RetrogeneDB ID: retro_sara_33

Retrocopy location

• Organism: Shrew (Sorex araneus)
• Coordinates: scaffold_216050:7710..8715(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSSARG00000001029
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: CSNK1D
• Ensembl ID: ENSSARG00000005475
• Aliases: None
• Description: casein kinase 1, delta [Source:HGNC Symbol;Acc:2452]

Sequence

>retro_sara_33
ATGGCGAACATCAGCGACTCCAAAGCCGATTTCGTGGTCGGCGGGAAATACAAGCTGGTACGGAAGATCGGGTCCGGCTC
CTTCGGGGACATTTACCTGGCGGTCAACATCACCAGCGGCGAGGAGGTGGCCGTGAAGCTCGAGTCGCAGAAGGCGCGGC
ACCCGCAGCTGCTGTACGAGAGTAAACTCTACAAGATCCTTCAAGGCGGGGTGGGCATCCCCCACATACGGTGGTATGGT
CAGGAAAAAGACCACAACATACTAGTCATGGATCTTCTTGGACCCAGCCTCGAAGATCTGTTCAATTTCTGTTCCAGAAG
GTTCACCATGAAAACGGTACTTATGTTAGCTGACCAGATGATCAGTAGAATTGAATATGTGCATACAAAGAATTTTATAC
ACAGAGACATTAAACCAGATAACTTCCTGATGGGTATTGGACATCACTGTAATAAGTTATTCCTTATTGATTTTGGCTTG
GCCAAAAAGTACAGAGACAACAGGACAAGGCAACACATACCGTACAGAGAAGATAAAAATCTGACTGGCACTGCCCGGTA
TGCTAGCATCAATGCACATCTTGGTATTGAACAAAGTCGCCGAGATGACATGGAATCATTAGGATATGTTTTGATGTATT
TCAATAGAACCAATCTGCCGTGGCAAGGACTAAAGGCTGCGACAAAGAAACAAAAATATGAAAAGATTAGTGAAAAGAAG
ATGTCCACTCCTGTTGAAGTTTTATGTAAGGGATTTCCTGCAGAATTTGCCATGTACTTAAACTATTGTCGTGGGCTGCG
CTTTGAGGAGGCCCCAGATTACACGTATTTGAGGCAGCTATTTCGCATTCTTTTCAGGACCCTGAACCACCAATACGACT
ACACATTTGATTGGACAATGTTAAAGCAGAAAGCAGCACAACAGGCAGCCTCTTCAAGTGGGCCGGGTCATCAGGCCCAA
CCCCACACAGGCAAGCAAACTGACAAAAACAAGACTAATGTGAAA

Alignment

ORF - retro_sara_33 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.98 %
• Parental protein coverage: 70.44 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  DIAAGEEVAIKLECVKTKHPQLHIESKIYKMMQGGVGIPTIRWCGAEGDYNVMVMELLGPSLEDLFNFCS
          .I..GEEVA.KLE..K..HPQL..ESK.YK..QGGVGIP.IRW.G.E.D.N..VM.LLGPSLEDLFNFCS
Retrocopy NITSGEEVAVKLESQKARHPQLLYESKLYKILQGGVGIPHIRWYGQEKDHNILVMDLLGPSLEDLFNFCS

Parental  RKFSLKTVLLLADQMISRIEYFLSKNFIHRDVSPDIFLKGLGKKGNPVYIIDFWWAKKNREPLAHQHIPY
          R.F..KTVL.LADQMISRIEY...KNFIHRD..PD.FL.G.G...N....IDF..AKK.R.....QHIPY
Retrocopy RRFTMKTVLMLADQMISRIEYVHTKNFIHRDIKPDNFLMGIGHHCNKLFLIDFGLAKKYRDNRTRQHIPY

Parental  RKNMNLTGTGRYPPINTHLGIEQSRRDDLESLGYVLMYFNLGSLPWQGLKAATKRQKYERISEKKMSTPI
          R...NLTGT.RY..IN.HLGIEQSRRDD.ESLGYVLMYFN...LPWQGLKAATK.QKYE.ISEKKMSTP.
Retrocopy REDKNLTGTARYASINAHLGIEQSRRDDMESLGYVLMYFNRTNLPWQGLKAATKKQKYEKISEKKMSTPV

Parental  EVLCKGYPSEFATYLNFCRSLRFDDKPDYSYLRQLFRNLFHRQGFSYDYVFDWNMLKFGASRAA
          EVLCKG.P.EFA.YLN.CR.LRF...PDY.YLRQLFR.LF......YDY.FDW.MLK..A...A
Retrocopy EVLCKGFPAEFAMYLNYCRGLRFEEAPDYTYLRQLFRILFRTLNHQYDYTFDWTMLKQKAAQQA

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_33 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 6 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Macropus eugenii	ENSMEUG00000008792	1 retrocopy	retro_meug_543,
Otolemur garnettii	ENSOGAG00000014866	1 retrocopy	retro_ogar_264,
Sorex araneus	ENSSARG00000005475	1 retrocopy	retro_sara_33 ,
Sorex araneus	ENSSARG00000009110	2 retrocopies	retro_sara_287, retro_sara_337,
Sorex araneus	ENSSARG00000011446	1 retrocopy	retro_sara_518,
Sarcophilus harrisii	ENSSHAG00000007638	2 retrocopies	retro_shar_260, retro_shar_710,