RetrogeneDB ID: retro_shar_80

Retrocopy location

• Organism: Tasmanian devil (Sarcophilus harrisii)
• Coordinates: GL867605.1:1176756..1177395(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSSHAG00000013149
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: RAB14
• Ensembl ID: ENSSHAG00000017800
• Aliases: None
• Description: RAB14, member RAS oncogene family [Source:HGNC Symbol;Acc:16524]

Sequence

>retro_shar_80
ATGGCATATGCTTATCTATTCAAGTACATCATCATCGGCGATACTGGGGTGGGCAAATCATGCCTATTACTGCAATTTAC
TGACAAGAGGTTCCAGCCAGTACATGACCTCACCATTGGTGTGGAATTTGGGGCCCGTTTAGTATCCATCGATGGCAAGC
AGATCAAGCTCCAGATCTGGGATACAGCTGGGCAAGAATCCTTTCGCTCCATCACAAGATCCTATTACCGGGGAGCTGCT
GGAGCCCTGCTGGTGTATGACATCACCCGGAGAGATACCTTCAATCACCTGACAACATGGCTGGAAGATGCTCGTCAGCA
TGCCAATGCCAACATGGTCATCATGCTGATTGGGAACAAAAGTGATCTGGACATCAGACGAGAAGTATCAAAGGAAGAAG
GGGAAGCTTTTGCCCAAGAACATGGACTCATCTTCATGGAAACCTCAGCGAAGACAGCAGTCAATGTAGAAGATGCTTTC
ATCAGTACAGCCAGGGGGATTTATGAGAAGATCCAAGAAGGCATCTTTGATATGAGTAATGAGACCAGTGGCATTAAGAT
AGGTCCTCAGCATGTTGGGGCTGCTCCTACACATGCCGGGAATCAGGGAGTACCGCGTTCAGGAGGAGGTTGCTGCTGA

Alignment

ORF - retro_shar_80 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 62.03 %
• Parental protein coverage: 86.98 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  YSYIFKYIIIGDMGVGKSCLLHQFTEKKFMADCPHTIGVEFGTRIIEVSGQKIKLQIWDTAGQERFRAVT
          Y.Y.FKYIIIGD.GVGKSCLL.QFT.K.F......TIGVEFG.R.....G..IKLQIWDTAGQE.FR..T
Retrocopy YAYLFKYIIIGDTGVGKSCLLLQFTDKRFQPVHDLTIGVEFGARLVSIDGKQIKLQIWDTAGQESFRSIT

Parental  RSYYRGAAGALMVYDITRRSTYNHLSSWLTDARNLTNPNTVIILIGNKADLEAQRDVTYEEAKQFAEENG
          RSYYRGAAGAL.VYDITRR.T.NHL..WL.DAR...N.N.VI.LIGNK.DL...R.V..EE...FA.E.G
Retrocopy RSYYRGAAGALLVYDITRRDTFNHLTTWLEDARQHANANMVIMLIGNKSDLDIRREVSKEEGEAFAQEHG

Parental  LLFLEASAKTGENVEDAFLEAAKKIYQNIQDGSLDLNAAESGVQHKP
          L.F.E.SAKT..NVEDAF...A..IY..IQ.G..D.....SG....P
Retrocopy LIFMETSAKTAVNVEDAFISTARGIYEKIQEGIFDMSNETSGIKIGP

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_80 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 8 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000003669	1 retrocopy	retro_chof_2175,
Cavia porcellus	ENSCPOG00000006688	1 retrocopy	retro_cpor_1081,
Myotis lucifugus	ENSMLUG00000009818	1 retrocopy	retro_mluc_1875,
Oryctolagus cuniculus	ENSOCUG00000013654	1 retrocopy	retro_ocun_1667,
Otolemur garnettii	ENSOGAG00000012973	1 retrocopy	retro_ogar_710,
Pelodiscus sinensis	ENSPSIG00000003919	1 retrocopy	retro_psin_66,
Sarcophilus harrisii	ENSSHAG00000006816	1 retrocopy	retro_shar_189,
Sarcophilus harrisii	ENSSHAG00000017800	1 retrocopy	retro_shar_80 ,