RetrogeneDB ID: retro_ttru_1584

Retrocopy location

• Organism: Dolphin (Tursiops truncatus)
• Coordinates: scaffold_30136:401..1326(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PPP2CA
• Ensembl ID: ENSTTRG00000016859
• Aliases: None
• Description: protein phosphatase 2, catalytic subunit, alpha isozyme [Source:HGNC Symbol;Acc:9299]

Sequence

>retro_ttru_1584
ATGGACGACAAGGCGTTCACCAAGGAGCTGGACCAGTGGGTCGAGCAGCTGAACGAGTGTAAACAACTGAACGAGAACCA
GGTGCGGACGCTGTGCGAAAAGGCTAAGGAAATTTTAACAAAAGAATCAAATGTGCAAGAGGTCCGTTGTCCTGTTACCG
TCTGTGGAGATGTGCATGGTCAATTCCATGATCTTATGGAACTCTTTAGAATCGGTGGGAAGTCACCAGATACAAACTAT
CTATTCATGGGTGACTATGTAGACAGAGGTTATTATTCTGTGGAGACTGTGACTCTTCTTGTGGCATTAAAGGTGCGTTA
CCCAGAACGTATTACAATATTGAGAGGAAACCACGAAAGCCGACAAATTACCCAAGTATATGGCTTTTATGATGAATGTC
TGCGAAAGTATGGGAATGCCAATGTTTGGAAATACTTTACAGATCTGTTTGACTATCTGCCACTTACAGCTTTAGTAGAT
GGGCAGATATTCTGCCTCCATGGTGGCCTCTCCCCATCCATAGATACACTGGATCATATAAGAGCCCTGGATCGTTTACA
GAAGTTCCACATGAGGGCCCAATGTGTGATCTATATGGTCAGATCCAGATGATAGTAGTGGGTGGTGTATTTCACCACGT
GGCGATGGATACACATTCGGACAAGATATTTACAAAACGTTTAACCAAGCCAATGGTTTCACAATGGTTTGTCGTGATCA
CCAACTTGTAATGGAGGTATTCAATTGGTGTCACGATCGGAATGTGGTTACCATTTTCAGCGCACCGAATTACTGTTATT
TTTGTGGGAGGCAGGCGGTTATCATGGAATTAGATGACACTTAGAAGTATTCCTTCCTTCAGTTTGACCCAGCACCTCGT
CGTGGAGAGCCTCACGTGATCCGGCGCACCCCAGCATACTTTCTG

Alignment

ORF - retro_ttru_1584 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.68 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MDEKVFTKELDQWVEQLNECKQLSESQVKSLCEKAKEILTKESNVQEVRCPVTVCGDVHGQFHDLMELFR
          MD.K.FTKELDQWVEQLNECKQL.E.QV..LCEKAKEILTKESNVQEVRCPVTVCGDVHGQFHDLMELFR
Retrocopy MDDKAFTKELDQWVEQLNECKQLNENQVRTLCEKAKEILTKESNVQEVRCPVTVCGDVHGQFHDLMELFR

Parental  IGGKSPDTNYLFMGDYVDRGYYSVETVTLLVALKVRYRERITILRGNHESRQITQVYGFYDECLRKYGNA
          IGGKSPDTNYLFMGDYVDRGYYSVETVTLLVALKVRY.ERITILRGNHESRQITQVYGFYDECLRKYGNA
Retrocopy IGGKSPDTNYLFMGDYVDRGYYSVETVTLLVALKVRYPERITILRGNHESRQITQVYGFYDECLRKYGNA

Parental  NVWKYFTDLFDYLPLTALVDGQIFCLHGGLSPSIDTLDHIRALDRLQ-EVPHEGPMCDL-LWSDPDDRGG
          NVWKYFTDLFDYLPLTALVDGQIFCLHGGLSPSIDTLDHIRALDRLQ.EVPHEGPMCDL..WSDPDD..G
Retrocopy NVWKYFTDLFDYLPLTALVDGQIFCLHGGLSPSIDTLDHIRALDRLQ<EVPHEGPMCDL<IWSDPDDSSG

Parental  WGISPRGAGYTFGQDISETFNHANGLTLVSRAHQLVMEGYNWCHDRNVVTIFSAPNYCYRCGNQAAIMEL
          W.ISPRG.GYTFGQDI..TFN.ANG.T.V.R.HQLVME..NWCHDRNVVTIFSAPNYCY.CG.QA.IMEL
Retrocopy WCISPRGDGYTFGQDIYKTFNQANGFTMVCRDHQLVMEVFNWCHDRNVVTIFSAPNYCYFCGRQAVIMEL

Parental  DDTLKYSFLQFDPAPRRGEPHVTRRTPDYFL
          DDT.KYSFLQFDPAPRRGEPHV.RRTP.YFL
Retrocopy DDT*KYSFLQFDPAPRRGEPHVIRRTPAYFL

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Tursiops truncatus was not studied using RNA-Seq expression data.

ChIP-Seq

Tursiops truncatus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ttru_1584 retrocopy.

TSS

Tursiops truncatus was not studied using FANTOM5 data.

Lab

retro_ttru_1584 was not experimentally validated.

Homology

Retrocopy orthology:

Tursiops truncatus 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 11 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000002653	1 retrocopy	retro_acar_69,
Bos taurus	ENSBTAG00000000469	1 retrocopy	retro_btau_1754,
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,
Mustela putorius furo	ENSMPUG00000010169	1 retrocopy	retro_mputfur_633,
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,
Tursiops truncatus	ENSTTRG00000000102	1 retrocopy	retro_ttru_1576,
Tursiops truncatus	ENSTTRG00000005532	1 retrocopy	retro_ttru_1015,
Tursiops truncatus	ENSTTRG00000016859	1 retrocopy	retro_ttru_1584 ,