RetrogeneDB ID: retro_sara_568

Retrocopy location

• Organism: Shrew (Sorex araneus)
• Coordinates: scaffold_234856:41952..42831(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SNW1
• Ensembl ID: ENSSARG00000002279
• Aliases: None
• Description: SNW domain containing 1 [Source:HGNC Symbol;Acc:16696]

Sequence

>retro_sara_568
ATGGTGCTCAGCAGCTTGTTACCTGCACCAGGTCAGCAGGCTCAGGACGAGCGTGAGGTAGAGGAAAGGGCAGGATCCCA
CAGGTCCCCACAGACCTCACTGGTGTCCTCCCGGAGAGAACCCCCAGCATACGGGTACAGGAAAGGGTGGACACCTCGCT
TACTGGAGGATTTTGGAGATGGAGGTGCTTTTCCAGAGATCCACGTGGCCCAATATCCACTGGCAAGGGGACAGAAGGAA
AAAATGTCAAATGCACTGGACATTCAGGAGGATGTGCAAGAAAAATCGAGTATGATGCAACTTCTCGACAAGGACAGTCC
AAAGACAAGGTGATTTACAGCAAGTACAGTGACTGATGCCCAAAGAAGTCACCAACGCAGATGAACCAGACCTCCAGACA
CCCGATGAAGAAGCCTTTCAAGAGATAACTGAAACGAGCAGACGAGCCTTAGAGAGGTTTGTGTCTCAGAAGCTGGCTGT
CACCATGCCTCCCTGAGCGGCTGACAAGCGGGCTCCTGCTCAGTATATCTGATACACTCCATCCCGGCAGGGGGCGGCTT
TCAACTCTGGAGACAAACACAGGGTTATTCTGTGCTGGAAATGCAGAAAGATCCCACAGAGCCTCCAAGATTCAAAGTTA
ATAAGAAAATTCCTCGGGGACCACCTTCTCCCCCCGCGCCCCTCATGCATTCTCCCAGCCAGAAGATGACTGTGAAGGAG
CAGCAAGCAGGGAGGATTCCTCCTTGTCTCTCCAGCAGGAAGAACGCGAAGGGGTACACAATCCCCTTAGACAAACGCCT
GGCTGCCGCTGGAGGGGGAGTGCAGACCGTCCGCATCAGTGAGAACTTTGCCAAGCTGGCAGAAGCGCTGTACATCGCC

Alignment

ORF - retro_sara_568 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.43 %
• Parental protein coverage: 57.2 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MALTSFLPAPTQLSQDQLEAEEKARSQRSRQTSLVSSRREPPPYGYRKGWIPRLLEDFGDGGAFPEIHVA
          M.L.S.LPAP.Q..QD..E.EE.A.S.RS.QTSLVSSRREPP.YGYRKGW.PRLLEDFGDGGAFPEIHVA
Retrocopy MVLSSLLPAPGQQAQDEREVEERAGSHRSPQTSLVSSRREPPAYGYRKGWTPRLLEDFGDGGAFPEIHVA

Parental  QYPLDMGRKKKMSNALAIQVDAEGK-IKYDAIARQGQSKDKVIYSKYSD-LVPKEVMNADDPDLQRPDEE
          QYPL..G.K.KMSNAL.IQ.D...K.I.YDA..RQGQSKDKVIYSKYSD.L.PKEV.NAD.PDLQ.PDEE
Retrocopy QYPLARGQKEKMSNALDIQEDVQEK<IEYDATSRQGQSKDKVIYSKYSD<LMPKEVTNADEPDLQTPDEE

Parental  AIKEITEKTRVALEKSVSQKVAAAMPVRAADKLAPAQYIRYTPSQQGVAFNSGAKQRVI-RMVEMQKDPM
          A..EITE..R.ALE..VSQK.A..MP..AADK.APAQYI.YTPS.QG.AFNSG.K.RVI....EMQKDP.
Retrocopy AFQEITETSRRALERFVSQKLAVTMPP*AADKRAPAQYI*YTPSRQGAAFNSGDKHRVI<SVLEMQKDPT

Parental  EPPRFKINKKIPRGPPSPPAPVMHSPSRKMTVKEQQEWKIPPCISNWKNAKGYTIPLDKRLAADGRGLQT
          EPPRFK.NKKIPRGPPSPPAP.MHSPS.KMTVKEQQ...IPPC.S..KNAKGYTIPLDKRLAA.G.G.QT
Retrocopy EPPRFKVNKKIPRGPPSPPAPLMHSPSQKMTVKEQQAGRIPPCLSSRKNAKGYTIPLDKRLAAAGGGVQT

Parental  VHINENFAKLAEALYIA
          V.I.ENFAKLAEALYIA
Retrocopy VRISENFAKLAEALYIA

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_568 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 33 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000003976	2 retrocopies	retro_amel_163, retro_amel_912,
Canis familiaris	ENSCAFG00000030409	1 retrocopy	retro_cfam_195,
Callithrix jacchus	ENSCJAG00000016947	2 retrocopies	retro_cjac_2932, retro_cjac_576,
Dipodomys ordii	ENSDORG00000012380	3 retrocopies	retro_dord_693, retro_dord_781, retro_dord_782,
Felis catus	ENSFCAG00000001637	1 retrocopy	retro_fcat_635,
Homo sapiens	ENSG00000100603	1 retrocopy	retro_hsap_174,
Gorilla gorilla	ENSGGOG00000026016	1 retrocopy	retro_ggor_257,
Loxodonta africana	ENSLAFG00000003482	2 retrocopies	retro_lafr_474, retro_lafr_787,
Myotis lucifugus	ENSMLUG00000005228	2 retrocopies	retro_mluc_387, retro_mluc_805,
Monodelphis domestica	ENSMODG00000005252	1 retrocopy	retro_mdom_1841,
Mustela putorius furo	ENSMPUG00000008724	1 retrocopy	retro_mputfur_551,
Mus musculus	ENSMUSG00000021039	2 retrocopies	retro_mmus_1022, retro_mmus_387,
Nomascus leucogenys	ENSNLEG00000016771	1 retrocopy	retro_nleu_982,
Otolemur garnettii	ENSOGAG00000029825	1 retrocopy	retro_ogar_1404,
Ochotona princeps	ENSOPRG00000007568	1 retrocopy	retro_opri_737,
Pongo abelii	ENSPPYG00000006031	1 retrocopy	retro_pabe_454,
Pan troglodytes	ENSPTRG00000006587	1 retrocopy	retro_ptro_165,
Sorex araneus	ENSSARG00000002279	3 retrocopies	retro_sara_403, retro_sara_568 , retro_sara_727,
Tupaia belangeri	ENSTBEG00000014074	3 retrocopies	retro_tbel_2575, retro_tbel_2927, retro_tbel_3536,
Taeniopygia guttata	ENSTGUG00000012340	2 retrocopies	retro_tgut_15, retro_tgut_30,
Tarsius syrichta	ENSTSYG00000010951	1 retrocopy	retro_tsyr_1871,