RetrogeneDB ID: retro_sara_121

Retrocopy location

• Organism: Shrew (Sorex araneus)
• Coordinates: GeneScaffold_3737:76431..76901(-)
• 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_121
GCGGCCGAGGAGCCGCAGCTGCTGCACCAGGCCGGCATCTGTAAGTGGTTCAACGTGCGCATGGGGTTCGGCTTCCTGTC
CATGACCGCCCGCGCCGGGGTCGCGCTCTACCCCCCGGTGGACGTCTTTGTGCATCAGAGTAAACTGCACATGGAGGGTT
TCCGAAGCCTAAAGGAGGGGAGGCAGTGGAATTCACCTTTAAGAAGTCTGCCAAGGGCCTGGAATCTATTCGAGTTACTG
GTCCTGGTGGGGTGTTCTGTATTGGAAGTGAGAGGCGGCCCAAAGGGAAGAACATGCAGAAGCGGAGATCTAAGGGAGAC
AGGTGCTACAACTGCGGCGGTCTAGACCATCATGCCAAAGAGTGTAAGCTGCCACCCCAGCCCAAGAAGTGCCACTTCTG
CCAGAGCATCAACCATATGGTGGCCTCCTGTCCACTGAAGGCCCAGCAAGCCCCCAGCTCCCAGGGGAAG

Alignment

ORF - retro_sara_121 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.25 %
• Parental protein coverage: 63.6 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  AEEESQILRGTGHCKWFNVRMGFGFISMINREGRPLDIPVDVFVHQSKLFMEGFRSLKEG-EPVEFTFKK
          A.EE.Q.L...G.CKWFNVRMGFGF.SM..R.G..L..PVDVFVHQSKL.MEGFRSLKEG.E.VEFTFKK
Retrocopy AAEEPQLLHQAGICKWFNVRMGFGFLSMTARAGVALYPPVDVFVHQSKLHMEGFRSLKEG<EAVEFTFKK

Parental  SSKGLESIRVTGPGGSPCVGSERRPKGKTLQKRKPKGDRCYNCGGLDHHAKECSLPPQPKKCHYCQSISH
          S.KGLESIRVTGPGG..C.GSERRPKGK..QKR..KGDRCYNCGGLDHHAKEC.LPPQPKKCH.CQSI.H
Retrocopy SAKGLESIRVTGPGGVFCIGSERRPKGKNMQKRRSKGDRCYNCGGLDHHAKECKLPPQPKKCHFCQSINH

Parental  MVANCPHKTGAQPPATSQGR
          MVA.CP.K..AQ....SQG.
Retrocopy MVASCPLK--AQQAPSSQGK

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_121 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,