RetrogeneDB ID: retro_sara_166

Retrocopy location

• Organism: Shrew (Sorex araneus)
• Coordinates: GeneScaffold_5452:22653..23354(-)
• Located in intron of: ENSSARG00000004993

Retrocopy information

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

Parental gene information

• Parental gene symbol: CAPZA1
• Ensembl ID: ENSSARG00000001278
• Aliases: None
• Description: capping protein (actin filament) muscle Z-line, alpha 1 [Source:HGNC Symbol;Acc:1488]

Sequence

>retro_sara_166
GCATTTGCCCAATATAGCATGGATCAATTCACGCCTGTAAAGATAGAAGGATATGAAGATCAGGTTTTAATTACAGAACA
TGGTGACCTGGGCAATAGCAGATTTTTAGATCCAAGAAACAAGATTTCCTTTAAGTTTGACCACTTACTGAAAGAAGCCA
GTGACCCCCAGCCCGAGGACATAGATGGTAGTCTGAAGACGTGGAGAGAATCCTGTGACAGTGCTTTAAGGACCTATGTG
AAAGATCACTATTCCAACGGCTTCTGTACTGTTTATGCTAAAACTATAGATGGGCAACAGACCATTATTGCATGCACTGA
AAGCCACCAGTTTCAGCCTAAAAATTTCTGGAATGGTCTTTGGAGATCAGAGTGGAAGTTCACCATCACCCCACTTACAG
CTCAAGTGGTGGGAGTACTTTAAATACAGGTTCACTATTATGAAGATGGGAATGTTCAGTTAGTTAGTCATAAAGATGTA
CAAGATTCAGTTACTGTTTCGAATGAAGTCCAAACTGCCAAGGAATTTATTAAAATCATAGAGCATGCAGAAAATGAGTA
TCAGACAGCAATTAGTGAGAACTACTAAACAATGTCAGATACCACGTTCAGGGCTTTGCGCAGGCAGCTTCCGTCAACCG
CACCAAGATCAAGTGGAATAAGATCCTCAGCTACAAGATCAGGAAGGAAATGCAGAATGCT

Alignment

ORF - retro_sara_166 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.62 %
• Parental protein coverage: 81.82 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  AFAQYNMDQFTPVKIEGYEDQVLITEHGDLGNSRFLDPRNKISFKFDHLRKEASDPQPEDVDGSLKLWRE
          AFAQY.MDQFTPVKIEGYEDQVLITEHGDLGNSRFLDPRNKISFKFDHL.KEASDPQPED.DGSLK.WRE
Retrocopy AFAQYSMDQFTPVKIEGYEDQVLITEHGDLGNSRFLDPRNKISFKFDHLLKEASDPQPEDIDGSLKTWRE

Parental  SCDSALRTYVKDHYSNGFCTVYAKTIDGQQTIIACIESHQFQPKNFWNGRWRSEWKFTIAPPTAQVVGVL
          SCDSALRTYVKDHYSNGFCTVYAKTIDGQQTIIAC.ESHQFQPKNFWNG.WRSEWKFTI.P.TAQVVGVL
Retrocopy SCDSALRTYVKDHYSNGFCTVYAKTIDGQQTIIACTESHQFQPKNFWNGLWRSEWKFTITPLTAQVVGVL

Parental  KIQVHYYEDGNVQLVSHKDVQDSVTVSNEVQTAKEFIKIIEHAENEYQTAISENYQTMSDTTFKALRRQL
          .IQVHYYEDGNVQLVSHKDVQDSVTVSNEVQTAKEFIKIIEHAENEYQTAISENY.TMSDTTF.ALRRQL
Retrocopy *IQVHYYEDGNVQLVSHKDVQDSVTVSNEVQTAKEFIKIIEHAENEYQTAISENY*TMSDTTFRALRRQL

Parental  P-VTRTKIDWNKILSYKIGKEMQNA
          P.V.RTKI.WNKILSYKI.KEMQNA
Retrocopy P<VNRTKIKWNKILSYKIRKEMQNA

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_166 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 11 parental genes, and 20 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000003570	1 retrocopy	retro_amel_219,
Latimeria chalumnae	ENSLACG00000017963	1 retrocopy	retro_lcha_20,
Myotis lucifugus	ENSMLUG00000009796	1 retrocopy	retro_mluc_2483,
Mustela putorius furo	ENSMPUG00000004977	1 retrocopy	retro_mputfur_616,
Mus musculus	ENSMUSG00000070372	4 retrocopies	retro_mmus_179, retro_mmus_1828, retro_mmus_3370, retro_mmus_349,
Oryctolagus cuniculus	ENSOCUG00000000270	6 retrocopies	retro_ocun_1315, retro_ocun_1417, retro_ocun_1787, retro_ocun_301, retro_ocun_527, retro_ocun_555,
Rattus norvegicus	ENSRNOG00000013538	1 retrocopy	retro_rnor_77,
Sorex araneus	ENSSARG00000001278	1 retrocopy	retro_sara_166 ,
Ictidomys tridecemlineatus	ENSSTOG00000015956	1 retrocopy	retro_itri_1044,
Tarsius syrichta	ENSTSYG00000006259	2 retrocopies	retro_tsyr_179, retro_tsyr_471,
Vicugna pacos	ENSVPAG00000005361	1 retrocopy	retro_vpac_579,