RetrogeneDB ID: retro_shar_6

Retrocopy location

• Organism: Tasmanian devil (Sarcophilus harrisii)
• Coordinates: GL850966.1:25512..26193(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSSHAG00000002184
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSSHAG00000015103
• Aliases: None
• Description: None

Sequence

>retro_shar_6
GAGGCAGTGGGAGCCTGTACTATAAAGCTGGTGATTGCTGTAGCAGTATTTCTACTGACATTTTATGTTATATCTCAAGT
ATTTGAAATAAAGTTAGATTCAAATTTAGGAAATTTATTTGCAAGGTCAGCACTGCAGATAGCTTACACAAAATCTCCCA
GATATAAATGTGGGATTTCAAAGGCCCCCCAAAAAAAAAATTTTGCCTTCAAAATGGCAAGTGGAGCAGCTAATGTTGTT
GGCCCCAAAATTTGTGTAGAAGAAAATATTTTAATGAGTGGTGTTAAGAATAATGTTAGAAGAGGAATCAATGTTGCATT
GGTAAATGGAAAAACTGGAGAAGCATTACACACTGAATACTTTGATATGTGGGGAAGAGATGTGACACCATTTATTGAAT
TCCTCAAGTATATTCAAGATGGAACCATAGTTTTAATGGGAACATATGATGATGGAGCAACCAAACTCACTAATGAAGCA
AGATTATTGATTGCTGCCTTGGGAAGTACAGCTATCAGTAACCTTGATTTTAGAGACAACTGGGTCTTCTGTGGTGGAAA
AGGTATCAAGACAAAAAGCCCCTTTAAAAAGCACATAAAGAACAACAAGAATACAAATAAATATGAAGGATGGCCAGAAC
TTGTAGAAATGAAAGGATGTATCCCCCAAAAGCAAGACTGA

Alignment

ORF - retro_shar_6 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.18 %
• Parental protein coverage: 99.56 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  AGAIKLVVAVAVFLLTFYVISQVFEIKLDSNLGNLFARSALQIACKDTKPPRYKCGISKACPEKHFAFKM
          A..IKLV.AVAVFLLTFYVISQVFEIKLDSNLGNLFARSALQIA...TK.PRYKCGISKA...K.FAFKM
Retrocopy ACTIKLVIAVAVFLLTFYVISQVFEIKLDSNLGNLFARSALQIAY--TKSPRYKCGISKAPQKKNFAFKM

Parental  ASGAANVVGPKICVEDNILMSGVKNNVGRGINVALVNGKTGEALRTEYFDMWGGDVAPFIEFLKSIQDGT
          ASGAANVVGPKICVE.NILMSGVKNNV.RGINVALVNGKTGEAL.TEYFDMWG.DV.PFIEFLK.IQDGT
Retrocopy ASGAANVVGPKICVEENILMSGVKNNVRRGINVALVNGKTGEALHTEYFDMWGRDVTPFIEFLKYIQDGT

Parental  IVLMGTYDDGATKLTNEARLLIAALGSTAISNLDFRDNWVFCGGKGIKTKSPFEQHIKNNKDTNKYEGWP
          IVLMGTYDDGATKLTNEARLLIAALGSTAISNLDFRDNWVFCGGKGIKTKSPF..HIKNNK.TNKYEGWP
Retrocopy IVLMGTYDDGATKLTNEARLLIAALGSTAISNLDFRDNWVFCGGKGIKTKSPFKKHIKNNKNTNKYEGWP

Parental  EVVEMEGCIPQKQD
          E.VEM.GCIPQKQD
Retrocopy ELVEMKGCIPQKQD

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_6 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 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000003224	1 retrocopy	retro_chof_1467,
Felis catus	ENSFCAG00000023087	1 retrocopy	retro_fcat_1392,
Homo sapiens	ENSG00000196937	1 retrocopy	retro_hsap_4657,
Loxodonta africana	ENSLAFG00000010029	1 retrocopy	retro_lafr_1169,
Macropus eugenii	ENSMEUG00000006906	2 retrocopies	retro_meug_2057, retro_meug_536,
Monodelphis domestica	ENSMODG00000015478	1 retrocopy	retro_mdom_1392,
Sarcophilus harrisii	ENSSHAG00000015103	1 retrocopy	retro_shar_6 ,
Tursiops truncatus	ENSTTRG00000016229	2 retrocopies	retro_ttru_1219, retro_ttru_855,