RetrogeneDB ID: retro_sara_530

Retrocopy location

• Organism: Shrew (Sorex araneus)
• Coordinates: scaffold_231087:26180..26687(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CHMP4A
• Ensembl ID: ENSSARG00000008328
• Aliases: None
• Description: charged multivesicular body protein 4A [Source:HGNC Symbol;Acc:20274]

Sequence

>retro_sara_530
AAGGCCGTGGGCAGTGGCGGGAGAGGTGAGGTCGCGATGATTGGTCTCTGCCGGCTCTTCAGGAGGGGAAAGAAAGAGAA
AGGGCCAACCCCAGAAGAGGCAATTCAGAAACTGAAGGAGACAGAGGAGATTCTGATCAAGAAACAGGAGTTCCTGGAGC
AGAAGATTCAACAGGAACTACAGACAGCCAAGAAGCATGGGACCAAGAATAAGAGAGCTGCCCTGCAGGCTCTTCGGAGG
AAGAAAAGTTTGGAACAGCAGCTGGCACAAACTGATGGGACATTATCTACCCTGGAGTTTCAGCGTGAGGCCATTGAAAA
TGCCACCACCAACACCAAAGTCCTTCGTACCATGGAACTTGCTGCCAAAGGCATGAAGAAGGCCTACTAGGACATGGACA
TTGAGACGGTGGATGAACTAACGGCTGACATCACAGAGCAACAGGAAGTGGCCCAGCAGATCTCAGATGCCATTTCTCGG
CCTGTGGGCTTTGGAGATGTGGATGAG

Alignment

ORF - retro_sara_530 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.18 %
• Parental protein coverage: 86.22 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  RAPGGGGRGEVAMSGFGRLFGRGKKEKGPTPEEAIQKLKETEEILIKKQEFLEQKIQQELQTAKKHGTKN
          .A.G.GGRGEVAM.G..RLF.RGKKEKGPTPEEAIQKLKETEEILIKKQEFLEQKIQQELQTAKKHGTKN
Retrocopy KAVGSGGRGEVAMIGLCRLFRRGKKEKGPTPEEAIQKLKETEEILIKKQEFLEQKIQQELQTAKKHGTKN

Parental  KRAALQALRRKKRLEQQLAQTDGTLSTLEFQREAIENATTNTEVLRTMELAAKGMKKAYQDMDIDKVDEL
          KRAALQALRRKK.LEQQLAQTDGTLSTLEFQREAIENATTNT.VLRTMELAAKGMKKAY.DMDI..VDEL
Retrocopy KRAALQALRRKKSLEQQLAQTDGTLSTLEFQREAIENATTNTKVLRTMELAAKGMKKAY*DMDIETVDEL

Parental  MADITEQQ-VAQQISDAISRPVGFGDDVDE
          .ADITEQQ.VAQQISDAISRPVGFG.DVDE
Retrocopy TADITEQQEVAQQISDAISRPVGFG-DVDE

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_530 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 6 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000254505	1 retrocopy	retro_hsap_2284,
Gorilla gorilla	ENSGGOG00000016091	1 retrocopy	retro_ggor_1697,
Microcebus murinus	ENSMICG00000001732	1 retrocopy	retro_mmur_1101,
Macaca mulatta	ENSMMUG00000012476	2 retrocopies	retro_mmul_1035, retro_mmul_1694,
Pongo abelii	ENSPPYG00000005691	1 retrocopy	retro_pabe_1937,
Sorex araneus	ENSSARG00000008328	1 retrocopy	retro_sara_530 ,