RetrogeneDB ID: retro_sara_663

Retrocopy location

• Organism: Shrew (Sorex araneus)
• Coordinates: scaffold_254805:4035..4935(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NONO
• Ensembl ID: ENSSARG00000007959
• Aliases: None
• Description: non-POU domain containing, octamer-binding [Source:HGNC Symbol;Acc:7871]

Sequence

>retro_sara_663
AGCAATAAAACCTTTAACTTGGAGAAGCAAAACCATGCTCCAAGGAAGCATCATCAACATCATCACCAGCAGCAGCAGCA
ACAGCCACCACCAATACCTGCAAATGGGCAACAAGCCAGCAGCCAAAATGAAGACTTGACTATTGACCTTAAGAATTTCA
GAAAACCAGGAGAGAAGACCTTTACCCAGCAGAGCCAGCTGTTTGTGGGCAATCTTCCTCCTGATATCACCGAGGAGGAA
ATGAGGAAACTGCTTGAGAAATATGGAAAAGCTGGTGAAGTCTTCATTCATAAGGATAAGGGCTTTGGCTTTATTCACTT
GGAAGCATGAACTCTAGCCGAGATTGCCAAAGTGGAGCTGGACAACATGCCACTTTGTGGCAAGCAGCTTTGTGTGCGCT
TTTCTTGTCATAGTGTATCCCTCACAGTTTCTCAATATGTGTCCAGTGAACTACTGGAGGAGGCCTTTTCTGTGTTTGGC
CAGGTAGAGAGGGCTGTGGTCATTGTGGATGATCGAGGAACGTCCTCTGGAAAAGGCATTGTTGAATTGTCAGGGAAACC
AGCTGCTCTGAAAGCTCTGGACAGATGTAGTGAAGGTTCTTTCCTACTAACCACATTTCCAAGGCCTGTGACTGTGGAGC
CCGTGGACCAGTTAGATGATGAAGAGGGATTACCAGAAAAACTGAAGAACCAGCAAGTTCACAAGGAAAGAGAACAACCA
CCCAGATTTGCCCAGCCTGGCTCATTTGAGTATGAGTACGCCATGCGCTGGAAGGCACTCACTGAGATGGAGAAACAGCA
GCAAGACCAAGTGGACTGTACTATCAAGGAAGCTCGTGAGAAGCTGGAAATGGAGAAGGAGGCTGCTCGTCATGAGCACC
AGGTCATGCTCATGAGGCAG

Alignment

ORF - retro_sara_663 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.64 %
• Parental protein coverage: 65.95 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  SNKTFNLEKQNHAPRKHHQHHHQQHHQQQQQQPPPIPANGQQASSQNEGLTIDLKNFRKPGEKTFTQRSR
          SNKTFNLEKQNHAPRKHHQH....HHQQQQQQPPPIPANGQQASSQNE.LTIDLKNFRKPGEKTFTQ.S.
Retrocopy SNKTFNLEKQNHAPRKHHQH----HHQQQQQQPPPIPANGQQASSQNEDLTIDLKNFRKPGEKTFTQQSQ

Parental  LFVGNLPPDITEEEMRKL-EKYGKAGEVFIHKDKGFGFIRLETRTLAEIAKVELDNMPLRGKQLRVRFAC
          LFVGNLPPDITEEEMRKL.EKYGKAGEVFIHKDKGFGFI.LE..TLAEIAKVELDNMPL.GKQL.VRF.C
Retrocopy LFVGNLPPDITEEEMRKLLEKYGKAGEVFIHKDKGFGFIHLEA*TLAEIAKVELDNMPLCGKQLCVRFSC

Parental  HSASLTVRNLPQYVSNELLEEAFSVFGQVERAVVIVDDRGRPSGKGIVEFSGKPAARKALDRCSEGSFLL
          HS.SLTV....QYVS.ELLEEAFSVFGQVERAVVIVDDRG..SGKGIVE.SGKPAA.KALDRCSEGSFLL
Retrocopy HSVSLTVS---QYVSSELLEEAFSVFGQVERAVVIVDDRGTSSGKGIVELSGKPAALKALDRCSEGSFLL

Parental  TTFPRPVTVEPMDQLDDEEGLPEKLVIKNQQFHKEREQPPRFAQPGSFEYEYAMRWKALIEMEKQQQDQV
          TTFPRPVTVEP.DQLDDEEGLPEKL..KNQQ.HKEREQPPRFAQPGSFEYEYAMRWKAL.EMEKQQQDQV
Retrocopy TTFPRPVTVEPVDQLDDEEGLPEKL--KNQQVHKEREQPPRFAQPGSFEYEYAMRWKALTEMEKQQQDQV

Parental  DRNIKEAREKLEMEMEAARHEHQVMLMRQ
          D..IKEAREKLEME.EAARHEHQVMLMRQ
Retrocopy DCTIKEAREKLEMEKEAARHEHQVMLMRQ

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_663 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 21 parental genes, and 31 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000016057	2 retrocopies	retro_amel_1438, retro_amel_795,
Bos taurus	ENSBTAG00000012152	2 retrocopies	retro_btau_1027, retro_btau_313,
Canis familiaris	ENSCAFG00000017071	1 retrocopy	retro_cfam_98,
Callithrix jacchus	ENSCJAG00000036744	1 retrocopy	retro_cjac_3990,
Equus caballus	ENSECAG00000008502	2 retrocopies	retro_ecab_357, retro_ecab_427,
Felis catus	ENSFCAG00000014807	2 retrocopies	retro_fcat_1219, retro_fcat_147,
Homo sapiens	ENSG00000147140	1 retrocopy	retro_hsap_1699,
Gorilla gorilla	ENSGGOG00000006194	1 retrocopy	retro_ggor_1273,
Microcebus murinus	ENSMICG00000000232	1 retrocopy	retro_mmur_569,
Myotis lucifugus	ENSMLUG00000002489	1 retrocopy	retro_mluc_622,
Mustela putorius furo	ENSMPUG00000004937	1 retrocopy	retro_mputfur_937,
Mus musculus	ENSMUSG00000031311	2 retrocopies	retro_mmus_3652, retro_mmus_632,
Nomascus leucogenys	ENSNLEG00000001278	1 retrocopy	retro_nleu_1344,
Oryctolagus cuniculus	ENSOCUG00000021848	2 retrocopies	retro_ocun_1317, retro_ocun_1804,
Otolemur garnettii	ENSOGAG00000004834	3 retrocopies	retro_ogar_1525, retro_ogar_546, retro_ogar_593,
Pongo abelii	ENSPPYG00000020451	1 retrocopy	retro_pabe_1398,
Pan troglodytes	ENSPTRG00000022010	1 retrocopy	retro_ptro_1150,
Pteropus vampyrus	ENSPVAG00000016503	1 retrocopy	retro_pvam_444,
Rattus norvegicus	ENSRNOG00000003689	2 retrocopies	retro_rnor_1178, retro_rnor_1503,
Sorex araneus	ENSSARG00000007959	2 retrocopies	retro_sara_661, retro_sara_663 ,
Drosophila melanogaster	FBgn0004227	1 retrocopy	retro_dmel_11,