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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGAGCAAGATCGCTTGCAATCGGCTGCAGAAGGAACTCGCCGAGTGGCAACTCAGCCCCCCTGCTGGATTCAAGCACAAGGTCTCCGATAACCTACAAAGgtgccgcctttcgcatcgcatcccgccctccttgcaattgcgtttgcctttttttatttatgtagttttttttttcttttgccttgttgctgtctcttct...

Basic information

species Zea mays
transcript GRMZM2G018447_T01
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G018447_T01 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os12g44000.1 (Oryza sativa), 5'ss of exon 2
TGAGCAAGATCGCTTGCAATCGGCTGCAGAAGGAACTCGCCGAGTGGCAACTCAGCCCCCCTGCTGGATTCAAGCACAAGGTCTCCGATAACCTACAAAGgtg------ccgcctttcgc--atcgcatcccgccctccttgcaattgcgt---ttgcctttttttatttatgtagttttttttttcttttgccttgttgctgtctcttct-----------------------------------------------------------------------------------
|||||||||||||||||||||||||||||||||| ||||||||||||||  ||||||| ||  | || |||||| ||| ||||||||||||||| |||||||         | |||   |   | |  | |     || |  |   ||  |     ||    |   || | |  | ||  ||  || | ||  ||||    | | | ||||                                                                                   
TGAGCAAGATCGCTTGCAATCGGCTGCAGAAGGAGCTCGCCGAGTGGCAGGTCAGCCCTCCCTCCGGGTTCAAGTACAGGGTCTCCGATAACCTCCAAAGgtcgtcatcttgtcttctactggttgatttcttgtttcttctcctgtggatgaaccgcgggatcccatct-tacaattgattccttttcttttcttgactgtatatgttcttgattttggggatttttggtgggtttttattattagtattgttgttaatctgtggagatggattcgtacgattcgcctaatag
















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|211424407|gb|FL084942.1|FL084942
EST:     CTCAGCCCCCCTGCTGGATTCAAGCACAAGGTCTCCGATAACCTACAAAG                         GTGGGTAATTGAGGTCACTGGAGCGGCGGGCACCCTTTACGCCGGCGAGAC
genomic: CTCAGCCCCCCTGCTGGATTCAAGCACAAGGTCTCCGATAACCTACAAAGgtgccgcctt ... aactgaccagGTGGGTAATTGAGGTCACTGGAGCGGCGGGCACCCTTTACGCCGGCGAGAC
EST: gi|32868298|gb|CF007980.1|CF007980
EST:     CTCAGCCCCCCTGCTGGATTCAAGCACAAGGTCTCCGATAACCTACAAAG                         GTGGGTAATTGAGGTCACTGGAGCGGCGGGCACCCTTTACGCCGGCGAGAC
genomic: CTCAGCCCCCCTGCTGGATTCAAGCACAAGGTCTCCGATAACCTACAAAGgtgccgcctt ... aactgaccagGTGGGTAATTGAGGTCACTGGAGCGGCGGGCACCCTTTACGCCGGCGAGAC
EST: gi|211424414|gb|FL084949.1|FL084949
EST:     CTCAGCCCCCCTGCTGGATTCAAGCACAAGGTCTCCGATAACCTACAAAG                         GTGGGTAATTGAGGTCACTGGAGCGGCGGGCACCCTTTACGCCGGCGAGAC
genomic: CTCAGCCCCCCTGCTGGATTCAAGCACAAGGTCTCCGATAACCTACAAAGgtgccgcctt ... aactgaccagGTGGGTAATTGAGGTCACTGGAGCGGCGGGCACCCTTTACGCCGGCGAGAC
EST: gi|211424415|gb|FL084950.1|FL084950
EST:     CTCAGCCCCCCTGCTGGATTCAAGCACAAGGTCTCCGATAACCTACAAAG                         GTGGGTAATTGAGGTCACTGGAGCGGCGGGCACCCTTTACGCCGGCGAGAC
genomic: CTCAGCCCCCCTGCTGGATTCAAGCACAAGGTCTCCGATAACCTACAAAGgtgccgcctt ... aactgaccagGTGGGTAATTGAGGTCACTGGAGCGGCGGGCACCCTTTACGCCGGCGAGAC
EST: gi|76018971|gb|DT946141.1|DT946141
EST:     CTCAGCCCCCCTGCTGGATTCAAGCACAAGGTCTCCGATAACCTACAAAG                         GTGGGTAATTGAGGTCACTGGAGCGGCGGGCACCCTTTACGCCGGCGAGAC
genomic: CTCAGCCCCCCTGCTGGATTCAAGCACAAGGTCTCCGATAACCTACAAAGgtgccgcctt ... aactgaccagGTGGGTAATTGAGGTCACTGGAGCGGCGGGCACCCTTTACGCCGGCGAGAC
EST: gi|211424413|gb|FL084948.1|FL084948
EST:     CTCAGCCCCCCTGCTGGATTCAAGCACAAGGTCTCCGATAACCTACAAAG                         GTGGGTAATTGAGGTCACTGGAGCGGCGGGCACCCTTTACGCCGGCGAGAC
genomic: CTCAGCCCCCCTGCTGGATTCAAGCACAAGGTCTCCGATAACCTACAAAGgtgccgcctt ... aactgaccagGTGGGTAATTGAGGTCACTGGAGCGGCGGGCACCCTTTACGCCGGCGAGAC
EST: gi|32869440|gb|CF009122.1|CF009122
EST:     CTCAGCCCCCCTGCTGGATTCAAGCACAAGGTCTCCGATAACCTACAAAG                         GTGGGTAATTGAGGTCACTGGAGCGGCGGGCACCCTTTACGCCGGCGAGAC
genomic: CTCAGCCCCCCTGCTGGATTCAAGCACAAGGTCTCCGATAACCTACAAAGgtgccgcctt ... aactgaccagGTGGGTAATTGAGGTCACTGGAGCGGCGGGCACCCTTTACGCCGGCGAGAC
EST: gi|211424416|gb|FL084951.1|FL084951
EST:     CTCAGCCCCCCTGCTGGATTCAAGCACAAGGTCTCCGATAACCTACAAAG                         GTGGGTAATTGAGGTCACTGGAGCGGCGGGCACCCTTTACGCCGGCGAGAC
genomic: CTCAGCCCCCCTGCTGGATTCAAGCACAAGGTCTCCGATAACCTACAAAGgtgccgcctt ... aactgaccagGTGGGTAATTGAGGTCACTGGAGCGGCGGGCACCCTTTACGCCGGCGAGAC
EST: gi|211421813|gb|FL084940.1|FL084940
EST:     CTCAGCCCCCCTGCTGGATTCAAGCACAAGGTCTCCGATAACCTACAAAG                         GTGGGTAATTGAGGTCACTGGAGCGGCGGGCACCCTTTACGCCGGCGAGAC
genomic: CTCAGCCCCCCTGCTGGATTCAAGCACAAGGTCTCCGATAACCTACAAAGgtgccgcctt ... aactgaccagGTGGGTAATTGAGGTCACTGGAGCGGCGGGCACCCTTTACGCCGGCGAGAC
EST: gi|32856121|gb|CD995802.1|CD995802
EST:     CTCAGCCCCCCTGCTGGATTCAAGCACAAGGTCTCCGATAACCTACAAAG                         GTGGGTAATTGAGGTCACTGGAGCGGCGGGCACCCTTTACGCCGGCGAGAC
genomic: CTCAGCCCCCCTGCTGGATTCAAGCACAAGGTCTCCGATAACCTACAAAGgtgccgcctt ... aactgaccagGTGGGTAATTGAGGTCACTGGAGCGGCGGGCACCCTTTACGCCGGCGAGAC
EST: gi|211421814|gb|FL084941.1|FL084941
EST:     CTCAGCCCCCCTGCTGGATTCAAGCACAAGGTCTCCGATAACCTACAAAG                         GTGGGTAATTGAGGTCACTGGAGCGGCGGGCACCCTTTACGCCGGCGAGAC
genomic: CTCAGCCCCCCTGCTGGATTCAAGCACAAGGTCTCCGATAACCTACAAAGgtgccgcctt ... aactgaccagGTGGGTAATTGAGGTCACTGGAGCGGCGGGCACCCTTTACGCCGGCGAGAC
EST: gi|89756005|gb|DY686208.1|DY686208
EST:     CTCAGCCCCCCTGCTGGATTCAAGCACAAGGTCTCCGATAACCTACAAAG                         GTGGGTAATTGAGGTCACTGGAGCGGCGGGCACCCTTTACGCCGGCGAGAC
genomic: CTCAGCCCCCCTGCTGGATTCAAGCACAAGGTCTCCGATAACCTACAAAGgtgccgcctt ... aactgaccagGTGGGTAATTGAGGTCACTGGAGCGGCGGGCACCCTTTACGCCGGCGAGAC
EST: gi|211421803|gb|FL084930.1|FL084930
EST:     CTCAGCCCCCCTGCTGGATTCAAGCACAAGGTCTCCGATAACCTACAAAG                         GTGGGTAATTGAGGTCACTGGAGCGGCGGGCACCCTTTACGCCGGCGAGAC
genomic: CTCAGCCCCCCTGCTGGATTCAAGCACAAGGTCTCCGATAACCTACAAAGgtgccgcctt ... aactgaccagGTGGGTAATTGAGGTCACTGGAGCGGCGGGCACCCTTTACGCCGGCGAGAC
EST: gi|67016859|gb|CO445608.1|CO445608
EST:     CTCAGTCCCCCTGCTGGATTCAAGCACAAGGTCTCCGATAACCTACAAAG                         GTGGGTAATTGAGGTCACTGGAGCGGCGGGCACCCTTTACGCCGGCGAGAC
genomic: CTCAGCCCCCCTGCTGGATTCAAGCACAAGGTCTCCGATAACCTACAAAGgtgccgcctt ... aactgaccagGTGGGTAATTGAGGTCACTGGAGCGGCGGGCACCCTTTACGCCGGCGAGAC
EST: gi|89246821|gb|DY618608.1|DY618608
EST:     CTCAGCCCCCCTGCTGGATTCAAGCACAAGGTCTCCGATAACCTACAAAG                         GTGGGTAATTGAGGTCACTGGAGCGGCGGGCACCCTTTACGCCGGCGAGAC
genomic: CTCAGCCCCCCTGCTGGATTCAAGCACAAGGTCTCCGATAACCTACAAAGgtgccgcctt ... aactgaccagGTGGGTAATTGAGGTCACTGGAGCGGCGGGCACCCTTTACGCCGGCGAGAC
EST: gi|211424417|gb|FL084952.1|FL084952
EST:     CTCAGCCCCCCTGCTGGATTCAAGCACAAGGTCTCCGATAACCTACAAAG                         GTGGGTAATTGAGGTCACTGGAGCGGCGGGCACCCTTTACGCCGGCGAGAC
genomic: CTCAGCCCCCCTGCTGGATTCAAGCACAAGGTCTCCGATAACCTACAAAGgtgccgcctt ... aactgaccagGTGGGTAATTGAGGTCACTGGAGCGGCGGGCACCCTTTACGCCGGCGAGAC
EST: gi|211421809|gb|FL084936.1|FL084936
EST:     CTCAGCCCCCCTGCTGGATTCAAGCACAAGGTCTCCGATAACCTACAAAG                         GTGGGTAATTGAGGTCACTGGAGCGGCGGGCACCCTTTACGCCGGCGAGAC
genomic: CTCAGCCCCCCTGCTGGATTCAAGCACAAGGTCTCCGATAACCTACAAAGgtgccgcctt ... aactgaccagGTGGGTAATTGAGGTCACTGGAGCGGCGGGCACCCTTTACGCCGGCGAGAC
EST: gi|76288121|gb|DV027689.1|DV027689
EST:     CTCAGCCCCCCTGCTGGATTCAAGCACAAGGTCTCCGATAACCTACAAAG                         GTGGGTAATTGAGGTCACTGGAGCGGCGGGCACCCTTTACGCCGGCGAGAC
genomic: CTCAGCCCCCCTGCTGGATTCAAGCACAAGGTCTCCGATAACCTACAAAGgtgccgcctt ... aactgaccagGTGGGTAATTGAGGTCACTGGAGCGGCGGGCACCCTTTACGCCGGCGAGAC
EST: gi|60394784|gb|DN227654.1|DN227654
EST:     CTCAGCCCCCCTGCTGGATTCAAGCACAAGGTCTCCGATAACCTACAAAG                         GTGGGTAATTGAGGTCACTGGAGCGGCGGGCACCCTTTACGCCGGCGAGAC
genomic: CTCAGCCCCCCTGCTGGATTCAAGCACAAGGTCTCCGATAACCTACAAAGgtgccgcctt ... aactgaccagGTGGGTAATTGAGGTCACTGGAGCGGCGGGCACCCTTTACGCCGGCGAGAC
EST: gi|32935782|gb|CF040594.1|CF040594
EST:     CTCAGCCCCCCTGCTGGATTCAAGCACAAGGTCTCCGATAACCTACAAAG                         GTGGGTAATTGAGGTCACTGGAGCGGCGGGCACCCTTTACGCCGGCGAGAC
genomic: CTCAGCCCCCCTGCTGGATTCAAGCACAAGGTCTCCGATAACCTACAAAGgtgccgcctt ... aactgaccagGTGGGTAATTGAGGTCACTGGAGCGGCGGGCACCCTTTACGCCGGCGAGAC
EST: gi|211421810|gb|FL084937.1|FL084937
EST:     CTCAGCCCCCCTGCTGGATTCAAGCACAAGGTCTCCGATAACCTACAAAG                         GTGGGTAATTGAGGTCACTGGAGCGGCGGGCACCCTTTACGCCGGCGAGAC
genomic: CTCAGCCCCCCTGCTGGATTCAAGCACAAGGTCTCCGATAACCTACAAAGgtgccgcctt ... aactgaccagGTGGGTAATTGAGGTCACTGGAGCGGCGGGCACCCTTTACGCCGGCGAGAC
EST: gi|76018970|gb|DT946140.1|DT946140
EST:     CTCAGCCCCCCTGCTGGATTCAAGCACAAGGTCTCCGATAACCTACAAAG                         GTGGGTAATTGAGGTCACTGGAGCGGCGGGCACCCTTTACGCCGGCGAGAC
genomic: CTCAGCCCCCCTGCTGGATTCAAGCACAAGGTCTCCGATAACCTACAAAGgtgccgcctt ... aactgaccagGTGGGTAATTGAGGTCACTGGAGCGGCGGGCACCCTTTACGCCGGCGAGAC
EST: gi|18172273|gb|BM347661.1|BM347661
EST:     CTCAGCCCCCCTGCTGGATTCAAGCACAAGGTCTCCGATAACCTACAAAG                         GTGGGTAATTGAGGTCACTGGAGCGGCGGGCACCCTTTACGCCGGCGAGAC
genomic: CTCAGCCCCCCTGCTGGATTCAAGCACAAGGTCTCCGATAACCTACAAAGgtgccgcctt ... aactgaccagGTGGGTAATTGAGGTCACTGGAGCGGCGGGCACCCTTTACGCCGGCGAGAC
EST: gi|211424418|gb|FL084953.1|FL084953
EST:     CTCAGCCCCCCTGCTGGATTCAAGCACAAGGTCTCCGATAACCTACAAAG                         GTGGGTAATTGAGGTCACTGGAGCGGCGGGCACCCTTTACGCCGGCGAGAC
genomic: CTCAGCCCCCCTGCTGGATTCAAGCACAAGGTCTCCGATAACCTACAAAGgtgccgcctt ... aactgaccagGTGGGTAATTGAGGTCACTGGAGCGGCGGGCACCCTTTACGCCGGCGAGAC
EST: gi|116821688|gb|EC865015.1|EC865015
EST:     CTCAGCCCCCCTGCTGGATTCAAGCACAAGGTCTCCGATAACCTACAAAG                         GTGGGTAATTGAGGTCACTGGAGCGGCGGGCACCCTTTACGCCGGCGAGAC
genomic: CTCAGCCCCCCTGCTGGATTCAAGCACAAGGTCTCCGATAACCTACAAAGgtgccgcctt ... aactgaccagGTGGGTAATTGAGGTCACTGGAGCGGCGGGCACCCTTTACGCCGGCGAGAC
EST: gi|29947193|gb|CB816528.1|CB816528
EST:     CTCAGCCCCCCTGCTGGATTCAAGCACAAGGTCTCCGATAACCTACAAAG                         GTGGGTAATTGAGGTCACTGGAGCGGCGGGCACCCTTTACGCCGGCGAGAC
genomic: CTCAGCCCCCCTGCTGGATTCAAGCACAAGGTCTCCGATAACCTACAAAGgtgccgcctt ... aactgaccagGTGGGTAATTGAGGTCACTGGAGCGGCGGGCACCCTTTACGCCGGCGAGAC
EST: gi|211421805|gb|FL084932.1|FL084932
EST:     CTCAGCCCCCCTGCTGGATTCAAGCACAAGGTCTCCGATAACCTATAAAG                         GTGGGTAATTGAGGTCACTGGAGCGGCGGGCACCCTTTACGCCGGCGAGAC
genomic: CTCAGCCCCCCTGCTGGATTCAAGCACAAGGTCTCCGATAACCTACAAAGgtgccgcctt ... aactgaccagGTGGGTAATTGAGGTCACTGGAGCGGCGGGCACCCTTTACGCCGGCGAGAC
EST: gi|211421806|gb|FL084933.1|FL084933
EST:     CTCAGCCCCCCTGCTGGATTCAAGCACAAGGTCTCCGATAACCTACAAAG                         GTGGGTAATTGAGGTCACTGGAGCGGCGGGCACCCTTTACGCCGGCGAGAC
genomic: CTCAGCCCCCCTGCTGGATTCAAGCACAAGGTCTCCGATAACCTACAAAGgtgccgcctt ... aactgaccagGTGGGTAATTGAGGTCACTGGAGCGGCGGGCACCCTTTACGCCGGCGAGAC
EST: gi|211421802|gb|FL084929.1|FL084929
EST:     CTCAGCCCCCCTGCTGGATTCAAGCACAAGGTCTCCGATAACCTACAAAG                         GTGGGTAATTGAGGTCACTGGAGCGGCGGGCACCCTTTACGCCGGCGAGAC
genomic: CTCAGCCCCCCTGCTGGATTCAAGCACAAGGTCTCCGATAACCTACAAAGgtgccgcctt ... aactgaccagGTGGGTAATTGAGGTCACTGGAGCGGCGGGCACCCTTTACGCCGGCGAGAC
EST: gi|211424411|gb|FL084946.1|FL084946
EST:     CTCAGCCCCCCTGCTGGATTCAAGCACAAGGTCTCCGATAACCTACAAAG                         GTGGGTAATTGAGGTCACTGGAGCGGCGGGCACCCTTTACGCCGGCGAGAC
genomic: CTCAGCCCCCCTGCTGGATTCAAGCACAAGGTCTCCGATAACCTACAAAGgtgccgcctt ... aactgaccagGTGGGTAATTGAGGTCACTGGAGCGGCGGGCACCCTTTACGCCGGCGAGAC
EST: gi|211421808|gb|FL084935.1|FL084935
EST:     CTCAGCCCCCCTGCTGGATTCAAGCACAAGGTCTCCGATAACCTACAAAG                         GTGGGTAATTGAGGTCACTGGAGCGGCGGGCACCCTTTACGCCGGCGAGAC
genomic: CTCAGCCCCCCTGCTGGATTCAAGCACAAGGTCTCCGATAACCTACAAAGgtgccgcctt ... aactgaccagGTGGGTAATTGAGGTCACTGGAGCGGCGGGCACCCTTTACGCCGGCGAGAC
EST: gi|18169036|gb|BM338876.1|BM338876
EST:     CTCAGCCCCCCTGCTGGATTCAAGCACAAGGTCTCCGATAACCTACAAAG                         GTGGGTAATTGAGGTCACTGGAGCGGCGGGCACCCTTTACGCCGGCGAGAC
genomic: CTCAGCCCCCCTGCTGGATTCAAGCACAAGGTCTCCGATAACCTACAAAGgtgccgcctt ... aactgaccagGTGGGTAATTGAGGTCACTGGAGCGGCGGGCACCCTTTACGCCGGCGAGAC

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: 73

TGAGCAAGATCGCTTGCAATCGGCTGCAGAAGGAACTCGCCGAGTGGCAACTCAGCCCCCCTGCTGGATTCAAGCACAAGGTCTCCGATAACCTACAAAGgtgccgcctt ... aactgaccagGTGGGTAATTGAGGTCACTGGAGCGGCGGGCACCCTTTACGCCGGCGAGACCTACCAGTTGCAGGTTGACTTCCCTGAGCATTATCCTATGGAGGCACCT


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 153

TGAGCAAGATCGCTTGCAATCGGCTGCAGAAGGAACTCGCCGAGTGGCAACTCAGCCCCCCTGCTGGATTCAAGCACAAGGTCTCCGATAACCTACAAAGgtgccgcctt ... aactgaccagGTGGGTAATTGAGGTCACTGGAGCGGCGGGCACCCTTTACGCCGGCGAGACCTACCAGTTGCAGGTTGACTTCCCTGAGCATTATCCTATGGAGGCACCT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 247

TGAGCAAGATCGCTTGCAATCGGCTGCAGAAGGAACTCGCCGAGTGGCAACTCAGCCCCCCTGCTGGATTCAAGCACAAGGTCTCCGATAACCTACAAAGgtgccgcctt ... aactgaccagGTGGGTAATTGAGGTCACTGGAGCGGCGGGCACCCTTTACGCCGGCGAGACCTACCAGTTGCAGGTTGACTTCCCTGAGCATTATCCTATGGAGGCACCT


Block sizes: 47 (upstream exon), 48 (downstream exon)
Score: 145

TGAGCAAGATCGCTTGCAATCGGCTGCAGAAGGAACTCGCCGAGTGGCAACTCAGCCCCCCTGCTGGATTCAAGCACAAGGTCTCCGATAACCTACAAAGgtgccgcctt ... aactgaccagGTGGGTAATTGAGGTCACTGGAGCGGCGGGCACCCTTTACGCCGGCGAGACCTACCAGTTGCAGGTTGACTTCCCTGAGCATTATCCTATGGAGGCACCT


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGAGCAAGATCGCTTGCAATCGGCTGCAGAAGGAACTCGCCGAGTGGCAACTCAGCCCCCCTGCTGGATTCAAGCACAAGGTCTCCGATAACCTACAAAGgtgccgcctttcgcatcgcatcccgccctccttgcaattgcgtttgcctttttttatttatgtagttttttttttcttttgccttgttgctgtctcttct

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA