RetrogeneDB ID: retro_sara_394

Retrocopy location

• Organism: Shrew (Sorex araneus)
• Coordinates: scaffold_191091:476..1065(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TRAPPC13
• Ensembl ID: ENSSARG00000000639
• Aliases: None
• Description: trafficking protein particle complex 13 [Source:HGNC Symbol;Acc:25828]

Sequence

>retro_sara_394
TTACTTCTTGATGATCAGATTCAAAATACTTTATCTTCAACTGTCTTTATAGAAAATGTCACCTTACAGCCATCTGAAAT
GTCCAGTGTGGCTGAATTAAATACTACAGTCCAGTCTGGAGAAGAGAACTGAGCATTTGGAACAAGAACATATTTGCAGC
CAGTTGAAGGAAGCCAGTATCTATATCACTTTTAGCTCAAGCAGGAACTTTTAGAAAAAGCTGGTATTGTTAAAGGACAA
GCAGAAATGGAAAATTGGATATAGTGTGGAAAAGAAAACCGAGTGGCATGCCAGTAATAGAGACAATCCAACTTGAAAAA
GAGGCTCGAGATTATAGAAAATTAAGACTCTCCTTGAAGGTAATTCCAGATACTATAAATCTAGAAGAAACTTTTCATAT
CACCTGCAAGTTAACAAATTGCAGCAATAAAAAAATGGAATTGGTTCTAAAGATGAGCGATACAGATTCTATTAGTTGAT
GTGGACATTCAGAAAGGTACCTTGGGAATCTGCCTCCAAATTCATCTCTCTGCTTACAATGACACTACTATTCTTAAAAG
CAGGTCTGCAAAGTATCTCTGGCATAAAG

Alignment

ORF - retro_sara_394 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 53.27 %
• Parental protein coverage: 55.49 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  VFLEAQIQNITTSPMFMEKVSLEPSIMYNVAELNSVNQAGKCITTFGSRTYLQPMDTRQYLYCLKPKKEF
          ..L..QIQN...S..F.E.V.L.PS.M..VAELN...Q.G.....FG.RTYLQP....QYLY....K.E.
Retrocopy LLLDDQIQNTLSSTVFIENVTLQPSEMSSVAELNTTVQSGEEN*AFGTRTYLQPVEGSQYLYHF*LKQEL

Parental  AEKAGIIKGVTVI-GKLDIVWKTNLGERGRLQTSQLQRMAPGYGDVRLSLEAIPDTVNLEEPFHITCKIT
          .EKAGI.KG.....GKLDIVWK..........T.QL...A..Y...RLSL..IPDT.NLEE.FHITCK.T
Retrocopy LEKAGIVKGQAEM<GKLDIVWKRKPSGMPVIETIQLEKEARDYRKLRLSLKVIPDTINLEETFHITCKLT

Parental  NCSERTMDLVLEMCNTNSIHWCGISGRQLGKLHPSSSLC-LALTLLSSVQGLQSVSGLR
          NCS...M.LVL.M..T.SI..CG.S.R.LG.L.P.SSLC.L..TLL....GLQS.SG..
Retrocopy NCSNKKMELVLKMSDTDSIS*CGHSERYLGNLPPNSSLC<LTMTLLFLKAGLQSISGIK

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_394 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 8 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000006026	1 retrocopy	retro_chof_1834,
Dasypus novemcinctus	ENSDNOG00000006386	1 retrocopy	retro_dnov_1288,
Equus caballus	ENSECAG00000011983	1 retrocopy	retro_ecab_1074,
Pteropus vampyrus	ENSPVAG00000008275	1 retrocopy	retro_pvam_980,
Sorex araneus	ENSSARG00000000639	1 retrocopy	retro_sara_394 ,
Ictidomys tridecemlineatus	ENSSTOG00000021318	1 retrocopy	retro_itri_1455,
Tarsius syrichta	ENSTSYG00000004582	1 retrocopy	retro_tsyr_18,
Tursiops truncatus	ENSTTRG00000006537	1 retrocopy	retro_ttru_1068,