RetrogeneDB ID: retro_sara_142

Retrocopy location

• Organism: Shrew (Sorex araneus)
• Coordinates: GeneScaffold_4315:14110..14439(+)
• Located in intron of: ENSSARG00000009355

Retrocopy information

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

Parental gene information

• Parental gene symbol: MAGOH
• Ensembl ID: ENSSARG00000012081
• Aliases: None
• Description: mago-nashi homolog, proliferation-associated (Drosophila) [Source:HGNC Symbol;Acc:6815]

Sequence

>retro_sara_142
AACAGCAATTATAAAAATGATGTCATGATCAGAAAAGAGGCCTACGTACACAAGAGTGTAATGGAAGAACTGAAGAGAAT
CATTGATGACAGTGAAATTACAAAAGAAGACGACGCCTTGTGGCCTCCCCTGACAGGGATGGCTGGCAGGAGCTTGAAAT
TGTAATTGGAGATGAACACATTTCTTTTACTACATCAAAAATAGGATCTCTTATTGATGTCACTCAGTCTAAGGGTCCTG
AAGGTCTTCGAGTATTTTACTATTTGGTACAGGACCTGAAATGTTTAGTTTTTAGTCTTATTGGATTACATTTCAAGATC
AAGCCTATC

Alignment

ORF - retro_sara_142 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.5 %
• Parental protein coverage: 75.34 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  NSNYKNDVMIRKEAYVHKSVMEELKRIIDDSEITKEDDALWPP-PDRVGRQELEIVIGDEHISFTTSKIG
          NSNYKNDVMIRKEAYVHKSVMEELKRIIDDSEITKEDDALWPP.PDR.G.QELEIVIGDEHISFTTSKIG
Retrocopy NSNYKNDVMIRKEAYVHKSVMEELKRIIDDSEITKEDDALWPP<PDRDGWQELEIVIGDEHISFTTSKIG

Parental  SLIDVNQSKDPEGLRVFYYLVQDLKCLVFSLIGLHFKIKPI
          SLIDV.QSK.PEGLRVFYYLVQDLKCLVFSLIGLHFKIKPI
Retrocopy SLIDVTQSKGPEGLRVFYYLVQDLKCLVFSLIGLHFKIKPI

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_142 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 6 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000009587	1 retrocopy	retro_amel_853,
Erinaceus europaeus	ENSEEUG00000015908	6 retrocopies	retro_eeur_232, retro_eeur_275, retro_eeur_387, retro_eeur_45, retro_eeur_463, retro_eeur_568,
Felis catus	ENSFCAG00000025232	2 retrocopies	retro_fcat_1246, retro_fcat_980,
Rattus norvegicus	ENSRNOG00000012778	1 retrocopy	retro_rnor_1168,
Sorex araneus	ENSSARG00000012081	2 retrocopies	retro_sara_142 , retro_sara_150,
Sus scrofa	ENSSSCG00000003849	3 retrocopies	retro_sscr_1007, retro_sscr_706, retro_sscr_977,