RetrogeneDB ID: retro_sara_590

Retrocopy location

• Organism: Shrew (Sorex araneus)
• Coordinates: scaffold_236117:72480..72903(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TRAPPC1
• Ensembl ID: ENSSARG00000010582
• Aliases: None
• Description: trafficking protein particle complex 1 [Source:HGNC Symbol;Acc:19894]

Sequence

>retro_sara_590
AGCGTGTACCTGTTTGATCGGAATGGAGTGTGACTGCATTACAGCGAGTGGCATCGCAAGAAGCAAGTGGGGATCCCCAA
AGAGGAGGAATACAATCTGATGTACGGAATGCTCTTCTCTATCCGCTCCTTTGTCAGCAAGATGTCCCCGCTAGACATAA
AGGACAGCTTCCTTGCTTTCCAAACAAGCCGCTACAAACTCCATTACTATGAGACACCTACTGGGATCAAGGTTGTCCTG
AATACTGACTTGGGCGTGGGACTTATCCGAGATGTACTGCACCATATCTATAGTGCGCTGTATGTGGAGCTGGTGGTGAA
CAATCTGCTCTGTCCATTGGGCCAAACTGTGCAAAGTGAGCTCTTCCGCTCCCGGCTGGATTCCTACATCCGCTCACTAC
CCTTCTTCTCCGCCCGGCCTGGC

Alignment

ORF - retro_sara_590 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.2 %
• Parental protein coverage: 97.24 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  NLYLFDRNGVCLHYSEWHRKKQAGIPKEEEYKLMYGMLFSIRSFVSKMSPLDMKDGFLAFQTSRYKLHYY
          ..YLFDRNGV.LHYSEWHRKKQ.GIPKEEEY.LMYGMLFSIRSFVSKMSPLD.KD.FLAFQTSRYKLHYY
Retrocopy SVYLFDRNGV*LHYSEWHRKKQVGIPKEEEYNLMYGMLFSIRSFVSKMSPLDIKDSFLAFQTSRYKLHYY

Parental  ETPTGIKVVMNTDLGVGPIRDVLHHIYSALYVELVVKNPLCPLGQTVQSELFRSRLDSYIRSLPFFSARP
          ETPTGIKVV.NTDLGVG.IRDVLHHIYSALYVELVV.N.LCPLGQTVQSELFRSRLDSYIRSLPFFSARP
Retrocopy ETPTGIKVVLNTDLGVGLIRDVLHHIYSALYVELVVNNLLCPLGQTVQSELFRSRLDSYIRSLPFFSARP

Parental  G
          G
Retrocopy G

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_590 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 5 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000047214	1 retrocopy	retro_btau_280,
Callithrix jacchus	ENSCJAG00000014756	1 retrocopy	retro_cjac_1057,
Erinaceus europaeus	ENSEEUG00000004320	1 retrocopy	retro_eeur_665,
Sorex araneus	ENSSARG00000010582	1 retrocopy	retro_sara_590 ,
Tursiops truncatus	ENSTTRG00000010306	1 retrocopy	retro_ttru_403,