RetrogeneDB ID: retro_shar_594

Retrocopy location

• Organism: Tasmanian devil (Sarcophilus harrisii)
• Coordinates: GL851184.1:27417..27773(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CINP
• Ensembl ID: ENSSHAG00000007660
• Aliases: None
• Description: cyclin-dependent kinase 2 interacting protein [Source:HGNC Symbol;Acc:23789]

Sequence

>retro_shar_594
AAACGTACATCTAAATATAATGAGGAACTTCAGAAGTTGTACAAGGAACTTCATGATACCTTAGAAAACTTGGCTAAGAT
ACAGGTGACAATGGAAAAGTTAACATCAACAACTAAAGGGATTTCTAACCCAGAAAATTACCATGTGGAAATGGAAATTA
TAAAACACTCCTTTTCCATATATGGTCCACACCTTACTCTTATAAAGTTTTCCATAAGTTTTCAGGAATGTACAAGAAAG
AAATACTCCTCAAAAACTTCATCGTTGAAGAGCTCACTCATGTCATCATGACAGTCCAGGATCCCATATTAAGCTTCCTA
TCTATGTGGCTGTATCAGCCTTGTGTGGAGAACACA

Alignment

ORF - retro_shar_594 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70. %
• Parental protein coverage: 54.46 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  KAHPKYNEELEMLCKELHDTLANLAKVQMKMEKLTSTTKGICNLENYH-RGNGN-QTPLFHTWPTTYFYE
          K...KYNEEL..L.KELHDTL.NLAK.Q..MEKLTSTTKGI.N.ENYH..GNGN..T.LFH.W.T.Y.Y.
Retrocopy KRTSKYNEELQKLYKELHDTLENLAKIQVTMEKLTSTTKGISNPENYH<CGNGNYKTLLFHIWSTPYSYK

Parental  VSHKLSEMYKKEILLKRIIVEELAHA--TNQDLILSYLSMWLYQPYVENS
          V.HK.S.MYKKEILLK..IVEEL.H...T.QD.ILS.LSMWLYQP.VEN.
Retrocopy VFHKFSGMYKKEILLKNFIVEELTHVIMTVQDPILSFLSMWLYQPCVENT

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Sarcophilus harrisii was not studied using RNA-Seq expression data.

ChIP-Seq

Sarcophilus harrisii was not studied using ChIP-Seq data.

EST

Sarcophilus harrisii was not studied using EST data.

TSS

Sarcophilus harrisii was not studied using FANTOM5 data.

Lab

retro_shar_594 was not experimentally validated.

Homology

Retrocopy orthology:

Sarcophilus harrisii 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 4 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Monodelphis domestica	ENSMODG00000013323	1 retrocopy	retro_mdom_1091,
Oryctolagus cuniculus	ENSOCUG00000026866	1 retrocopy	retro_ocun_1274,
Otolemur garnettii	ENSOGAG00000009451	1 retrocopy	retro_ogar_321,
Sarcophilus harrisii	ENSSHAG00000007660	3 retrocopies	retro_shar_293, retro_shar_294, retro_shar_594 ,