Skip to another splice site:
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 5'  3'   		2  
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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtcggtgccacccatactcctacccactccccgtcagggtattggctccttttctggtattctcgtttttttctgaccttctggtggggtttctgtctgtcttggcgtgcgcagAGGTTTCGACGTTCCTGCACGCGTGCGAGGGGGAGGCGGTGACGAAGCTCACCAACGAGAAGGTGCCCTACTTCAACGCGCCCATCTATCTGCAGAACAA

Basic information

species Zea mays
transcript GRMZM2G032419_T01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G032419_T01 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os11g37080.1 (Oryza sativa), 3'ss of exon 1
gtcggtgccacccatactcctacccactccccgtcagggtattggctccttttctggtattctcgtttttttctgaccttctggtggggtttc-tgtctgtcttggcg-tgcgcagAGGTTTCGACGTTCCTGCACGCGTGCGAGGGGGAGGCGGTGACGAAGCTCACCAACGAGAAGGTGCCCTACTTCAACGCGCCCATCTATCTGCAGAACAA
||  | ||  | | | ||||| | | || |||         | |  ||  | |||| |  |    ||||     ||  ||| | |||  | |  ||  ||  |  ||  || |||||||| ||||||||| ||||||||||||||||||| |||||||||||||| || ||||||||||||||||||||||||||||||||||| || ||||||||
gtgagcgcgtctcctcctcctcctcccttccc---------tggattctctctctgtttgtgggtttttccggcgagattcggttggtttctgatgcgtgcgtgagcactgagcagAGGTGTCGACGTTCATGCACGCGTGCGAGGGGGACGCGGTGACGAAGCTGACGAACGAGAAGGTGCCCTACTTCAACGCGCCCATCTACCTCCAGAACAA
















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|31357816|gb|CD442173.1|CD442173
EST:     CCGCTTCGGCGGCGGGTTCCGCGACGAGGGCCCGCCCGCGGAGGTCGTCG                         AGGTTTCGACGTTCCTGCACGCGTGCGAGGGGGAGGCGGTGACNAAGCTCA
genomic: CCGCTTCGGCGGCGGGTTCCGCGACGAGGGCCCGCCCGCGGAGGTCGTCGgtcggtgcca ... gcgtgcgcagAGGTTTCGACGTTCCTGCACGCGTGCGAGGGGGAGGCGGTGACGAAGCTCA
EST: gi|211457053|gb|FL081470.1|FL081470
EST:     CCGCTTCGGCGGCGGGTTCCGCGACGAGGGCCCGCCCGCGGAGGTCGTCG                         AGGTTTCGACGTTCCTGCACGCGTGCGAGGGGGAGGCGGTGACGAAGCTCA
genomic: CCGCTTCGGCGGCGGGTTCCGCGACGAGGGCCCGCCCGCGGAGGTCGTCGgtcggtgcca ... gcgtgcgcagAGGTTTCGACGTTCCTGCACGCGTGCGAGGGGGAGGCGGTGACGAAGCTCA
EST: gi|211003881|gb|FL081488.1|FL081488
EST:     CGCTTCGGCG-CGGGTTTCCGCGACGAGGGCCCGCCCGCGGAGGTCGTCG                         AGGTTTCGACGTTCCTGCACGCGTGCGAGGGGGAGGCGGTGACGAAGCTCA
genomic: CGCTTCGGCGGCGGGTT-CCGCGACGAGGGCCCGCCCGCGGAGGTCGTCGgtcggtgcca ... gcgtgcgcagAGGTTTCGACGTTCCTGCACGCGTGCGAGGGGGAGGCGGTGACGAAGCTCA
EST: gi|60344900|gb|DN211873.1|DN211873
EST:     CCGCTTCGGCGGCGGGTTCCGCGACGAGGGCCCGCCCGCGGAGGTCGTCG                         AGGTTTCGACGTTCCTGCACGCGTGCGAGGGGGAGGCGGTGACGAAGCTCA
genomic: CCGCTTCGGCGGCGGGTTCCGCGACGAGGGCCCGCCCGCGGAGGTCGTCGgtcggtgcca ... gcgtgcgcagAGGTTTCGACGTTCCTGCACGCGTGCGAGGGGGAGGCGGTGACGAAGCTCA
EST: gi|29130259|gb|CB380963.1|CB380963
EST:     CCGCTTCGGCGGCGGGTTCCGCGACGAGGGCCCGCCCGCGGAGGTCGTCG                         AGGTTTCGACGTTCCTGCACGCGTGCGAGGGGGAGGCGGTGACGAAGCTCA
genomic: CCGCTTCGGCGGCGGGTTCCGCGACGAGGGCCCGCCCGCGGAGGTCGTCGgtcggtgcca ... gcgtgcgcagAGGTTTCGACGTTCCTGCACGCGTGCGAGGGGGAGGCGGTGACGAAGCTCA
EST: gi|211454925|gb|FL081458.1|FL081458
EST:     CCGCTTCGGCGGCGGGTTCCGCGACGAGGGCCCGCCCGCGGAGGTCGTCG                         AGGTTTCGACGTTCCTGCACGCGTGCGAGGGGGAGGCGGTGACGAAGCTCA
genomic: CCGCTTCGGCGGCGGGTTCCGCGACGAGGGCCCGCCCGCGGAGGTCGTCGgtcggtgcca ... gcgtgcgcagAGGTTTCGACGTTCCTGCACGCGTGCGAGGGGGAGGCGGTGACGAAGCTCA
EST: gi|211454927|gb|FL081460.1|FL081460
EST:     CCGCTTCGGCGGCGGGTTCCGCGACGAGGGCCCGCCCGCGGAGGTCGTCG                         AGGTTTCGACGTTCCTGCACGCGTGCGAGGGGGAGGCGGTGACGAAGCTCA
genomic: CCGCTTCGGCGGCGGGTTCCGCGACGAGGGCCCGCCCGCGGAGGTCGTCGgtcggtgcca ... gcgtgcgcagAGGTTTCGACGTTCCTGCACGCGTGCGAGGGGGAGGCGGTGACGAAGCTCA
EST: gi|211457052|gb|FL081469.1|FL081469
EST:     CCGCTTCGGCGGCGGGTTCCGCGACGAGGGCCCGCCCGCGGAGGTCGTCG                         AGGTTTCGACGTT
genomic: CCGCTTCGGCGGCGGGTTCCGCGACGAGGGCCCGCCCGCGGAGGTCGTCGgtcggtgcca ... gcgtgcgcagAGGTTTCGACGTT
EST: gi|211003875|gb|FL081482.1|FL081482
EST:     CCGCTTCGGCGGCGGGTTCCGCGACGAGGGCCCGCCCGCGGAGGTCGTCG                         AGGTTTCGACGTTCCTGCACGCGTGCGAGGGGGAGGCGGTGACGAAGCTCA
genomic: CCGCTTCGGCGGCGGGTTCCGCGACGAGGGCCCGCCCGCGGAGGTCGTCGgtcggtgcca ... gcgtgcgcagAGGTTTCGACGTTCCTGCACGCGTGCGAGGGGGAGGCGGTGACGAAGCTCA
EST: gi|148990163|gb|EE031870.2|EE031870
EST:     CCGCTTCGGCGGCGGGTTCCGCGACGAGGGCCCGCCCGCGGAGGTCGCCG                         AGGTTTCGACGTTCCTGCACGCGTGCGAGGGGGAGGCGGTGACGAAGCTCA
genomic: CCGCTTCGGCGGCGGGTTCCGCGACGAGGGCCCGCCCGCGGAGGTCGTCGgtcggtgcca ... gcgtgcgcagAGGTTTCGACGTTCCTGCACGCGTGCGAGGGGGAGGCGGTGACGAAGCTCA
EST: gi|211457047|gb|FL081464.1|FL081464
EST:     CCGCTTCGGCGGCGGGTTCCGCGACGAGGGCCCGCCCGCGGAGGTCGTCG                         AGGTTTCGACGTTCCTGCACGCGTGCGAGGGGGAGGCGGTGACGAAGCTCA
genomic: CCGCTTCGGCGGCGGGTTCCGCGACGAGGGCCCGCCCGCGGAGGTCGTCGgtcggtgcca ... gcgtgcgcagAGGTTTCGACGTTCCTGCACGCGTGCGAGGGGGAGGCGGTGACGAAGCTCA
EST: gi|211003882|gb|FL081489.1|FL081489
EST:     CCGCTTCGGCGGCGGGTTCCGCGACGAGGGCCCGCCCGCGGAGGTCGTCG                         AGGTTTCGACGTTCCTGCACGCGTGCGAGGGGGAGGCGGTGACGAAGCTCA
genomic: CCGCTTCGGCGGCGGGTTCCGCGACGAGGGCCCGCCCGCGGAGGTCGTCGgtcggtgcca ... gcgtgcgcagAGGTTTCGACGTTCCTGCACGCGTGCGAGGGGGAGGCGGTGACGAAGCTCA
EST: gi|60343373|gb|DN210346.1|DN210346
EST:     AGGGCCCGCCCGCGGAGGTCGTCG                         AGGTTTCGACGTTCCTGCACGCGTGCGAGGGGGAGGCGGTGACGAAGCTCA
genomic: AGGGCCCGCCCGCGGAGGTCGTCGgtcggtgcca ... gcgtgcgcagAGGTTTCGACGTTCCTGCACGCGTGCGAGGGGGAGGCGGTGACGAAGCTCA
EST: gi|211457055|gb|FL081472.1|FL081472
EST:     CCGCTTCGGCGGCGGGTTCCGCGACGAGGGCCCGCCCGCGGAGGTCGTCG                         AAGTTTCGACGTT
genomic: CCGCTTCGGCGGCGGGTTCCGCGACGAGGGCCCGCCCGCGGAGGTCGTCGgtcggtgcca ... gcgtgcgcagAGGTTTCGACGTT
EST: gi|211457061|gb|FL081478.1|FL081478
EST:     CCGTTTCGGC-GCGGGTTCCGCGACGAGGGCCCGCCCGCGGAGGTCGTCG                         AGGTTTCGACGTTCCTGCACGCGTGCGAGGGGGAGGCGGTGACGAAGCTCA
genomic: CCGCTTCGGCGGCGGGTTCCGCGACGAGGGCCCGCCCGCGGAGGTCGTCGgtcggtgcca ... gcgtgcgcagAGGTTTCGACGTTCCTGCACGCGTGCGAGGGGGAGGCGGTGACGAAGCTCA
EST: gi|211003885|gb|FL081492.1|FL081492
EST:     CCGCTTCGGCGGCGGGTTCCGCGACGAGGGCCCGCCCGCGGAGGTCGTCG                         AGGTTTCGACGTTCCTGCACGCGTGCGAGGGGGAGGCGGTGACGAAGCTCA
genomic: CCGCTTCGGCGGCGGGTTCCGCGACGAGGGCCCGCCCGCGGAGGTCGTCGgtcggtgcca ... gcgtgcgcagAGGTTTCGACGTTCCTGCACGCGTGCGAGGGGGAGGCGGTGACGAAGCTCA
EST: gi|211003880|gb|FL081487.1|FL081487
EST:     CCGCTTCGGCGGCGGGTTCCGCGACGAGGGCCCGCCCGCGGAGGTCGTCG                         AGGTTTCGACGTTCCTGCACGCGTGCGAGGGGGAGGCGGTGACGAAGCTCA
genomic: CCGCTTCGGCGGCGGGTTCCGCGACGAGGGCCCGCCCGCGGAGGTCGTCGgtcggtgcca ... gcgtgcgcagAGGTTTCGACGTTCCTGCACGCGTGCGAGGGGGAGGCGGTGACGAAGCTCA
EST: gi|211457056|gb|FL081473.1|FL081473
EST:     CCGCTTCGGCGGCGGGTTCCGCGACGAGGGCCCGCCCGCGGAGGTCGTCT                         AGGTTTCGACGTTCCTGCACGCGTGCGAGGGGGAGGCGGTGACGAAGCTCA
genomic: CCGCTTCGGCGGCGGGTTCCGCGACGAGGGCCCGCCCGCGGAGGTCGTCGgtcggtgcca ... gcgtgcgcagAGGTTTCGACGTTCCTGCACGCGTGCGAGGGGGAGGCGGTGACGAAGCTCA
EST: gi|211003883|gb|FL081490.1|FL081490
EST:     CCGCTTCGGCGGCGGGTTCCGCGACGAGGGCCCGCCCGCGGAGGTCGTCG                         AGGTTTCGACGTTCCTGCACGCGTGCGAGGGGGAGGCGGTGACGAAGCTCA
genomic: CCGCTTCGGCGGCGGGTTCCGCGACGAGGGCCCGCCCGCGGAGGTCGTCGgtcggtgcca ... gcgtgcgcagAGGTTTCGACGTTCCTGCACGCGTGCGAGGGGGAGGCGGTGACGAAGCTCA
EST: gi|211457048|gb|FL081465.1|FL081465
EST:     CCGCTTCGGCGGCGGGTTCCGCGACGAGGGCCCGCCCGCGGAGGTCGTCG                         AGGTTTCGACGTTCCTGCACGCGTGCGAGGGGGAGGCGGTGACGAAGCTCA
genomic: CCGCTTCGGCGGCGGGTTCCGCGACGAGGGCCCGCCCGCGGAGGTCGTCGgtcggtgcca ... gcgtgcgcagAGGTTTCGACGTTCCTGCACGCGTGCGAGGGGGAGGCGGTGACGAAGCTCA
EST: gi|211454926|gb|FL081459.1|FL081459
EST:     CCGCTTCGGCGGCGGGTTCCGCGACGAGGGCCCGCCCGCGGAGGTCGTCG                         AGGTTTCGACGTTCCTGCACGCGTGCGAGGGGGAGGCGGTGACGAAGCTCA
genomic: CCGCTTCGGCGGCGGGTTCCGCGACGAGGGCCCGCCCGCGGAGGTCGTCGgtcggtgcca ... gcgtgcgcagAGGTTTCGACGTTCCTGCACGCGTGCGAGGGGGAGGCGGTGACGAAGCTCA
EST: gi|211457057|gb|FL081474.1|FL081474
EST:     CCGCTTCGGCGGCGGGTTCCGCGACGAGGGCCCGCCCGCGGAGGTCGTCG                         AGGTTTCGACGTTCCTGCACGCGTGCGAGGGGGAGGCGGTGACGAAGCTCA
genomic: CCGCTTCGGCGGCGGGTTCCGCGACGAGGGCCCGCCCGCGGAGGTCGTCGgtcggtgcca ... gcgtgcgcagAGGTTTCGACGTTCCTGCACGCGTGCGAGGGGGAGGCGGTGACGAAGCTCA
EST: gi|211454928|gb|FL081461.1|FL081461
EST:     CCGCTTCGGCGGCGGGTTCCGCGACGAGGGCCCGCCCGCGGAGGTCGTCG                         AGGTTTCGACGTTCCTGCACGCGTGCGAGGGGGAGGCGGTGACGAAGCTCA
genomic: CCGCTTCGGCGGCGGGTTCCGCGACGAGGGCCCGCCCGCGGAGGTCGTCGgtcggtgcca ... gcgtgcgcagAGGTTTCGACGTTCCTGCACGCGTGCGAGGGGGAGGCGGTGACGAAGCTCA
EST: gi|211003874|gb|FL081481.1|FL081481
EST:     CCGCTTCGGCGGCGGGTTCCGCGACGAGGGCCCGCCCGCGGAGGTCGTCT                         AGGTTTCGACGTTCCTGCACGCGTGCGAGGGGGAGGCGGTGACGAAGCTCA
genomic: CCGCTTCGGCGGCGGGTTCCGCGACGAGGGCCCGCCCGCGGAGGTCGTCGgtcggtgcca ... gcgtgcgcagAGGTTTCGACGTTCCTGCACGCGTGCGAGGGGGAGGCGGTGACGAAGCTCA
EST: gi|211457060|gb|FL081477.1|FL081477
EST:     CCGCTTCGGCGGCGGGTTCCGCGACGAGGGCCCGCCCGCGGAGGTCGTCG                         AGGTTTCGACGTTCCTGCACGCGTGCGAGGGGGAGGCGGTGACGAAGCTCA
genomic: CCGCTTCGGCGGCGGGTTCCGCGACGAGGGCCCGCCCGCGGAGGTCGTCGgtcggtgcca ... gcgtgcgcagAGGTTTCGACGTTCCTGCACGCGTGCGAGGGGGAGGCGGTGACGAAGCTCA
EST: gi|211454930|gb|FL081463.1|FL081463
EST:     CCGCTTCGGCGGCGGGTTCCGCGACGAGGGCCCGCCCGCGGAGGTCGTCG                         AGGTTTCGACGTTCCTGCACGCGTGCGAGGGGGAGGCGGTGACGAAGCTCA
genomic: CCGCTTCGGCGGCGGGTTCCGCGACGAGGGCCCGCCCGCGGAGGTCGTCGgtcggtgcca ... gcgtgcgcagAGGTTTCGACGTTCCTGCACGCGTGCGAGGGGGAGGCGGTGACGAAGCTCA
EST: gi|211003872|gb|FL081479.1|FL081479
EST:     CCGCTTCGGCGGCGGGTTCCGCGACGAGGGCCCGCCCGCGGAGGTCGTCG                         AGGTTTCGACGTTCCTGCACGCGTGCGAGGGGGAGGCGGTGACGAAGCTCA
genomic: CCGCTTCGGCGGCGGGTTCCGCGACGAGGGCCCGCCCGCGGAGGTCGTCGgtcggtgcca ... gcgtgcgcagAGGTTTCGACGTTCCTGCACGCGTGCGAGGGGGAGGCGGTGACGAAGCTCA
EST: gi|211003878|gb|FL081485.1|FL081485
EST:     CCGCTTCGGCGGCGGGTTCCGCGACGAGGGCCCGCCCGCGGAGGTCGTCG                         AGGTTTCGACGTTCCTGCACGCGTGCGAGGGGGAGG
genomic: CCGCTTCGGCGGCGGGTTCCGCGACGAGGGCCCGCCCGCGGAGGTCGTCGgtcggtgcca ... gcgtgcgcagAGGTTTCGACGTTCCTGCACGCGTGCGAGGGGGAGG

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: 190

GGCCGCGGCGGGGGCCGATTCAGCGGTGGTGGCCGAGGTGGCGGCGGGGGCCGCTTCGGCGGCGGGTTCCGCGACGAGGGCCCGCCCGCGGAGGTCGTCGgtcggtgcca ... gcgtgcgcagAGGTTTCGACGTTCCTGCACGCGTGCGAGGGGGAGGCGGTGACGAAGCTCACCAACGAGAAGGTGCCCTACTTCAACGCGCCCATCTATCTGCAGAACAA


Block sizes: 33 (upstream exon), 48 (downstream exon)
Score: 38

GGCCGCGGCGGGGGCCGATTCAGCGGTGGTGGCCGAGGTGGCGGCGGGGGCCGCTTCGGCGGCGGGTTCCGCGACGAGGGCCCGCCCGCGGAGGTCGTCGgtcggtgcca ... gcgtgcgcagAGGTTTCGACGTTCCTGCACGCGTGCGAGGGGGAGGCGGTGACGAAGCTCACCAACGAGAAGGTGCCCTACTTCAACGCGCCCATCTATCTGCAGAACAA


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

GGCCGCGGCGGGGGCCGATTCAGCGGTGGTGGCCGAGGTGGCGGCGGGGGCCGCTTCGGCGGCGGGTTCCGCGACGAGGGCCCGCCCGCGGAGGTCGTCGgtcggtgcca ... gcgtgcgcagAGGTTTCGACGTTCCTGCACGCGTGCGAGGGGGAGGCGGTGACGAAGCTCACCAACGAGAAGGTGCCCTACTTCAACGCGCCCATCTATCTGCAGAACAA


Block sizes: 41 (upstream exon), 48 (downstream exon)
Score: 25

GGCCGCGGCGGGGGCCGATTCAGCGGTGGTGGCCGAGGTGGCGGCGGGGGCCGCTTCGGCGGCGGGTTCCGCGACGAGGGCCCGCCCGCGGAGGTCGTCGgtcggtgcca ... gcgtgcgcagAGGTTTCGACGTTCCTGCACGCGTGCGAGGGGGAGGCGGTGACGAAGCTCACCAACGAGAAGGTGCCCTACTTCAACGCGCCCATCTATCTGCAGAACAA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttctcgtttttttctgaccttctggtggggtttctgtctgtcttggcgtgcgcagAGGTTTCGACGTTCCTGCACGCGTGCGAGGGGGAGGCGGTGACGAAGCTCACCAACGAGAAGGTGCCCTACTTCAACGCGCCCATCTATCTGCAGAACAA
           ttctgac  putative branch site (score: 25)
      tttttttct  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtcggtgccacccatactcctacccactccccgtcagggtattggctccttttctggtattctcgtttttttctgaccttctggtggggtttctgtctgtcttggcgtgcgcagAGGTTTCGACGTTCCTGCACGCGTGCGAGGGGGAGGCGGTGACGAAGCTCACCAACGAGAAGGTGCCCTACTTCAACGCGCCCATCTATCTGCAGAACAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGCAG