RetrogeneDB ID: retro_ttru_1015

Retrocopy location

• Organism: Dolphin (Tursiops truncatus)
• Coordinates: scaffold_100052:29495..30004(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PPP4C
• Ensembl ID: ENSTTRG00000005532
• Aliases: None
• Description: protein phosphatase 4, catalytic subunit [Source:HGNC Symbol;Acc:9319]

Sequence

>retro_ttru_1015
GGCTCCGTCACCATGTAGCACTACTGCTCTGAGATCTTTGACTACCTCAGCCTGTTGGCCGTCGCTGATCACAAGATCTT
TTGTGTGCACAGGGCCTCTCCACCTCCATCTAGGCCCTGGACTAGATGCAGATGATTGACCAAAAGCAAGACGTGCCCCT
TGATGGACTGTGTGTGACCTGCTCTGGTTCGACCCTCAAGACACAACAGGATGGTGTGGGAGTCCTGTGGGACCGGCTAC
GTATTTCGCAGTGATGTGGTGACCCAGTTCCATTCAACCAAGGACACTGACATGATCCGGGCCCACCACCTGGTGACAGG
TTACGAATGGCACTTCAGTGAAACTGTGCTCACTGTTCAGTTGTCACCCAACTACTGCTACAACTGTGGGAATATGGCAG
CTATCCTGGAGCTGGATAAGCATCTTCAGGAAGATTTCAGTATATTTGAGGCTACTCCTGAGGGACATGGGGCATCCCCT
TCAAGAAGCCAGTGGCTGAATACTTCCTG

Alignment

ORF - retro_ttru_1015 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.67 %
• Parental protein coverage: 56.35 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  GSVTVWRYCTEIFDYLSLSAIIDGKIFCVHG-GLSPSIQTLDQIRTIDRKQEVPHDG-PMCDLLWSDPED
          GSVT...YC.EIFDYLSL.A..D.KIFCVH..GLS.SI..LD....ID.KQ.VP.DG...CDLLW.DP.D
Retrocopy GSVTM*HYCSEIFDYLSLLAVADHKIFCVHR<GLSTSI*ALD*MQMIDQKQDVPLDG<TVCDLLWFDPQD

Parental  TTGWGVSPRG-AGYLFGSDVVAQFNAANDIDMICRAHQLVMEGYKWHFNETVLTVWSAPNYCYRCGNVAA
          TTGW..SP.G..GY.F.SDVV.QF....D.DMI.RAH.LV..GY.WHF.ETVLTV...PNYCY.CGN.AA
Retrocopy TTGWCGSPVG<TGYVFRSDVVTQFHSTKDTDMI-RAHHLVT-GYEWHFSETVLTVQLSPNYCYNCGNMAA

Parental  ILELDEHLQKDFIIFEAAPQ-ETRGIPSKKPVADYFL
          ILELD.HLQ.DF.IFEA.P...T.GIP.KKPVA.YFL
Retrocopy ILELDKHLQEDFSIFEATPE<GTWGIPFKKPVAEYFL

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_1015 retrocopy.

TSS

Tursiops truncatus was not studied using FANTOM5 data.

Lab

retro_ttru_1015 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 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000015223	1 retrocopy	retro_amel_286,
Canis familiaris	ENSCAFG00000017089	1 retrocopy	retro_cfam_16,
Ciona savignyi	ENSCSAVG00000004266	1 retrocopy	retro_csav_27,
Equus caballus	ENSECAG00000022179	1 retrocopy	retro_ecab_911,
Felis catus	ENSFCAG00000014171	1 retrocopy	retro_fcat_1043,
Macropus eugenii	ENSMEUG00000000397	5 retrocopies	retro_meug_1014, retro_meug_1188, retro_meug_1336, retro_meug_560, retro_meug_859,
Ornithorhynchus anatinus	ENSOANG00000008136	1 retrocopy	retro_oana_25,
Pan troglodytes	ENSPTRG00000007984	1 retrocopy	retro_ptro_28,
Tursiops truncatus	ENSTTRG00000000102	1 retrocopy	retro_ttru_1576,
Tursiops truncatus	ENSTTRG00000005532	1 retrocopy	retro_ttru_1015 ,
Tursiops truncatus	ENSTTRG00000016859	1 retrocopy	retro_ttru_1584,