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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCCCCCCTCCCCGCCGGTTGCCGCGCTCGTGCCACGGTGCGGTAGCCCCGTCGACGCCGGCGGACAGCGTGCACTATGGGTTGCTCCTCCTCCGTGCCAGgttcgcacctcctctccctcgagtcttcaaaattcgaaggttgcggtgtaggattgttgtattttctattcaattagttgccggagggaacagattcaaa...

Basic information

species Zea mays
transcript GRMZM2G362088_T01
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G362088_T02 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os03g05740.1 (Oryza sativa), 5'ss of exon 1
-TCCCCCCTCCCCGCCGGTTGCCGCGCTCGTGCCACGGTGCGGTAGCCC-CGTCGACGCCGGCGGACAGCGTGCACTATGGGTTGCTCCTCCTCCGTGCCAGgttcgcacctcctctccctcgagtcttcaaaattcga---aggttgcggtgtaggattgttgtattttctattcaattagttgccggagggaacagattcaaa
 || || |   || |||    ||||   |   || ||   |  |  | | | |||||||||||   || ||    | ||||||||||||||||||||||||||||| | |   | | |  |    ||  |    ||      || || |   || || |   ||| |   ||    |  | ||||     | |       | |  
CTCACCTCCGGCCACCGACCACCGCCGCCT--CCGCGTCCCTCTGCCTCACCTCGACGCCGGCTAGCATCGCCGGCGATGGGTTGCTCCTCCTCCGTGCCAGgttctctctctcacacgtttccatcccccttttttagattagatttcctcgttggcta--tgtttcggctgcggatattgttggtaccgagtgttaggtaag-
















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|211329193|gb|FL235162.1|FL235162
EST:     TCGACGCCGGCGGACAGCGTGCACTATGGGTTGCTCCTCCTCCGTGCCAG                         CTAGAAATACTGGAGGGCTGAACACTATCAGCAACGATAGCTCTCCAGCCA
genomic: TCGACGCCGGCGGACAGCGTGCACTATGGGTTGCTCCTCCTCCGTGCCAGgttcgcacct ... tcccattcagCTAGAAATACTGGAGGGCTGAACACTATCAGCAACGATAGCTCTCCAGACG
EST: gi|211331361|gb|FL235186.1|FL235186
EST:     TCGACGCCGGCGGACAGCGTGCACTATGGGTTGCTCCTCCTCCGTGCCAG                         CTAGAAATACTGGAGGGCTGAACACTATCAGCAACGATAGCTCTCCAGCCA
genomic: TCGACGCCGGCGGACAGCGTGCACTATGGGTTGCTCCTCCTCCGTGCCAGgttcgcacct ... tcccattcagCTAGAAATACTGGAGGGCTGAACACTATCAGCAACGATAGCTCTCCAGACG
EST: gi|211329196|gb|FL235165.1|FL235165
EST:     TCGACGCCGGCGGACAGCGTGCACTATGGGTTGCTCCTCCTCCGTGCCAG                         CTAGAAATACTGGAGGGCTGAACACTATCAGCAACGATAGCTCTCCAGCCA
genomic: TCGACGCCGGCGGACAGCGTGCACTATGGGTTGCTCCTCCTCCGTGCCAGgttcgcacct ... tcccattcagCTAGAAATACTGGAGGGCTGAACACTATCAGCAACGATAGCTCTCCAGACG
EST: gi|211329195|gb|FL235164.1|FL235164
EST:     TCGACGCCGGCGGACAGCGTGCACTATGGGTTGCTCCTCCTCCGTGCCAG                         CTAGAAATACTGGAGGGCTGAACACTATCA
genomic: TCGACGCCGGCGGACAGCGTGCACTATGGGTTGCTCCTCCTCCGTGCCAGgttcgcacct ... tcccattcagCTAGAAATACTGGAGGGCTGAACACTATCA
EST: gi|211331350|gb|FL235175.1|FL235175
EST:     TCGACGCCGGCGGACAGCGTGCACTATGGGTTGCTCCTCCTCCGTGCCAG                         CTAGAAATACTGGAGGGCTGAACACTATCAGCAACGATAGCTCTCCAGACG
genomic: TCGACGCCGGCGGACAGCGTGCACTATGGGTTGCTCCTCCTCCGTGCCAGgttcgcacct ... tcccattcagCTAGAAATACTGGAGGGCTGAACACTATCAGCAACGATAGCTCTCCAGACG
EST: gi|211329203|gb|FL235172.1|FL235172
EST:     TCGACGCCGGCGGACAGCGTGCACTATGGGTTGCTCCTCCTCCGTGCCAG                         CTAGAAATACTGGAGGGCTGAACACTATCAGCAACGATAGCTCTCCAGCCA
genomic: TCGACGCCGGCGGACAGCGTGCACTATGGGTTGCTCCTCCTCCGTGCCAGgttcgcacct ... tcccattcagCTAGAAATACTGGAGGGCTGAACACTATCAGCAACGATAGCTCTCCAGACG
EST: gi|211331353|gb|FL235178.1|FL235178
EST:     TCGACGCCGGCGGACAGCGTGCACTATGGGTTGCTCCTCCTCCGTGCCAG                         CTAGAAATACTGGAGGGCTGAACACTATCAGCAACGATAGCTCTCCAGCCA
genomic: TCGACGCCGGCGGACAGCGTGCACTATGGGTTGCTCCTCCTCCGTGCCAGgttcgcacct ... tcccattcagCTAGAAATACTGGAGGGCTGAACACTATCAGCAACGATAGCTCTCCAGACG
EST: gi|50330001|gb|CO525127.1|CO525127
EST:     TCGACGCCGGCGGACAGCGTGCACTATGGGTTGCTCCTCCTCCGTGCCAG                         CTAGAAATACTGGAGGGCTGAACACTATCAGCAACGATAGCTCTCCAGACG
genomic: TCGACGCCGGCGGACAGCGTGCACTATGGGTTGCTCCTCCTCCGTGCCAGgttcgcacct ... tcccattcagCTAGAAATACTGGAGGGCTGAACACTATCAGCAACGATAGCTCTCCAGACG
EST: gi|211329194|gb|FL235163.1|FL235163
EST:     TCGACGCCGGCGGACAGCGTGCACTATGGGTTGCTCCTCCTCCGTGCCAG                         CTAGAAATACTGGAGGGCTGAACACTATCAGCAACGATAGCTCTCCAGACG
genomic: TCGACGCCGGCGGACAGCGTGCACTATGGGTTGCTCCTCCTCCGTGCCAGgttcgcacct ... tcccattcagCTAGAAATACTGGAGGGCTGAACACTATCAGCAACGATAGCTCTCCAGACG
EST: gi|148937431|gb|EC881612.2|EC881612
EST:     TCGACGCCGGCGGACAGCGTGCACTATGGGTTGCTCCTCCTCCGTGCCAG                         CTAGAAATACTGGAGGGCTGAACACTATCAGCAACGATAGCTCTCCAGACG
genomic: TCGACGCCGGCGGACAGCGTGCACTATGGGTTGCTCCTCCTCCGTGCCAGgttcgcacct ... tcccattcagCTAGAAATACTGGAGGGCTGAACACTATCAGCAACGATAGCTCTCCAGACG
EST: gi|211331363|gb|FL235188.1|FL235188
EST:     TCGACGCCGGCGGACAGCGTGCACTATGGGTTGCTCCTCCTCCGTGCCAG                         CTAGAAATACTGGAGGGCTGAACACTATCAGCAACGATAGCTCTCCAGCCA
genomic: TCGACGCCGGCGGACAGCGTGCACTATGGGTTGCTCCTCCTCCGTGCCAGgttcgcacct ... tcccattcagCTAGAAATACTGGAGGGCTGAACACTATCAGCAACGATAGCTCTCCAGACG
EST: gi|211329202|gb|FL235171.1|FL235171
EST:     TCGACGCCGGCGGACAGCGTGCACTATGGGTTGCTCCTCCTCCGTGCCAG                         CTAGAAATACTGGAGGGCTGAACACTATCAGCAACGATAGCTCTCCAGCCA
genomic: TCGACGCCGGCGGACAGCGTGCACTATGGGTTGCTCCTCCTCCGTGCCAGgttcgcacct ... tcccattcagCTAGAAATACTGGAGGGCTGAACACTATCAGCAACGATAGCTCTCCAGACG
EST: gi|211331355|gb|FL235180.1|FL235180
EST:     TCGACGCCGGCGGACAGCGTGCACTATGGGTTGCTCCTCCTCCGTGCCAG                         CTAGAAATACTGGAGGGCTGAACACTATCAGCAACGATAGCTCTCCAGCCA
genomic: TCGACGCCGGCGGACAGCGTGCACTATGGGTTGCTCCTCCTCCGTGCCAGgttcgcacct ... tcccattcagCTAGAAATACTGGAGGGCTGAACACTATCAGCAACGATAGCTCTCCAGACG
EST: gi|60336834|gb|DN203807.1|DN203807
EST:     TCGACGCCGGCGGACAGCGTGCACTATGGGTTGCTCCTCCTCCGTGCCAG                         CTAGAAATACTGGAGGGCTGAACACTATCAGCAACGATAGCTCTCCAGACG
genomic: TCGACGCCGGCGGACAGCGTGCACTATGGGTTGCTCCTCCTCCGTGCCAGgttcgcacct ... tcccattcagCTAGAAATACTGGAGGGCTGAACACTATCAGCAACGATAGCTCTCCAGACG
EST: gi|211331359|gb|FL235184.1|FL235184
EST:     TCGACGCCGGCGGACAGCGTGCACTATGGGTTGCTCCTCCTCCGTGCCAG                         CTAGAAATACTGGAGGGCTGAACACTATCAGCAACGATAGCTCTCCAGCCA
genomic: TCGACGCCGGCGGACAGCGTGCACTATGGGTTGCTCCTCCTCCGTGCCAGgttcgcacct ... tcccattcagCTAGAAATACTGGAGGGCTGAACACTATCAGCAACGATAGCTCTCCAGACG
EST: gi|211331360|gb|FL235185.1|FL235185
EST:     TCGACGCCGGCGGACAGCGTGCACTATGGGTTGCTCCTCCTCCGTGCCAG                         CTAGAAATACTGGAGGGCTGAACACTATCAGCAACGATAGCTCTCCAGACG
genomic: TCGACGCCGGCGGACAGCGTGCACTATGGGTTGCTCCTCCTCCGTGCCAGgttcgcacct ... tcccattcagCTAGAAATACTGGAGGGCTGAACACTATCAGCAACGATAGCTCTCCAGACG
EST: gi|211331354|gb|FL235179.1|FL235179
EST:     TCGACGCCGGCGGACAGCGTGCACTATGGGTTGCTCCTCCTCCGTGCCAG                         CTAGAAATACTGGAGGGCTGAACACTATCAGCAACGATAGCTCTCCAGCCA
genomic: TCGACGCCGGCGGACAGCGTGCACTATGGGTTGCTCCTCCTCCGTGCCAGgttcgcacct ... tcccattcagCTAGAAATACTGGAGGGCTGAACACTATCAGCAACGATAGCTCTCCAGACG
EST: gi|211329201|gb|FL235170.1|FL235170
EST:     TCGACGCCGGCGGACAGCGTGCACTATGGGTTGCTCCTCCTCCGTGCCAG                         CTAGAAATACTGGAGGGCTGAACACTATCAGCAACGATAGCTCTCCAGACG
genomic: TCGACGCCGGCGGACAGCGTGCACTATGGGTTGCTCCTCCTCCGTGCCAGgttcgcacct ... tcccattcagCTAGAAATACTGGAGGGCTGAACACTATCAGCAACGATAGCTCTCCAGACG
EST: gi|211329198|gb|FL235167.1|FL235167
EST:     TCGACGCCGGCGGACAGCGTGCACTATGGGTTGCTCCTCCTCCGTGCCAG                         CTAGAAATACTGGAGGGCTGAACACTATCAGCAACGATAGCTCTCCAGCCA
genomic: TCGACGCCGGCGGACAGCGTGCACTATGGGTTGCTCCTCCTCCGTGCCAGgttcgcacct ... tcccattcagCTAGAAATACTGGAGGGCTGAACACTATCAGCAACGATAGCTCTCCAGACG
EST: gi|211331364|gb|FL235189.1|FL235189
EST:     TCGACGCCGGCGGACAGCGTGCACTATGGGTTGCTCCTCCTCCGTGCCAG                         CTAGAAATACTGGAGGGCTGAACACTATCAGCAACGATAGCTCTCCAGACG
genomic: TCGACGCCGGCGGACAGCGTGCACTATGGGTTGCTCCTCCTCCGTGCCAGgttcgcacct ... tcccattcagCTAGAAATACTGGAGGGCTGAACACTATCAGCAACGATAGCTCTCCAGACG
EST: gi|211333515|gb|FL235190.1|FL235190
EST:     TCGACGCCGGCGGACAGCGTGCACTATGGGTTGCTCCTCCTCCGTGCCAG                         CTAGAAATACTGGAGGGCTGAACACTATCAGCAACGATAGCTCTCCAGCCA
genomic: TCGACGCCGGCGGACAGCGTGCACTATGGGTTGCTCCTCCTCCGTGCCAGgttcgcacct ... tcccattcagCTAGAAATACTGGAGGGCTGAACACTATCAGCAACGATAGCTCTCCAGACG
EST: gi|78089132|gb|DV517518.1|DV517518
EST:     TCGACGCCGGCGGACAGCGTGCACTATGGGTTGCTCCTCCTCCGTGCCAG                         CTAGAAATACTGGAGGGCTGAACACTATCAGCAACGATAGCTCTCCAGACG
genomic: TCGACGCCGGCGGACAGCGTGCACTATGGGTTGCTCCTCCTCCGTGCCAGgttcgcacct ... tcccattcagCTAGAAATACTGGAGGGCTGAACACTATCAGCAACGATAGCTCTCCAGACG
EST: gi|211329204|gb|FL235173.1|FL235173
EST:     TCGACGCCGGCGGACAGCGTGCACTATGGGTTGCTCCTCCTCCGTGCCAG                         CTAGAAATACTGGAGGGCTGAACACTATCAGCAACGATAGCTCTCCAGACG
genomic: TCGACGCCGGCGGACAGCGTGCACTATGGGTTGCTCCTCCTCCGTGCCAGgttcgcacct ... tcccattcagCTAGAAATACTGGAGGGCTGAACACTATCAGCAACGATAGCTCTCCAGACG
EST: gi|211331358|gb|FL235183.1|FL235183
EST:     TCGACGCCGGCGGACAGCGTGCACTATGGGTTGCTCCTCCTCCGTGCCAG                         CTAGAAATACTGGAGGGCTGAACACTATCAGCAACGATAGCTCTCCAGACG
genomic: TCGACGCCGGCGGACAGCGTGCACTATGGGTTGCTCCTCCTCCGTGCCAGgttcgcacct ... tcccattcagCTAGAAATACTGGAGGGCTGAACACTATCAGCAACGATAGCTCTCCAGACG
EST: gi|211329197|gb|FL235166.1|FL235166
EST:     TCGACGCCGGCGGACAGCGTGCACTATGGGTTGCTCCTCCTCCGTGCCAG                         CTAGAAAWACTGGAGGGCTGAACACTATCAGCAACGATAGCTCTCCAGACG
genomic: TCGACGCCGGCGGACAGCGTGCACTATGGGTTGCTCCTCCTCCGTGCCAGgttcgcacct ... tcccattcagCTAGAAATACTGGAGGGCTGAACACTATCAGCAACGATAGCTCTCCAGACG
EST: gi|211329200|gb|FL235169.1|FL235169
EST:     TCGACGCCGGCGGACAGCGTGCACTATGGGTTGCTCCTCCTCCGTGCCAG                         CTAGAAATACTGGAGGGCTGAACACTATCAGCAACGATAGCTCTCCAGCCA
genomic: TCGACGCCGGCGGACAGCGTGCACTATGGGTTGCTCCTCCTCCGTGCCAGgttcgcacct ... tcccattcagCTAGAAATACTGGAGGGCTGAACACTATCAGCAACGATAGCTCTCCAGACG

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), 47 (downstream exon)
Score: 146

TCCCCCCTCCCCGCCGGTTGCCGCGCTCGTGCCACGGTGCGGTAGCCCCGTCGACGCCGGCGGACAGCGTGCACTATGGGTTGCTCCTCCTCCGTGCCAGgttcgcacct ... tcccattcagCTAGAAATACTGGAGGGCTGAACACTATCAGCAACGATAGCTCTCCAGACGCCAGTTCAAAGGACTTGCGTGCTAAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 164

TCCCCCCTCCCCGCCGGTTGCCGCGCTCGTGCCACGGTGCGGTAGCCCCGTCGACGCCGGCGGACAGCGTGCACTATGGGTTGCTCCTCCTCCGTGCCAGgttcgcacct ... tcccattcagCTAGAAATACTGGAGGGCTGAACACTATCAGCAACGATAGCTCTCCAGACGCCAGTTCAAAGGACTTGCGTGCTAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 245

TCCCCCCTCCCCGCCGGTTGCCGCGCTCGTGCCACGGTGCGGTAGCCCCGTCGACGCCGGCGGACAGCGTGCACTATGGGTTGCTCCTCCTCCGTGCCAGgttcgcacct ... tcccattcagCTAGAAATACTGGAGGGCTGAACACTATCAGCAACGATAGCTCTCCAGACGCCAGTTCAAAGGACTTGCGTGCTAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 221

TCCCCCCTCCCCGCCGGTTGCCGCGCTCGTGCCACGGTGCGGTAGCCCCGTCGACGCCGGCGGACAGCGTGCACTATGGGTTGCTCCTCCTCCGTGCCAGgttcgcacct ... tcccattcagCTAGAAATACTGGAGGGCTGAACACTATCAGCAACGATAGCTCTCCAGACGCCAGTTCAAAGGACTTGCGTGCTAAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TCCCCCCTCCCCGCCGGTTGCCGCGCTCGTGCCACGGTGCGGTAGCCCCGTCGACGCCGGCGGACAGCGTGCACTATGGGTTGCTCCTCCTCCGTGCCAGgttcgcacctcctctccctcgagtcttcaaaattcgaaggttgcggtgtaggattgttgtattttctattcaattagttgccggagggaacagattcaaa

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTCCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC