RetrogeneDB ID: retro_sara_608

Retrocopy location

• Organism: Shrew (Sorex araneus)
• Coordinates: scaffold_237976:65335..65781(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSSARG00000001396
• Aliases: None
• Description: None

Sequence

>retro_sara_608
GGGTACCACCACATGGACTGTGCCCACGTCTACCAGAACGAGAATGAGGTGGGCGCGGCCATCCAGGAGAAGATCCAGCA
GAAGGTGGTGAAGCGGCAGGACCTCTTCATCGTCAGCAAGCTGTGGTGCATGTACCACGAGAAAGGCCTGGTGAGGGGCG
TGTGCCAGAAGACGCTGGGTGACCTCTAGCTGGACTACCTGGACCTCTACCTGATGCAGTGGCACACCGGCTTCAGGCCA
GCCAAGGAGTTTTTCCTGCTGGATGGTGACAACAAAGTGATCCCTGTGAGGCAGACTTCGTGGACACGTGGACGGCCATG
GAAGAGCTGGTGGATGAAGCGCTGGTGAAAGCCATCGGAATCTCCAGCTTCAACCCCCTGCAGATCGAGAAGATCCTAAA
CAAGCCTGGCCTCCTTCCCTCCCCCCTCAATAAAAAGTGTTTTTGT

Alignment

ORF - retro_sara_608 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 60.0 %
• Parental protein coverage: 53.21 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  GYRHIDCAYVYQNENEVGEAIQEKIQEKAVKREDLFIVSKLWPTFFDRPLVKQACQKTLRDLKLDYLDLY
          GY.H.DCA.VYQNENEVG.AIQEKIQ.K.VKR.DLFIVSKLW.......LV...CQKTL.DL.LDYLDLY
Retrocopy GYHHMDCAHVYQNENEVGAAIQEKIQQKVVKRQDLFIVSKLWCMYHEKGLVRGVCQKTLGDL*LDYLDLY

Parental  LIHWPQGLQAGEVFMPKDDKGNIIPSNIT-FLEAWEAMEELVDEGLVKALGVSNFNHLQIEKIFNKPGLK
          L..W..G......F...D.....IP...T.F...W.AMEELVDE.LVKA.G.S.FN.LQIEKI.NKPGL.
Retrocopy LMQWHTGFRPAKEFFLLDGDNKVIPVRQT<FVDTWTAMEELVDEALVKAIGISSFNPLQIEKILNKPGLL

Parental  HKPVTNQVEC
          ..P......C
Retrocopy PSPLNKKCFC

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_608 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 14 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000000166	1 retrocopy	retro_chof_400,
Callithrix jacchus	ENSCJAG00000012250	1 retrocopy	retro_cjac_3038,
Erinaceus europaeus	ENSEEUG00000004422	1 retrocopy	retro_eeur_681,
Echinops telfairi	ENSETEG00000006005	3 retrocopies	retro_etel_1055, retro_etel_1643, retro_etel_748,
Homo sapiens	ENSG00000198074	1 retrocopy	retro_hsap_581,
Macaca mulatta	ENSMMUG00000013098	2 retrocopies	retro_mmul_1357, retro_mmul_2455,
Mus musculus	ENSMUSG00000029762	1 retrocopy	retro_mmus_627,
Mus musculus	ENSMUSG00000052131	1 retrocopy	retro_mmus_2860,
Mus musculus	ENSMUSG00000061758	1 retrocopy	retro_mmus_1490,
Nomascus leucogenys	ENSNLEG00000013088	1 retrocopy	retro_nleu_801,
Pongo abelii	ENSPPYG00000018018	1 retrocopy	retro_pabe_606,
Pan troglodytes	ENSPTRG00000019718	1 retrocopy	retro_ptro_428,
Rattus norvegicus	ENSRNOG00000009734	3 retrocopies	retro_rnor_2380, retro_rnor_2588, retro_rnor_657,
Sorex araneus	ENSSARG00000001396	1 retrocopy	retro_sara_608 ,