RetrogeneDB ID: retro_shar_215

Retrocopy location

• Organism: Tasmanian devil (Sarcophilus harrisii)
• Coordinates: GL834687.1:213194..213605(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSSHAG00000017480
• Aliases: None
• Description: None

Sequence

>retro_shar_215
TATATCAAATGTCCATCCTTTTTTGATAAACTTGTCAAAGAGCCAGTTTCACTGCAGCCCATTGAAAATGCCCATGTCTT
GCTCTATTTGGGAGATGCTGTCACCAACAGATCATATATCACCTGCTGGAAGCATTGCCACTTTAAGTATGTTGTTAAAT
TTCTGACAAATAGAGGGTTTACACCTTGTGAATTCAATCTTTGTGGAGCCTGGAGGGATAATGATGTTGTGATGATGAGA
GGCACCTTTGCAAATATCAAGTTCCTGAATAAGTTTATTAGAAAACCATCTTCCAGAACAATTAATTTTTCCATCAGGAC
AAACATTGAATATATTTGAGGCTGAGAATTATACAGAGTACATATTATGATTATTTTAGCAAAGAAGAAATATGGGTCTA
AAAATTGAAGA

Alignment

ORF - retro_shar_215 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.03 %
• Parental protein coverage: 53.26 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  YIRCPSFFDKLAKEPVALQPIENAHVLLYLGDSVT-TDHISPAGSIARSSA-AAKYLTNRGLTPREFNSY
          YI.CPSFFDKL.KEPV.LQPIENAHVLLYLGD.VT.TDHISPAGSIA..S....K.LTNRG.TP.EFN..
Retrocopy YIKCPSFFDKLVKEPVSLQPIENAHVLLYLGDAVT>TDHISPAGSIATLSM<VVKFLTNRGFTPCEFNLC

Parental  GARRGNDAVMTRGTFANIKLLNKFIGKPAPKTIH-FPSGQTLDVFEAA-ELYQREGIPLIILAGKKYGSG
          GA.R.ND.VM.RGTFANIK.LNKFI.KP...TI..FPSGQTL..FEA..ELY.R..I..I.LA.KKYGS.
Retrocopy GAWRDNDVVMMRGTFANIKFLNKFIRKPSSRTIN>FPSGQTLNIFEAE<ELY-RVHIMII-LAKKKYGSK

Parental  NSR
          N.R
Retrocopy N*R

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_215 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 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Monodelphis domestica	ENSMODG00000011768	1 retrocopy	retro_mdom_889,
Sarcophilus harrisii	ENSSHAG00000017480	1 retrocopy	retro_shar_215 ,