RetrogeneDB ID: retro_sara_676

Retrocopy location

• Organism: Shrew (Sorex araneus)
• Coordinates: scaffold_256985:242811..243243(+)
• 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_676
ACCATGACTGAAACCCACATTGATGTCAAGACGATTGATAGTTATTTGATGGTCGAATCTATTGCTTTCATGAAGAAATG
CAACCACCCGATTCTGAAGACCTCTTATGCTCAGCAACAGCAAGTCACCAGATCCTGAAGATGATGGAAATCATGACCCC
AACGATGCAAAAAAAATGACGTGAAAAAGGCGGTTGATAAATTGATTTCAGACAGTTTTAGGAAAAGATATAGAAAAAGC
TCACCAATTGATTTACCTGGTTCATATCTTTTTCAGAAAAATTTAAAAGCTGAAGCTCAAGTTTGAATTGGGAAATCTTG
TGTAGTCTCATGGTAAGAGTAGTTGTGGTTTTGGAAAAACAGTTGAGTATGAGACAGATACTAAAGTTGAAGAGCCGATA
GATATGAGCAGCCACCAATCAGTGAATCTATT

Alignment

ORF - retro_sara_676 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 54.61 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 2
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  TMIEAHVDVKTTDGYLLRLFCVGFTKKRNNQIRKTSYAQHQQV-RQIRKKMMEIMT-REVQTNDLKEVVN
          TM.E.H.DVKT.D.YL.......F.KK.N..I.KTSYAQ.QQV..QI.K.MMEIMT.......D.K..V.
Retrocopy TMTETHIDVKTIDSYLM-VESIAFMKKCNHPILKTSYAQQQQV<HQILK-MMEIMT>QRCXXXDVKKAVD

Parental  KLIPDS-IGKDIEKACQSIYPLHDVFVRKVKMLKKPKFELGKLMELHGEGSSS-GKATGDETGAKVE-RA
          KLI.DS..GKDIEKA.Q.IY..H..F.RK...LK..KFELG.L...HG..S...GK....ET..KVE.RA
Retrocopy KLISDS>LGKDIEKAHQLIYLVH-IFFRKI*KLKL-KFELGNLV*SHGKSSCGFGKTVEYETDTKVE<RA

Parental  DGYE-PPVQESV
          D.YE.PP..ES.
Retrocopy DRYEQPPISESI

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_676 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,