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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tagcaacttcttaaatctatgatttagagagctaaaatttacataactattagagttgctcttagttcttcatggactgattttgacacccctcatgcagAGTTCTTGCACAAGGTCAGAGCTGGAGGCTGAAAGTAAGCAAACAGACAACATTTTGGAGTATAAGCAATCAACTCAAAGGCACTTGTCTATTCCTAGCC

Basic information

species Zea mays
transcript GRMZM2G179024_T01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G179024_T01 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os09g36220.2 (Oryza sativa), 3'ss of exon 4
tagcaacttcttaaatctatgatttagagagctaaaatttacataacta--ttagagttgctcttagttcttcatggactga-ttttgacacccctcatgcagAGTTCTTGCACAAGGTCAGAGCTGGAGGCTGAAAGTAAGCAAACAGACAACATTTTGGAGTATAAGCAATCAACTCAAAGGCACTTGTCTATTCCTAGCC
     | |  ||| |||  |        |  ||    ||   ||    |  | |||  || ||   ||| ||| |||||||| |||||   |||||| |||||||||| || ||||||||||| ||||||||||| |||| ||||||  ||||  |  |||| ||||||||  |||    |||||| || || |  |||  ||
---atagtctttatatccttagcagtagggactgtcgttattatgctgagttcagatctgttcgctgttgttcgtggactgaattttggatcccctcttgcagAGTTCATGTACAAGGTCAGAACTGGAGGCTGACAGTAGGCAAACCAACAATTTACTGGAATATAAGCAGCCAATGGGAAGGCATTTCTCCAAGCCTGACC
















Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|211068419|gb|FL394011.1|FL394011
EST:     ATGTGCCCTGTAAAAATAGAGAATGCAGTGAACAAGAAAGTGATGCTCAA                         AGTTCTTGCACAAGGTCAGAGCTGGAGGCTGAAAGTAAGCAAACAGACAAC
genomic: ATGTGCCCTGTAAAAATAGAGAATGCAGTGAACAAGAAAGTGATGCTCAAgtaagtttta ... cctcatgcagAGTTCTTGCACAAGGTCAGAGCTGGAGGCTGAAAGTAAGCAAACAGACAAC
EST: gi|211271454|gb|FL402761.1|FL402761
EST:     ATGTGCCCTGTAAAAATAGAGAATGCAGTGAACAAGAAAGTGATGCTCAA                         AGTTCTTGCACAAGGTCAGAGCTGGAGGCTGAAAGTAAGCAAACAGACAAC
genomic: ATGTGCCCTGTAAAAATAGAGAATGCAGTGAACAAGAAAGTGATGCTCAAgtaagtttta ... cctcatgcagAGTTCTTGCACAAGGTCAGAGCTGGAGGCTGAAAGTAAGCAAACAGACAAC
EST: gi|211464201|gb|FL411568.1|FL411568
EST:     ATGTGCCCTGTAAAAATAGAGAATGCAGTGAACAAGAAAGTGATGCTCAA                         AGTTCTTGCACAAGGTCAGAGCTGGAGGCTGAAAGTAAGCAAACAGACAAC
genomic: ATGTGCCCTGTAAAAATAGAGAATGCAGTGAACAAGAAAGTGATGCTCAAgtaagtttta ... cctcatgcagAGTTCTTGCACAAGGTCAGAGCTGGAGGCTGAAAGTAAGCAAACAGACAAC
EST: gi|211074649|gb|FL417767.1|FL417767
EST:     ATGTGCCCTGTAAAAATAGAGAATGCAGTGAACAAGAAAGTGATGCTCAA                         AGTTCTTGCACAAGGTCAGAGCTGGAGGCTGAAAGTAAGCAAACAGACAAC
genomic: ATGTGCCCTGTAAAAATAGAGAATGCAGTGAACAAGAAAGTGATGCTCAAgtaagtttta ... cctcatgcagAGTTCTTGCACAAGGTCAGAGCTGGAGGCTGAAAGTAAGCAAACAGACAAC
EST: gi|211283973|gb|FL373342.1|FL373342
EST:     ATGTGCCCTGTAAAAATAGAGAATGCAGTGAACAAGAAAGTGATGCTCAA                         AGTTCTTGCACAAGGTCAGAGCTGGAGGCTGAAAGTAAGCAAACAGACAAC
genomic: ATGTGCCCTGTAAAAATAGAGAATGCAGTGAACAAGAAAGTGATGCTCAAgtaagtttta ... cctcatgcagAGTTCTTGCACAAGGTCAGAGCTGGAGGCTGAAAGTAAGCAAACAGACAAC
EST: gi|211068119|gb|FL380670.1|FL380670
EST:     ATGTGCCCTGTAAAAATAGAGAATGCAGTGAACAAGAAAGTGATGCTCAA                         AGTTCTTGCACAAGGTCAGAGCTGGAGGCTGAAAGTAAGCAAACAGACAAC
genomic: ATGTGCCCTGTAAAAATAGAGAATGCAGTGAACAAGAAAGTGATGCTCAAgtaagtttta ... cctcatgcagAGTTCTTGCACAAGGTCAGAGCTGGAGGCTGAAAGTAAGCAAACAGACAAC
EST: gi|211009321|gb|FL418112.1|FL418112
EST:     ATGTGCCCTGTAAAAATAGAGAATGCAGTGAACAAGAAAGTGATGCTCAA                         AGTTCTTGCACAAGGTCAGAGCTGGAGGCTGAAAGTAAGCAAACAGACAAC
genomic: ATGTGCCCTGTAAAAATAGAGAATGCAGTGAACAAGAAAGTGATGCTCAAgtaagtttta ... cctcatgcagAGTTCTTGCACAAGGTCAGAGCTGGAGGCTGAAAGTAAGCAAACAGACAAC
EST: gi|211447902|gb|FL396731.1|FL396731
EST:     ATGTGCCCTGTAAAAATAGAGAATGCAGTGAACAAGAAAGTGATGCTCAA                         AGTTCTTGCACAAGGTCAGAGCTGGAGGCTGAAAGTAAGCAAACAGACAAC
genomic: ATGTGCCCTGTAAAAATAGAGAATGCAGTGAACAAGAAAGTGATGCTCAAgtaagtttta ... cctcatgcagAGTTCTTGCACAAGGTCAGAGCTGGAGGCTGAAAGTAAGCAAACAGACAAC
EST: gi|211311125|gb|FL384821.1|FL384821
EST:     ATGTGCCCTGTAAAAATAGAGAATGCAGTGAACAAGAAAGTGATGCTCAA                         AGTTCTTGCACAAGGTCAGAGCTGGAGGCTGAAAGTAAGCAAACAGACAAC
genomic: ATGTGCCCTGTAAAAATAGAGAATGCAGTGAACAAGAAAGTGATGCTCAAgtaagtttta ... cctcatgcagAGTTCTTGCACAAGGTCAGAGCTGGAGGCTGAAAGTAAGCAAACAGACAAC
EST: gi|211211823|gb|FL379549.1|FL379549
EST:     ATGTGCCCTGTAAAAATAGAGAATGCAGTGAACAAGAAAGTGATGCTCAA                         AGTTCTTGCACAAGGTCAGAGCTGGAGGCTGAAAGTAAGCAAACAGACAAC
genomic: ATGTGCCCTGTAAAAATAGAGAATGCAGTGAACAAGAAAGTGATGCTCAAgtaagtttta ... cctcatgcagAGTTCTTGCACAAGGTCAGAGCTGGAGGCTGAAAGTAAGCAAACAGACAAC
EST: gi|211160047|gb|FL415234.1|FL415234
EST:     ATGTGCCCTGTAAAAATAGAGAATGCAGTGAACAAGAAAGTGATGCTCAA                         AGTTCTTGCACAAGGTCAGAGCTGGAGGCTGAAAGTAAGCAAACAGACAAC
genomic: ATGTGCCCTGTAAAAATAGAGAATGCAGTGAACAAGAAAGTGATGCTCAAgtaagtttta ... cctcatgcagAGTTCTTGCACAAGGTCAGAGCTGGAGGCTGAAAGTAAGCAAACAGACAAC
EST: gi|211363255|gb|FL387048.1|FL387048
EST:     ATGTGCCCTGTAAAAATAGAGAATGCAGTGAACAAGAAAGTGATGCTCAA                         AGTTCTTGCACAAGGTCAGAGCTGGAGGCTGAAAGTAAGCAAACAGACAAC
genomic: ATGTGCCCTGTAAAAATAGAGAATGCAGTGAACAAGAAAGTGATGCTCAAgtaagtttta ... cctcatgcagAGTTCTTGCACAAGGTCAGAGCTGGAGGCTGAAAGTAAGCAAACAGACAAC
EST: gi|148953113|gb|EE152594.2|EE152594
EST:     ATGTGCCCTGTAAAAATAGAGAATGCAGTGAACAAGAAAGTGATGCTCAA                         AGTTCTTGCACAAGGTCAGAGCTGGAGGCTGAAAG
genomic: ATGTGCCCTGTAAAAATAGAGAATGCAGTGAACAAGAAAGTGATGCTCAAgtaagtttta ... cctcatgcagAGTTCTTGCACAAGGTCAGAGCTGGAGGCTGAAAG

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 4 RNA-Seq libraries.


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 102

AAGAATCCAACAGAAGACTGGCGTGACAAAATCTGATAATTTGGACAGAGATGTGCCCTGTAAAAATAGAGAATGCAGTGAACAAGAAAGTGATGCTCAAgtaagtttta ... cctcatgcagAGTTCTTGCACAAGGTCAGAGCTGGAGGCTGAAAGTAAGCAAACAGACAACATTTTGGAGTATAAGCAATCAACTCAAAGGCACTTGTCTATTCCTAGCC


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 171

AAGAATCCAACAGAAGACTGGCGTGACAAAATCTGATAATTTGGACAGAGATGTGCCCTGTAAAAATAGAGAATGCAGTGAACAAGAAAGTGATGCTCAAgtaagtttta ... cctcatgcagAGTTCTTGCACAAGGTCAGAGCTGGAGGCTGAAAGTAAGCAAACAGACAACATTTTGGAGTATAAGCAATCAACTCAAAGGCACTTGTCTATTCCTAGCC


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 193

AAGAATCCAACAGAAGACTGGCGTGACAAAATCTGATAATTTGGACAGAGATGTGCCCTGTAAAAATAGAGAATGCAGTGAACAAGAAAGTGATGCTCAAgtaagtttta ... cctcatgcagAGTTCTTGCACAAGGTCAGAGCTGGAGGCTGAAAGTAAGCAAACAGACAACATTTTGGAGTATAAGCAATCAACTCAAAGGCACTTGTCTATTCCTAGCC


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 175

AAGAATCCAACAGAAGACTGGCGTGACAAAATCTGATAATTTGGACAGAGATGTGCCCTGTAAAAATAGAGAATGCAGTGAACAAGAAAGTGATGCTCAAgtaagtttta ... cctcatgcagAGTTCTTGCACAAGGTCAGAGCTGGAGGCTGAAAGTAAGCAAACAGACAACATTTTGGAGTATAAGCAATCAACTCAAAGGCACTTGTCTATTCCTAGCC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

actattagagttgctcttagttcttcatggactgattttgacacccctcatgcagAGTTCTTGCACAAGGTCAGAGCTGGAGGCTGAAAGTAAGCAAACAGACAACATTTTGGAGTATAAGCAATCAACTCAAAGGCACTTGTCTATTCCTAGCC
                                   ttttgac  putative branch site (score: 175)
                                         cacccctc  CT-rich tract
                                tgatttt  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tagcaacttcttaaatctatgatttagagagctaaaatttacataactattagagttgctcttagttcttcatggactgattttgacacccctcatgcagAGTTCTTGCACAAGGTCAGAGCTGGAGGCTGAAAGTAAGCAAACAGACAACATTTTGGAGTATAAGCAATCAACTCAAAGGCACTTGTCTATTCCTAGCC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - catggac