPQGGEG.
Retrocopy EPMEERRVKRRSPKSFSAHSTQGISAPKNAVAVSKSTGFSNPASQSTSLRPKL<KRVMKETTKPQGGEGQ

Parental  GAQATPIQHSFLTDVSDVQEM-ERGLLSLLNDFHSGKLQAFGNECSIEQMEHVRGMQEKLARLNLELYGE
          GAQATPIQ.SFLT.VS.VQEM.ERGLLSLLND.HSGKLQAFGNECSIEQMEHVRGMQEKLAR.NLELYGE
Retrocopy GAQATPIQRSFLTGVSGVQEM<ERGLLSLLNDSHSGKLQAFGNECSIEQMEHVRGMQEKLARWNLELYGE

Parental  LEELPEDKRKAASDANLDRLLSDLEELNSSIQKLHLADAQDVPNTSAG
          LEELPEDKRKAA.DANLDRLLSDLEEL.SSIQKLH.A.A.DVPNTSAG
Retrocopy LEELPEDKRKAARDANLDRLLSDLEELSSSIQKLHWAHARDVPNTSAG

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_117 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 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000007605	1 retrocopy	retro_chof_810,
Mustela putorius furo	ENSMPUG00000014889	1 retrocopy	retro_mputfur_1437,
Sorex araneus	ENSSARG00000002666	1 retrocopy	retro_sara_117 ,