RetrogeneDB ID: retro_shar_428

Retrocopy location

• Organism: Tasmanian devil (Sarcophilus harrisii)
• Coordinates: GL842388.1:19551..20094(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PPP2CA
• Ensembl ID: ENSSHAG00000016632
• Aliases: None
• Description: protein phosphatase 2, catalytic subunit, alpha isozyme [Source:HGNC Symbol;Acc:9299]

Sequence

>retro_shar_428
AGACAATATGGAAATGCAAATGTTTGGAAATATTTTACAGACTTTTTGATCATCTTCCTCTAACTGCCTTGGTGTATGGT
CAGATATTCTGTCTACATGGTGGTCTCTCACTAGGCATAGATACACTGGATCATATCAAAGCACTTGATCGCCTACAAGA
AGTTCCTCATGAGAGTCCAATGTGTGACTTGCTTTGTCAGATCCAGATGACTGTGGTGGTTGGGGTATTTCTCCTCGAGG
TGCTGGACATACAATTGGACAAGATATTTCAGAGATATTTAATTATGCCAATGGCCTCAACATTGATATCCAGAGCTCAA
CAGCTGGTGATGAAGGGATATAATTGATGTCATGACAGGGATGTAGTAACAATATTCAGTGCTCTAAACTATTGCTACTG
TGCTGGTAACCAAGCTGCAGTCATGGAACTTGATGATACGCTAGTGAACTCCTTCTTGCAAGTTTGATCCAACACCATGC
AGAGGTGAACCACATTTTATTAGCTGTACCCCAGATTACTTCCTGTAATGAGATTTTAAATGT

Alignment

ORF - retro_shar_428 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.92 %
• Parental protein coverage: 54.35 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  RKYGNANVWKYFTD-LFDYLPLTALVDGQIFCLHGGLSPSIDTLDHIRALDRLQEVPHEGPMCDLL-WSD
          R.YGNANVWKYFTD.LFD.LPLTALV.GQIFCLHGGLS..IDTLDHI.ALDRLQEVPHE.PMCDLL..SD
Retrocopy RQYGNANVWKYFTD<LFDHLPLTALVYGQIFCLHGGLSLGIDTLDHIKALDRLQEVPHESPMCDLL<LSD

Parental  PDDRGGWGISPRGAGYTFGQDISETFNHANGL-TLVSRAHQLVMEGYNWCHDRNVVTIFSAPNYCYRCGN
          PDD.GGWGISPRGAG.T.GQDISE.FN.ANGL.TL.SRA.QLVM.GYN.CHDR.VVTIFSA.NYCY..GN
Retrocopy PDDCGGWGISPRGAGHTIGQDISEIFNYANGL>TLISRAQQLVMKGYN*CHDRDVVTIFSALNYCYCAGN

Parental  QAAIMELDDTLKYSFLQ-FDPAPRRGEPHVTRRTPDYFLCLQLSC
          QAA.MELDDTL..SFLQ.FDP.P.RGEPH....TPDYFL.....C
Retrocopy QAAVMELDDTLVNSFLQ>FDPTPCRGEPHFISCTPDYFL**DFKC

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_428 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 15 parental genes, and 29 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000002653	1 retrocopy	retro_acar_69,
Bos taurus	ENSBTAG00000000469	1 retrocopy	retro_btau_1754,
Callithrix jacchus	ENSCJAG00000013634	2 retrocopies	retro_cjac_1346, retro_cjac_4113,
Dasypus novemcinctus	ENSDNOG00000013011	4 retrocopies	retro_dnov_1025, retro_dnov_1844, retro_dnov_2100, retro_dnov_2122,
Echinops telfairi	ENSETEG00000007561	2 retrocopies	retro_etel_1233, retro_etel_659,
Felis catus	ENSFCAG00000029685	1 retrocopy	retro_fcat_1086,
Homo sapiens	ENSG00000113575	1 retrocopy	retro_hsap_369,
Mustela putorius furo	ENSMPUG00000010169	1 retrocopy	retro_mputfur_633,
Nomascus leucogenys	ENSNLEG00000026729	1 retrocopy	retro_nleu_2441,
Otolemur garnettii	ENSOGAG00000009695	2 retrocopies	retro_ogar_3414, retro_ogar_921,
Rattus norvegicus	ENSRNOG00000005389	5 retrocopies	retro_rnor_1263, retro_rnor_1264, retro_rnor_1265, retro_rnor_1266, retro_rnor_817,
Sorex araneus	ENSSARG00000005447	3 retrocopies	retro_sara_296, retro_sara_385, retro_sara_715,
Sarcophilus harrisii	ENSSHAG00000016632	3 retrocopies	retro_shar_313, retro_shar_428 , retro_shar_471,
Ictidomys tridecemlineatus	ENSSTOG00000010560	1 retrocopy	retro_itri_258,
Tursiops truncatus	ENSTTRG00000016859	1 retrocopy	retro_ttru_1584,