RetrogeneDB ID: retro_sara_178

Retrocopy location

• Organism: Shrew (Sorex araneus)
• Coordinates: GeneScaffold_5966:30705..31106(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RPS3A
• Ensembl ID: ENSSARG00000000717
• Aliases: None
• Description: ribosomal protein S3A [Source:HGNC Symbol;Acc:10421]

Sequence

>retro_sara_178
GAGGCTCATATTGATGTCAAGACTAATGATGGTTATTTGTTTTGTCTATTCGTGTTGGTTGCACTAAGAAGCACAACAGC
AAGATCTGGAAGGCCTCATGCTCAACTCCAACAAGTCCACCAGATTTGGAAGCAGATAACAGAAATCAAGACTCAAGAGC
TGCAGACAAATGACTTCAAAGAAGCAGTCAATAAAGACATGGAAAAGCCCACCAATCTGTTTATTCACTCCATGATGTCT
TTGTTAGAAAAGTAGAAATGCTGAAGAAGCCTAAGTTCGAATTGAGAAAACTCCCAGAGCTTCATGGTGAATGTAGCAGG
TATGGAAAAGCTACAGGGGATGAGACAGATGCTAAAGTTGAAAGTGCCATTGAATATGAACCACCAGTGAAGGAATCTGT
T

Alignment

ORF - retro_sara_178 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 53.47 %
• Parental protein coverage: 97.95 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  EAHVDVKTTDGYLLRLFCVGFTKKRNNQIRKTSYAQHQQVRQIRKKMMEIMTREVQTNDLKEVVNKLIPD
          EAH.DVKT.DGY...LFC..F...........S...H.Q..Q.......I...E..T....E........
Retrocopy EAHIDVKTNDGY---LFCL-FVLVALRSTTARSGRPHAQLQQVHQIWKQIT--EIKT---QELQTNDFKE

Parental  SIGKDIEK-ACQSIYPLHDVFVRKVKMLKKPKFELGKLMELHGEGSSSGKATGDETGAKVERADGYEPPV
          ...KD.EK.A.QS.Y.LHDVFVRKV.MLKKPKFEL.KL.ELHGE.S..GKATGDET.AKVE.A..YEPPV
Retrocopy AVNKDMEK<AHQSVYSLHDVFVRKVEMLKKPKFELRKLPELHGECSRYGKATGDETDAKVESAIEYEPPV

Parental  QESV
          .ESV
Retrocopy KESV

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_178 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 27 retrocopies.

Species	Parental gene accession	Retrocopies number
Macaca mulatta	ENSMMUG00000021821	1 retrocopy	retro_mmul_2297,
Monodelphis domestica	ENSMODG00000000969	6 retrocopies	retro_mdom_1040, retro_mdom_1229, retro_mdom_1396, retro_mdom_1480, retro_mdom_627, retro_mdom_694,
Mus musculus	ENSMUSG00000028081	2 retrocopies	retro_mmus_218, retro_mmus_254,
Rattus norvegicus	ENSRNOG00000011893	1 retrocopy	retro_rnor_198,
Sorex araneus	ENSSARG00000000717	15 retrocopies	retro_sara_103, retro_sara_178 , retro_sara_238, retro_sara_257, retro_sara_390, retro_sara_401, retro_sara_449, retro_sara_451, retro_sara_482, retro_sara_63, retro_sara_666, retro_sara_676, retro_sara_723, retro_sara_762, retro_sara_91,
Sarcophilus harrisii	ENSSHAG00000015088	2 retrocopies	retro_shar_777, retro_shar_95,