RetrogeneDB ID: retro_sara_582

Retrocopy location

• Organism: Shrew (Sorex araneus)
• Coordinates: scaffold_235858:45275..46025(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CNN3
• Ensembl ID: ENSSARG00000012874
• Aliases: None
• Description: calponin 3, acidic [Source:HGNC Symbol;Acc:2157]

Sequence

>retro_sara_582
AAGTAGGACCGGCAGAAGGAGGCAGAGCTCCGCAGCTGGATCCAGAGACTAACCGGCCTGTCCATCGGCGCCGACTTTCA
GAAGGGCCTGAATGATGGGGTGATCTTGTGCACATTGATGAATAAATTACAGCCGGGCTCCGTCCATAAGATCAACCGCT
CCATGAAGAACTGGCATCAGCTGGAGAACCTTTCCAACTTCATCAAAGCCATGGCGAGCTACGGCATGAACCCCGTGGAT
CTGTTTGAGGCCAACGACCTGTTTCAGAGCGGCAACATGACGCAGATGCAGGTGTCTCTCCTTGCCCTAGCGGGGAAGGC
CAAGACCAAGGGCCTGCAGAGTGATGTGGACATTGGCTTCAAGTACTCGGAGAAGCAGGAGCGGAACTTTGATGACGCCA
CCATGAAGGCGGGCCAGTGTGTCATCAGGCTCCAGATGGGCACCAACAAGTGTGCCAACCAGTCGGGGATGACGGCATAT
GGCATGAGAAGGCAACTTTATGACCCAAAGAACCACATCCTGCCCCCCATGGACCACTCAACCATGAGCCTGCAAATGGG
CACCAACAAGTGTGCCAGCCAGGTGGACATGATGGCCCCTAGCACCCGGCGTTACATCTATGACACCAAGCTGGGCACCG
ACAAGTGCGACAACTCCTCCATGTCCCTGCAGATGGGCTACACGCAGGGCGCCAACCAGAGCAGACAGGTGTTTGGGCTG
GGCCGGCAGATCTACGATTCCAAGTATTGC

Alignment

ORF - retro_sara_582 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 63.35 %
• Parental protein coverage: 80.97 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  KYDHQAEEDLRNWIEEVTGMSIGTNFQLGLKDGIILCELINKLQPGSVKKVNESPLNWPQLENIGNFIKA
          K.D.Q.E..LR.WI...TG.SIG..FQ.GL.DG.ILC.L.NKLQPGSV.K.N.S..NW.QLEN..NFIKA
Retrocopy K*DRQKEAELRSWIQRLTGLSIGADFQKGLNDGVILCTLMNKLQPGSVHKINRSMKNWHQLENLSNFIKA

Parental  IQAYGMKPHDIFEANDLFENGNMTQVQTTLVALAGLAKTKGFHTTIDIGVKYAEKQTRRFDEGKLKAGQS
          ...YGM.P.D.FEANDLF..GNMTQ.Q..L.ALAG.AKTKG.....DIG.KY.EKQ.R.FD....KAGQ.
Retrocopy MASYGMNPVDLFEANDLFQSGNMTQMQVSLLALAGKAKTKGLQSDVDIGFKYSEKQERNFDDATMKAGQC

Parental  VIGLQMGTNKCASQAGMTAYGTRRHLYDPKMQTDKPFDQTTISLQMGTNKGASQAGMLAPGTRRDIYDQK
          VI.LQMGTNKCA.Q.GMTAYG.RR.LYDPK.....P.D..T.SLQMGTNK.ASQ..M.AP.TRR.IYD.K
Retrocopy VIRLQMGTNKCANQSGMTAYGMRRQLYDPKNHILPPMDHSTMSLQMGTNKCASQVDMMAPSTRRYIYDTK

Parental  LTLQPVDNSTISLQMGTNKVASQKGMSVYGLGRQVYDPKYC
          L.....DNS..SLQMG....A.Q....V.GLGRQ.YD.KYC
Retrocopy LGTDKCDNSSMSLQMGYTQGANQ-SRQVFGLGRQIYDSKYC

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_582 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 5 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000020345	1 retrocopy	retro_btau_1211,
Callithrix jacchus	ENSCJAG00000018128	3 retrocopies	retro_cjac_1331, retro_cjac_533, retro_cjac_861,
Macropus eugenii	ENSMEUG00000002921	2 retrocopies	retro_meug_2020, retro_meug_42,
Mustela putorius furo	ENSMPUG00000003332	1 retrocopy	retro_mputfur_896,
Sorex araneus	ENSSARG00000012874	1 retrocopy	retro_sara_582 ,