RetrogeneDB ID: retro_sara_601

Retrocopy location

• Organism: Shrew (Sorex araneus)
• Coordinates: scaffold_237339:52718..53139(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ARPC3
• Ensembl ID: ENSSARG00000000546
• Aliases: None
• Description: actin related protein 2/3 complex, subunit 3, 21kDa [Source:HGNC Symbol;Acc:706]

Sequence

>retro_sara_601
AAAGACACAGATATTGTGAATGAAGCTATCTATTACTTCAAGGCCAATGTCTTCTTCAAAAACTAGGAAATTAAGAATGA
CGCTGACAGAACCTTGATATATATCACTCTCTATATTTCTGAGTGTCTGAAGAAACTCTAGCAGTGCAATTCCAAAAGCA
AAGGTGAGAAGGAAATGTATACCCTGGGAATCACTAATTTCCCCATTCCTGGAGAGCCGGTTTCCACTGAAAGCAATTTG
TGACAAACCAGCTAACAAACAAGAAGACGAAGTGATGTGGGCCTACCTGCAGCAGCTGAGGCAGGAGACGAGCCTGAGAC
TCTGTGAGAAAGTCTTTGACCCTCAGAATTATAAGCCCAGTAAGTGGTGGACTTGCTTCATGAAGAGACAGTTCATGAAC
AAGAGTCTTTCCGGACCTGGT

Alignment

ORF - retro_sara_601 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.11 %
• Parental protein coverage: 79.21 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  KDTDIVDEAIYYFKANVFFKNYEIKNEADRTLIYITLYISECLKKLQKCNPKSQCEKEMYTLGITNFPIP
          KDTDIV.EAIYYFKANVFFKN.EIKN.ADRTLIYITLYISECLKKL..CN.KS..EKEMYTLGITNFPIP
Retrocopy KDTDIVNEAIYYFKANVFFKN*EIKNDADRTLIYITLYISECLKKL*QCNSKSKGEKEMYTLGITNFPIP

Parental  GEP-GF-PLNAIYAKPANKQEDEVMRAYLQQLRQETGLRLCEKVFDPQNDKPSKWWTCFVKRQFMNKSLS
          GEP.GF.PL.AI..KPANKQEDEVM.AYLQQLRQET.LRLCEKVFDPQN.KPSKWWTCF.KRQFMNKSLS
Retrocopy GEP<GF<PLKAICDKPANKQEDEVMWAYLQQLRQETSLRLCEKVFDPQNYKPSKWWTCFMKRQFMNKSLS

Parental  GPG
          GPG
Retrocopy GPG

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_601 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 10 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000008456	1 retrocopy	retro_cfam_11,
Callithrix jacchus	ENSCJAG00000009360	1 retrocopy	retro_cjac_242,
Echinops telfairi	ENSETEG00000006992	2 retrocopies	retro_etel_116, retro_etel_1323,
Felis catus	ENSFCAG00000004132	2 retrocopies	retro_fcat_1048, retro_fcat_73,
Monodelphis domestica	ENSMODG00000011628	1 retrocopy	retro_mdom_71,
Oryctolagus cuniculus	ENSOCUG00000011908	1 retrocopy	retro_ocun_1252,
Oreochromis niloticus	ENSONIG00000003785	1 retrocopy	retro_onil_18,
Sorex araneus	ENSSARG00000000546	2 retrocopies	retro_sara_529, retro_sara_601 ,
Sarcophilus harrisii	ENSSHAG00000014805	3 retrocopies	retro_shar_144, retro_shar_439, retro_shar_576,
Ictidomys tridecemlineatus	ENSSTOG00000011979	1 retrocopy	retro_itri_1350,