RetrogeneDB ID: retro_shar_66

Retrocopy location

• Organism: Tasmanian devil (Sarcophilus harrisii)
• Coordinates: GL867637.1:80578..81220(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSSHAG00000003926
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSSHAG00000009125
• Aliases: None
• Description: None

Sequence

>retro_shar_66
AGCGAATTGCGGAAAGGTAAACTGAGGCCCGGGCGCCTGCGACTGGCCAACCGCCCGCACCGCCGCCTGGGGCCCACGGG
CCGCGACGTGCACTCCCTGAAGAAACTGAGGGAAGCCGCCAACGCCAACGACTTGGAGACGGTGAAGCAGCTGCTGGAGG
ATGGAGTGGATCCGATGTCGACCGACGATAAAGGCCGCAGCGCCCTGCACTACGCCGCTTGCAACGGCAACGACCAGATG
GTGCAGCTGCTCCTGAGCCACGGCGCCGATCCCGACCAGAGGGACGGGCTGGGCAACACCGCGCTGCACCTAGCCGCCTG
CACCAACCAGGTCCCGGTCATCACCACGCTGCTCCGGAGAGGGGCCCGGGTGGACGTCCTGGACCGCGCCGGCAGGACCC
CCCTGCACCTCGCCAAGAACAAGCTGACCATTCTGCAGGGGAGCCAGCCGCAGTGCCTGGAAGCCGTCCGCCTGGAGGTG
AAGCAGATCATTCAGATGCTCAAGGAGTACCTGGAGCGCCTGGGGCAGCACGAGCAGCGCGTCCGGCTGGACGATCTCTG
CAACCGCCTCCAGATGACGAGCACCAAAGAGCAGGTGGACGAGGTGACGGATCTCCTGGCCAGCTTCACCTCGCTCAGCC
TG

Alignment

ORF - retro_shar_66 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.04 %
• Parental protein coverage: 91.03 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  TERVKRPARRGRLR-SSSPHANARPPPFSSTALKRLREAANANDLETVQQLLEDGADPCTADDKGRTALH
          .E..K...R.GRLR....PH....P.......LK.LREAANANDLETV.QLLEDG.DP...DDKGR.ALH
Retrocopy SELRKGKLRPGRLRLANRPHRRLGPTGRDVHSLKKLREAANANDLETVKQLLEDGVDPMSTDDKGRSALH

Parental  FASCNGNDQIVQLLLDHGADPNQRDGLGNTPLHLAACTNHVPVITTLLRGGARVDALDRAGRTPLHLAKS
          .A.CNGNDQ.VQLLL.HGADP.QRDGLGNT.LHLAACTN.VPVITTLLR.GARVD.LDRAGRTPLHLAK.
Retrocopy YAACNGNDQMVQLLLSHGADPDQRDGLGNTALHLAACTNQVPVITTLLRRGARVDVLDRAGRTPLHLAKN

Parental  KLNILQEGQSQCLEAVRLEVKQIIHMLREYLERLGQHEQRDRLDDLCTRLQMTSTKEQVDEVTDLLASFT
          KL.ILQ..Q.QCLEAVRLEVKQII.ML.EYLERLGQHEQR.RLDDLC.RLQMTSTKEQVDEVTDLLASFT
Retrocopy KLTILQGSQPQCLEAVRLEVKQIIQMLKEYLERLGQHEQRVRLDDLCNRLQMTSTKEQVDEVTDLLASFT

Parental  SLSL
          SLSL
Retrocopy SLSL

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_66 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 3 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Macropus eugenii	ENSMEUG00000013953	1 retrocopy	retro_meug_1876,
Macaca mulatta	ENSMMUG00000015254	2 retrocopies	retro_mmul_2397, retro_mmul_2444,
Sarcophilus harrisii	ENSSHAG00000009125	1 retrocopy	retro_shar_66 ,