RetrogeneDB ID: retro_shar_371

Retrocopy location

• Organism: Tasmanian devil (Sarcophilus harrisii)
• Coordinates: GL841524.1:16508..16810(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSSHAG00000011251
• Aliases: None
• Description: None

Sequence

>retro_shar_371
GAAAAGAATTCATGGAAAGTGACAATTTCAGATGAAATGCTTCAGAAAAAGAGGATAAGGAAGAAAGAGAAAGCAGAGAT
AAAACCCATTAAAACTTCAGTTGTTGGGGAATCTAAGTGGGATTTCATCTGAGAAGGGAAGCCAAGAGATCATATGGAGT
TAACAACTAGGAATTCACTTTATAGGAAGGCAGATACTATGATACACTGAGATGAAGAAAGTGACTCCTTGGCCATTAAA
CCACATCAGCAAATGTTACCTAAGGAAAAAAAGATCACCACAGAAAGGATGAGAAGAGAAAG

Alignment

ORF - retro_shar_371 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 58.1 %
• Parental protein coverage: 62.05 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  EKDSWKVKTLDEILQEKKRRKEQEEKAEIKRIKNSDDRDSKRDSLEEGELRDHRMEITIRNSPYRREDSM
          EK.SWKV...DE.LQ.K..RK...EKAEIK.IK.S....SK.D...EG..RDH.ME.T.RNS.YR..D.M
Retrocopy EKNSWKVTISDEMLQKKRIRKK--EKAEIKPIKTSVVGESKWDFI*EGKPRDH-MELTTRNSLYRKADTM

Parental  EDRGEEDDSLAIKPPQQMSRKE-KAHHRK-DEKRK
          ....EE.DSLAIKP.QQM..KE.K..H...DEKRK
Retrocopy IH*DEESDSLAIKPHQQMLPKE<KKDHHRKDEKRK

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_371 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 2 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Rattus norvegicus	ENSRNOG00000046253	1 retrocopy	retro_rnor_2850,
Sarcophilus harrisii	ENSSHAG00000011251	3 retrocopies	retro_shar_219, retro_shar_371 , retro_shar_509,