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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GATCTGGTGGAGATTGGCTCCTCTGGTGTCCTAGATCCTAGTTTTATTGAGAAGCTGAGTGAAGAAAACATCGCTCTGTTTTCAAGgtaaaattgcttttactattgctttcatgttgtatcttggtgagttttggaaaggtagtctttatgcatggttactaaagtcgttgaagagtttctgcat...

Basic information

species Zea mays
transcript GRMZM2G021864_T01
intron # 17
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G021864_T01 (Zea mays), 5'ss of exon 17
lower sequence: LOC_Os10g10190.1 (Oryza sativa), 5'ss of exon 17
GATCTGGTGGAGATTGGCTCCTCTGGTGTCCTAGATCCTAGTTTTATTGAGAAGCTGAGTGAAGAAAACATCGCTCTGTTTTCAAGgtaaaattgcttttactattgctttcatgttgtatcttggtgagttttg-gaaaggtagtctttatgcatggttactaaagtcgttgaagagtttctgcat
 ||   || || ||||||||    ||||  || |||||   | | || || |||||||||||||||||||||| ||||||  ||||||||  ||| |  |      |   | | | || || |    |  ||||| |  | |  |    |||   | |  | ||  ||| |  |   |||       
AATTCAGTAGATATTGGCTCTGAAGGTGCACTTGATCCCTATATCATGGAAAAGCTGAGTGAAGAAAACATCGGTCTGTTCACAAGgtaatgttgatcattgatgagtcatgagggtgcatatataggccttttgcgttatgatggaactattt-tagcaattactgtcatacatatgttcagattc
















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|33091337|gb|CF051331.1|CF051331
EST:     CCTAGTTTTATTGAGAAGCTGAGTGAAGAAAACATCGCTCTGTTTTCAAG                         GCGTGAAGAGCTTCGACAACGAGATACACGACTGAAGCAGACG
genomic: CCTAGTTTTATTGAGAAGCTGAGTGAAGAAAACATCGCTCTGTTTTCAAGgtaaaattgc ... ttttttacagGCGTGAAGAGCTTCGACAACGAGATACACAACTGAAGCAGACG
EST: gi|211215778|gb|FL437224.1|FL437224
EST:     CCTAGTTTTATTGAGAAGCTGAGTGAAGAAAACATCGCTCTGTTTTCAAG                         GCGTGAAGAGCTTCGACAACGAGATACACAACTGAAGCAGACG
genomic: CCTAGTTTTATTGAGAAGCTGAGTGAAGAAAACATCGCTCTGTTTTCAAGgtaaaattgc ... ttttttacagGCGTGAAGAGCTTCGACAACGAGATACACAACTGAAGCAGACG
EST: gi|32804257|gb|CD956493.1|CD956493
EST:     CCTAGTTTTATTGAGAAGCTGAGTGAAGAAAACATCGCTCTGTTTTCAAG                         GCGTGAAGAGCTTCGACAACGAGATACACAACTGAAGCAGACG
genomic: CCTAGTTTTATTGAGAAGCTGAGTGAAGAAAACATCGCTCTGTTTTCAAGgtaaaattgc ... ttttttacagGCGTGAAGAGCTTCGACAACGAGATACACAACTGAAGCAGACG
EST: gi|78022987|gb|DV491374.1|DV491374
EST:     CCTAGTTTTATTGAGAAGCTGAGTGAAGAAAACATCGCTCTGTTTTCAAG                         GCGTGAAGAGCTTCGACAACGAGATACACAACTGAAGCAGACG
genomic: CCTAGTTTTATTGAGAAGCTGAGTGAAGAAAACATCGCTCTGTTTTCAAGgtaaaattgc ... ttttttacagGCGTGAAGAGCTTCGACAACGAGATACACAACTGAAGCAGACG
EST: gi|32909144|gb|CF013956.1|CF013956
EST:     CCTAGTTTTATTGAGAAGCTGAGTGAAGAAAACATCGCTCTGTTTTCAAG                         GCGTGAAGAGCTTCGGCAACGAGATACCCAACTGAAGCAGACG
genomic: CCTAGTTTTATTGAGAAGCTGAGTGAAGAAAACATCGCTCTGTTTTCAAGgtaaaattgc ... ttttttacagGCGTGAAGAGCTTCGACAACGAGATACACAACTGAAGCAGACG
EST: gi|32931903|gb|CF036715.1|CF036715
EST:     CCTAGTTTTATTGAGAAGCTGAGTGAAGAAAACATCGCTCTGTTTTCAAG                         GCGTGAAGAGCTTCGACAACGAGATACACAACTGAAGCAGACG
genomic: CCTAGTTTTATTGAGAAGCTGAGTGAAGAAAACATCGCTCTGTTTTCAAGgtaaaattgc ... ttttttacagGCGTGAAGAGCTTCGACAACGAGATACACAACTGAAGCAGACG
EST: gi|211458170|gb|FL127582.1|FL127582
EST:     CCTAGTTTTATTGAGAAGCTGAGTGAAGAAAACATCGCTCTGTTTTCAAG                         GCGTGAAGAGCTTCGACAACGAGATACACAACTGAAGCAGACG
genomic: CCTAGTTTTATTGAGAAGCTGAGTGAAGAAAACATCGCTCTGTTTTCAAGgtaaaattgc ... ttttttacagGCGTGAAGAGCTTCGACAACGAGATACACAACTGAAGCAGACG
EST: gi|89248917|gb|DY620703.1|DY620703
EST:     CCTAGTTTTATTGAGAAGGTGAGTGAAGAAAACATCGCTCTGTTTTCAAG                         GCGTGAAGAGCTTCGACAACGAGATACACAACTGAAGCAGACG
genomic: CCTAGTTTTATTGAGAAGCTGAGTGAAGAAAACATCGCTCTGTTTTCAAGgtaaaattgc ... ttttttacagGCGTGAAGAGCTTCGACAACGAGATACACAACTGAAGCAGACG
EST: gi|89758497|gb|DY687658.1|DY687658
EST:     CTAGTTTTATTGAGAAGCTGAGTGAAGAAAACATCGCTCTGTTTTTCAGG                         GCGTGA-GAGCTTCGACAACGAGATACACAACTGAGGCAGACG
genomic: CTAGTTTTATTGAGAAGCTGAGTGAAGAAAACATCGCTCTGTTTT-CAAGgtaaaattgc ... ttttttacagGCGTGAAGAGCTTCGACAACGAGATACACAACTGAAGCAGACG
EST: gi|5608024|gb|AI901691.1|AI901691
EST:     CTGTTTTCAAG                         GCGTGAAGAGCTTCGACAACGAGATACACAACTGAAGCAGACG
genomic: CTGTTTTCAAGgtaaaattgc ... ttttttacagGCGTGAAGAGCTTCGACAACGAGATACACAACTGAAGCAGACG
EST: gi|6194461|gb|AW146565.1|AW146565
EST:     CCTAGTTTTATTGAGAAGCTGAGTGAAGAAAACATCGCTCTGTTTTCAAG                         GCGTGAAGAGCTTCGACAACGAGATACACAACTGAAGCAGACG
genomic: CCTAGTTTTATTGAGAAGCTGAGTGAAGAAAACATCGCTCTGTTTTCAAGgtaaaattgc ... ttttttacagGCGTGAAGAGCTTCGACAACGAGATACACAACTGAAGCAGACG
EST: gi|211460681|gb|FL127583.1|FL127583
EST:     CCTAGTTTTATTGAGAAGCTGAGTGAAGAAAACATCGCTCTGTTTTCAAG                         GCGTGAAGAGCTTCGACAACGAGATACACAACTGAAGCAGACGATTGGAGA
genomic: CCTAGTTTTATTGAGAAGCTGAGTGAAGAAAACATCGCTCTGTTTTCAAGgtaaaattgc ... ttttttacagGCGTGAAGAGCTTCGACAACGAGATACACAACTGAAGCAGACGATTGGAGA
EST: gi|32934210|gb|CF039022.1|CF039022
EST:     CCTAGTTTTATTGAGAAGCTGAGTGAAGAAAACATCGCTCTGTTTTCAAG                         GCGTGAAGAGCTTCGACAACGAGATACACAACTGAAGCAGACG
genomic: CCTAGTTTTATTGAGAAGCTGAGTGAAGAAAACATCGCTCTGTTTTCAAGgtaaaattgc ... ttttttacagGCGTGAAGAGCTTCGACAACGAGATACACAACTGAAGCAGACG
EST: gi|78106767|gb|DV525185.1|DV525185
EST:     CCTAGTTTTATTGAGAAGCTGAGTGAAGAAAACATCGCTCTGTTTTCAAG                         GCGTGAAGAGCTTCGACAACGAGATACACAACTGAAGCAGACG
genomic: CCTAGTTTTATTGAGAAGCTGAGTGAAGAAAACATCGCTCTGTTTTCAAGgtaaaattgc ... ttttttacagGCGTGAAGAGCTTCGACAACGAGATACACAACTGAAGCAGACG
EST: gi|116827696|gb|EC871624.1|EC871624
EST:     CCTAGTTTTATTGAGAAGCTGAGTGAAG-AAACATCGCTCTGTTTTCAA-                         GCGTGAAGAGCTTCGACAACGAGATACACAACTGAAGCAGACG
genomic: CCTAGTTTTATTGAGAAGCTGAGTGAAGAAAACATCGCTCTGTTTTCAAGgtaaaattgc ... ttttttacagGCGTGAAGAGCTTCGACAACGAGATACACAACTGAAGCAGACG
EST: gi|32930527|gb|CF035339.1|CF035339
EST:     CCTAGTTTTATTGAGAAGCTGAGTGAAGAAAACATCGCTCTGTTTTCAAG                         GCGTGAAGAGCTTCGACACCGAGATACCCAACTGAAGCAGACG
genomic: CCTAGTTTTATTGAGAAGCTGAGTGAAGAAAACATCGCTCTGTTTTCAAGgtaaaattgc ... ttttttacagGCGTGAAGAGCTTCGACAACGAGATACACAACTGAAGCAGACG
EST: gi|5915604|gb|AW053245.1|AW053245
EST:     CCTAGTTTTATTGAGAAGCTGAGTGAAGAAAACATCGCTCTGTTTTCAAG                         GCGTGAAGAGCTTCGACAACGAGATACACAACTGAAGCAGACG
genomic: CCTAGTTTTATTGAGAAGCTGAGTGAAGAAAACATCGCTCTGTTTTCAAGgtaaaattgc ... ttttttacagGCGTGAAGAGCTTCGACAACGAGATACACAACTGAAGCAGACG
EST: gi|32932800|gb|CF037612.1|CF037612
EST:     CCTAGTTTTATTGAGAAGCTGAGTGAAGAAAACATCGCTCTGTTTTCAAG                         GCGTGAAGAGCTTCGACAACGAGATACACAACTGAAGCAGACG
genomic: CCTAGTTTTATTGAGAAGCTGAGTGAAGAAAACATCGCTCTGTTTTCAAGgtaaaattgc ... ttttttacagGCGTGAAGAGCTTCGACAACGAGATACACAACTGAAGCAGACG
EST: gi|5713643|gb|AI943635.1|AI943635
EST:     CCTAGTTTTATTGAGAAGCTGAGTGAAGAAAACATCGCTCTGTTTTCAAG                         GCGTGAAGAGCTTCGACAACGAGATACACAACTGAAGCAGACG
genomic: CCTAGTTTTATTGAGAAGCTGAGTGAAGAAAACATCGCTCTGTTTTCAAGgtaaaattgc ... ttttttacagGCGTGAAGAGCTTCGACAACGAGATACACAACTGAAGCAGACG
EST: gi|5361116|gb|AI795731.1|AI795731
EST:     CCTAGTTTTATTGAGAAGCTGAGTGAAGAAAACATCGCTCTGTTTTCAAG                         GCGTGAAGAGCTTCGACAACGAGATACACAACTGAAG
genomic: CCTAGTTTTATTGAGAAGCTGAGTGAAGAAAACATCGCTCTGTTTTCAAGgtaaaattgc ... ttttttacagGCGTGAAGAGCTTCGACAACGAGATACACAACTGAAG
EST: gi|32932808|gb|CF037620.1|CF037620
EST:     CCTAGTTTTATTGAGAAGCTGAGTGAAGAAAACATCGCTCTGTTTTCAAG                         GCGTGAAGAGCTTCGACAACGAGATACACAACTGAAGCAGACG
genomic: CCTAGTTTTATTGAGAAGCTGAGTGAAGAAAACATCGCTCTGTTTTCAAGgtaaaattgc ... ttttttacagGCGTGAAGAGCTTCGACAACGAGATACACAACTGAAGCAGACG
EST: gi|91054831|gb|EB165249.1|EB165249
EST:     CCTAGTTTTATTGAGAAGCTGAGTGAAGAAAACATCGCTCTGTTTTCAAG                         GCGTGAAGAGCTTCGACAACGAGATACACAACTGAAGCAGACG
genomic: CCTAGTTTTATTGAGAAGCTGAGTGAAGAAAACATCGCTCTGTTTTCAAGgtaaaattgc ... ttttttacagGCGTGAAGAGCTTCGACAACGAGATACACAACTGAAGCAGACG
EST: gi|13381810|gb|BG458485.1|BG458485
EST:     CCTAGTTTTATTGAGAAGCTGAGTGAAGAAAACATCGCTCTGTTTTCAAG                         GCGTGAAGAGCTTCGACAACGAGATACACAACTGAAGCAGACG
genomic: CCTAGTTTTATTGAGAAGCTGAGTGAAGAAAACATCGCTCTGTTTTCAAGgtaaaattgc ... ttttttacagGCGTGAAGAGCTTCGACAACGAGATACACAACTGAAGCAGACG
EST: gi|12968788|gb|BG265825.1|BG265825
EST:     CCTAGTTTTATTGAGAAGCTGAGTGAAGAAAACATCGCTCTGTTTTCAAG                         GCGTGAAGAGCTTCGACAACGAGATACACAACTGAAGCAGACG
genomic: CCTAGTTTTATTGAGAAGCTGAGTGAAGAAAACATCGCTCTGTTTTCAAGgtaaaattgc ... ttttttacagGCGTGAAGAGCTTCGACAACGAGATACACAACTGAAGCAGACG

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: 47 (upstream exon), 43 (downstream exon)
Score: 113

GATCTGGTGGAGATTGGCTCCTCTGGTGTCCTAGATCCTAGTTTTATTGAGAAGCTGAGTGAAGAAAACATCGCTCTGTTTTCAAGgtaaaattgc ... ttttttacagGCGTGAAGAGCTTCGACAACGAGATACACAACTGAAGCAGACG


Block sizes: 47 (upstream exon), 43 (downstream exon)
Score: 85

GATCTGGTGGAGATTGGCTCCTCTGGTGTCCTAGATCCTAGTTTTATTGAGAAGCTGAGTGAAGAAAACATCGCTCTGTTTTCAAGgtaaaattgc ... ttttttacagGCGTGAAGAGCTTCGACAACGAGATACACAACTGAAGCAGACG


Block sizes: 49 (upstream exon), 43 (downstream exon)
Score: 131

GATCTGGTGGAGATTGGCTCCTCTGGTGTCCTAGATCCTAGTTTTATTGAGAAGCTGAGTGAAGAAAACATCGCTCTGTTTTCAAGgtaaaattgc ... ttttttacagGCGTGAAGAGCTTCGACAACGAGATACACAACTGAAGCAGACG


Block sizes: 49 (upstream exon), 43 (downstream exon)
Score: 83

GATCTGGTGGAGATTGGCTCCTCTGGTGTCCTAGATCCTAGTTTTATTGAGAAGCTGAGTGAAGAAAACATCGCTCTGTTTTCAAGgtaaaattgc ... ttttttacagGCGTGAAGAGCTTCGACAACGAGATACACAACTGAAGCAGACG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GATCTGGTGGAGATTGGCTCCTCTGGTGTCCTAGATCCTAGTTTTATTGAGAAGCTGAGTGAAGAAAACATCGCTCTGTTTTCAAGgtaaaattgcttttactattgctttcatgttgtatcttggtgagttttggaaaggtagtctttatgcatggttactaaagtcgttgaagagtttctgcat

- - - - - - - - - - - - - - - - - - - - - - - -  AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA