RetrogeneDB ID: retro_sara_16

Retrocopy location

• Organism: Shrew (Sorex araneus)
• Coordinates: GeneScaffold_4117:168355..169120(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSSARG00000001950
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: NTF3
• Ensembl ID: ENSSARG00000006682
• Aliases: None
• Description: neurotrophin 3 [Source:HGNC Symbol;Acc:8023]

Sequence

>retro_sara_16
TTCCACCAGGTGAGAAGAGTGATGACCATCCTTTTCCTTACTATGGTTATTTCATACTTCGGTTGCATGAAGGCTGCCCC
CATGAAAGAAGCAAACATCCGAGGACAAGGCAGCTTGGCCTACCCAGGAGTGCGGACCCATGGGACTCTGGAGAGCGTGA
ATGGGCCCCAGGCAGGTTCACGAGGCCTGACATCATTGGCTGACACTTTTGAACATGTGATAGAAGAGCTGCTGGATGAG
GACCAGAAAGTTCGGCCCCACGAAGAAAACAATAAGGACGCGGACTTGTACACTTCCCGAGTGATGCTCAGTAGTCAAGT
GCCTTTGGAGCCTCCTCTTCTCTTTCTGCTGGAGGAATACAAAAATTACCTGGATGCTGCAAACATGTCGATGAGGGTCC
GGCGCCACTCTGACCCTGCCCGCCGTGGGGAGCTGAGCGTGTGCGACAGCATTAGCGAGTGGGTGACGGCGGCAGATAAA
AAGACTGCAGTGGACATGTCGGGCGGGACAGTCACTGTCCTTGAAAAAGTCCCTGTATCAAAAGGCCAACTGAAGCAGTA
CTTCTATGAGACCAAGTGCAATCCCATGGGTTACACGAAGGAGGGCTGCAGGGGCATAGACAAAAGGCATTGGAATTCCC
AGTGCCGAACTACCCAGTCGTACGTGCGGGCCCTTACCATGGATAGCAAAAAGAGAATTGGCTGGCGATTCATAAGGATA
GACACTTCCTGTGTATGTACATTGACCATTAAAAGGGGAAGATAG

Alignment

ORF - retro_sara_16 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 53.85 %
• Parental protein coverage: 59. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  RVLLSDSTPLEPPPLYLMEDYVGNPAGANRTSRRKRYAEHKSHRGEYSVCDSESLWVT--DKSSAIDIRG
          RV.LS...PLEPP.L.L.E.Y......AN...R..R.......RGE.SVCDS.S.WVT..DK..A.D..G
Retrocopy RVMLSSQVPLEPPLLFLLEEYKNYLDAANMSMRVRRHSD-PARRGELSVCDSISEWVTAADKKTAVDMSG

Parental  HQVTVLGEIKTGNSPVKQYFYETRCKEARPVKNGCRGIDDKHWNSQCKTSQTYVRALTSENNKLVGWRWI
          ..VTVL..........KQYFYET.C......K.GCRGID..HWNSQC.T.Q.YVRALT....K..GWR.I
Retrocopy GTVTVLEKVPVSKGQLKQYFYETKCNPMGYTKEGCRGIDKRHWNSQCRTTQSYVRALTMDSKKRIGWRFI

Parental  RIDTSCVCALSRKVGR
          RIDTSCVC.L..K.GR
Retrocopy RIDTSCVCTLTIKRGR

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_16 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 1 parental gene, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Sorex araneus	ENSSARG00000006682	2 retrocopies	retro_sara_16 , retro_sara_27,