RetrogeneDB ID: retro_ttru_1359

Retrocopy location

• Organism: Dolphin (Tursiops truncatus)
• Coordinates: scaffold_111343:22772..23684(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: FBXO28
• Ensembl ID: ENSTTRG00000013708
• Aliases: None
• Description: F-box protein 28 [Source:HGNC Symbol;Acc:29046]

Sequence

>retro_ttru_1359
ATGGCGGCGGCATCGGAGGAGCGGTTGGCTGAGGAAGGAGGCGGTGGCCCCGGCGACTGCGGCTCCCCTTCCGCCATCGG
CTCTACCCAGCGACTGCCCTCACCGACCCCGCCCGCCCCAGTCCCTGCAGCCGGGGTCCCAGGCGCCCCCAGCCTCGGCG
CTGGCTCCGGACCAGCTGCCTCAAAACAACATGCTCATGGCGCTGTCCATCGTAGCCATCGAAAACATCCCCAGCTTTAT
GTCCCAGGATGAAATTAGCCAGCTCCACCTGGTTTGTAAAAGAATGGACTTGGTCTGCCAGAGAATGTTGAATCAGGGAT
TTCTAAAAGTGGAGAGGTACCATAATCCATGTCAGAACAAGTTAAAGCACAACTCCCAAGGAGAGAGTCAGAAAGGAGAA
ACCGTTCATTAGCTCCTCATGCAGACATCCTCGCTGCGGTTGAAACAAAGCTGTCTCTCTTAAATGTGACTTTCATGAAG
CTTGTGGACTCCAATCTCTGTTGCTTCATCCCAGGAAAGGTGATTGGTGAGATTTATCATGTGTTGAGATATGTCCATTC
TACCAGAGCCCCTCAGCGAGCTCATGAAGTACTTCAAGAGTTAAGGGATATTTCCTCCATGGCAACAGAATACTTTGATG
AAAAGATTGTTCCAGTTCTAAAGAGGAAATTACCAGGATCAGATGTATCTGGAAGGCTCATGGGCTCTCCTCCAGTTCCA
GGACCTTCTGTAGCCCTGACAACAATGCAACTCTTCTCCAAGCAAAACCCTTCAAGACAAGAGGTTACCAAACTCCAGCA
GCAGGTTAAGACAAATGGTGCTGAGGTGACTGTTCTCAGGCATGAAATTTCTGAGCTTCGCACCAAAGAGCAAGAACAGC
AGAAACAGCTTCAAGACCAGGACCAGAAACTG

Alignment

ORF - retro_ttru_1359 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.22 %
• Parental protein coverage: 82.34 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MAAASEERMAEEGGGGHGDGGSPSAIGSTQRLP-PPPP-PQAPQPGSQAPPVPALAPDQLPQNNTLVALP
          MAAASEER.AEEGGGG.GD.GSPSAIGSTQRLP.P.PP.PQ..QPGSQAPP..ALAPDQLPQNN.L.AL.
Retrocopy MAAASEERLAEEGGGGPGDCGSPSAIGSTQRLPSPTPP>PQSLQPGSQAPPASALAPDQLPQNNMLMALS

Parental  IVAIENILSFMSYDEISQLRLVCKRMDLVCQRMLNQGFLKVERYHNLCQ-KQVKAQLPRRESERRNHSLA
          IVAIENI.SFMS.DEISQL.LVCKRMDLVCQRMLNQGFLKVERYHN.CQ..QVKAQLPRRESERRN.SLA
Retrocopy IVAIENIPSFMSQDEISQLHLVCKRMDLVCQRMLNQGFLKVERYHNPCQ<EQVKAQLPRRESERRNRSLA

Parental  RHADILAAVETRLSLLNMTFMKYVDSNLCCFIPGKVIDEIYRVLRYVNSTRAPQRAHEVLQELRDISSMA
          .HADILAAVET.LSLLN.TFMK.VDSNLCCFIPGKVI.EIY.VLRYV.STRAPQRAHEVLQELRDISSMA
Retrocopy PHADILAAVETKLSLLNVTFMKLVDSNLCCFIPGKVIGEIYHVLRYVHSTRAPQRAHEVLQELRDISSMA

Parental  MEYFDEKIVPILKRKLPGSDVSGRLMGSPPVPGPSAALTTMQLFSKQNPSRQEVTKLQQQVKTNGAGVTV
          .EYFDEKIVP.LKRKLPGSDVSGRLMGSPPVPGPS.ALTTMQLFSKQNPSRQEVTKLQQQVKTNGA.VTV
Retrocopy TEYFDEKIVPVLKRKLPGSDVSGRLMGSPPVPGPSVALTTMQLFSKQNPSRQEVTKLQQQVKTNGAEVTV

Parental  LRREISELRTKVQEQQKQLQDQDQKL
          LR.EISELRTK.QEQQKQLQDQDQKL
Retrocopy LRHEISELRTKEQEQQKQLQDQDQKL

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_1359 retrocopy.

TSS

Tursiops truncatus was not studied using FANTOM5 data.

Lab

retro_ttru_1359 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 3 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000010255	5 retrocopies	retro_chof_1637, retro_chof_2403, retro_chof_247, retro_chof_730, retro_chof_903,
Dipodomys ordii	ENSDORG00000004351	1 retrocopy	retro_dord_773,
Tursiops truncatus	ENSTTRG00000013708	1 retrocopy	retro_ttru_1359 ,