RetrogeneDB ID: retro_sara_688

Retrocopy location

• Organism: Shrew (Sorex araneus)
• Coordinates: scaffold_258952:2269..2719(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RAB2A
• Ensembl ID: ENSSARG00000013511
• Aliases: None
• Description: RAB2A, member RAS oncogene family [Source:HGNC Symbol;Acc:9763]

Sequence

>retro_sara_688
GTTGGTAAACCATGCTTATTGCTACAGTTTACAGACAAGAGGTCTCAGCCAGTGCATGACCTTACTATTGGTGTGGAATT
TGGTGCTCGAATGATAACTATTGATGAAAAACAGATAAAACTCCAAATATGGGATACGGCAGGACAAGAGTCTTTTCGTT
CCATCACAAGGTCATATTACAGAGGTGCCGCAGGGGCTTTACTAGTGTATGATATTACAAGGAGGGATACATTCAACTAC
TTGACAACCTGGTTAGAAGATGCCTGCCAGCATTCCAATTCCAACATGGTCATTATGCTTATTGGAAATAAAAGTGATTT
AGAATCTACAAGAGAAGTGAAAAAAGAGGAAGGTGAAGCTTTTGCACCAGAGCATGGTCTTATTTTCATGGAAACTTCTG
CTAAGACTGCTTCTAACGTAGAAGAGGCATTTATGAAAAAATTCAAGAAG

Alignment

ORF - retro_sara_688 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.0 %
• Parental protein coverage: 71.43 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  VGKSCLLLQFTDKRFQPVHDLTIGVEFGARMITIDGKQIKLQIWDTAGQESFRSITRSYYRGAAGALLVY
          VGK.CLLLQFTDKR.QPVHDLTIGVEFGARMITID.KQIKLQIWDTAGQESFRSITRSYYRGAAGALLVY
Retrocopy VGKPCLLLQFTDKRSQPVHDLTIGVEFGARMITIDEKQIKLQIWDTAGQESFRSITRSYYRGAAGALLVY

Parental  DITRRDTFNHLTTWLEDARQHSNSNMVIMLIGNKSDLESRREVKKEEGEAFAREHGLIFMETSAKTASNV
          DITRRDTFN.LTTWLEDA.QHSNSNMVIMLIGNKSDLES.REVKKEEGEAFA.EHGLIFMETSAKTASNV
Retrocopy DITRRDTFNYLTTWLEDACQHSNSNMVIMLIGNKSDLESTREVKKEEGEAFAPEHGLIFMETSAKTASNV

Parental  EEAFINTAKE
          EEAF....K.
Retrocopy EEAFMKKFKK

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_688 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 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000007153	1 retrocopy	retro_cfam_2057,
Equus caballus	ENSECAG00000012124	1 retrocopy	retro_ecab_970,
Monodelphis domestica	ENSMODG00000008556	2 retrocopies	retro_mdom_1999, retro_mdom_989,
Sorex araneus	ENSSARG00000004969	1 retrocopy	retro_sara_97,
Sorex araneus	ENSSARG00000013511	2 retrocopies	retro_sara_688 , retro_sara_744,
Tarsius syrichta	ENSTSYG00000013060	1 retrocopy	retro_tsyr_1215,
Tursiops truncatus	ENSTTRG00000009615	1 retrocopy	retro_ttru_1377,