RetrogeneDB ID: retro_sara_92

Retrocopy location

• Organism: Shrew (Sorex araneus)
• Coordinates: GeneScaffold_257:88699..88983(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: FHIT
• Ensembl ID: ENSSARG00000008738
• Aliases: None
• Description: fragile histidine triad [Source:HGNC Symbol;Acc:3701]

Sequence

>retro_sara_92
TTCAGACTTGGCCAGCATTTCATCAAACCCTGTGTGGTGGTTCTTAAAACAGAACTGCCCTTTGCCCCTGTGAACAGGAA
GCCTGTGGTACCAGGACATGTCCTCATGTGTCCCTTCAGCCAGTGGACTGCTTCCAGGATTTGCCTCCTGATGAAGTGGC
CAATTTGTGTCAGGCAGCCCAGAGAGTTGACATGTTGGTGAAGCGTTTCCAGGGGACTCCTCTCACCTTTTCTGTGCAGG
ATGGCTCTGAGGCCAGACACACTGAAGCACGTGTATGTCCACAT

Alignment

ORF - retro_sara_92 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.13 %
• Parental protein coverage: 64.43 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  FRFGQHLIKPSVVFLKTELSFALVNRKPVVPGHVLVCP-LRPVDRFQDLRPDEVADLFQATQRVGMVVEK
          FR.GQH.IKP.VV.LKTEL.FA.VNRKPVVPGHVL.CP.L.PVD.FQDL.PDEVA.L.QA.QRV.M.V.K
Retrocopy FRLGQHFIKPCVVVLKTELPFAPVNRKPVVPGHVLMCP<LQPVDCFQDLPPDEVANLCQAAQRVDMLV-K

Parental  HFQGTSLTFSMQDGPEAGQTVKHVHVH
          .FQGT.LTFS.QDG.EA..T...V..H
Retrocopy RFQGTPLTFSVQDGSEARHTEARVCPH

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_92 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 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000017139	1 retrocopy	retro_amel_680,
Canis familiaris	ENSCAFG00000007194	1 retrocopy	retro_cfam_840,
Myotis lucifugus	ENSMLUG00000013987	1 retrocopy	retro_mluc_156,
Pteropus vampyrus	ENSPVAG00000016009	1 retrocopy	retro_pvam_1319,
Sorex araneus	ENSSARG00000008738	1 retrocopy	retro_sara_92 ,
Tarsius syrichta	ENSTSYG00000010547	1 retrocopy	retro_tsyr_1570,