RetrogeneDB ID: retro_sara_684

Retrocopy location

• Organism: Shrew (Sorex araneus)
• Coordinates: scaffold_258280:1901..2645(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSSARG00000003923
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: CLMP
• Ensembl ID: ENSSARG00000012393
• Aliases: None
• Description: CXADR-like membrane protein [Source:HGNC Symbol;Acc:24039]

Sequence

>retro_sara_684
GTGATCACTTACTCCAGCCGCCATGTCTACAATAACCTGACCGAGGAACAGAAGGGCCGAGTGGCCTTTGCTTCCAATTT
CCTGGCAGGAGATGCCTCCCTGCAGATCGAACCCCTGAAGCCCAGTGATGAGGGCCGCTACACCTGCAAGGTGAAGAACT
CGGGGCGCTATGTGTGGAGCCACGTCATCTTAAAAGTCTTAGTGAGACCATCCAAGCCCAAATGTGAGCTGGAAGGAGAG
CTGACGGAAGGCAGTGACCTCACCCTGCAGTGCGAGTCATCCTCAGGCACCAAGCCCATCGTGTATAACTGGCAGCGGGT
CCGAGAGAAGGAGGGAGAAGATGAACATCTGCCTCCCAACTCTCGGATTGACTACAACCACCCAGGGCGCGTCCTGCTGC
AGAATCTCACCATGTCCTCCTCTGGCCTGTACCAGTGCACAGCGGACAACGAGGCGGGCAAGGAGAGCTGCGTGGTGAGA
GTGACTGTGCAGTATGTGCAAAGCATAGGCATGTTGGCAGGGGCAGTTACCGGCATGGTGGCTGGCGCGATGCTGATTGT
CTTCTTAGTGTGGCTGCTGATCCGAAGGAAAGACAAAGAGAGATACGAGGAAGAGGAGAGACCCAATGAGATCCGAGAGG
ATGCAGAAGCCCCCAAAGCACGCCTGGTGAAACCCAGCTCCTCTTCCTCAGGCTCTCAGAGCTCCCGCTCGGGCTCGTCC
TCCACACGCTCCACTGCAAATAGT

Alignment

ORF - retro_sara_684 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 99.19 %
• Parental protein coverage: 68.32 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  VITYSSRHVYNNLTEEQKGRVAFASNFLAGDASLQIEPLKPSDEGRYTCKVKNSGRYVWSHVILKVLVRP
          VITYSSRHVYNNLTEEQKGRVAFASNFLAGDASLQIEPLKPSDEGRYTCKVKNSGRYVWSHVILKVLVRP
Retrocopy VITYSSRHVYNNLTEEQKGRVAFASNFLAGDASLQIEPLKPSDEGRYTCKVKNSGRYVWSHVILKVLVRP

Parental  SKPKCELEGELTEGSDLTLQCESSSGTKPIVYNWQRVREKEGEDEHLPPKSRIDYNHPGRVLLQNLTMSS
          SKPKCELEGELTEGSDLTLQCESSSGTKPIVYNWQRVREKEGEDEHLPP.SRIDYNHPGRVLLQNLTMSS
Retrocopy SKPKCELEGELTEGSDLTLQCESSSGTKPIVYNWQRVREKEGEDEHLPPNSRIDYNHPGRVLLQNLTMSS

Parental  SGLYQCTAGNEAGKESCVVRVTVQYVQSIGMLAGAVTGMVAGAMLIVFLVWLLIRRKDKERYEEEERPNE
          SGLYQCTA.NEAGKESCVVRVTVQYVQSIGMLAGAVTGMVAGAMLIVFLVWLLIRRKDKERYEEEERPNE
Retrocopy SGLYQCTADNEAGKESCVVRVTVQYVQSIGMLAGAVTGMVAGAMLIVFLVWLLIRRKDKERYEEEERPNE

Parental  IREDAEAPKARLVKPSSSSSGSQSSRSGSSSTRSTANS
          IREDAEAPKARLVKPSSSSSGSQSSRSGSSSTRSTANS
Retrocopy IREDAEAPKARLVKPSSSSSGSQSSRSGSSSTRSTANS

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_684 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 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Sorex araneus	ENSSARG00000012393	1 retrocopy	retro_sara_684 ,