RetrogeneDB ID: retro_sara_271

Retrocopy location

• Organism: Shrew (Sorex araneus)
• Coordinates: scaffold_140194:4974..5417(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: STMN1
• Ensembl ID: ENSSARG00000011057
• Aliases: None
• Description: stathmin 1 [Source:HGNC Symbol;Acc:6510]

Sequence

>retro_sara_271
ATGGCTTCTTCTGATATCCAGGTGAAAGAACTGGAGAAACATGCAACTGGCCAGGCTTTTGAACTGATTCTTAGCCCTTG
ATCAAAAGAATCTGTCCCTGAATTCACCCTTTTCCCCCAAAGAAGATGAATCTTTCTCTGGAGGAAATCCAGAGGAAATT
AGAAGCTACAGAAGAAAGACGAAAGTCCCATGAAGCTGAAGTCTTGAAGCAGTTTGCTGAGAAGCGAGAGCATGAGAAAG
AAGTGCTTCAAAAAGCGATAGAAGAGAACAACTTCAGTAAAATGGCGGAAGAGAAACTGACCCACAAAATGGAAGCCAAC
AAAGAAAACCGAGAGGCACAGATGGCTGCCAAACAGGAGCATTTGCGAGCGAAGGACAAGCATGTTGAAAAAGTGTGGAA
GAACAAAGAATCCAAAGATCCTGCTGATGAGACTGAAGCTGAC

Alignment

ORF - retro_sara_271 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.67 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MASSDIQVKELEKRASGQAFELILSPRSKESVPEFPLSP-PKKKDLSLEEIQKKLEAAEERRKSHEAEVL
          MASSDIQVKELEK.A.GQAFELILSP.SKESVPEF.L.P.PKK..LSLEEIQ.KLEA.EERRKSHEAEVL
Retrocopy MASSDIQVKELEKHATGQAFELILSP*SKESVPEFTLFP<PKKMNLSLEEIQRKLEATEERRKSHEAEVL

Parental  KQLAEKREHEKEVLQKAIEENNNFSKMAEEKLTHKMEANKENREAQMAAKLERLREKDKHVEEVRKNKES
          KQ.AEKREHEKEVLQKAIEE.NNFSKMAEEKLTHKMEANKENREAQMAAK.E.LR.KDKHVE.V.KNKES
Retrocopy KQFAEKREHEKEVLQKAIEE-NNFSKMAEEKLTHKMEANKENREAQMAAKQEHLRAKDKHVEKVWKNKES

Parental  KDPADETEAD
          KDPADETEAD
Retrocopy KDPADETEAD

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_271 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 9 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000013761	1 retrocopy	retro_btau_247,
Callithrix jacchus	ENSCJAG00000009462	2 retrocopies	retro_cjac_3206, retro_cjac_474,
Equus caballus	ENSECAG00000021662	1 retrocopy	retro_ecab_490,
Loxodonta africana	ENSLAFG00000006089	1 retrocopy	retro_lafr_84,
Mustela putorius furo	ENSMPUG00000015774	1 retrocopy	retro_mputfur_1191,
Oryctolagus cuniculus	ENSOCUG00000006493	1 retrocopy	retro_ocun_56,
Rattus norvegicus	ENSRNOG00000016810	4 retrocopies	retro_rnor_1604, retro_rnor_1855, retro_rnor_2048, retro_rnor_765,
Sorex araneus	ENSSARG00000010989	1 retrocopy	retro_sara_756,
Sorex araneus	ENSSARG00000011057	2 retrocopies	retro_sara_271 , retro_sara_764,