RetrogeneDB ID: retro_sara_450

Retrocopy location

• Organism: Shrew (Sorex araneus)
• Coordinates: scaffold_213173:12025..12651(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SYPL1
• Ensembl ID: ENSSARG00000013935
• Aliases: None
• Description: synaptophysin-like 1 [Source:HGNC Symbol;Acc:11507]

Sequence

>retro_sara_450
GTTGTTTCTATCTTTGTTTTTGCCAGCTGTGGGGGCTTTAAGGGCAAAATATATTCTACTCACTTGTCCCCCTAAACTTA
ATGAAAATAAAATGATTCTAGCTGCTTTTGGTTATCTATTTAGGTTGAATGGAGCATGATTTCAGACACCTCTGCAAGTA
AATATGTGTGCAGTAGATTGGAGTAAACATGTCCTTATTGGAGATTATACTTCTTTTGCACAATTCTTTGTTAACGCAGT
CTTTGTCTTCCTGTACTGCATCACTGCTCTTCTGCTCTATGTCAGTTATAAAAACTTGCACTAGGATAGTTGAAAGCATC
CTGTGATCGACTTTGTCATTACTCTTGTGGCTACTTTTATTGCCTGGTGAGCCCTACAGCCTGCAATAAAAACTTACAAA
ATATTAAAATAGCTACTGACCACAGTATTGTCGAGGAACTTACCTCTTGTAATAGTAATGGAGTGACCTGTCATTTTAAT
TCTGTGACTTAGTATAGGATGCCTAAATGTATCTGTGATCTGTGACTTTCTGAATATAATATTTTGGGGAGGAAAAGCAT
AAGTTCGTATACAAGGAGACCAATTTACACAGTCCATCAGGTGTGACAGCTTCCAATAGCCAAGGG

Alignment

ORF - retro_sara_450 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 62.91 %
• Parental protein coverage: 96.31 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  VASIFSIATCGGFKG-KTSIVVSCPKENQNHTVTADFGYPFRLNQASFQSSSQQNVCQVDWSKYVLIGDY
          V.SIF..A.CGGFKG.K.......PK.N.N....A.FGY.FRLN.A.FQ...Q.N.C.VDWSK.VLIGDY
Retrocopy VVSIFVFASCGGFKG>KYILLTCPPKLNENKMILAAFGYLFRLNGA*FQTPLQVNMCAVDWSKHVLIGDY

Parental  ASSAQFYVTFAVFVFLYCIAALLLYLGYTNMYRDSRKLPMIDFIITLVATFL-WLVSTSAWAKALTDIKI
          .S.AQF.V..AVFVFLYCI.ALLLY..Y.N...DS.K.P.IDF.ITLVATF...LVS..A..K.L..IKI
Retrocopy TSFAQFFVN-AVFVFLYCITALLLYVSYKNLH*DS*KHPVIDFVITLVATFI<CLVSPTACNKNLQNIKI

Parental  ATGHNIVEELDPCIGQSVKCSFGSVS-SMGSLNVSVICGFLNMILWGGNA-WFVYKETNLHSPSDATASQ
          AT.H.IVEEL..C....V.C.F.SV..S.G.LNVSVIC.FLN.I.WGG.A..FVYKETNLHSPS..TAS.
Retrocopy ATDHSIVEELTSCNSNGVTCHFNSVT>SIGCLNVSVICDFLNIIFWGGKA>KFVYKETNLHSPSGVTASN

Parental  SQG
          SQG
Retrocopy SQG

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_450 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 20 parental genes, and 32 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000016176	2 retrocopies	retro_cjac_1588, retro_cjac_2483,
Cavia porcellus	ENSCPOG00000009221	1 retrocopy	retro_cpor_239,
Equus caballus	ENSECAG00000009695	1 retrocopy	retro_ecab_340,
Homo sapiens	ENSG00000008282	1 retrocopy	retro_hsap_1817,
Gorilla gorilla	ENSGGOG00000006497	1 retrocopy	retro_ggor_1984,
Myotis lucifugus	ENSMLUG00000014980	3 retrocopies	retro_mluc_1884, retro_mluc_2083, retro_mluc_449,
Macaca mulatta	ENSMMUG00000019593	2 retrocopies	retro_mmul_1251, retro_mmul_1464,
Mus musculus	ENSMUSG00000020570	1 retrocopy	retro_mmus_3470,
Nomascus leucogenys	ENSNLEG00000008861	1 retrocopy	retro_nleu_2720,
Oryctolagus cuniculus	ENSOCUG00000015127	3 retrocopies	retro_ocun_1000, retro_ocun_1569, retro_ocun_331,
Otolemur garnettii	ENSOGAG00000008079	2 retrocopies	retro_ogar_1970, retro_ogar_2520,
Ochotona princeps	ENSOPRG00000006755	2 retrocopies	retro_opri_210, retro_opri_448,
Pongo abelii	ENSPPYG00000018292	1 retrocopy	retro_pabe_2370,
Pan troglodytes	ENSPTRG00000019570	2 retrocopies	retro_ptro_1173, retro_ptro_1939,
Rattus norvegicus	ENSRNOG00000009856	2 retrocopies	retro_rnor_2273, retro_rnor_2992,
Sorex araneus	ENSSARG00000013935	1 retrocopy	retro_sara_450 ,
Ictidomys tridecemlineatus	ENSSTOG00000020871	1 retrocopy	retro_itri_1243,
Tupaia belangeri	ENSTBEG00000009095	2 retrocopies	retro_tbel_2025, retro_tbel_2566,
Tarsius syrichta	ENSTSYG00000013296	2 retrocopies	retro_tsyr_1768, retro_tsyr_775,
Tursiops truncatus	ENSTTRG00000002848	1 retrocopy	retro_ttru_661,