RetrogeneDB ID: retro_shar_87

Retrocopy location

• Organism: Tasmanian devil (Sarcophilus harrisii)
• Coordinates: GL841397.1:1442796..1443612(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSSHAG00000014297
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSSHAG00000004156
• Aliases: None
• Description: None

Sequence

>retro_shar_87
ATGGCGGCGGAGGAACCTCATCAGCAGAATCCGGAGCCATTGGAAAGTGACTCTGAAGGAATTAACAGTTTGGCCTACGA
TGAAGCCATCATGGCCCAGCAGGACCGAATTCAGCAAGAGATTGCTGTTCAAAATCCCCTGGTGTCCGAGCGCCTGGAGC
TCTCCGTGCTTTACAAGGAGTACGCCGAAGATGACAACATCTACCAACAGAAGATCAAGGACCTACACAAAAAGTACTCC
TACATCCGAAAGACCAGGCCCGATGGCAACTGCTTCTACCGGGCTTTCGGCTTCTCCCACCTGGAGGCCCTTCTGGAGGA
CAAGAAGGAGCTGCAGAGGCTCAAAGCCGTCTCCGCCAAGAGCAAGGACGACCTGGTGGCCCAGGGCTTCGCCGAGTTCA
CAATTGAAGATTTCCACAACACATTCATGGACCTGATCGAACAGGTGGAGAGGGGAACCTCAGCAACGGAACTGCTGGCC
TCCTTCAATGACCAGAGCACCTCCGACTACCTGGTGGTTTACCTGCGGCTGCTCACCTCAGGCCACCTGCAGCGTGAGAG
CAAGTTCTTCGAGCATTTCATCGAGGGGGGACAGACGGTCAAGGAGTTTTGTCAGCAGGAGGTGGAGCCCATGTGCAAGG
AGAGTGACCACATCCACATCATGGCGCTGGCGCAGGCCCTCAGCATCTCCATCCAGGTGGAGTACATGGACCGCGGTGAG
GGCGGCACCACCAACACCCACGTCTTCTCTGAGGGCTCCGAGACCAAGGTGTACCTTCTGTACAGACCCGGACACTACGA
CATCCTTTACAAATAG

Alignment

ORF - retro_shar_87 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.38 %
• Parental protein coverage: 91.3 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAAEEPQQQKPEEAPLVAPPRGVNCLAYDEAIMAQQDRIQQEIAVQNPLVSERLELSVLYKEYAEDDNIY
          MAAEEP.QQ.PE..PL.....G.N.LAYDEAIMAQQDRIQQEIAVQNPLVSERLELSVLYKEYAEDDNIY
Retrocopy MAAEEPHQQNPE--PLESDSEGINSLAYDEAIMAQQDRIQQEIAVQNPLVSERLELSVLYKEYAEDDNIY

Parental  QQKIKDLHKKYSYIRKTRPDGNCFYRAFGFSHLEALLEDSKELQRFKAISAKSKEDLVSQGFTEFTIEDF
          QQKIKDLHKKYSYIRKTRPDGNCFYRAFGFSHLEALLED.KELQR.KA.SAKSK.DLV.QGF.EFTIEDF
Retrocopy QQKIKDLHKKYSYIRKTRPDGNCFYRAFGFSHLEALLEDKKELQRLKAVSAKSKDDLVAQGFAEFTIEDF

Parental  HNTFMDLIEQVEKRTSVADLLASFNDQSTSDYLVVYLRLLTSGYLQRESKFFEHFIEGGRTVKEFCQQEV
          HNTFMDLIEQVE..TS...LLASFNDQSTSDYLVVYLRLLTSG.LQRESKFFEHFIEGG.TVKEFCQQEV
Retrocopy HNTFMDLIEQVERGTSATELLASFNDQSTSDYLVVYLRLLTSGHLQRESKFFEHFIEGGQTVKEFCQQEV

Parental  EPMCKESDHIHIIALAQALSVSIQVEYMDRGEGGTTNPHVFPEGSEPKVYLLYRPGHYDILYK
          EPMCKESDHIHI.ALAQALS.SIQVEYMDRGEGGTTN.HVF.EGSE.KVYLLYRPGHYDILYK
Retrocopy EPMCKESDHIHIMALAQALSISIQVEYMDRGEGGTTNTHVFSEGSETKVYLLYRPGHYDILYK

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_87 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 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000018084	1 retrocopy	retro_amel_1270,
Bos taurus	ENSBTAG00000003967	1 retrocopy	retro_btau_1119,
Canis familiaris	ENSCAFG00000014729	2 retrocopies	retro_cfam_1376, retro_cfam_2023,
Equus caballus	ENSECAG00000002621	1 retrocopy	retro_ecab_760,
Myotis lucifugus	ENSMLUG00000012235	2 retrocopies	retro_mluc_1257, retro_mluc_614,
Mustela putorius furo	ENSMPUG00000013314	1 retrocopy	retro_mputfur_1057,
Pteropus vampyrus	ENSPVAG00000017099	2 retrocopies	retro_pvam_131, retro_pvam_274,
Rattus norvegicus	ENSRNOG00000021175	1 retrocopy	retro_rnor_2431,
Sarcophilus harrisii	ENSSHAG00000004156	1 retrocopy	retro_shar_87 ,