RetrogeneDB ID: retro_shar_588

Retrocopy location

• Organism: Tasmanian devil (Sarcophilus harrisii)
• Coordinates: GL850806.1:29839..30302(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: DERL1
• Ensembl ID: ENSSHAG00000011915
• Aliases: None
• Description: derlin 1 [Source:HGNC Symbol;Acc:28454]

Sequence

>retro_shar_588
TATATGTTCATGCTCTTTTTTAACTGGATTTGCATCATTGTTACTAGTTTAATGATGGACATGCAGTTGCTGACTATTCT
TTTGATCATATCAGTACTCTTTGTCTAGACCCATTTGAAGAGAGAAATGATTGTTATCATTTTGGTTTGGAACACTATTT
AACGCCTATTACTTGCCTTGGGTTATTCTTGTATTCAACTACATTACTGGAAGATCGCTTTTCAATGAACTGATAAGAAA
TCTTTTTGGACATGTGTCTTACTTCTTAATGTTCAAATACCCAATTGATGTGGGAGGAATAACTTTTTTGTGTACCCCTC
AGTGTCTATATCTCTGGCATTCCAGTAGGAGAGGAACCATCTCTAAATTTGGTGTTTCACCTTCAAGCATAAGATGAGCT
GCAGAACAATAGCTTGGTGGAGGTGGTCCACACAATTGGAGCCAGGGCTTCCAACTAGGAGAT

Alignment

ORF - retro_shar_588 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 62.18 %
• Parental protein coverage: 61.51 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  YMFMLLFNWVCIVITGLIMDMQLLMIPLIMSVLYVWAQLNREMIV-SFWFGTRFKFFFFFFFFFFFSFFF
          YMFML.FNW.CI..T.L.MDMQLL.I.LI.SVL.V...L.REMIV.SFWFGT.F...........F....
Retrocopy YMFMLFFNWICIIVTSLMMDMQLLTILLIISVLFV*THLKREMIV>SFWFGTLFNAYYLPWVILVFNYI-

Parental  SPPRVINELIGNLVGHLYYFLMFKYPMDLGGRTFLCTPQCLYRWLPSRRGNVSGFGVPPASMRRAAEHQL
          ......NELI.NL.GH..YFLMFKYP.D.GG.TFLCTPQCLY.W..SRRG..S.FGV.P.S.R.AAE..L
Retrocopy TGRSLFNELIRNLFGHVSYFLMFKYPIDVGGITFLCTPQCLYLWHSSRRGTISKFGVSPSSIR*AAEQ*L

Parental  GGGGRHNWGQGFRLGD
          GGGG.HNW.QGF.LGD
Retrocopy GGGGPHNWSQGFQLGD

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_588 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 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000006519	1 retrocopy	retro_amel_364,
Canis familiaris	ENSCAFG00000000974	1 retrocopy	retro_cfam_754,
Cavia porcellus	ENSCPOG00000011870	1 retrocopy	retro_cpor_1520,
Myotis lucifugus	ENSMLUG00000009085	1 retrocopy	retro_mluc_2035,
Mustela putorius furo	ENSMPUG00000001132	1 retrocopy	retro_mputfur_1082,
Mus musculus	ENSMUSG00000022365	1 retrocopy	retro_mmus_919,
Rattus norvegicus	ENSRNOG00000005551	2 retrocopies	retro_rnor_1206, retro_rnor_2717,
Sarcophilus harrisii	ENSSHAG00000011915	1 retrocopy	retro_shar_588 ,