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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttaatcttcttttggtggagcatctttaaacactgacagcagacgatttatatgagtgggtcatggaaattgatgtgaacatgtgctctattgcagATTACAATGGCTATTGCAAGAGAAGTTGCTTCTGTCACCAAACTAGGTGTAGAG

Basic information

species Zea mays
transcript GRMZM2G139462_T03
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G139462_T06 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os01g73450.1 (Oryza sativa), 3'ss of exon 2
gttaatcttcttttggtggagcatctttaaacactgacagcagacgatttatatgagtgggtcatggaaattgatgtgaacatgtgctctattgcagATTACAATGGCTATTGCAAGAGAAGTTGCTTCTGTCACCAAACTAGGTGTAGAG
|| |   | ||||| |||||||||  | |||     |   | ||  ||||    ||   ||||||| || |   ||| |   |||    | |||||||| || ||||| ||||||||||| |||||||||||||||| |||||||||||||
gtgaggttgcttttagtggagcattatcaaatttaaaatactgaatatttgatggaacaggtcatgtaagt--gtgtaa---tgt----tgttgcagATCACGATGGCAATTGCAAGAGAGGTTGCTTCTGTCACCAGACTAGGTGTAGAG
















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|76917142|gb|DV166699.1|DV166699
EST:     TAAGTGGGGAAGCTCTTGCCGGGAATCACACAGAAAACATCGACCCAGAG                         ATTACAATGGCTATTGCAAGAGAAGTTGCTTCTGTCACCAAACTAGGTGTA
genomic: TAAGTGGGGAAGCTCTTGCCGGGAATCACACAGAAAACATCGACCCAAAGgttaatcttc ... tctattgcagATTACAATGGCTATTGCAAGAGAAGTTGCTTCTGTCACCAAACTAGGTGTA
EST: gi|211175205|gb|FL094962.1|FL094962
EST:     TAAGTGGGGAAGCTCTTGCCGGGAATCACACAGAAAACATCGACCCAAAG                         ATTACAATGGCTATTGCAAGAGAAGTTGCTTCTGTCACCAAACTAGGTGTA
genomic: TAAGTGGGGAAGCTCTTGCCGGGAATCACACAGAAAACATCGACCCAAAGgttaatcttc ... tctattgcagATTACAATGGCTATTGCAAGAGAAGTTGCTTCTGTCACCAAACTAGGTGTA
EST: gi|211173537|gb|FL094957.1|FL094957
EST:     TAAGTGGGGAAGCTCTTGCCGGGAATCACACAGAAAACATCGACCCAAAG                         ATTACAATGGCTATTGCAAGAGAAGTTGCTTCTGTCACCAAACTAGGTGTA
genomic: TAAGTGGGGAAGCTCTTGCCGGGAATCACACAGAAAACATCGACCCAAAGgttaatcttc ... tctattgcagATTACAATGGCTATTGCAAGAGAAGTTGCTTCTGTCACCAAACTAGGTGTA
EST: gi|84980665|gb|DW531014.1|DW531014
EST:     TAAGTGGGGAAGCTCTTGCCGGGAATCACACAGAAAACATCGACCCAAAG                         ATTACAATGGCTATTGCAAGAGAAGTTGCTTCTGTCACCAAACTAGGTGTA
genomic: TAAGTGGGGAAGCTCTTGCCGGGAATCACACAGAAAACATCGACCCAAAGgttaatcttc ... tctattgcagATTACAATGGCTATTGCAAGAGAAGTTGCTTCTGTCACCAAACTAGGTGTA
EST: gi|76013765|gb|DT940935.1|DT940935
EST:     TAAGTGGGGAAGCTCTTGCCGGGAATCACACAGAAAACATCGACCCAAAG                         ATTACAATGGCTATTGCAAGAGAAGTTGCTTCTGTCACCAAACTAGGTGTA
genomic: TAAGTGGGGAAGCTCTTGCCGGGAATCACACAGAAAACATCGACCCAAAGgttaatcttc ... tctattgcagATTACAATGGCTATTGCAAGAGAAGTTGCTTCTGTCACCAAACTAGGTGTA
EST: gi|50338057|gb|CO533183.1|CO533183
EST:     TAAGTGGGGAAGCTCTTGCCGGGAATCACACAGAAAACATCGACCCAAAG                         ATTACAATGGCTATTGCAAGAGAAGTTGCTTCTGTCACCAAACTAGGTGTA
genomic: TAAGTGGGGAAGCTCTTGCCGGGAATCACACAGAAAACATCGACCCAAAGgttaatcttc ... tctattgcagATTACAATGGCTATTGCAAGAGAAGTTGCTTCTGTCACCAAACTAGGTGTA
EST: gi|211173536|gb|FL094956.1|FL094956
EST:     TAAGTGGGGAAGCTCTTGCCGGGAATCACACAGAAAACATCGACCCAAAG                         ATTACAATGGCTATTGCAAGAGAAGTTGCTTCTGTCACCAAACTAGGTGTA
genomic: TAAGTGGGGAAGCTCTTGCCGGGAATCACACAGAAAACATCGACCCAAAGgttaatcttc ... tctattgcagATTACAATGGCTATTGCAAGAGAAGTTGCTTCTGTCACCAAACTAGGTGTA
EST: gi|50326142|gb|CO521268.1|CO521268
EST:     TAAGTGGGGAAGCTCTTGCCGGGAATCACACAGAAAACATCGACCCAAAG                         ATTACAATGGCTATTGCAAGAGAAGTTGCTTCTGTCACCAAACTAGGTGTA
genomic: TAAGTGGGGAAGCTCTTGCCGGGAATCACACAGAAAACATCGACCCAAAGgttaatcttc ... tctattgcagATTACAATGGCTATTGCAAGAGAAGTTGCTTCTGTCACCAAACTAGGTGTA
EST: gi|211175204|gb|FL094961.1|FL094961
EST:     TAAGTGGGGAAGCTCTTGCCGGGAATCACACAGAAAACATCGACCCAAAG                         ATTACAATGGCTATTGCAAGAGAAGTTGCTTCTGTCACCAAACTAGGTGTA
genomic: TAAGTGGGGAAGCTCTTGCCGGGAATCACACAGAAAACATCGACCCAAAGgttaatcttc ... tctattgcagATTACAATGGCTATTGCAAGAGAAGTTGCTTCTGTCACCAAACTAGGTGTA
EST: gi|211175207|gb|FL094964.1|FL094964
EST:     TAAGTGGGGAAGCTCTTGCCGGGAATCACACAGAAAACATCGACCCAAAG                         ATTACAATGGCTATTGCAAGAGAAGTTGCTTCTGTCACCAAACTAGGTGTA
genomic: TAAGTGGGGAAGCTCTTGCCGGGAATCACACAGAAAACATCGACCCAAAGgttaatcttc ... tctattgcagATTACAATGGCTATTGCAAGAGAAGTTGCTTCTGTCACCAAACTAGGTGTA
EST: gi|211175211|gb|FL094968.1|FL094968
EST:     TAAGTGGGGAAGCTCTTGCCGGGAATCACACAGAAAACATCGACCCAAAG                         ATTACAATGGCTATTGCAAGAGAAGTTGCTTCTGTCACCAAACTAGGTGTA
genomic: TAAGTGGGGAAGCTCTTGCCGGGAATCACACAGAAAACATCGACCCAAAGgttaatcttc ... tctattgcagATTACAATGGCTATTGCAAGAGAAGTTGCTTCTGTCACCAAACTAGGTGTA
EST: gi|211175206|gb|FL094963.1|FL094963
EST:     TAAGTGGGGAAGCTCTTGCCGGGAATCACACAGAAAACATCGACCCAAAG                         AT-ACAATGGCTATTGCAAGAGAA
genomic: TAAGTGGGGAAGCTCTTGCCGGGAATCACACAGAAAACATCGACCCAAAGgttaatcttc ... tctattgcagATTACAATGGCTATTGCAAGAGAA
EST: gi|211173530|gb|FL094950.1|FL094950
EST:     TAAGTGGGGAAGCTCTTGCCGGGAATCACACAGAAAACATCGACCCAAAG                         ATTACAATGGCTATTGCAAGAGAAGT-GCTTCTGTCACCAAACTAGGTGTA
genomic: TAAGTGGGGAAGCTCTTGCCGGGAATCACACAGAAAACATCGACCCAAAGgttaatcttc ... tctattgcagATTACAATGGCTATTGCAAGAGAAGTTGCTTCTGTCACCAAACTAGGTGTA
EST: gi|86466839|gb|DY233209.1|DY233209
EST:     TAAGTGGGGAAGCTCTTGCCGGGAATCACACAAAAAACATCGACCCAAAG                         ATTACAATGGCTATTGCAAGAGAAGTTGCTTCTGTCACCAAACTAGGTGTA
genomic: TAAGTGGGGAAGCTCTTGCCGGGAATCACACAGAAAACATCGACCCAAAGgttaatcttc ... tctattgcagATTACAATGGCTATTGCAAGAGAAGTTGCTTCTGTCACCAAACTAGGTGTA
EST: gi|211175215|gb|FL094972.1|FL094972
EST:     TAAGTGGGGAAGCTCTTGCCGGGAATCACACAGAAAACATCGACCCAAAG                         ATTACAATGGCTATTGCAAGAGAAGTTGCTTCTGTCACCAAACTAGGTGTA
genomic: TAAGTGGGGAAGCTCTTGCCGGGAATCACACAGAAAACATCGACCCAAAGgttaatcttc ... tctattgcagATTACAATGGCTATTGCAAGAGAAGTTGCTTCTGTCACCAAACTAGGTGTA
EST: gi|211175210|gb|FL094967.1|FL094967
EST:     TAAGTGGGGAAGCTCTTGCCGGGAATCACACAGAAAACATCGACCCAAAG                         ATTACAATGGCTATTGCAAGAGAAGTTGCTTCTGTCACCAAA
genomic: TAAGTGGGGAAGCTCTTGCCGGGAATCACACAGAAAACATCGACCCAAAGgttaatcttc ... tctattgcagATTACAATGGCTATTGCAAGAGAAGTTGCTTCTGTCACCAAA
EST: gi|211175212|gb|FL094969.1|FL094969
EST:     TAAGTGGGGAAGCTCTTGCCGGGAATCACACAGAAAACATCGACCCAAAG                         ATTACAATGGCTATTGCAAGAGAAGTTGCTTCTGTCACCAAACTAGGTGTA
genomic: TAAGTGGGGAAGCTCTTGCCGGGAATCACACAGAAAACATCGACCCAAAGgttaatcttc ... tctattgcagATTACAATGGCTATTGCAAGAGAAGTTGCTTCTGTCACCAAACTAGGTGTA
EST: gi|211173535|gb|FL094955.1|FL094955
EST:     TAAGTGGGGAAGCTCTTGCCGGGAATCACACAGAAAACATCGACCCAAAG                         ATTACAATGGCTATTGCAAGAGAAG
genomic: TAAGTGGGGAAGCTCTTGCCGGGAATCACACAGAAAACATCGACCCAAAGgttaatcttc ... tctattgcagATTACAATGGCTATTGCAAGAGAAG
EST: gi|33467006|gb|CF244055.1|CF244055
EST:     TAAGTGGGGAAGCTCTTGCCGGGAATCACACAGAAAACATCGACCCAAAG                         ATTACAATGGCTATTGCAAGAGAAGTTGCTTCTGTCACCAAACTAGGTGTA
genomic: TAAGTGGGGAAGCTCTTGCCGGGAATCACACAGAAAACATCGACCCAAAGgttaatcttc ... tctattgcagATTACAATGGCTATTGCAAGAGAAGTTGCTTCTGTCACCAAACTAGGTGTA
EST: gi|86468321|gb|DY234691.1|DY234691
EST:     TAAGTGGGGAAGCTCTTGCCGGGAATCACACAAAAAACATCGACCCAAAG                         ATTACAATGGCTATTGCAAGAAAAGTTGCTTCTGTCACCAAACTAGGTGTA
genomic: TAAGTGGGGAAGCTCTTGCCGGGAATCACACAGAAAACATCGACCCAAAGgttaatcttc ... tctattgcagATTACAATGGCTATTGCAAGAGAAGTTGCTTCTGTCACCAAACTAGGTGTA
EST: gi|211173532|gb|FL094952.1|FL094952
EST:     TAAGTGGGGAAGCTCTTGCCGGGAATCACACAGAAAACATCGACCCAAAG                         ATTACAATGGCTATTGCAAGAGAAGTTGCTTCTGTCACCAAACTAGGTGTA
genomic: TAAGTGGGGAAGCTCTTGCCGGGAATCACACAGAAAACATCGACCCAAAGgttaatcttc ... tctattgcagATTACAATGGCTATTGCAAGAGAAGTTGCTTCTGTCACCAAACTAGGTGTA
EST: gi|148960321|gb|EE153577.2|EE153577
EST:     TAAGTGGGGAAGCTCTTGCCGGGAATCACACAGAAAACATCGACCCAAAG                         ATTACAATGGCTATTGCAAGAGAAGTTGCTTCTGTCACCAAACTAGGTGTA
genomic: TAAGTGGGGAAGCTCTTGCCGGGAATCACACAGAAAACATCGACCCAAAGgttaatcttc ... tctattgcagATTACAATGGCTATTGCAAGAGAAGTTGCTTCTGTCACCAAACTAGGTGTA
EST: gi|211173531|gb|FL094951.1|FL094951
EST:     TAAGTGGGGAAGCTCTTGCCGGGAATCACACAGAAAACATCGACCCAAAG                         ATTACAATGGCTATTGGCAAGAGAAGTTGCTTCTGTCACCAAACTAGG
genomic: TAAGTGGGGAAGCTCTTGCCGGGAATCACACAGAAAACATCGACCCAAAGgttaatcttc ... tctattgcagATTACAATGGCTATTG-CAAGAGAAGTTGCTTCTGTCACCAAACTAGG
EST: gi|211175202|gb|FL094959.1|FL094959
EST:     TAAGTGGGGAAGCTCTTGCCGGGAATCACACAGAAAACATCGACCCAAAG                         ATTACAATGGCTATTGCAAGAGAAGTTGCTTCTGTCACCAAACTA
genomic: TAAGTGGGGAAGCTCTTGCCGGGAATCACACAGAAAACATCGACCCAAAGgttaatcttc ... tctattgcagATTACAATGGCTATTGCAAGAGAAGTTGCTTCTGTCACCAAACTA

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), 49 (downstream exon)
Score: 138

TTCTTCTAGTTCCAGAAGGCTATATAGATGGAAAAGGGTATTGCTCAAAGTAAGTGGGGAAGCTCTTGCCGGGAATCACACAGAAAACATCGACCCAAAGgttaatcttc ... tctattgcagATTACAATGGCTATTGCAAGAGAAGTTGCTTCTGTCACCAAACTAGGTGTAGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 253

TTCTTCTAGTTCCAGAAGGCTATATAGATGGAAAAGGGTATTGCTCAAAGTAAGTGGGGAAGCTCTTGCCGGGAATCACACAGAAAACATCGACCCAAAGgttaatcttc ... tctattgcagATTACAATGGCTATTGCAAGAGAAGTTGCTTCTGTCACCAAACTAGGTGTAGAG


Block sizes: 45 (upstream exon), 49 (downstream exon)
Score: 33

TTCTTCTAGTTCCAGAAGGCTATATAGATGGAAAAGGGTATTGCTCAAAGTAAGTGGGGAAGCTCTTGCCGGGAATCACACAGAAAACATCGACCCAAAGgttaatcttc ... tctattgcagATTACAATGGCTATTGCAAGAGAAGTTGCTTCTGTCACCAAACTAGGTGTAGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 164

TTCTTCTAGTTCCAGAAGGCTATATAGATGGAAAAGGGTATTGCTCAAAGTAAGTGGGGAAGCTCTTGCCGGGAATCACACAGAAAACATCGACCCAAAGgttaatcttc ... tctattgcagATTACAATGGCTATTGCAAGAGAAGTTGCTTCTGTCACCAAACTAGGTGTAGAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gacgatttatatgagtgggtcatggaaattgatgtgaacatgtgctctattgcagATTACAATGGCTATTGCAAGAGAAGTTGCTTCTGTCACCAAACTAGGTGTAGAG
                          aattgat  putative branch site (score: 164)
                                            ctctatt  putative PPT
     tttatatga  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttaatcttcttttggtggagcatctttaaacactgacagcagacgatttatatgagtgggtcatggaaattgatgtgaacatgtgctctattgcagATTACAATGGCTATTGCAAGAGAAGTTGCTTCTGTCACCAAACTAGGTGTAGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGT