RetrogeneDB ID: retro_sara_239

Retrocopy location

• Organism: Shrew (Sorex araneus)
• Coordinates: scaffold_123939:81..458(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: EAF1
• Ensembl ID: ENSSARG00000014007
• Aliases: None
• Description: ELL associated factor 1 [Source:HGNC Symbol;Acc:20907]

Sequence

>retro_sara_239
GTGCCCTTTAGAGCCCCAACGAAGCCCCCAGATATACCCCAAACATCTCCCTTGAAAGATAACCCCTCACCTGAACCTCA
GCTGGATGACATCAAAAGAGAGCTGAGGGCCGAGGTCGACCTCATCGAGCAGATGAGCAGCAGCAGCGGCAGCAGCAACT
CGGACTCCGAGAGCTCCTCGGGCAGCGACGACGACCACAACGACGACAGCTCCAGCAGCGGCGGGGAGGAGCCCCGCCTC
CCCGCTGCCCTGGCACCAGCTGTCCTACAGCAGCCGGAAGTGGCCAGCGGGACCGGCGGCCCCAGGGAAGCAGCCAGCTC
ATGAACAGCCTCCCGAGTGACTTGCAGCTGAGTGAGTCCGGCAGTGACAGCGATGAC

Alignment

ORF - retro_sara_239 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.76 %
• Parental protein coverage: 63.11 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MPFRAPTKPPAGPKTSPLKDNPSPEPQLDDIKRELRAEVDLIEQMSSSSGSSSSDSESSSGSDDDDSSSS
          .PFRAPTKPP..P.TSPLKDNPSPEPQLDDIKRELRAEVDLIEQMSSSSGSS.SDSESSSGSD.DD....
Retrocopy VPFRAPTKPPDIPQTSPLKDNPSPEPQLDDIKRELRAEVDLIEQMSSSSGSSNSDSESSSGSD-DDHNDD

Parental  GGEEHGPASPPPPPPASHQQSYGGRPDVANGTG-RPQGSSQLMNTLRNDLQLSESGSDSDD
          .....G.....P..PA.........P.VA.GTG.RPQGSSQLMN.L..DLQLSESGSDSDD
Retrocopy SSSSGGEE---PRLPAALAPAVLQQPEVASGTG<RPQGSSQLMNSLPSDLQLSESGSDSDD

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_239 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 3 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Monodelphis domestica	ENSMODG00000014543	1 retrocopy	retro_mdom_290,
Sorex araneus	ENSSARG00000014007	1 retrocopy	retro_sara_239 ,
Sarcophilus harrisii	ENSSHAG00000006597	2 retrocopies	retro_shar_485, retro_shar_56,