RetrogeneDB ID: retro_sara_351

Retrocopy location

• Organism: Shrew (Sorex araneus)
• Coordinates: scaffold_176141:3288..3801(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: OIP5
• Ensembl ID: ENSSARG00000009593
• Aliases: None
• Description: Opa interacting protein 5 [Source:HGNC Symbol;Acc:20300]

Sequence

>retro_sara_351
CCCACAGGGCTGAGGATGGAGGAGTCACCATCGTGGCTGTAGCTGCAGAGGTGTGCAGTGTTCCAGGTGCAGTGCCATGC
AGTGCTGGCAGACTCCATGCTCCCTCACCTGGAACCTGACTCCAACCCTGGAGACTGTGGTCTTCTCCAGAGTCACAAAC
AATGTGGTTTTAGAAGCGCCTTTTATGGTGGGCATTGGAGGCTTGCTCAAAGGCAGCACTGGAAACATTTTATTCTGTTG
TCCATGTGGAATTCTGGTTGGTTTCTATCTACATTCAACCCATGCTTCCACGGCTGCCTTAAAAGGCCACTTCTGCCTTT
CCAGTGACAAAATAGCATGCTATCTCTTAACAACAAATGCCATAGTGCCTGCATCCAAGATGGAGATTCACAACGTCCCT
CTTGCAAAGAAGATGGCAGAACTGAACGAGAACATAATGTTAACAATGTCTGCTTAAATTCACTGATGAAAATTCTGAAG
GACATGACTCCTGCCAAGTCCAAGGCAGAAAAC

Alignment

ORF - retro_sara_351 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.11 %
• Parental protein coverage: 72.84 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  PSGARL---PWWLQPERCAVFQCARCHAVLADSV-HLAWNLTATLGAVVFSRVTNNVVLEEPFLVGIDGL
          P.G.R....P.WL...RCAVFQ...CHAVLADS...L.WNLT.TL..VVFSRVTNNVVLE.PF.VGI.GL
Retrocopy PTGLRMEESPSWL*LQRCAVFQ-VQCHAVLADSM>SLTWNLTPTLETVVFSRVTNNVVLEAPFMVGIGGL

Parental  LKGSTYNLLFCCSCEVPVGFHLYSTHAAMAALRGHFCLSSDKMMCYLLSTKAIVPASKMEIHNVPLEQKV
          LKGST.N.LFCC.C...VGF.L.STHA..AAL.GHFCLSSDK..CYLL.T.AIVPASKMEIHNVPL..K.
Retrocopy LKGSTGNILFCCPCGILVGFYLHSTHASTAALKGHFCLSSDKIACYLLTTNAIVPASKMEIHNVPLAKKM

Parental  LELKEKIMLT-HVHLSSLMKIPKDKAPAKSKTEN
          .EL.E.IMLT..V.L.SLMKI.KD..PAKSK.EN
Retrocopy AELNENIMLT<NVCLNSLMKILKDMTPAKSKAEN

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_351 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 7 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000016777	1 retrocopy	retro_amel_242,
Bos taurus	ENSBTAG00000010766	1 retrocopy	retro_btau_1700,
Felis catus	ENSFCAG00000030520	1 retrocopy	retro_fcat_1387,
Myotis lucifugus	ENSMLUG00000009765	2 retrocopies	retro_mluc_2106, retro_mluc_2341,
Mustela putorius furo	ENSMPUG00000008828	2 retrocopies	retro_mputfur_1518, retro_mputfur_1534,
Otolemur garnettii	ENSOGAG00000033746	1 retrocopy	retro_ogar_1761,
Sorex araneus	ENSSARG00000009593	2 retrocopies	retro_sara_351 , retro_sara_629,