RetrogeneDB ID: retro_shar_32

Retrocopy location

• Organism: Tasmanian devil (Sarcophilus harrisii)
• Coordinates: GL867601.1:148865..149450(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSSHAG00000005282
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSSHAG00000009747
• Aliases: None
• Description: None

Sequence

>retro_shar_32
ATGCCGTTATCGCCACTTCGACTGGCAGTTGTGTGCTCTAGTAACCAGAACCGCAGTATGGAGGCCCACAATATCCTCCT
TAAACGGGGATTCAGTGTCAGATCCTTTGGGTCGGGCAGCCGCGTGAAACTCCCAGGGCCGGCGCCAGACAAGCCAAATA
TTTATGACTTCAAGACAACTTATGATCAGATTTACAACGATCTCCTCAAGAAGGACAAGAAGCTCTACACCCAGAATGGG
ATTCTGCATATGTTGAACAGAAACAAGAGGATCAAGCCCGGGCCAGAACGATTCCAGAATTGCGAAGATTTGTTTGACCT
CATCCTTACCTGTGAAGAAAAAGTCTATGACCAGGTAGTGGAATATCTAACTTCCAGAGAGCAAGAAACCTGCCAGCCGG
TTCATGTCGTGAATGTGGATATAAAAGATGACCAGGAGGAAGCCATCCTAGGAGCCTTTCTCATTTGTGAACTCTGCCAG
TGTATACAGCTCACAGAAGATATGGAGAATGAGATCGATGAGCTCTTGCAGGAATTTGAGGAGAAGAGCAACAAGAGCTT
CCTTCACACTGTCTGCTTTTACTGA

Alignment

ORF - retro_shar_32 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.83 %
• Parental protein coverage: 99.4 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  KRGFSVRSFGTGTHVKLPGPAPDKPNVYDFKTTYDQMYNDLLRKDKELYTQNGILHMLDRNKRIKPRPER
          KRGFSVRSFG.G..VKLPGPAPDKPN.YDFKTTYDQ.YNDLL.KDK.LYTQNGILHML.RNKRIKP.PER
Retrocopy KRGFSVRSFGSGSRVKLPGPAPDKPNIYDFKTTYDQIYNDLLKKDKKLYTQNGILHMLNRNKRIKPGPER

Parental  FQNCKDLFDLILTCEERVYDQVVEDLNSREQETCQPVHVINVDIQDNHEEATLGAFLICELCQCIQHTED
          FQNC.DLFDLILTCEE.VYDQVVE.L.SREQETCQPVHV.NVDI.D..EEA.LGAFLICELCQCIQ.TED
Retrocopy FQNCEDLFDLILTCEEKVYDQVVEYLTSREQETCQPVHVVNVDIKDDQEEAILGAFLICELCQCIQLTED

Parental  MENEIDELLQEFEEKSSRTFLHTVCFY
          MENEIDELLQEFEEKS...FLHTVCFY
Retrocopy MENEIDELLQEFEEKSNKSFLHTVCFY

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_32 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 17 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000013736	3 retrocopies	retro_amel_1930, retro_amel_292, retro_amel_84,
Dipodomys ordii	ENSDORG00000011714	1 retrocopy	retro_dord_433,
Erinaceus europaeus	ENSEEUG00000010799	1 retrocopy	retro_eeur_648,
Felis catus	ENSFCAG00000003318	1 retrocopy	retro_fcat_54,
Microcebus murinus	ENSMICG00000011016	5 retrocopies	retro_mmur_1057, retro_mmur_1081, retro_mmur_1353, retro_mmur_890, retro_mmur_891,
Mustela putorius furo	ENSMPUG00000014394	2 retrocopies	retro_mputfur_108, retro_mputfur_1408,
Sarcophilus harrisii	ENSSHAG00000009747	1 retrocopy	retro_shar_32 ,
Tupaia belangeri	ENSTBEG00000010136	3 retrocopies	retro_tbel_1675, retro_tbel_2435, retro_tbel_2704,