RetrogeneDB ID: retro_sara_27

Retrocopy location

• Organism: Shrew (Sorex araneus)
• Coordinates: scaffold_259450:46863..47586(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSSARG00000002533
• 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_27
ATGTCCATGTTGTTCTACACTCTGATCACAGCGCTTCTGATTGGCATCCAGGCAGAACCACTGGCAGAGAGCAATGTCCC
AGCAGGACACACTATTCCCCAAGCCCACTGGACCAAGCTTCAGCATTCCCTTGACACAGCCCTCCGCAGAGTCCACAATG
CCCCAGCAGGGGCGATAGCCGCCCGGGTATCTGGACAGAGCAGCAACATCACCGTGGACCCCAAACTCTTCAAAAAGCGC
AGACTGCATTCTCCTCGTGTGCTGTTCAGCACCCAGCCACCCCCACTGTCTGCCGACTCTCAGGATCTGGACTTAGAGGC
TGGCAGCACCTCCCCTTTCAACAGGACTCACAGGAGCAAGAGGTCGTCCCACCCCATCCACCAGCGGGGCGAGTTCTCTG
TGTGCGATAGTGTCAGCGTGTGGGTCGGAGACAAGACCACAGCCACAGACATTAAGGGCAAGGAGGTGATGGTGTTGGGG
GAGGTGAACATCAACAACAGTGTCTTCAAACAGTACTTTTTTGAGACCAAGTGCCAAGTGCCCAATCCTTCAGACAGCGG
GTGCAGGGGCATCGACTCCAAGCACTGGAATTCCTATTGCACCACCACACACACCTTCGTCAGGGCTCTGACCATGGACG
ACAAGCAGGCGGCCTGGCGGTTCATCCGGATCGACACAGCCTGTGTATGTGTGCTCAGCAGGAAGACAGGGAGAAGAGCC
TGA

Alignment

ORF - retro_sara_27 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 50.29 %
• Parental protein coverage: 65.52 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  VAMDTELLRQQRRYNSPRVLLSDSTPLEPPPLYLMEDYVGNPAGANRTSRRKRYAEHKSHRGEYSVCDSE
          ...D..L....RR..SPRVL.S...P.............G.....NRT.R.KR.......RGE.SVCDS.
Retrocopy ITVDPKLFKK-RRLHSPRVLFSTQPPPLSADSQDLDLEAGSTSPFNRTHRSKRSSHPIHQRGEFSVCDSV

Parental  SLWVTDKSSAIDIRGHQVTVLGEIKTGNSPVKQYFYETRCKEARPVKNGCRGIDDKHWNSQCKTSQTYVR
          S.WV.DK..A.DI.G..V.VLGE....NS..KQYF.ET.C....P...GCRGID.KHWNS.C.T..T.VR
Retrocopy SVWVGDKTTATDIKGKEVMVLGEVNINNSVFKQYFFETKCQVPNPSDSGCRGIDSKHWNSYCTTTHTFVR

Parental  ALTSENNKLVGWRWIRIDTSCVCALSRKVGR
          ALT....K...WR.IRIDT.CVC.LSRK.GR
Retrocopy ALTMD-DKQAAWRFIRIDTACVCVLSRKTGR

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_27 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 ,