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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttgtcaggagttaatcacatgtttctatgttgttgacctcttctattagatctgcttaatcttaatgattaaactgtcctattctgattccacaacccagGTAGTCACAGAATACTCTGAGGATCAGCTTGAGTTGGTCTTAGAAGCCTGCGAAAGGATGAATGCGCATCTGACAGCTGCAGTTGTCTCAAACGACCCGC

Basic information

species Zea mays
transcript GRMZM2G090087_T03
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G090087_T03 (Zea mays), 3'ss of exon 12
lower sequence: LOC_Os05g45960.1 (Oryza sativa), 3'ss of exon 12
ttgtcaggagttaatcacatgtttctatgttgttgacctcttctattagatctgcttaatcttaatgattaa--actgtcctattctgattccaca-acccagGTAGTCACAGAATACTCTGAGGATCAGCTTGAGTTGGTCTTAGAAGCCTGCGAAAGGATGAATGCGCATCTGACAGCTGCAGTTGTCTCAAACGACCCGC-
          |  ||   |  |||| ||    ||||   |  |    |  | |   |  || |  ||||  |  |||  |||||||  | | || |  | ||||| || ||||| || ||||| ||| ||||||| || || ||||||||||| ||||||||||| ||  ||||||| ||||||||||| |||||||||||   
---gtgcatatgcatgctagctttcaatagaattgataacaacctacaagtttcaattgtcattgtgatatagtactaacctattccaagttcatatgcgcagGTGGTTACAGAGTATTCTGATGATGAGCTTGAATTAGTATTAGAAGCCTGTGAAAGGATGAACGC-TATCTGACGGCTGCAGTTGTTTCAAACGACCCTTT
















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|18383619|gb|BM416819.1|BM416819
EST:     AAAGTGGGAACTTCGAGCTTGTGACAAAGGAGATATTTGGTCCATTCCAG                         GTAGTCACAGAATACTCTGAGGATCAGCTTGAGTTGGTCTTAGAAGCCTGC
genomic: AAAGTGGGAACTTCGAGCTTGTGACAAAGGAGATATTTGGTCCATTCCAGgtaatagatc ... cacaacccagGTAGTCACAGAATACTCTGAGGATCAGCTTGAGTTGGTCTTAGAAGCCTGC
EST: gi|211120257|gb|FL200678.1|FL200678
EST:     AAAGTGGGAACTTCGAGCTTGTGACAAAGGAGATATTTGGTCCATTCCAG                         GTAGTCACAGAATACTCTGAGGATCAGCTTGAGTTGGTCTTAGAAGCCTGC
genomic: AAAGTGGGAACTTCGAGCTTGTGACAAAGGAGATATTTGGTCCATTCCAGgtaatagatc ... cacaacccagGTAGTCACAGAATACTCTGAGGATCAGCTTGAGTTGGTCTTAGAAGCCTGC
EST: gi|67020094|gb|CO448843.1|CO448843
EST:     AAAGTGGGAACTTCGAGCTTGTGACAAAGGAGATATTTGGTCCATTCCAG                         GTAGTCACAGAATACTCTGAGGACCAGCTTGAGTTGGTCTTAGAAGCCTGC
genomic: AAAGTGGGAACTTCGAGCTTGTGACAAAGGAGATATTTGGTCCATTCCAGgtaatagatc ... cacaacccagGTAGTCACAGAATACTCTGAGGATCAGCTTGAGTTGGTCTTAGAAGCCTGC
EST: gi|6827469|gb|AW331112.1|AW331112
EST:     AAAGTGGGAACTTCGAGCTTGTGACAAAGGAGATATTTGGTCCATTCCAG                         GTAGTCACAGAATACTCTGAGGACCAGCTTGAGTTGGTCTTAGAAGCCTGC
genomic: AAAGTGGGAACTTCGAGCTTGTGACAAAGGAGATATTTGGTCCATTCCAGgtaatagatc ... cacaacccagGTAGTCACAGAATACTCTGAGGATCAGCTTGAGTTGGTCTTAGAAGCCTGC
EST: gi|18659076|gb|BM500142.1|BM500142
EST:     AAAGTGGGAACTTCGAGCTTGTGACAAAGGAGATATTTGGTCCATTCCAG                         GTAGTCACAGAATACTCTGAGGATCAGCTTGAGTTGGTCTTAGAAGCCTGC
genomic: AAAGTGGGAACTTCGAGCTTGTGACAAAGGAGATATTTGGTCCATTCCAGgtaatagatc ... cacaacccagGTAGTCACAGAATACTCTGAGGATCAGCTTGAGTTGGTCTTAGAAGCCTGC
EST: gi|67024223|gb|CO452972.1|CO452972
EST:     AAAGTGGGAACTTCGAGCTTGTGACANAGGAGATATTTGGTCCATTCCAG                         GTAGTCACAGAATACTCTNGAG-ACCAGCTTGAGTTGGTCTTANAAGCCCT
genomic: AAAGTGGGAACTTCGAGCTTGTGACAAAGGAGATATTTGGTCCATTCCAGgtaatagatc ... cacaacccagGTAGTCACAGAATACTCT-GAGGATCAGCTTGAGTTGGTCTTAGAAGCC-T
EST: gi|24773212|gb|CA408466.1|CA408466
EST:     AAAGTGGGAACTTCGAGCTTGTGACAAAGGAGATATTTGGTCCATTCCAG                         GTAGTCACAGAATACTCTGAGGATCAGCTTGAGTTGGTCTTAGAAGCCTGC
genomic: AAAGTGGGAACTTCGAGCTTGTGACAAAGGAGATATTTGGTCCATTCCAGgtaatagatc ... cacaacccagGTAGTCACAGAATACTCTGAGGATCAGCTTGAGTTGGTCTTAGAAGCCTGC
EST: gi|67023454|gb|CO452203.1|CO452203
EST:     AAAGTGGGAACTTCGAGCTTGTGACAAAGGAGATATTTGGTCCATTCCAG                         GTAGTCACAGAATACTCTGAGGACCAGCTTGAGTTGGTCTTANAAGCCTGC
genomic: AAAGTGGGAACTTCGAGCTTGTGACAAAGGAGATATTTGGTCCATTCCAGgtaatagatc ... cacaacccagGTAGTCACAGAATACTCTGAGGATCAGCTTGAGTTGGTCTTAGAAGCCTGC
EST: gi|33102441|gb|CF062401.1|CF062401
EST:     AAAGTGGGAACTTCGAGCTTGTGACAAAGGAGATATTTGGTCCATTCCAG                         GTAGTCACAGAATACTCTGAGGATCAGCTTGAGTTGGTCTTAGAAGCCTGC
genomic: AAAGTGGGAACTTCGAGCTTGTGACAAAGGAGATATTTGGTCCATTCCAGgtaatagatc ... cacaacccagGTAGTCACAGAATACTCTGAGGATCAGCTTGAGTTGGTCTTAGAAGCCTGC
EST: gi|211120258|gb|FL200679.1|FL200679
EST:     AAAGTGGGAACTTCGAGCTTGTGACAAAGGAGATATTTGGTCCATTCCAG                         GTAGTCACGGAATACTCTGAGGATCAGCTTGAGTTGGTCTTAGAAGCCTGC
genomic: AAAGTGGGAACTTCGAGCTTGTGACAAAGGAGATATTTGGTCCATTCCAGgtaatagatc ... cacaacccagGTAGTCACAGAATACTCTGAGGATCAGCTTGAGTTGGTCTTAGAAGCCTGC
EST: gi|211507628|gb|FL212141.1|FL212141
EST:     AAAGTGGGAACTTCGAGCTTGTGACAAAGGAGATATTTGGTCCATTCCAG                         GTAGTCACAGAATACTCTGAGGATCAGCTTGAGTTGGTCTTAGAAGCCTGC
genomic: AAAGTGGGAACTTCGAGCTTGTGACAAAGGAGATATTTGGTCCATTCCAGgtaatagatc ... cacaacccagGTAGTCACAGAATACTCTGAGGATCAGCTTGAGTTGGTCTTAGAAGCCTGC
EST: gi|67014372|gb|CO443121.1|CO443121
EST:     GGAGAT-TTTGGTCCATTCCAG                         GTAGTCACAGAATCCTCTGAGGACCAGCTTGAGTTGGTCTTAGAAGCCTGC
genomic: GGAGATATTTGGTCCATTCCAGgtaatagatc ... cacaacccagGTAGTCACAGAATACTCTGAGGATCAGCTTGAGTTGGTCTTAGAAGCCTGC
EST: gi|32847832|gb|CD987513.1|CD987513
EST:     AAAGTGGGAACTTCGAGCTTGTGACAAAGGAGATATTTGGTCCATTCCAG                         GTAGTCACAGAATACTCCGAGGATCAGCTTGAGTTGGTCTTAGAAGCCTGC
genomic: AAAGTGGGAACTTCGAGCTTGTGACAAAGGAGATATTTGGTCCATTCCAGgtaatagatc ... cacaacccagGTAGTCACAGAATACTCTGAGGATCAGCTTGAGTTGGTCTTAGAAGCCTGC
EST: gi|60349947|gb|DN216920.1|DN216920
EST:     AAAGTGGGAACTTCGAGCTTGTGACAAAGGAGATATTTGGTCCATTCCAG                         GTAGTCACAGAATACTCTGAGGATCAGCTTGAGTTGGTCTTAGAAGCCTGC
genomic: AAAGTGGGAACTTCGAGCTTGTGACAAAGGAGATATTTGGTCCATTCCAGgtaatagatc ... cacaacccagGTAGTCACAGAATACTCTGAGGATCAGCTTGAGTTGGTCTTAGAAGCCTGC
EST: gi|211342162|gb|FL434432.1|FL434432
EST:     AAAGTGGGAACTTCGAGCTTGTGACAAAGGAGATATTTGGTCCATTCCAG                         GTAGTCACAGAATACTCTGAGGATCAGCTTGAGTTGGTCTTAGAAGCCTGC
genomic: AAAGTGGGAACTTCGAGCTTGTGACAAAGGAGATATTTGGTCCATTCCAGgtaatagatc ... cacaacccagGTAGTCACAGAATACTCTGAGGATCAGCTTGAGTTGGTCTTAGAAGCCTGC

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: 363

TGGTGCCATGAAGCCTACTGCTGTATTTGTTCCTCTAGAAGAAATTCTAAAAAGTGGGAACTTCGAGCTTGTGACAAAGGAGATATTTGGTCCATTCCAGgtaatagatc ... cacaacccagGTAGTCACAGAATACTCTGAGGATCAGCTTGAGTTGGTCTTAGAAGCCTGCGAAAGGATGAATGCGCATCTGACAGCTGCAGTTGTCTCAAACGACCCGC


Block sizes: 48 (upstream exon), 47 (downstream exon)
Score: 166

TGGTGCCATGAAGCCTACTGCTGTATTTGTTCCTCTAGAAGAAATTCTAAAAAGTGGGAACTTCGAGCTTGTGACAAAGGAGATATTTGGTCCATTCCAGgtaatagatc ... cacaacccagGTAGTCACAGAATACTCTGAGGATCAGCTTGAGTTGGTCTTAGAAGCCTGCGAAAGGATGAATGCGCATCTGACAGCTGCAGTTGTCTCAAACGACCCGC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 73

TGGTGCCATGAAGCCTACTGCTGTATTTGTTCCTCTAGAAGAAATTCTAAAAAGTGGGAACTTCGAGCTTGTGACAAAGGAGATATTTGGTCCATTCCAGgtaatagatc ... cacaacccagGTAGTCACAGAATACTCTGAGGATCAGCTTGAGTTGGTCTTAGAAGCCTGCGAAAGGATGAATGCGCATCTGACAGCTGCAGTTGTCTCAAACGACCCGC


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 212

TGGTGCCATGAAGCCTACTGCTGTATTTGTTCCTCTAGAAGAAATTCTAAAAAGTGGGAACTTCGAGCTTGTGACAAAGGAGATATTTGGTCCATTCCAGgtaatagatc ... cacaacccagGTAGTCACAGAATACTCTGAGGATCAGCTTGAGTTGGTCTTAGAAGCCTGCGAAAGGATGAATGCGCATCTGACAGCTGCAGTTGTCTCAAACGACCCGC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttagatctgcttaatcttaatgattaaactgtcctattctgattccacaacccagGTAGTCACAGAATACTCTGAGGATCAGCTTGAGTTGGTCTTAGAAGCCTGCGAAAGGATGAATGCGCATCTGACAGCTGCAGTTGTCTCAAACGACCCGC
                                    ttctgat  putative branch site (score: 212)
          ttaatcttaatgatta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttgtcaggagttaatcacatgtttctatgttgttgacctcttctattagatctgcttaatcttaatgattaaactgtcctattctgattccacaacccagGTAGTCACAGAATACTCTGAGGATCAGCTTGAGTTGGTCTTAGAAGCCTGCGAAAGGATGAATGCGCATCTGACAGCTGCAGTTGTCTCAAACGACCCGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG
- - - - - - aatcaca
- - - - - - - - - -tgtttct
- - - - - - - - - - - - - -tgttgtt
- - - - - - - - - - - - - - - - - - - - - - - - - -ctgctta