RetrogeneDB ID: retro_shar_31

Retrocopy location

• Organism: Tasmanian devil (Sarcophilus harrisii)
• Coordinates: GL849632.1:1690041..1690692(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSSHAG00000015111
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSSHAG00000009111
• Aliases: None
• Description: None

Sequence

>retro_shar_31
ATGACCCTCCAGTGGATGGCAGTGGCCTCCTTCTTTTATGCTGAGATCATGGCTGTGCTGCTGCTCTGCAGCCCCTTCAT
CTCCCCGCAGAAATGGGAGAAAATCTTTAGCTCCCGCCTGGTGCACTGGCTGGTGACCTACGGGCAGCCCTTCTTTGGGA
TCCTGCTGTTGATCCTGGCGCTGCTATTCCTGGAGGCCCTGTGGGAGATTAGGAAGTTTGAAAGCATGGAGAAGGAGAGC
CTGCTAAAGTGCCCAGCGGTCATGGAGCATCACCAAATGAAGCTCTTCCGAGCCCAACGGAACCTGCACATCACAGGCTT
CGCGTTGCTGCTGTCGCTGCTGCTACCCCGCCTCACCGCCCTCCAGAAGCAGCAGGCCTCGCTGCAGGACGAGAACGAGA
GGCTACTGGAGGAGGCCGAGACCCAGATGATCCAGCGCATCGCTGCCGAGGTGAGCGAGAACCAGTCCCTGAGGGAGGAC
CTCTTGAAGCTGACGCAGGAGCTGGAGGCCTGCCGCAGGAGCCTTGGGCGGGCCCAGGACGAGAACATTCACCTGCGCAA
GCGCTGCGAGAAACGGGACCCCAAGAATCTGCCGTCGGACTCGGACCGGTCAGAGGCCGACAGGAAGCCTGAAGACCAAA
AGCGGGAGTGA

Alignment

ORF - retro_shar_31 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 57.45 %
• Parental protein coverage: 59. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MSLQWSAVATFLYAEVVAVLLLCIPFISPKRWQKIFKSSLVQLIVSYGNTFFVVLIVILVLLLIDAVREI
          M.LQW.AVA.F.YAE..AVLLLC.PFISP..W.KIF.S.LV...V.YG..FF..L..IL.LL...A..EI
Retrocopy MTLQWMAVASFFYAEIMAVLLLCSPFISPQKWEKIFSSRLVHWLVTYGQPFFGILLLILALLFLEALWEI

Parental  RKYDDVTEKVNLQNNPGAMEHFHMKLFRAQRNLHIAGFSLLLSFLIRRLVTLISQQATLLASNEAFKKQA
          RK.....EK..L...P..MEH..MKLFRAQRNLHI.GF.LLLS.L..RL..L..QQA.L...NE.....A
Retrocopy RKFESM-EKESLLKCPAVMEHHQMKLFRAQRNLHITGFALLLSLLLPRLTALQKQQASLQDENERLLEEA

Parental  E
          E
Retrocopy E

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_31 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 6 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000019245	1 retrocopy	retro_cfam_482,
Callithrix jacchus	ENSCJAG00000011348	1 retrocopy	retro_cjac_2552,
Echinops telfairi	ENSETEG00000008662	1 retrocopy	retro_etel_1522,
Macropus eugenii	ENSMEUG00000007345	3 retrocopies	retro_meug_1017, retro_meug_1867, retro_meug_208,
Monodelphis domestica	ENSMODG00000008300	2 retrocopies	retro_mdom_1110, retro_mdom_24,
Sarcophilus harrisii	ENSSHAG00000009111	1 retrocopy	retro_shar_31 ,