RetrogeneDB ID: retro_sara_746

Retrocopy location

• Organism: Shrew (Sorex araneus)
• Coordinates: scaffold_65096:3648..4147(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: LIN28B
• Ensembl ID: ENSSARG00000008374
• Aliases: None
• Description: lin-28 homolog B (C. elegans) [Source:HGNC Symbol;Acc:32207]

Sequence

>retro_sara_746
GGCATCTGTAAGCGCTCCAATGTGCGCATGGGGTTCGGCTTCCTGTCCATGACTGCCCTCGCCGGGGTCGCGCTCGACCC
CCCCAGTGGACGTCTTTGTGTATCAGAGTAAACTGCACATGGAGGGTTTCCGAAGACTGAAGGAGGGGGAGGCAGTGGAA
TTCACCTCTAAGAAGTCCGCCAAGGCCCCTGGAATCTATTCGAGTTACTGGTCCTGGTGGGGTGTTCTGTATTGGAAGTG
AGAGGCGGCCCAAAGGGAAGAACATGCAGAAGCGGAGATCTAAGGGAGACAGGTGCCCCCATGATGGTCTAGACCATCAT
GCCAAAGAGTGCAAGCTGCCACCCCAGCCCAAGCATCAACCATATGGTAGCCTCCTGTCCACTGAAGGCCCAGCAAGCCC
CCAGCTCCCAGGGGAAGCCTGCCTACTTCTGGGAGGAAGAAGAGGAGATCCATTCCCCTGCCCTGCTGCCTGAGGCCCAA
AATTGAGCCAGTGGGTGGG

Alignment

ORF - retro_sara_746 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 58.24 %
• Parental protein coverage: 66.8 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  GHCKWFNVRMGFGFISMINREGRPLDIP-VDVFVHQSKLFMEGFRSLKEGEPVEFTFKKSSKG-LESIRV
          G.CK..NVRMGFGF.SM....G..LD.P.VDVFV.QSKL.MEGFR.LKEGE.VEFT.KKS.K..LESIRV
Retrocopy GICKRSNVRMGFGFLSMTALAGVALDPP>VDVFVYQSKLHMEGFRRLKEGEAVEFTSKKSAKA>LESIRV

Parental  TGPGGSPCVGSERRPKGKTLQKRKPKGDRCYNCGGLDHHAKECSLPPQPKKCHYCQSIS-HMVANCPHKT
          TGPGG..C.GSERRPKGK..QKR..KGDRC....GLDHHAKEC.LPPQPK...Y....S.H.....P...
Retrocopy TGPGGVFCIGSERRPKGKNMQKRRSKGDRCPH-DGLDHHAKECKLPPQPKHQPYGSLLS<H*RPSKPPAP

Parental  GAQPPATSQGRQEAESQPCTSTHPREVVGG
          ....P............PC......E.VGG
Retrocopy RGSLPTSGRKKRRSIPLPCCLRPKIEPVGG

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_746 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 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Echinops telfairi	ENSETEG00000015340	1 retrocopy	retro_etel_1927,
Microcebus murinus	ENSMICG00000002297	4 retrocopies	retro_mmur_1377, retro_mmur_1390, retro_mmur_660, retro_mmur_800,
Oryctolagus cuniculus	ENSOCUG00000017850	1 retrocopy	retro_ocun_532,
Otolemur garnettii	ENSOGAG00000011042	1 retrocopy	retro_ogar_645,
Sorex araneus	ENSSARG00000008374	2 retrocopies	retro_sara_121, retro_sara_746 ,
Tarsius syrichta	ENSTSYG00000006480	1 retrocopy	retro_tsyr_1815,