RetrogeneDB ID: retro_sara_719

Retrocopy location

• Organism: Shrew (Sorex araneus)
• Coordinates: scaffold_28567:143..935(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: IMPACT
• Ensembl ID: ENSSARG00000002836
• Aliases: None
• Description: impact RWD domain protein [Source:HGNC Symbol;Acc:20387]

Sequence

>retro_sara_719
TGTGTCATTGATGACTGTGCCCAAAACATTTTGTATTATAACTAGAGACTATATAGATGAACCCCAATGGACACTTTACT
TACAGATGATGTTACCTAGCGAGTATCCCTGAACTGCTCCACCTGTTTATCAACTAAATGCTCCATGGCTCAAAGGGCAA
GAACATACGTATTTATCAAATAGCTTTGAGGAAATATACATACAGAATATTGGTGAAAGTATTCTTTACCTGTGGGTGGA
GAAAATAAGAGATGTTCCAATACAGAAATATCAGATAACAGAACCCGGCCCAGACATAAAGAAGAAAACAGAAGAGGAAG
ATGTTGACACTGAAGAAGACGTGATTTTAGCATGTCGACCAGCAAATCCAGTAAAAGCATTAGATTTTGATATCAGTAAA
AATCGCATAGAAATAGAAGAATTACCTCCGATTGATCATGGAGTTCCTATCACAGACCAAAGAAGTACTTTTCAGGCCCA
CCTGGCTCCAGTAGTTTGTCCCCAACAGGTGAAAATGGTTCTCGCCAAATTGTATCAGAATAAGAAAATAGCTAGTGCCG
CCCACAGTATCTATGTGTACGGGATATATTGTGAGGATAAGCAGACTTCCTACAGGACTGTAAGGATGATGGGGAGACAG
TAGCTGGTGGGCGCCTTCTCCATTTCATGGAGATTTTGAACGTGAGGAATATCATGGTGGTGGTCTCATGCTGGTACGGG
GGAATTTTGCTGGGCCCAGATCATTTTAAGCACATCAACAACTGCGCCAGAAACATACTAGTGGAGAAGAAC

Alignment

ORF - retro_sara_719 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.45 %
• Parental protein coverage: 82.97 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  CVIDDCA-KIFCIRISDDIDDPKWTLCLQVMLPNEYPGTAPPVYQLNAPWLKGQERTDLSNSLEEIYIQN
          CVIDDCA.K.FCI...D.ID.P.WTL.LQ.MLP.EYP.TAPPVYQLNAPWLKGQE.T.LSNS.EEIYIQN
Retrocopy CVIDDCA>KTFCIITRDYIDEPQWTLYLQMMLPSEYP*TAPPVYQLNAPWLKGQEHTYLSNSFEEIYIQN

Parental  IGESILYLWVEKIRDVLIQKSQMTEPXXXXXXXXXXXXXXXXEDVILACRPANPVKALDFDISKNRTEIE
          IGESILYLWVEKIRDV.IQK.Q.TEP................EDVILACRPANPVKALDFDISKNR.EIE
Retrocopy IGESILYLWVEKIRDVPIQKYQITEPGPDIKKKTEEEDVDTEEDVILACRPANPVKALDFDISKNRIEIE

Parental  EL-RIDHGVPITDRRSTFQAPLAPVVCPQQVKMVLSKLYENKKIASATHNIYAYRIYCEDKQT-FLQDCE
          EL..IDHGVPITD.RSTFQA.LAPVVCPQQVKMVL.KLY.NKKIASA.H.IY.Y.IYCEDKQT.FLQDC.
Retrocopy ELPPIDHGVPITDQRSTFQAHLAPVVCPQQVKMVLAKLYQNKKIASAAHSIYVYGIYCEDKQT<FLQDCK

Parental  DDGETAAGGRLLHLMEILNVRNVMVVVSRWYGGILLGPDRFKHINNCARNILVEKN
          DDGET.AGGRLLH.MEILNVRN.MVVVS.WYGGILLGPD.FKHINNCARNILVEKN
Retrocopy DDGETVAGGRLLHFMEILNVRNIMVVVSCWYGGILLGPDHFKHINNCARNILVEKN

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_719 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 8 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000013068	1 retrocopy	retro_chof_2523,
Erinaceus europaeus	ENSEEUG00000003962	1 retrocopy	retro_eeur_409,
Homo sapiens	ENSG00000154059	1 retrocopy	retro_hsap_3341,
Macaca mulatta	ENSMMUG00000004664	1 retrocopy	retro_mmul_1041,
Nomascus leucogenys	ENSNLEG00000006582	1 retrocopy	retro_nleu_1166,
Pongo abelii	ENSPPYG00000009071	1 retrocopy	retro_pabe_2753,
Pan troglodytes	ENSPTRG00000009927	1 retrocopy	retro_ptro_2141,
Sorex araneus	ENSSARG00000002836	1 retrocopy	retro_sara_719 ,