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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AAGGAGGTCTTATCCGGTAGCTGCGGCGTGCCAGCACCGCAGCAGCGCCTGATCTACAAGGGCCGCATCCTCAAGGACGAGCAAACCCTAGACAGCTATGgtacgtgccacgccgaaacgctggttgtagtgtagagtaaagtaccttcagatttggtgtcgtagcgtgggattgtccgattctgttcatcaattcggcg...

Basic information

species Zea mays
transcript GRMZM2G170843_T02
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G170843_T02 (Zea mays), 5'ss of exon 1
lower sequence: LOC_Os10g39620.5 (Oryza sativa), 5'ss of exon 1
AAGGAGGTCTTATCCGGTAGCTGCGGCGTGCCAGCACCGCAGCAGCGCCTGATCTACAAGGGCCGCATCCTCAAGGACGAGCAAACCCTAGACAGCTATGgtacgtgccacgccgaaacgct-ggttgtagtgtagagtaaagtaccttcagat--ttggtgtcgtagcgtgggattgtccgattctgttcatcaattcggcg
||||||||  |  | || ||||||| |||||| ||  |||||||||||||||||||||||||||| |||||||||||||||||||||||||| |||||||||  ||| |     | |  | | ||| |  | | |||  |||   || ||| ||  |  |  |  | |    |    ||  || |         |  |   ||
AAGGAGGTGGTGGCGGGGAGCTGCGACGTGCCGGCGGCGCAGCAGCGCCTGATCTACAAGGGCCGGATCCTCAAGGACGAGCAAACCCTAGAAAGCTATGgtgagtgtc---taggactgttaggtagaggaggagaaaaaaaacccatcaaatcgtcaggatttttggtccgatgggttggaattgacatgctacgtgctcg

upper sequence: GRMZM2G170843_T02 (Zea mays), 5'ss of exon 1
lower sequence: GLYMA01G36410.1 (Glycine max), 5'ss of exon 1
AAGGAGGTCTTATCCGGTAGCTGCGGCGTGCCAGCACCGCAGCAGCGCCTGATCTACAAGGGCCGCATCCTCAAGGACGAGCAAACCCTAGACAGCTATGgtacgtgcc-acgccgaaacgctggttgtagtgtagagtaaagtaccttcagatttgg---tgtcgtagcgtgggattgtccgattctgttcatcaattcggcg
||||| |   |  |  | | ||| | | |  | ||    || ||||||||||| ||||||||||| || |||||||| || ||||||||  | ||||||||||  | || |    |     ||   |||| |      |    |    |  ||||||    | | | ||| | |  ||  | |||| || ||||   |||    
AAGGACGCGGTTGCACGCAACTGTGACATATCCGCGGATCAACAGCGCCTGATTTACAAGGGCCGGATTCTCAAGGATGATCAAACCCTCCAAAGCTATGgtatttaccgatcttgctgttctccgtgtatttctcttttgtattgactttgatttgagttttttgcagcatcgatttagc-gattttgctcat-gtttcat--

upper sequence: GRMZM2G170843_T02 (Zea mays), 5'ss of exon 1
lower sequence: AT2G17200.1 (Arabidopsis thaliana), 5'ss of exon 1
AAGGAGGTCTTATCCGGTAGCTGCGGCGTGCCAGCACCGCAGCAGCGCCTGATCTACAAGGGCCGCATCCTCAAGGACGAGCAAACCCTAGACAGCTATGgtacgtgccacgccgaaacgctggttgtagtgtagagtaaagtaccttcagatttggtgtcgtagcgtgggattgtcc--gattctgttcatcaattcggcg------------
|| ||| |  |  |    ||| |||  || |||||    ||||||||| |||| |||||||| || |||||||||||||| ||||| ||   |||||||||||     ||           |  ||   |||   | |   ||   |||   |      |  | |  ||  ||| |    |||||| ||| ||  |    |             
AAAGAGTTGGTGGCTCAGAGCAGCGATGTTCCAGCTAATCAGCAGCGCTTGATTTACAAGGGTCGTATCCTCAAGGACGATCAAACTCTCCTCAGCTATGgtaatcttcatcgtttctgatttattcgtgtgggtacttttgt-tgttctcgtagatccttattgattgaaattcttgtggattctattc-tctgtggaacatgttatacctag

upper sequence: GRMZM2G170843_T02 (Zea mays), 5'ss of exon 1
lower sequence: Vv04s0210g00220.t01 (Vitis vinifera), 5'ss of exon 1
AAGGAGGTCTTATCCGGTAGCTGCGGCGTGCCAGCACCGCAGCAGCGCCTGATCTACAAGGGCCGCATCCTCAAGGACGAGCAAACCCTAGACAGCTATGgtacgt-gccacgccgaaacgctggttgtagtgtagagtaaagtaccttcagatttggtgtcgtagcgtgggattgtccgattctgttcatcaattcggcg----
|| |  ||  | ||    | |||||   | || ||   |||||||||  |||| |||||||| || ||| | |||||||| ||||||||||| ||||| ||||  | | ||   | |  |  || |      | ||  |   ||    |  |  | | ||| |||  |   ||   | |||||    |  |   || |  |    
AAAGCCGTTCTCTCGCAGAACTGCGATATTCCCGCGGAGCAGCAGCGATTGATTTACAAGGGACGGATCTTGAAGGACGACCAAACCCTAGAGAGCTACGgtatattgacatttctatccattgctctccacgcagtctgttgt----tatgggtagttgtagtattgaaagaac-ttcgatttaagtttttgtttggttgcgtc

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|4152059|gb|AI372193.1|AI372193
EST:     GATCTACAAGGGCCGCATCCTCAAGGACGAGCAAACCCTAGACAGCTATG                         GCGTTGAGACGGATCACACAATTCACTTGGTGCGAGGTGTCGCCCCACCAG
genomic: GATCTACAAGGGCCGCATCCTCAAGGACGAGCAAACCCTAGACAGCTATGgtacgtgcca ... tatattgtagGCGTTGAGACGGATCACACAATTCACTTGGTGCGAGGTGTCGCCACACCAG
EST: gi|87156400|gb|DY401189.1|DY401189
EST:     GATCTACAAGGGCCGCATCCTCAAGGACGAGCAAACCCTAGACAGCTATG                         GCGTTGAGACGGATCACACAATTCACTTGGTGCGAGGTGTCGCCCCACCAG
genomic: GATCTACAAGGGCCGCATCCTCAAGGACGAGCAAACCCTAGACAGCTATGgtacgtgcca ... tatattgtagGCGTTGAGACGGATCACACAATTCACTTGGTGCGAGGTGTCGCCACACCAG
EST: gi|211453067|gb|FL216223.1|FL216223
EST:     GATCTACAAGGGCCGCATCCTCAAGGACGAGCAAACCCTAGACAGCTATG                         GCGTTGAGAAGGATCACACAATTCACTTGGGTGCGAGGTGTCGCCCCACCA
genomic: GATCTACAAGGGCCGCATCCTCAAGGACGAGCAAACCCTAGACAGCTATGgtacgtgcca ... tatattgtagGCGTTGAGACGGATCACACAATTCACTTGG-TGCGAGGTGTCGCCACACCA
EST: gi|211450935|gb|FL216216.1|FL216216
EST:     GATCTACAAGGGCCGCATCCTCAAGGACGAGCAAACCCTAGACAGCTATG                         GCGTTGAGAAGGATCACANCAATTCACTTGGTGCGAGGTGTCGCCCCACCA
genomic: GATCTACAAGGGCCGCATCCTCAAGGACGAGCAAACCCTAGACAGCTATGgtacgtgcca ... tatattgtagGCGTTGAGACGGATCACA-CAATTCACTTGGTGCGAGGTGTCGCCACACCA
EST: gi|87155559|gb|DY400348.1|DY400348
EST:     GATCTACAAGGGCCGCATCCTCAAGGACGAGCAAACCCTAGACAGCTATG                         GCGTTGAGACGGATCACACAATTCACTTGGTGCGAGGTGTCGCCCCACCAG
genomic: GATCTACAAGGGCCGCATCCTCAAGGACGAGCAAACCCTAGACAGCTATGgtacgtgcca ... tatattgtagGCGTTGAGACGGATCACACAATTCACTTGGTGCGAGGTGTCGCCACACCAG
EST: gi|26560110|gb|CA832345.1|CA832345
EST:     GATCTACAAGGGCCGCATCCTCAAGGACGAGCAAACCCTAGACAGCTATG                         GCGTTGAGACGGATCACACAATTCACTTGGTGCGAGGTGTCGCCCCACCAG
genomic: GATCTACAAGGGCCGCATCCTCAAGGACGAGCAAACCCTAGACAGCTATGgtacgtgcca ... tatattgtagGCGTTGAGACGGATCACACAATTCACTTGGTGCGAGGTGTCGCCACACCAG
EST: gi|211448821|gb|FL216208.1|FL216208
EST:     GATCTACAAGGGCCGCATCCTCAARGACGAGCAAACCCTAGACAGCTATG                         GCGTTGAGAAGGATCACACAATTCACTTGGTGCGAGGTGTCGCCCCACCAG
genomic: GATCTACAAGGGCCGCATCCTCAAGGACGAGCAAACCCTAGACAGCTATGgtacgtgcca ... tatattgtagGCGTTGAGACGGATCACACAATTCACTTGGTGCGAGGTGTCGCCACACCAG
EST: gi|148938301|gb|EC882608.2|EC882608
EST:     ATCTACAAGGGCCGCATCCCTCAAGGACGAGCAAACCCTAGACAGCTAGG                         GCGTTGAGACGGATCACACAA
genomic: ATCTACAAGGGCCGCATCC-TCAAGGACGAGCAAACCCTAGACAGCTATGgtacgtgcca ... tatattgtagGCGTTGAGACGGATCACACAA
EST: gi|22546476|gb|BU098787.1|BU098787
EST:     GATCTACAAGGGCCGCATCCTCAAGGACGAGCAAACCCTAGACAGCTATG                         GCGTTGAGACGGATCACACAATTCACTTGGTGCGAGGTGTCGCCCCACCAG
genomic: GATCTACAAGGGCCGCATCCTCAAGGACGAGCAAACCCTAGACAGCTATGgtacgtgcca ... tatattgtagGCGTTGAGACGGATCACACAATTCACTTGGTGCGAGGTGTCGCCACACCAG
EST: gi|23199685|gb|BU582250.1|BU582250
EST:     GATCTACAAGGGCCGCATCCTCAAGGACGAGCAAACCCTAGACAGCTATG                         GCGTTGAGACGGATCACACAATTCACTTGGTGCGAGGTGTCGCCCCACCAG
genomic: GATCTACAAGGGCCGCATCCTCAAGGACGAGCAAACCCTAGACAGCTATGgtacgtgcca ... tatattgtagGCGTTGAGACGGATCACACAATTCACTTGGTGCGAGGTGTCGCCACACCAG
EST: gi|211450941|gb|FL216222.1|FL216222
EST:     GATCTACAAGGGYCGCATCCTCAAGGACGAGCAAACCCTAGACAGCTATG                         GCGTTGAGAAGGATCACACAATTCACTTGGTGCGAGGTGTCGCCCCACCAG
genomic: GATCTACAAGGGCCGCATCCTCAAGGACGAGCAAACCCTAGACAGCTATGgtacgtgcca ... tatattgtagGCGTTGAGACGGATCACACAATTCACTTGGTGCGAGGTGTCGCCACACCAG
EST: gi|76015379|gb|DT942549.1|DT942549
EST:     GATCTACAAGGGCCGCATCCTCAAGGACGAGCAAACCCTAGACAGCTATG                         GCGTTGAGACGGATCACACAATTCACTTGGTGCGAGGTGTCGCCACACCAG
genomic: GATCTACAAGGGCCGCATCCTCAAGGACGAGCAAACCCTAGACAGCTATGgtacgtgcca ... tatattgtagGCGTTGAGACGGATCACACAATTCACTTGGTGCGAGGTGTCGCCACACCAG
EST: gi|211450937|gb|FL216218.1|FL216218
EST:     TACAAGGGCCGCATCCTCAAGGACGAGCAAACCCTAGACAGCTATG                         GCGTTGAGAAGGATCACACAATTCACTTGGTGCGAGGTGTCGCCCCACCAG
genomic: TACAAGGGCCGCATCCTCAAGGACGAGCAAACCCTAGACAGCTATGgtacgtgcca ... tatattgtagGCGTTGAGACGGATCACACAATTCACTTGGTGCGAGGTGTCGCCACACCAG
EST: gi|29543700|gb|CB604080.1|CB604080
EST:     GGCCGCATCCTCAAGGACGAGCAAACCCTAGACAGCTATG                         GCGTTGAGAC-GNTCACACAATTCACTTGG-GCGAGG-GTCGCCACACCAG
genomic: GGCCGCATCCTCAAGGACGAGCAAACCCTAGACAGCTATGgtacgtgcca ... tatattgtagGCGTTGAGACGGATCACACAATTCACTTGGTGCGAGGTGTCGCCACACCAG
EST: gi|211450932|gb|FL216213.1|FL216213
EST:     GATCTACAAGGGCCGCATCCTCAAGGACGAGCAAACCCTAGACAGCTATG                         GCGTTGAGAAGGATCACACAATTCACTTGGGTGCGAGGTGTCGCCCCACCA
genomic: GATCTACAAGGGCCGCATCCTCAAGGACGAGCAAACCCTAGACAGCTATGgtacgtgcca ... tatattgtagGCGTTGAGACGGATCACACAATTCACTTGG-TGCGAGGTGTCGCCACACCA
EST: gi|149008827|gb|EE041031.2|EE041031
EST:     GATCTACAAGGGCCGCATCCTCAAGGACGAGCAAACCCTAGACAGCTATG                         GCGTTGAGACGGATCACACAATTCACTTGGTGCGAGGTGTCGCCACACCAG
genomic: GATCTACAAGGGCCGCATCCTCAAGGACGAGCAAACCCTAGACAGCTATGgtacgtgcca ... tatattgtagGCGTTGAGACGGATCACACAATTCACTTGGTGCGAGGTGTCGCCACACCAG
EST: gi|26559202|gb|CA831437.1|CA831437
EST:     GATCTACAAGGGCCGCATCCTCAAGGACGAGCAAACCCTAGACAGCTATG                         GCGTTGAGACGGATCACACAATTCACTTGGTGCGAGGTGTCGCCCCACCAG
genomic: GATCTACAAGGGCCGCATCCTCAAGGACGAGCAAACCCTAGACAGCTATGgtacgtgcca ... tatattgtagGCGTTGAGACGGATCACACAATTCACTTGGTGCGAGGTGTCGCCACACCAG
EST: gi|91872506|gb|EB402463.1|EB402463
EST:     GATCTACAAGGGCCGCATCCTCAAGGACGAGCAAACCCTAGACAGCTATG                         GCGTTGAGACGGATCACACAATTCACTTGGTGCGAGGTGTCGCCACACCAG
genomic: GATCTACAAGGGCCGCATCCTCAAGGACGAGCAAACCCTAGACAGCTATGgtacgtgcca ... tatattgtagGCGTTGAGACGGATCACACAATTCACTTGGTGCGAGGTGTCGCCACACCAG
EST: gi|149062873|gb|EE157595.2|EE157595
EST:     GATCTACAAGGGCCGCATCCTCAAGGACGAGCAAACCCTAGACAGCTATG                         GCGTTGAGACGGATCACACAATTCACTTGGTGCGAGGTGTCGCCACACCAG
genomic: GATCTACAAGGGCCGCATCCTCAAGGACGAGCAAACCCTAGACAGCTATGgtacgtgcca ... tatattgtagGCGTTGAGACGGATCACACAATTCACTTGGTGCGAGGTGTCGCCACACCAG
EST: gi|211448818|gb|FL216205.1|FL216205
EST:     GATCTACAAGGGCCGCATCCTCAAGGACGAGCAAACCCTAGACAGCTATG                         GCGTTGAGACGGATCACACAATTCACTTGGTGCGAGGTGTCGCCACACCAG
genomic: GATCTACAAGGGCCGCATCCTCAAGGACGAGCAAACCCTAGACAGCTATGgtacgtgcca ... tatattgtagGCGTTGAGACGGATCACACAATTCACTTGGTGCGAGGTGTCGCCACACCAG
EST: gi|211448820|gb|FL216207.1|FL216207
EST:     GATCTACAAGGGCCGCATCCTCAAGGACGAGCAAACCCTAGACAGCTATG                         GCGTTGAGAAGGATCACACAATTCACTTGGTGCGAGGTGTCGCCCCACCAG
genomic: GATCTACAAGGGCCGCATCCTCAAGGACGAGCAAACCCTAGACAGCTATGgtacgtgcca ... tatattgtagGCGTTGAGACGGATCACACAATTCACTTGGTGCGAGGTGTCGCCACACCAG
EST: gi|211448819|gb|FL216206.1|FL216206
EST:     GATCTACAAGGGCCGCATCCTCAAGGACGAGCAAACCCTAGACAGCTATG                         GCGTTGAGAAGGATCACACAATTCACTTGGTGCGAGGTGTCGCCCCACCAG
genomic: GATCTACAAGGGCCGCATCCTCAAGGACGAGCAAACCCTAGACAGCTATGgtacgtgcca ... tatattgtagGCGTTGAGACGGATCACACAATTCACTTGGTGCGAGGTGTCGCCACACCAG

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: 60

AAGGAGGTCTTATCCGGTAGCTGCGGCGTGCCAGCACCGCAGCAGCGCCTGATCTACAAGGGCCGCATCCTCAAGGACGAGCAAACCCTAGACAGCTATGgtacgtgcca ... tatattgtagGCGTTGAGACGGATCACACAATTCACTTGGTGCGAGGTGTCGCCACACCAGCTGCATCCAGTGCACCTGCTGCTGCCAACCCCCTTGCTTCATTTACTCC


Block sizes: 47 (upstream exon), 45 (downstream exon)
Score: 84

AAGGAGGTCTTATCCGGTAGCTGCGGCGTGCCAGCACCGCAGCAGCGCCTGATCTACAAGGGCCGCATCCTCAAGGACGAGCAAACCCTAGACAGCTATGgtacgtgcca ... tatattgtagGCGTTGAGACGGATCACACAATTCACTTGGTGCGAGGTGTCGCCACACCAGCTGCATCCAGTGCACCTGCTGCTGCCAACCCCCTTGCTTCATTTACTCC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 93

AAGGAGGTCTTATCCGGTAGCTGCGGCGTGCCAGCACCGCAGCAGCGCCTGATCTACAAGGGCCGCATCCTCAAGGACGAGCAAACCCTAGACAGCTATGgtacgtgcca ... tatattgtagGCGTTGAGACGGATCACACAATTCACTTGGTGCGAGGTGTCGCCACACCAGCTGCATCCAGTGCACCTGCTGCTGCCAACCCCCTTGCTTCATTTACTCC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 85

AAGGAGGTCTTATCCGGTAGCTGCGGCGTGCCAGCACCGCAGCAGCGCCTGATCTACAAGGGCCGCATCCTCAAGGACGAGCAAACCCTAGACAGCTATGgtacgtgcca ... tatattgtagGCGTTGAGACGGATCACACAATTCACTTGGTGCGAGGTGTCGCCACACCAGCTGCATCCAGTGCACCTGCTGCTGCCAACCCCCTTGCTTCATTTACTCC


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AAGGAGGTCTTATCCGGTAGCTGCGGCGTGCCAGCACCGCAGCAGCGCCTGATCTACAAGGGCCGCATCCTCAAGGACGAGCAAACCCTAGACAGCTATGgtacgtgccacgccgaaacgctggttgtagtgtagagtaaagtaccttcagatttggtgtcgtagcgtgggattgtccgattctgttcatcaattcggcg

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ccacgcc