RetrogeneDB ID: retro_sara_768

Retrocopy location

• Organism: Shrew (Sorex araneus)
• Coordinates: scaffold_98809:124..955(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSSARG00000010747
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: FBL
• Ensembl ID: ENSSARG00000008709
• Aliases: None
• Description: fibrillarin [Source:HGNC Symbol;Acc:3599]

Sequence

>retro_sara_768
CGTAGGGGCGGCTTCGGGGGCCGCAGGGGCTTCGGAGACCAAGAAGGACGCAGTGGTGGCTGGGGTGGCCGCAGGGGCTA
CGGGGGCCGGGGCCACGGTGGAAAGCGCAGAGGCCAGTCGGGCAAGAACGTGGTGGTGGAGCCCATCGGCATGAGGGGGG
TCTTCATTTGCCGAGGGATGGAAGATGCTCTGGTCACCAGGAACCTGGTCCCGGGACAGTCGGTGTACGGAGAGAAGAGA
GTGTCCATTGCGGAAGGAGACGACAAAGTCGAGTACCGGGCGTGGAACCCCTTCCGCTCCACGGTGGCAGTGGCCATCCT
GGGAGGTGTGGACCAGATCCACATCAAGCCTGGGGTGCAAGGTGCTCTACCTGGGGGCTGCTTCAGGCACTACTGTCTCC
CACGTCTCTGACATTGTAGGGCCGAATGGTCTGGTCTATGCAGCTGAGTTTTCCCACCGCTCTGACCAAGGAGCTCATTA
ACTTTGGCCAAGAAGAGGACGAACATCATCCCGGTGTTGGAGGACGCGCGCCACCCGCTCAAGTACCGCATGCTCATCGG
CATGGTGGACGTCATCTTCGCCGACGTGGCGCAGCCCGACCAGTCGCGCATCGTGGCGCTCAACGCGCACACCTTCCTGC
GCAACGGCGGCCACTTCCTCATGTCCATCAAGGCCAACTGCATCGACTCCACCGCCTCGCCCGAGGCCGTGTTCGCCTCC
GAGGTGAAGAAGCTGCAGCAGGAGAACCTCAAGCCGCAGGAGCAGCTCACGCTGGAGCCCTACGAGCGCGACCACGCCGT
GGTCATCGGGGTCTACCGCCCCTCGGCCAAG

Alignment

ORF - retro_sara_768 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.2 %
• Parental protein coverage: 87.38 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  RGGGFRGGRGRGGG-GRGGGGGFQPGGGNRGRGRGGKRGGQSGKNVVVEP-HRHEG-VFICRGKEDALVT
          R.GGF.G.RG.G...GR.GG.G...G.G..GRG.GGKR.GQSGKNVVVEP.HRHEG.VFICRG.EDALVT
Retrocopy RRGGFGGRRGFGDQEGRSGGWGGRRGYG--GRGHGGKRRGQSGKNVVVEP<HRHEG>VFICRGMEDALVT

Parental  RNLVPGESVYGEKRVSIAXXXXXXXXXXXNPFRSTVAVAILGGVTQIHIKPG--KVLLGAASSH-TFSHV
          RNLVPG.SVYGEKRVSIA...........NPFRSTVAVAILGGV.QIHIKPG....L.G....H.T.SHV
Retrocopy RNLVPGQSVYGEKRVSIAEGDDKVEYRAWNPFRSTVAVAILGGVDQIHIKPGVQGALPGGCFRH>TVSHV

Parental  SDIV--DGLVYAAEFSHRSD-PELIN-LAKKRPNIIPVIEDARHPHKYRMLIAVVDVIFADMAQPDQTRI
          SDIV...GLVYAAEFSHRSD..ELIN.LAKKR.NIIPV.EDARHP.KYRMLI..VDVIFAD.AQPDQ.RI
Retrocopy SDIVGPNGLVYAAEFSHRSD>KELIN>LAKKRTNIIPVLEDARHPLKYRMLIGMVDVIFADVAQPDQSRI

Parental  VALNAHTFLRNGGHFVISIK---IDSTASAEVVFASEVKKMQQENMKSQEQLTLEPYERDHIVIMGVYPP
          VALNAHTFLRNGGHF..SIK...IDSTAS.E.VFASEVKK.QQEN.K.QEQLTLEPYERDH.V..GVY.P
Retrocopy VALNAHTFLRNGGHFLMSIKANCIDSTASPEAVFASEVKKLQQENLKPQEQLTLEPYERDHAVVIGVYRP

Parental  PVK
          ..K
Retrocopy SAK

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_768 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 7 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Equus caballus	ENSECAG00000023221	1 retrocopy	retro_ecab_308,
Loxodonta africana	ENSLAFG00000000171	1 retrocopy	retro_lafr_23,
Macropus eugenii	ENSMEUG00000014684	1 retrocopy	retro_meug_1077,
Rattus norvegicus	ENSRNOG00000019229	4 retrocopies	retro_rnor_1082, retro_rnor_1780, retro_rnor_643, retro_rnor_75,
Sorex araneus	ENSSARG00000008709	1 retrocopy	retro_sara_768 ,
Ictidomys tridecemlineatus	ENSSTOG00000012486	1 retrocopy	retro_itri_1302,
Tursiops truncatus	ENSTTRG00000003967	1 retrocopy	retro_ttru_30,