RetrogeneDB ID: retro_shar_657

Retrocopy location

• Organism: Tasmanian devil (Sarcophilus harrisii)
• Coordinates: GL856940.1:892892..893414(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: REEP6
• Ensembl ID: ENSSHAG00000012645
• Aliases: None
• Description: receptor accessory protein 6 [Source:HGNC Symbol;Acc:30078]

Sequence

>retro_shar_657
ATGGGTACCTTGAGACAATGCTTTCAGAGGTTCTTGGAGCAAAAAACATCATCACCGATGTCCTCAGGAAGCTGAGGAGA
TCACCAGTATCAAAAAATGCTACTTGGTTACAAATTCTGTTTTCTTCATGGCTCTCTATCTCATATTTGGCTATGGTGGC
TCCCTGTTTTGCAGTCTCACTGGATTCATCTACTTAGCATATGATTCCATCAAGGTCATTGAAAGCCCCAACAAAGATGA
TGATACCATTTAACTCATCTAGTGGGTGGAACATAGCATACCTGGCCTGGCTGACTTTTTCTCTGATATCTTACTTTTCT
GGTTCCCCTTCTTCTCTGCAGGAAAATGTGCCTTCTTGCTATGGTGCATCCTTCTAGTCTGAAATGGCTCACAGATCTTG
TATCATTACTTGATCCATGCCATTTCCTGAGGCATCAAGCTTCCATAGACAGTCTGGTGACTTACCTAAGTGGCCAAACC
TTGGACATGGCAACCAGTTTGATCCAGGAAGCAACCGAGGCA

Alignment

ORF - retro_shar_657 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.72 %
• Parental protein coverage: 84.62 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MASLRQRFQRFLEQK-NIVTDALGKL-EEITGVRKYYLATGSIAFVALYLIFGYGASLLCNLIGFMYPAY
          M..LRQ.FQRFLEQK.NI.TD.L.KL.EEIT...K.YL.T.S..F.ALYLIFGYG.SL.C.L.GF.Y.AY
Retrocopy MGTLRQCFQRFLEQK<NIITDVLRKL<EEITSIKKCYLVTNSVFFMALYLIFGYGGSLFCSLTGFIYLAY

Parental  ASIKAIESPNKDDDTIWLTYWVVYSIFGLAEFFSDIFLFWFPFYYAGKCAFLLWCMLPVTCNGSQILYHR
          .SIK.IESPNKDDDTI.L..WV..SI.GLA.FFSDI.LFWFPF..AGKCAFLLWC.L....NGSQILYH.
Retrocopy DSIKVIESPNKDDDTI*LI*WVEHSIPGLADFFSDILLFWFPFFSAGKCAFLLWCIL-LV*NGSQILYHY

Parental  LIRPI-FLRHQASMDSLVTDLSGRALDTAAHLTREVLQA
          LI..I.FLRHQAS.DSLVT.LSG..LD.A..L..E...A
Retrocopy LIHAI<FLRHQASIDSLVTYLSGQTLDMATSLIQEATEA

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_657 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.

---

Parental genes homology:

Parental genes homology involve 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Microcebus murinus	ENSMICG00000003588	1 retrocopy	retro_mmur_1072,
Monodelphis domestica	ENSMODG00000005050	1 retrocopy	retro_mdom_1574,
Sarcophilus harrisii	ENSSHAG00000012645	1 retrocopy	retro_shar_657 ,
Drosophila melanogaster	FBgn0033906	1 retrocopy	retro_dmel_12,