RetrogeneDB ID: retro_shar_269

Retrocopy location

• Organism: Tasmanian devil (Sarcophilus harrisii)
• Coordinates: GL840191.1:8453..8772(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CKLF
• Ensembl ID: ENSSHAG00000000837
• Aliases: None
• Description: chemokine-like factor [Source:HGNC Symbol;Acc:13253]

Sequence

>retro_shar_269
TATATAATAAGATCTGACCAAGTGCTGAAGTGTTTGTTTTGTCTTTTTTCAATATTGTAAAGTCATTTATGATCATAATA
CTCCTTATGATTGTGTCTGTTTTGGTACTGGTAACAGAAACTAAACTAGTAATCACTGTTGGAATGATCCTTGGGATTGT
GGCAATTGTGTTTACTTTTGCAAATGCTGCCTTCATATACAGAAAACTTATGTGTAATCTAAATAATCTCTATGAGAAAA
GGCACAGTCATGAAAAAGACTTCTCTTTCAACATTCTCACTATCATCATAATTATTACACTCATTAATCTGAGAGGGAA

Alignment

ORF - retro_shar_269 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 52.73 %
• Parental protein coverage: 71.05 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  YLLRLDLVLKFLFW-PLLDIINSLMTIVFLMIVSVLSLIPETKIQIAVAGILGIVATVFTVADAALIYRK
          Y..R.D.VLK.LF......I..S.M.I..LMIVSVL.L..ETK..I.V..ILGIVA.VFT.A.AA.IYRK
Retrocopy YIIRSDQVLKCLFC<SFFNIVKSFMIIILLMIVSVLVLVTETKLVITVGMILGIVAIVFTFANAAFIYRK

Parental  LMFNPSGPYEKRRTHE-KKRRSRHSRHSHHSYHPRLSQEK
          LM.N....YEKR..HE.K.....HS.H.HH.Y....S...
Retrocopy LMCNLNNLYEKRHSHE<KRLLFQHS-HYHHNYYTH*SERE

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_269 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.

---

Parental genes homology:

Parental genes homology involve 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Pteropus vampyrus	ENSPVAG00000000188	1 retrocopy	retro_pvam_1009,
Sarcophilus harrisii	ENSSHAG00000000837	1 retrocopy	retro_shar_269 ,
Tarsius syrichta	ENSTSYG00000014768	1 retrocopy	retro_tsyr_671,