RetrogeneDB ID: retro_shar_617

Retrocopy location

• Organism: Tasmanian devil (Sarcophilus harrisii)
• Coordinates: GL856790.1:1045639..1046180(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSSHAG00000012512
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: PAFAH1B2
• Ensembl ID: ENSSHAG00000011403
• Aliases: None
• Description: platelet-activating factor acetylhydrolase 1b, catalytic subunit 2 (30kDa) [Source:HGNC Symbol;Acc:8575]

Sequence

>retro_shar_617
GTGAGCCAGGGGGACTCAAACCCAGCAGCTATTCCACATGCAGCTGAAGATATTCAAGGAAATGACCGATGGATGTCTCA
GCACAACAGATTTGTCTTGGATTGTAAAGACAAAGAGCCTGACATCCTATTTGTGGGAGACTCAATGGTACAGTTGCTAC
AGCAGTATAAGATATGGCGAGAGCTTTTTTCCCCCCCTTCATGCACTGAATTTTGGAATTGGTGGTGACACCACAAGGCA
TGTTTTATGGAGACTGAAGAACGGAGAACTGGAAAATATTAAACCTAAGGTTATCGTTGTCTGGGTAGGAACAAACAACG
ATGAAAATACAGCAGAGGAGATAGTAGGTGGCATTGAGGCCTTTGTACAGTTGATTACCACAAGGCAGCCGCAGGCCAAA
GTCATCGTACTGCTTCTTCTTCCTCGAGGTGAAAAGCCTAATCCTTTGAGACAAAAGAATGCAAAGGTAAATCAGCTCCT
CAAGGTCTCACTGCCCAAGCTTACCAATGTTCAGCTCTTGGATACAGATGGGGGCTTTGTG

Alignment

ORF - retro_shar_617 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.37 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MSQGDSNPAAIPHAAEDIQGDDRWMSQHNRFVLDCKDKEPDVLFVGDSMVQLLQQYEIWRELFS-PLHAL
          .SQGDSNPAAIPHAAEDIQG.DRWMSQHNRFVLDCKDKEPD.LFVGDSMVQLLQQY.IWRELFS.PLHAL
Retrocopy VSQGDSNPAAIPHAAEDIQGNDRWMSQHNRFVLDCKDKEPDILFVGDSMVQLLQQYKIWRELFS>PLHAL

Parental  NFGIGGDTTRHVLWRLKNGELENIKPKVIVVWVGTNNHENTAEEVAGGIEAIVQLINTRQPQAKVIVLGL
          NFGIGGDTTRHVLWRLKNGELENIKPKVIVVWVGTNN.ENTAEE..GGIEA.VQLI.TRQPQAKVIVL.L
Retrocopy NFGIGGDTTRHVLWRLKNGELENIKPKVIVVWVGTNNDENTAEEIVGGIEAFVQLITTRQPQAKVIVLLL

Parental  LPRGEKPNPLRQKNAKVNQLLKVSLPKLANVQLLDTDGGFV
          LPRGEKPNPLRQKNAKVNQLLKVSLPKL.NVQLLDTDGGFV
Retrocopy LPRGEKPNPLRQKNAKVNQLLKVSLPKLTNVQLLDTDGGFV

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_617 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 14 parental genes, and 21 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000008628	2 retrocopies	retro_amel_1145, retro_amel_818,
Canis familiaris	ENSCAFG00000013226	1 retrocopy	retro_cfam_1335,
Callithrix jacchus	ENSCJAG00000012698	1 retrocopy	retro_cjac_3325,
Dipodomys ordii	ENSDORG00000011274	1 retrocopy	retro_dord_560,
Felis catus	ENSFCAG00000029945	1 retrocopy	retro_fcat_270,
Homo sapiens	ENSG00000168092	2 retrocopies	retro_hsap_1148, retro_hsap_4661,
Gorilla gorilla	ENSGGOG00000028197	2 retrocopies	retro_ggor_2893, retro_ggor_893,
Macaca mulatta	ENSMMUG00000002050	2 retrocopies	retro_mmul_2481, retro_mmul_892,
Mustela putorius furo	ENSMPUG00000004246	1 retrocopy	retro_mputfur_898,
Nomascus leucogenys	ENSNLEG00000007337	2 retrocopies	retro_nleu_1096, retro_nleu_946,
Pongo abelii	ENSPPYG00000003907	2 retrocopies	retro_pabe_3621, retro_pabe_953,
Pan troglodytes	ENSPTRG00000004318	2 retrocopies	retro_ptro_3097, retro_ptro_782,
Rattus norvegicus	ENSRNOG00000018032	1 retrocopy	retro_rnor_2585,
Sarcophilus harrisii	ENSSHAG00000011403	1 retrocopy	retro_shar_617 ,