RetrogeneDB ID: retro_sara_196

Retrocopy location

• Organism: Shrew (Sorex araneus)
• Coordinates: GeneScaffold_6714:297594..298022(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MYL1
• Ensembl ID: ENSSARG00000002568
• Aliases: None
• Description: myosin, light chain 1, alkali; skeletal, fast [Source:HGNC Symbol;Acc:7582]

Sequence

>retro_sara_196
GATTTCACCGAAGACCAGACCACAGAGTTCAAAGAGGCCTTCCAGCTGTTTGATCCAACTGGGGATAGCAAGATCCTGTA
CACACAGTTTGGAAATGTGATGTGCAACCTGGGTCAGAACCCCAACAATGCTGAGGTGCTCACGGTCCTGGGGAACCCTA
GGAGTTATGAGATGAAATAAAGGGGCTGAACTTTCAACACTTCCTGCCTATGCTGCAGACAGTGGCCAAGAACAAGGACC
AGAACACCTATCAGGACTATGTCAAAGGCCTCCAGGGATTTGATAAGGAAAGAAATGGCACCATCATGTGTGTTGAAATC
TGACATGTTCTTGTTACTCTTGGTGAGGAGACGGTCAAGTGAGAGGTTGAAAGACTGGTGTGCAGGCAAGAGGATAGAAA
TGATTGTATCAACTATAAAGAGCTCATA

Alignment

ORF - retro_sara_196 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 53.47 %
• Parental protein coverage: 76.06 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  EFSKEQQDDFKEAFLLFDRTGESKITLSQVGDVLRALGTNPTNAEVKKVLGNPSNEEM-NAKKIEFEQFL
          .F...Q...FKEAF.LFD.TG.SKI...Q.G.V...LG.NP.NAEV..VLGNP...EM...K...F..FL
Retrocopy DFTEDQTTEFKEAFQLFDPTGDSKILYTQFGNVMCNLGQNPNNAEVLTVLGNPRSYEM<EIKGLNFQHFL

Parental  PMMQAISNNKDQGGYEDFVEGLRVFDKEGNGTVMGAELRHVLATLGEKMKEEEVEALMAGQEDSNGCINY
          PM.Q....NKDQ..Y.D.V.GL..FDKE.NGT.M..E..HVL.TLGE.....EVE.L...QED.N.CINY
Retrocopy PMLQTVAKNKDQNTYQDYVKGLQGFDKERNGTIMCVEI*HVLVTLGEETVK*EVERLVCRQEDRNDCINY

Parental  EAFV
          ....
Retrocopy KELI

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_196 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 5 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000008609	2 retrocopies	retro_chof_1485, retro_chof_2467,
Macropus eugenii	ENSMEUG00000006905	5 retrocopies	retro_meug_1796, retro_meug_21, retro_meug_537, retro_meug_87, retro_meug_914,
Mus musculus	ENSMUSG00000061816	1 retrocopy	retro_mmus_973,
Sorex araneus	ENSSARG00000002568	1 retrocopy	retro_sara_196 ,
Tarsius syrichta	ENSTSYG00000007599	3 retrocopies	retro_tsyr_1284, retro_tsyr_1539, retro_tsyr_2003,