RetrogeneDB ID: retro_sara_445

Retrocopy location

• Organism: Shrew (Sorex araneus)
• Coordinates: scaffold_209984:0..480(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: UBXN1
• Ensembl ID: ENSSARG00000008689
• Aliases: None
• Description: UBX domain protein 1 [Source:HGNC Symbol;Acc:18402]

Sequence

>retro_sara_445
CCCCTCAGACACGTCCTGGGTCAGAAACCCACTTCCTTGAAGCAAAGTCATTCTGAAGGACCTGGGTTGGCTGCAGGCGA
ATGCAACCCGGACTGAGTGAACAGGAGAAACAGGAGCAGACTAAGAGAATGCTGGAGATGGAGGCGCAGAATCAGTGGGA
GCTAGAGGAGCGAGAGGAGCAGGAAGTGTTGGAACGGGAATGGCAGCACCAGAGACAAGGAGCTGTTGGCCACTTTCCAG
AGGCTCCAGGAGGACGAGATGCAGCAGGTTGAGGAGGAGCAGAGGTGGGAGAAGGCCTAAGAGTTGGAGGCCAGACAAAG
CGTCCATGAAAAGACTGAAAGGAACAAAGCAGAGAGAGCCAAGCCCGTTGGTAGTGTGGATACTCGGCCTTCCTCACCAA
CAGCAGAGCCGGGTCATGTTCACTGACCTCCCAGCCAGGAGCCTCCCACCAAGCGTGGGTATGACCAGTGCCGCATCCAG

Alignment

ORF - retro_sara_445 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.87 %
• Parental protein coverage: 65.73 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  PLGHVLGREPTSSEQSGPEGPGSAAGEG-KPGLSEEEKQEQTKRMLELVAQKQREREEREEREALERERQ
          PL.HVLG..PTS..QS..EGPG.AAGE...PGLSE.EKQEQTKRMLE..AQ.Q.E.EEREE.E.LE..R.
Retrocopy PLRHVLGQKPTSLKQSHSEGPGLAAGEC<QPGLSEQEKQEQTKRMLEMEAQNQWELEEREEQEVLE--RE

Parental  RRRQGQ-ELSAARQRLQEDEMRRAAEERRREKAEELAARQRVREKIERDKAERAKKYGGSVGSRPSAPAA
          ...Q.Q.EL.A..QRLQEDEM....EE.R.EKA.EL.ARQ.V.EK.ER.KAERAK...GSV..RPS.P.A
Retrocopy WQHQRQ>ELLATFQRLQEDEMQQVEEEQRWEKA*ELEARQSVHEKTERNKAERAKPV-GSVDTRPSSPTA

Parental  EPPGPVPSSPSQEPPTKR-YDQCRIQ
          E.PG.V...PSQEPPTKR.YDQCRIQ
Retrocopy E-PGHVH*PPSQEPPTKRGYDQCRIQ

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_445 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 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Rattus norvegicus	ENSRNOG00000019666	1 retrocopy	retro_rnor_1601,
Sorex araneus	ENSSARG00000008689	1 retrocopy	retro_sara_445 ,
Tupaia belangeri	ENSTBEG00000007971	1 retrocopy	retro_tbel_1413,