RetrogeneDB ID: retro_shar_650

Retrocopy location

• Organism: Tasmanian devil (Sarcophilus harrisii)
• Coordinates: GL856929.1:2740202..2740522(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RP9
• Ensembl ID: ENSSHAG00000001730
• Aliases: None
• Description: retinitis pigmentosa 9 (autosomal dominant) [Source:HGNC Symbol;Acc:10288]

Sequence

>retro_shar_650
TATGAAAAAGCTCCTCTTGGACTTATCAAGGAAGATGAGACCAAGCCAGAAGTCTGCAATATCAGAAATACCCAATAATG
AACATGCCAGAGAATTTCTGGCTAATGCTCCAACTAAAGGACTCTGGATGACCCTGGGGAAAAAAGTCAAGGTTATGTAA
TGTGGCACTATAAGCTGTATAGACTCAGAACAGGGGACAAAGACTGCTCATTCTTTATCAAAGGCAATCAGAAATTTAAA
AATAATTCAGTGTAGCAATAAAGATCCCTTGTATGACATCATAAGGGAAAATAAATGTCATAAAAAAAGATGTGAAGATA

Alignment

ORF - retro_shar_650 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.09 %
• Parental protein coverage: 61.99 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  YEKPPPGLIKEDETKPEDC-IPDVPGNEHAREFLAHAPTKGLWMPLGKEVKVMQC-WRCKRYGHRTGDKE
          YEK.P.GLIKEDETKPE.C.I...P.NEHAREFLA.APTKGLWM.LGK.VKVM.C.W..K.Y..RTGDK.
Retrocopy YEKAPLGLIKEDETKPEVC>ISEIPNNEHAREFLANAPTKGLWMTLGKKVKVM*C<WHYKLYRLRTGDKD

Parental  CPFFIKGNQK-LEQFRVAHEDPMYDIIRENKRH-EKDVRI
          C.FFIKGNQK.L........DP.YDIIRENK.H..KDV.I
Retrocopy CSFFIKGNQK>LKIIQCSNKDPLYDIIRENKCH>KKDVKI

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_650 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 3 parental genes, and 20 retrocopies.

Species	Parental gene accession	Retrocopies number
Monodelphis domestica	ENSMODG00000025514	17 retrocopies	retro_mdom_1205, retro_mdom_1515, retro_mdom_1553, retro_mdom_1622, retro_mdom_1759, retro_mdom_1840, retro_mdom_1905, retro_mdom_1912, retro_mdom_265, retro_mdom_317, retro_mdom_386, retro_mdom_560, retro_mdom_623, retro_mdom_687, retro_mdom_761, retro_mdom_818, retro_mdom_896,
Sarcophilus harrisii	ENSSHAG00000001730	2 retrocopies	retro_shar_440, retro_shar_650 ,
Tupaia belangeri	ENSTBEG00000009535	1 retrocopy	retro_tbel_280,