RetrogeneDB ID: retro_shar_515

Retrocopy location

• Organism: Tasmanian devil (Sarcophilus harrisii)
• Coordinates: GL849746.1:298905..299324(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TSPAN6
• Ensembl ID: ENSSHAG00000000274
• Aliases: None
• Description: tetraspanin 6 [Source:HGNC Symbol;Acc:11858]

Sequence

>retro_shar_515
GAGCTGGTGGCTACTATTATGGGATTTATTTTTAGGCAAGAGATTAAGAACAGCTTAAAGATGAAGTATGAGGCTTTCTT
GAAGCCGGCCAGTGATACAGGCAGTCACCGACGTGAGCCAGTGGGTACCATCTAGGAAACTTTGCAGTGCTGCAGGCCCA
GAGCAACACAGACTGAGAAATTCCTGCCTACTCTTGTGGAGAAAGGCGGCTTTCCCTGGGGTGGCTGCAGTGTCACAGCT
GTCCTTGGGCTGATAGAAAGGACCCAAAGAAGCAGAATCAAGACATCTGTTTTGTATAGAGTAGCAACTGCGATCCAGGC
AGACACGGGTCTTGTGGCAACGTTTCCTCTGGGGTTGCTTGTTTCTAGCTGACTGGTGTCGTTCTGGCCTGTGGCTTCTC
TCAGTGTGTTGCAGATCAC

Alignment

ORF - retro_shar_515 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 55.17 %
• Parental protein coverage: 63.76 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  ELVAAVVGFVFRHEIKDSFKMNYEASLKQYNDTGVQRSEAVDTIQKTLHCCG-VLSATDWESTAY-YVEK
          ELVA...GF.FR.EIK.S.KM.YEA.LK...DTG..R.E.V.TI..TL.CC....S.TD.E..AY..VEK
Retrocopy ELVATIMGFIFRQEIKNSLKMKYEAFLKPASDTGSHRREPVGTI*ETLQCCR<AQSNTD*EIPAY>LVEK

Parental  G-FPRSCC-RYHSCSWADRKDLKKQNQEGCFL-RVTTIIQSEMGVVA-GISFGVACFQLIGIFLACCLSR
          G.FP...C...HSC.WADRKD.KKQNQ..CF..RV.T.IQ...G.VA...S.GVACF.L.G..LAC..S.
Retrocopy GGFPWGGC<QCHSCPWADRKDPKKQNQDICFV>RVATAIQADTGLVA<NVSSGVACF*LTGVVLACGFSQ

Parental  SITNN
          .....
Retrocopy CVADH

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_515 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 9 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000017521	3 retrocopies	retro_cfam_1600, retro_cfam_1609, retro_cfam_878,
Callithrix jacchus	ENSCJAG00000004288	1 retrocopy	retro_cjac_2306,
Echinops telfairi	ENSETEG00000012276	1 retrocopy	retro_etel_1987,
Loxodonta africana	ENSLAFG00000027296	1 retrocopy	retro_lafr_994,
Microcebus murinus	ENSMICG00000011370	1 retrocopy	retro_mmur_447,
Nomascus leucogenys	ENSNLEG00000007505	1 retrocopy	retro_nleu_1186,
Otolemur garnettii	ENSOGAG00000004869	1 retrocopy	retro_ogar_2827,
Sarcophilus harrisii	ENSSHAG00000000274	1 retrocopy	retro_shar_515 ,
Sus scrofa	ENSSSCG00000012481	1 retrocopy	retro_sscr_84,