RetrogeneDB ID: retro_sara_56

Retrocopy location

• Organism: Shrew (Sorex araneus)
• Coordinates: GeneScaffold_165:3360..3671(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ERH
• Ensembl ID: ENSSARG00000005558
• Aliases: None
• Description: enhancer of rudimentary homolog (Drosophila) [Source:HGNC Symbol;Acc:3447]

Sequence

>retro_sara_56
ATGTCTGACACCATTTTGCTGGTCCAGCCTACCAAGAGGCCAGAAGGCAGAACTTATGCTGACTATGAATCTGTGAATGA
ATGCATGGAAGGTGTTTGTAAAATGTATGAAGAACATCTGAAGAGAATGAACCCCACAGCCCCTCTATCACATACGATAT
CAGTCAATTGTTTGATTTTATTGGTGATCTGGCAGACCTCAGCTGCCTTGTTTACTGAGCTGATACTCAGACAAACCAGC
CTTACAACAAAGACTGGATTAAAGAGAAGATGTACGTGCTTCTTCGTCGGCAGGCCCAGCAGGCCGGGAAA

Alignment

ORF - retro_sara_56 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.33 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MSHTILLVQPTKRPEGRTYADYESVNECMEGVCKMYEEHLKRMNP-NSPSITYDISQLFDFIDDLADLSC
          MS.TILLVQPTKRPEGRTYADYESVNECMEGVCKMYEEHLKRMNP..SPSITYDISQLFDFI.DLADLSC
Retrocopy MSDTILLVQPTKRPEGRTYADYESVNECMEGVCKMYEEHLKRMNP<HSPSITYDISQLFDFIGDLADLSC

Parental  LVYRADTQTYQPYNKDWIKEKIYVLLRRQAQQAGK
          LVY.ADTQT.QPYNKDWIKEK.YVLLRRQAQQAGK
Retrocopy LVY*ADTQTNQPYNKDWIKEKMYVLLRRQAQQAGK

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_56 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.

---

Parental genes homology:

Parental genes homology involve 9 parental genes, and 23 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000014940	2 retrocopies	retro_cjac_209, retro_cjac_846,
Equus caballus	ENSECAG00000019178	1 retrocopy	retro_ecab_45,
Gorilla gorilla	ENSGGOG00000004751	2 retrocopies	retro_ggor_2424, retro_ggor_2553,
Microcebus murinus	ENSMICG00000009623	1 retrocopy	retro_mmur_74,
Myotis lucifugus	ENSMLUG00000011879	1 retrocopy	retro_mluc_142,
Nomascus leucogenys	ENSNLEG00000001514	2 retrocopies	retro_nleu_1128, retro_nleu_1604,
Oryctolagus cuniculus	ENSOCUG00000004636	1 retrocopy	retro_ocun_42,
Pan troglodytes	ENSPTRG00000006482	2 retrocopies	retro_ptro_2433, retro_ptro_2577,
Sorex araneus	ENSSARG00000005558	11 retrocopies	retro_sara_114, retro_sara_127, retro_sara_151, retro_sara_221, retro_sara_251, retro_sara_295, retro_sara_298, retro_sara_490, retro_sara_56 , retro_sara_58, retro_sara_66,