RetrogeneDB ID: retro_ttru_1228

Retrocopy location

• Organism: Dolphin (Tursiops truncatus)
• Coordinates: scaffold_107703:10464..11868(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RBM46
• Ensembl ID: ENSTTRG00000001239
• Aliases: None
• Description: RNA binding motif protein 46 [Source:HGNC Symbol;Acc:28401]

Sequence

>retro_ttru_1228
ATGAATGAAGAAAATACAGATGGAACAAATGGATGCAGTAAAGTCCGAACTGGTACTCAGAATGAAGCAGCATTACTTGC
TTTGATGGAAAAGACTGGATACAACATGGTTCAAGAAAATGGGCAAAGGAAGTTTAGTGGTTCGCCTCCAGGTTGGGAAG
GTCCACCTCCACCTAGAGGCTGTGAAGTTTTTGTAGGAAAAATACCTCGTGATATGTACGAAGATGAATTAGTTCCTGTA
TTTGAAAGAGCTGGGAAGATATATGAATTTCGACTTATGATGGAATTTAGTGGTGAAAATCGAGGTTATGCTTTTGTGAT
GTGTACTACAAAAGAAGAAGCCCAGTTAGCCATCAGAATTCTTAATAATTATGAGATGCGACCAGGGAAGTTTATCGGTG
TGTGTGTAAGCTTGGATAATTACAGATTATTTATTGGAGTTATTCTGAAGGAAAAGAAGAAGGAAGAAATCTTGGATGAA
ATGAAGAAAGTTACAGAAGGAGTTGTAGATGTCATTGTTTACCCAAGCGCAACTGATAAGACCAAAAATCGCAGTTTTGC
GTTTGTTGAGTATGAATCTCAGAGAGCTACTGCTATGGCTAGGAGAAAACTAATTCCAGGAACCTTCAAACTGTAGGGCC
ATACCATTCAGGTAGATTGGACTGACCCAGAGAAAGAGGTTGATGAGGAAACCACGCAGAGAGTTAAAGTTCTCTATGTA
TGAAATGTAATGATCTCAACTACAGAGGAAACAATTAAAGCAGAATTCAATAAATTCAAACCTGGTGCAGTTGAATGAGT
AAAGAAACGTAGAGATTATGCTTTTGTTCACTTTTTCAACCGAGAAGATGCAGTGGCTGCTATGTCTGTTATGAATGGAA
AATGCATTGATGGAGCAAGTATTGAGGTAACACTGGGAAAACCTGTAAATAAAGAAAACACTTGGAGACAGCATCTTAAT
GGTCAGATCAGCCCCAATTCAGAAAACCTGATTGTGTTTGCTAACAAAGAAGAGAGCCACCCAAAAACTCTAGGCATGGT
ACCAACTCTTCCAGCTTGTCTCAATGGCCAGCATGGCCCAAGCCTCCCCGAAATTGAAAGATGCGCTTATCCATTTTTTC
CTGGAACAAAGCTTACTCCAATTAGTATGTATTCTTTAAAATCCAATCATTTCAATTCTGAAGTAATGCATTTGGATTAT
TACTGCAACAAAAATAATTGGGCACCACCAGAGTATTATTTATATTCAACAACAAGTCAAGATGGGAAAGTACTCTTGGC
ATATAAAATCGTTATTCCTGCTATTGCAAATGGATCCCAGAGTTACTTCATGCCAGACAAACTCTGTACTACATTGGAAG
ATGCAAAGGAACTGGCGGCCCAGCTTACGTTACTTCATTTGGAC

Alignment

ORF - retro_ttru_1228 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.09 %
• Parental protein coverage: 87.8 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MNEENTDGTNGCSKVRTGTQNEAALLALMEKTGYNMVQENGQRKFGGPPPGWEGPPPPRGCEVFVGKIPR
          MNEENTDGTNGCSKVRTGTQNEAALLALMEKTGYNMVQENGQRKF.G.PPGWEGPPPPRGCEVFVGKIPR
Retrocopy MNEENTDGTNGCSKVRTGTQNEAALLALMEKTGYNMVQENGQRKFSGSPPGWEGPPPPRGCEVFVGKIPR

Parental  DMYEDELVPVFERAGKIYEFRLMMEFSGENRGYAFVMYTTKEEAQLAIRILNNYEIRPGKFIGVCVSLDN
          DMYEDELVPVFERAGKIYEFRLMMEFSGENRGYAFVM.TTKEEAQLAIRILNNYE.RPGKFIGVCVSLDN
Retrocopy DMYEDELVPVFERAGKIYEFRLMMEFSGENRGYAFVMCTTKEEAQLAIRILNNYEMRPGKFIGVCVSLDN

Parental  CRLFIGAIPKEKKKEEILDEMKKVTEGVVDVIVYPSATDKTKNRGFAFVEYESHRAAAMARRKLIPGTFQ
          .RLFIG.I.KEKKKEEILDEMKKVTEGVVDVIVYPSATDKTKNR.FAFVEYES.RA.AMARRKLIPGTF.
Retrocopy YRLFIGVILKEKKKEEILDEMKKVTEGVVDVIVYPSATDKTKNRSFAFVEYESQRATAMARRKLIPGTFK

Parental  LWGHTIQVDWADPEKEVDEETMQRVKVLYVRNLMISTAEETIKVEFSKFKPGAVERVKKLRDYAFVHFFN
          L.GHTIQVDW.DPEKEVDEET.QRVKVLYV.N.MIST.EETIK.EF.KFKPGAVE.VKK.RDYAFVHFFN
Retrocopy L*GHTIQVDWTDPEKEVDEETTQRVKVLYV*NVMISTTEETIKAEFNKFKPGAVE*VKKRRDYAFVHFFN

Parental  REDAVAAMSVMNGKCIDGARIEVTLAKPVIKENTWRQHLNGQISPNSENLIVFANKEESYPKILGKPPTL
          REDAVAAMSVMNGKCIDGA.IEVTL.KPV.KENTWRQHLNGQISPNSENLIVFANKEES.PK.LG..PTL
Retrocopy REDAVAAMSVMNGKCIDGASIEVTLGKPVNKENTWRQHLNGQISPNSENLIVFANKEESHPKTLGMVPTL

Parental  PARLNGQHSPGLPEIERCTYPLFPGTKLTPISMYSLKSSHFNSAVMHLDYYCNKNNWAPPEYYLYSTTSQ
          PA.LNGQH.P.LPEIERC.YP.FPGTKLTPISMYSLKS.HFNS.VMHLDYYCNKNNWAPPEYYLYSTTSQ
Retrocopy PACLNGQHGPSLPEIERCAYPFFPGTKLTPISMYSLKSNHFNSEVMHLDYYCNKNNWAPPEYYLYSTTSQ

Parental  DGKVLLIYKIVIPAIANGSQSYFMPDKLCTTLEDAKELAAQFTLLHLD
          DGKVLL.YKIVIPAIANGSQSYFMPDKLCTTLEDAKELAAQ.TLLHLD
Retrocopy DGKVLLAYKIVIPAIANGSQSYFMPDKLCTTLEDAKELAAQLTLLHLD

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_1228 retrocopy.

TSS

Tursiops truncatus was not studied using FANTOM5 data.

Lab

retro_ttru_1228 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 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000010284	1 retrocopy	retro_cpor_809,
Tursiops truncatus	ENSTTRG00000001239	1 retrocopy	retro_ttru_1228 ,