RetrogeneDB ID: retro_shar_41

Retrocopy location

• Organism: Tasmanian devil (Sarcophilus harrisii)
• Coordinates: GL834808.1:497036..497660(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSSHAG00000009042
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: RDH12
• Ensembl ID: ENSSHAG00000012445
• Aliases: None
• Description: retinol dehydrogenase 12 (all-trans/9-cis/11-cis) [Source:HGNC Symbol;Acc:19977]

Sequence

>retro_shar_41
TTGCAGGAGGAGCCCCGGCTAGATGTCTTGATCAATAATGCAGGGGTCTTCCAGTGCCCCTATACAAAGACTGAAGATGG
CTTTGAGATGCAGTTTGGGGTGAATCACCTGGGCCACTTCTTGCTCACCAACCTGCTTCTCGACCGCCTTAAAGACTCGG
CCCCCAGCCGGATCGTGGTGGTTTCTTCCAAGCTTTACAAATACGGGGAAATCAACTTTGAAGATTTGAATAGTGAGGTA
AAGTATAATAAAAGTTTCTGTTATAGTCAGAGCAAGCTGGCCAATATTCTCTTTGCCAGAGAACTAGCTCGCCGGCTGGA
AGGCACGAATGTTACCGTCAATGTGCTTCACCCTGGTATTGTCCGGACCAATCTGGGGAGGCACATCAACATCCCCCTGC
TGGCCAAGCCGCTTTTCAACCTGGTGTCGTGGGCTTTTTTCAAAACCCCTGTGGAAGGAGCCCAAACCTCAGTCTACCTG
GCCTCCTCAGCAGAAGTGGAGGGGGTGTCGGGAAAGTACTTTGGGGACTGCAAAGAAGAAGAGCTTCTGCCCAAAGCCAT
GGATGACTCCGTGGCAAGAAAGCTCTGGGATATCAGTGAAGTGATGGTGGGCCTGTTAAAGTAG

Alignment

ORF - retro_shar_41 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 52.68 %
• Parental protein coverage: 64.22 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LAEEKQLHILINNAGVMMCPYSKTVDGFETQFGVNHLGHFLLTHLLLERLKESAPSRIVNLSSVIHHFGS
          L.EE..L..LINNAGV..CPY.KT.DGFE.QFGVNHLGHFLLT.LLL.RLK.SAPSRIV..SS.....G.
Retrocopy LQEEPRLDVLINNAGVFQCPYTKTEDGFEMQFGVNHLGHFLLTNLLLDRLKDSAPSRIVVVSSKLYKYGE

Parental  IYFRDLQGEKYYNRAFAYCHSKLANVLFTRELAYRLRGTGVTTYAVHPGIVQSELMRHSFLMCLLWRLFT
          I.F.DL..E..YN..F.Y..SKLAN.LF.RELA.RL.GT.VT....HPGIV...L.RH.....L...LF.
Retrocopy INFEDLNSEVKYNKSFCYSQSKLANILFARELARRLEGTNVTVNVLHPGIVRTNLGRHINIPLLAKPLFN

Parental  ----PFVKSTQQGAQTSLHCALAEGIESQSGRYFSDCRTAWVSPKGRNNKTAKRLWEVSCELLGI
          .....F.K....GAQTS...A.....E..SG.YF.DC......PK......A..LW..S....G.
Retrocopy LVSWAFFKTPVEGAQTSVYLASSAEVEGVSGKYFGDCKEEELLPKAMDDSVARKLWDISEVMVGL

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_41 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 13 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000008036	1 retrocopy	retro_amel_673,
Canis familiaris	ENSCAFG00000016446	1 retrocopy	retro_cfam_2068,
Equus caballus	ENSECAG00000015001	1 retrocopy	retro_ecab_1059,
Felis catus	ENSFCAG00000014092	1 retrocopy	retro_fcat_1910,
Loxodonta africana	ENSLAFG00000022637	1 retrocopy	retro_lafr_847,
Macropus eugenii	ENSMEUG00000001473	1 retrocopy	retro_meug_41,
Meleagris gallopavo	ENSMGAG00000011960	1 retrocopy	retro_mgal_16,
Microcebus murinus	ENSMICG00000010855	1 retrocopy	retro_mmur_432,
Ornithorhynchus anatinus	ENSOANG00000015759	1 retrocopy	retro_oana_89,
Procavia capensis	ENSPCAG00000009359	1 retrocopy	retro_pcap_1,
Pelodiscus sinensis	ENSPSIG00000010721	1 retrocopy	retro_psin_24,
Sarcophilus harrisii	ENSSHAG00000012445	1 retrocopy	retro_shar_41 ,
Drosophila melanogaster	FBgn0033203	1 retrocopy	retro_dmel_79,