RetrogeneDB ID: retro_ttru_1439

Retrocopy location

• Organism: Dolphin (Tursiops truncatus)
• Coordinates: scaffold_113240:645893..646686(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PITPNB
• Ensembl ID: ENSTTRG00000001278
• Aliases: None
• Description: phosphatidylinositol transfer protein, beta [Source:HGNC Symbol;Acc:9002]

Sequence

>retro_ttru_1439
ATGATGCTGTTCAAGGAGTATGGAGTCATCCTACCTGCGTCTGTAGAAGAGTGTCAAGTAGGGCAGCTGTATTCTGTGGT
GGAGGCCAGGGAAAATGGGAATGGGTGGTGGTGAAAGTGTGGAGGTTCTGGTGAATGAGACCTATGAAAAGAACGGTGAG
AAAGGCCAGTACATGCACAAGATCTACCACTTACAGGGCAAAGTGCCCACATTTGTTGGAATGCTGGCCCCAGATGGAGC
CCTGGATATATGAAAAAGCATGTAATGACTACTTTTATTACAGAACTGTTATTACAAATGAGTACCTGAAAGACTACTGT
CTGATTAAAATGGAAACCTGGCATAAACCAGATCTTGGCACCCAGGAAAATGTGCATAAACTGGAGCCTGAGGCATGGAA
ACATGTGGAAGCCATATATACAGACATTGCAGATTAAAGTGAAGTACTTAGACAGAATTACAAGGCAGAGGAAGATCCAG
AAAAATTTTTATCTATCAAAACAGGCCGAGGATCCTTGACCCCAATTGGAAATAAGAACTTGTAAATCAGAAAGACTGCC
CATACTTGTGTGCATATAAACTGGATACTGTCAAGTTCAAGGGGTGGGGCCTACAGAACAAAGTGGAAAATTTTATACAT
AAGCAAGAGAGACATCTGTTTACAAACTTCCACAGGCAGCTATTCTGTTGGATCAATAACTGGGTTGACCTGACTATGGA
GAACATTTGAAGGATGGAAGAAGAGACAAAGAGACAGCTGGATGAGATGAGACAGAAGGACCCAGTGAAAGGA

Alignment

ORF - retro_ttru_1439 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 60.45 %
• Parental protein coverage: 97.43 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MVLIKEFRVVLPCSVQEYQVGQLYSVAEASKNETG-GGEGIEVLKNEPYEKDGEKGQYTHKIYHL-KSKV
          M.L.KE..V.LP.SV.E.QVGQLYSV.EA..N..G.GGE..EVL.NE.YEK.GEKGQY.HKIYHL...K.
Retrocopy MMLFKEYGVILPASVEECQVGQLYSVVEARENGNG>GGESVEVLVNETYEKNGEKGQYMHKIYHL>RAKC

Parental  PAFVRMIAPEGSLVFHEKAWNAYPYCRTIVTNEYMKDDFFIKIETWHKPDLGTLENVHGLDPNTWKTVEV
          P.......P.......EKA.N.Y.Y.RT..TNEY.KD...IK.ETWHKPDLGT.ENVH.L.P..WK.VE.
Retrocopy PHLLECW-PQMEPWIYEKACNDYFYYRTVITNEYLKDYCLIKMETWHKPDLGTQENVHKLEPEAWKHVEA

Parental  VHIDIADRSQVEPADYKADEDPALFQSVKTKRGPL-GPNWKKELASNPDCPQMCAYKLVTIKFKWWGLQS
          ...DIAD.S.V....YKA.EDP..F.S.KT.RG.L..PNWK.EL....DCP..CAYKL.T.KFK.WGLQ.
Retrocopy IYTDIAD*SEVLRQNYKAEEDPEKFLSIKTGRGSL<DPNWK*ELVNQKDCPYLCAYKLDTVKFKGWGLQN

Parental  KVENFIQKQEKRIFTNFHRQLFCWIDKWIDLTMEDIRRMEDETQKELETLRNQGQVRG
          KVENFI.KQE...FTNFHRQLFCWI..W.DLTME.I.RME.ET...L...R....V.G
Retrocopy KVENFIHKQERHLFTNFHRQLFCWINNWVDLTMENI*RMEEETKRQLDEMRQKDPVKG

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_1439 retrocopy.

TSS

Tursiops truncatus was not studied using FANTOM5 data.

Lab

retro_ttru_1439 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 10 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000012309	2 retrocopies	retro_chof_2374, retro_chof_860,
Cavia porcellus	ENSCPOG00000012298	1 retrocopy	retro_cpor_957,
Macropus eugenii	ENSMEUG00000010442	3 retrocopies	retro_meug_392, retro_meug_689, retro_meug_786,
Oryctolagus cuniculus	ENSOCUG00000000511	1 retrocopy	retro_ocun_1620,
Otolemur garnettii	ENSOGAG00000000391	1 retrocopy	retro_ogar_1300,
Ochotona princeps	ENSOPRG00000002540	1 retrocopy	retro_opri_931,
Tupaia belangeri	ENSTBEG00000000293	1 retrocopy	retro_tbel_4285,
Takifugu rubripes	ENSTRUG00000018546	1 retrocopy	retro_trub_36,
Tarsius syrichta	ENSTSYG00000001148	1 retrocopy	retro_tsyr_503,
Tursiops truncatus	ENSTTRG00000001278	2 retrocopies	retro_ttru_1060, retro_ttru_1439 ,