RetrogeneDB ID: retro_shar_440

Retrocopy location

• Organism: Tasmanian devil (Sarcophilus harrisii)
• Coordinates: GL843206.1:39518..39911(-)
• 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_440
TATGAAAAACCTCCCCCAGAACTTATCAAGGAAGATGAGACCAAGCCAGAAGACTGCATACTGGATGTCCCGGGCAATGA
ACATGCCAGAGAATTTCTGGCTCACACTCCAACTAAAGGCCTCTGGATGCCCCTGGGGAAGGAAGTCAAGGTTATGCAAT
GCTGGCGCTGTAAACGGTATGGACACAGAACAGGTGACAAAGAGTGCCCGTTCTTTATCAAAGGCAATCAGAAATTGGAA
CAATTCAGAGTAGCACATGAAGATCCCATGTATGACATCATAAGGGAGAATAAACGTCATGAAAAAGATGTGAGGATACA
CCAGTTAAAGAAGCTGCTAGAGGATTCTAGCTACTACTACTCAGATAGCAGTACTTCCAGCTCCTCAGAATGT

Alignment

ORF - retro_shar_440 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.13 %
• Parental protein coverage: 76.02 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  YEKPPPGLIKEDETKPEDCIPDVPGNEHAREFLAHAPTKGLWMPLGKEVKVMQCWRCKRYGHRTGDKECP
          YEKPPP.LIKEDETKPEDCI.DVPGNEHAREFLAH.PTKGLWMPLGKEVKVMQCWRCKRYGHRTGDKECP
Retrocopy YEKPPPELIKEDETKPEDCILDVPGNEHAREFLAHTPTKGLWMPLGKEVKVMQCWRCKRYGHRTGDKECP

Parental  FFIKGNQKLEQFRVAHEDPMYDIIRENKRHEKDVRIQQLKKLLEDST-SDEDSSTSSSSEC
          FFIKGNQKLEQFRVAHEDPMYDIIRENKRHEKDVRI.QLKKLLEDS.....DSSTSSSSEC
Retrocopy FFIKGNQKLEQFRVAHEDPMYDIIRENKRHEKDVRIHQLKKLLEDSSYYYSDSSTSSSSEC

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_440 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,