RetrogeneDB ID: retro_sara_516

Retrocopy location

• Organism: Shrew (Sorex araneus)
• Coordinates: scaffold_229486:47263..47659(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: YIPF5
• Ensembl ID: ENSSARG00000013838
• Aliases: None
• Description: Yip1 domain family, member 5 [Source:HGNC Symbol;Acc:24877]

Sequence

>retro_sara_516
ATCACGGTGCCCAGGTAAGTGCAAGTAGCAGATGGCATTACCATGAATGAGACCGATTTGGCAGGACCCAGGGTGTTTCA
CCTTGCCTTTGAAGCCACGTTCTTCCTTGCTGGAAAAATCCAATTTGGCTCTGCATATGGAATCCGTGCAGTTGGATGTC
TCGGAAAAGTTCTGTCATTAAACTTAATGAGTGTGACACGTGTTTCATTTGCTTGTTTGGCAAATATTCTTGGGACACTT
TTCTTCCCACGATCCTCCTTTGCAGCTTTGCAGTGATATTTTCTTTGTAGGGAATGGCAAGAATCCTTTCCACTGCTGGA
ATTATTGGGTGCCATAGTTTTTCCTGCTTCCAAAAGCTTTATTTCTGCATTAGCCTTGGAAGAACATCAATTTCTA

Alignment

ORF - retro_sara_516 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.67 %
• Parental protein coverage: 55.98 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  LTVLHPLKVADGSIMNETDLAGPMVFCLAFGATLLLAGKIQFGYVYGISAIGCLGMFCLLNLMSMTGVSF
          .TV.....VADG..MNETDLAGP.VF.LAF.AT..LAGKIQFG..YGI.A.GCLG....LNLMS.T.VSF
Retrocopy ITVPR*VQVADGITMNETDLAGPRVFHLAFEATFFLAGKIQFGSAYGIRAVGCLGKVLSLNLMSVTRVSF

Parental  GCVASVLGY-CLLPMILLSSFAVIFSLQGMAGIILTAAIIGWCSFS-ASK-FISALAMEGQQLL
          .C.A..LG....LP.ILL.SFAVIFSL.GMA.I..TA.IIG..SFS.ASK.FISALA.E..Q.L
Retrocopy ACLANILGT<TFLPTILLCSFAVIFSL*GMARILSTAGIIGCHSFS>ASKSFISALALEEHQFL

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_516 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 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000014497	1 retrocopy	retro_dnov_16,
Mus musculus	ENSMUSG00000024487	1 retrocopy	retro_mmus_3086,
Sorex araneus	ENSSARG00000013838	1 retrocopy	retro_sara_516 ,
Tarsius syrichta	ENSTSYG00000008071	1 retrocopy	retro_tsyr_16,