RetrogeneDB ID: retro_sara_410

Retrocopy location

• Organism: Shrew (Sorex araneus)
• Coordinates: scaffold_195581:12419..12986(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: POP4
• Ensembl ID: ENSSARG00000004748
• Aliases: None
• Description: processing of precursor 4, ribonuclease P/MRP subunit (S. cerevisiae) [Source:HGNC Symbol;Acc:30081]

Sequence

>retro_sara_410
AAACATTCAGAAACCAGGCAGGCAGAAGGCTTTGTGGGGGCCTTCCTGAAGCACAGTATGCCTCACATGAGCCAGCAAGC
CTGTGATGACTATTTACAAAGAAAGGCCGTGGTTCTGGAATACTTCACTGATTGAGGAATAAAAGAGAAGGAAAAGAAAT
CCAGAGGTATCTCTGCCAGGCAGAGAAGGGAAATGCAGCTCTTTGACATTAAACCAGATCAGCATCAGCAGAGGTAGAGT
CTTTTTCTCCCTTTCTATGAACTCCGGAAACAATACATTCAGAATCTGTGTGGTGGGCTCAAACCAGACATGCAGCCCCA
GATGATTCAGACCAAAATGTAAAAGGGAGATCTTGGTGCTATATTTTCAGTTGCAAAATCCAAAGGCCCTTCCTAGGTGG
GTGTGACAGGAATCATTCTATAGGAAACAAAGCATGTTTTCAAAATCATCACCAGAGAAGACCACCTGAAGGTTATCCCT
AAGCTAAACTTGTGTACACTGTGGAAACAGATGAGTTCTCTTTTCTACATTTATGGGAGCAAATTCTAGCTTCGGAAAAG
TGAACGG

Alignment

ORF - retro_sara_410 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.0 %
• Parental protein coverage: 86.64 %
• Number of stop codons detected: 6
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  KHSGTKRAEAFVRAFLKRSMPHMSQQACEDHLQRKAVVLEYFTRRKKKEKRKKSKGLSARQRREMRLFDI
          KHS.T..AE.FV.AFLK.SMPHMSQQAC.D.LQRKAVVLEYFT....KEK.KKS.G.SARQRREM.LFDI
Retrocopy KHSETRQAEGFVGAFLKHSMPHMSQQACDDYLQRKAVVLEYFTD*GIKEKEKKSRGISARQRREMQLFDI

Parental  KPE--QQRYSLFLPLHELWKQYIRDLCNGLKPDTQPQMIQAKLLKGDLHGAIISVAKSKCPSYVGVTGIL
          KP...QQR.SLFLP..EL.KQYI..LC.GLKPD.QPQMIQ.K..KGDL.GAI.SVAKSK.PS.VGVTGI.
Retrocopy KPDQHQQR*SLFLPFYELRKQYIQNLCGGLKPDMQPQMIQTKM*KGDL-GAIFSVAKSKGPS*VGVTGII

Parental  LQETKHVFKIITKEDQLKVIPKQN-CVFTVEIDGF-LSYIYGSKFQLRSSER
          L.ETKHVFKIIT.ED.LKVIPK.N..V.TVE.D.F.L.YIYGSKF.LR.SER
Retrocopy L*ETKHVFKIITREDHLKVIPKLN<LVYTVETDEF>LFYIYGSKF*LRKSER

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_410 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 5 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Mustela putorius furo	ENSMPUG00000008041	1 retrocopy	retro_mputfur_1088,
Oryctolagus cuniculus	ENSOCUG00000015974	1 retrocopy	retro_ocun_1367,
Otolemur garnettii	ENSOGAG00000011168	2 retrocopies	retro_ogar_3293, retro_ogar_541,
Sorex araneus	ENSSARG00000004748	1 retrocopy	retro_sara_410 ,
Tupaia belangeri	ENSTBEG00000002194	6 retrocopies	retro_tbel_1225, retro_tbel_1516, retro_tbel_2043, retro_tbel_3671, retro_tbel_3821, retro_tbel_89,