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 5'  3'   		2  
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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tacggatggaatttatatccacatttctacttgaaaaacgtcactttttggtaaggggctgcatcttttgtaagtaacagcttctgctaatgttctgtagATTGACGACATGGATCGACTTATTGAGGTAATAAAGCAAGCAGCAAAGGAAGGGGCACTGGTTCTCTACACCCTTGCCGATCCTTCAATGGCCGAGGCGA

Basic information

species Zea mays
transcript GRMZM2G131286_T01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G131286_T01 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os07g34640.1 (Oryza sativa), 3'ss of exon 1
tacggatgg-aatttatatccacatttctacttgaaaaacgtcactttttg-gtaaggggctgcatcttttgtaagtaacagctt-ctgctaatgttctgtagATTGACGACATGGATCGACTTATTGAGGTAATAAAGCAAGCAGCAAAGGAAGGGGCACTGGTTCTCTACACCCTTGCCGATCCTTCAATGGCCGAGGCGA
 || ||    |||||  |    ||||      ||| ||| |   ||   || |||     ||  || ||   ||  |      || || | ||| | || |||||||| ||||||||| ||||||||||| || |||||||||||||||| ||||| ||||||||| | || || ||||| |||||||||||||| ||||| |
cactgaccctaatttgcacttgcatt---gactgataaatgaagctagctgtgtagttttcttgatattgattattttgtcttttgctacaaatttgctttagATTGATGACATGGATAGACTTATTGAGATAGTAAAGCAAGCAGCAAAAGAAGGAGCACTGGTTTTATATACTCTTGCTGATCCTTCAATGGCTGAGGCAA
















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|149089654|gb|EE178908.2|EE178908
EST:     ACTGCCTCGCCGACCGCGGCTGCGCTGTCAACACCCACCTCTTCTCCTTG                         ATTGACGACATGGATCGACTTATTGAGGTAATAAAGCAAGCAGCAAAGGAA
genomic: ACTGCCTCGCCGACCGCGGCTGCGCTGTCAACACCCACCTCTTCTCCTTGgtaaaatatc ... tgttctgtagATTGACGACATGGATCGACTTATTGAGGTAATAAAGCAAGCAGCAAAGGAA
EST: gi|71430620|gb|DR811670.1|DR811670
EST:     ACTGCCTCGCCGACCGCGGCTGCGCTGTCAACACCCACCTCTTCTCCTTG                         ATTGACGACATGGATCGACTTATTGAGGTAATAAAGCAAGCAGCAAAGGAA
genomic: ACTGCCTCGCCGACCGCGGCTGCGCTGTCAACACCCACCTCTTCTCCTTGgtaaaatatc ... tgttctgtagATTGACGACATGGATCGACTTATTGAGGTAATAAAGCAAGCAGCAAAGGAA
EST: gi|149110473|gb|EE190435.2|EE190435
EST:     ACTGCCTCGCCGACCGCGGCTGCGCTGTCAACACCCACCTCTTCTCCTTG                         ATTGACGACATGGATCGACTTATTGAGGTAATAAAGCAAGCAGCAAAGGAA
genomic: ACTGCCTCGCCGACCGCGGCTGCGCTGTCAACACCCACCTCTTCTCCTTGgtaaaatatc ... tgttctgtagATTGACGACATGGATCGACTTATTGAGGTAATAAAGCAAGCAGCAAAGGAA
EST: gi|78110243|gb|DV528658.1|DV528658
EST:     ACTGCCTCGCCGACCGCGGCTGCGCTGTCAACACCCACCTCTTCTCCTTG                         ATTGACGACATGGATCGACTTATTGAGGTAATAAAGCAAGCAGCAAAGGAA
genomic: ACTGCCTCGCCGACCGCGGCTGCGCTGTCAACACCCACCTCTTCTCCTTGgtaaaatatc ... tgttctgtagATTGACGACATGGATCGACTTATTGAGGTAATAAAGCAAGCAGCAAAGGAA
EST: gi|149046888|gb|EE048098.2|EE048098
EST:     ACTGCCTCGCCGACCGCGGCTGCGCTGTCAACACCCACCTCTTCTCCTTG                         ATTGACGACATGGATCGACTTATTGAGGTAATAAAGCAAGCAGCAAAGGAA
genomic: ACTGCCTCGCCGACCGCGGCTGCGCTGTCAACACCCACCTCTTCTCCTTGgtaaaatatc ... tgttctgtagATTGACGACATGGATCGACTTATTGAGGTAATAAAGCAAGCAGCAAAGGAA
EST: gi|211210467|gb|FL316814.1|FL316814
EST:     ACTGCCTCGCCGACCGCGGCTGCGCTGTCAACACCCACCTCTTCTCCTTG                         ATTGACGACATGGATCGACTTATTGAGGTAATAAAGCAAGCAGCAAAGGAA
genomic: ACTGCCTCGCCGACCGCGGCTGCGCTGTCAACACCCACCTCTTCTCCTTGgtaaaatatc ... tgttctgtagATTGACGACATGGATCGACTTATTGAGGTAATAAAGCAAGCAGCAAAGGAA
EST: gi|149072724|gb|EE160962.2|EE160962
EST:     ACTGCCTCGCCGACCGCGGCTGCGCTGTCAACACCCACCTCTTCTCCTTG                         ATTGACGACATGGATCGACTTATTGAGGTAATAAAGCAAGCAGCAAAGGAA
genomic: ACTGCCTCGCCGACCGCGGCTGCGCTGTCAACACCCACCTCTTCTCCTTGgtaaaatatc ... tgttctgtagATTGACGACATGGATCGACTTATTGAGGTAATAAAGCAAGCAGCAAAGGAA
EST: gi|94478256|gb|EB707214.1|EB707214
EST:     ACTGCCTCGCCGACCGCGGCTGCGCTGTCAACACCCACCTCTTCTCCTTG                         ATTGACGACATGGATCGACTTATTGAGGTAATAAAGCAAGCAGCAAAGGAG
genomic: ACTGCCTCGCCGACCGCGGCTGCGCTGTCAACACCCACCTCTTCTCCTTGgtaaaatatc ... tgttctgtagATTGACGACATGGATCGACTTATTGAGGTAATAAAGCAAGCAGCAAAGGAA
EST: gi|76019440|gb|DT946610.1|DT946610
EST:     ACTGCCTCGCCGACCGCGGCTGCGCTGTCAACACCCACCTCTTCTCCTTG                         ATTGACGACATGGATCGACTTATTGAGGTAATAAAGCAAGCAGCAAAGGAA
genomic: ACTGCCTCGCCGACCGCGGCTGCGCTGTCAACACCCACCTCTTCTCCTTGgtaaaatatc ... tgttctgtagATTGACGACATGGATCGACTTATTGAGGTAATAAAGCAAGCAGCAAAGGAA
EST: gi|101398506|gb|EB821126.1|EB821126
EST:     ACTGCCTCGCCGACCGCGGCTGCGCTGTCAACACCCACCTCTTCTCCTTG                         ATTGACGACATGGATCGACTTATTGAGGTAATAAAAGCAAGCAGCAAAAGA
genomic: ACTGCCTCGCCGACCGCGGCTGCGCTGTCAACACCCACCTCTTCTCCTTGgtaaaatatc ... tgttctgtagATTGACGACATGGATCGACTTATTGAGGTAATAAA-GCAAGCAGCAAAGGA
EST: gi|211010783|gb|FL360718.1|FL360718
EST:     ACTGCCTCGCCGACCGCGGCTGCGCTGTCAACACCCACCTCTTCTCCTTG                         ATTGACGACATGGATCGACTTATTGAGGTAATAAAGCAAGCAGCAAAGGAA
genomic: ACTGCCTCGCCGACCGCGGCTGCGCTGTCAACACCCACCTCTTCTCCTTGgtaaaatatc ... tgttctgtagATTGACGACATGGATCGACTTATTGAGGTAATAAAGCAAGCAGCAAAGGAA
EST: gi|78086221|gb|DV514614.1|DV514614
EST:     ACTGCCTCGCCGACCGCGGCTGCGCTGTCAACACCCACCTCTTCTCCTTG                         ATTGACGACATGGATCGACTTATTGAGGTAATAAAGCAAGCAGCAAAGGAA
genomic: ACTGCCTCGCCGACCGCGGCTGCGCTGTCAACACCCACCTCTTCTCCTTGgtaaaatatc ... tgttctgtagATTGACGACATGGATCGACTTATTGAGGTAATAAAGCAAGCAGCAAAGGAA
EST: gi|50322291|gb|CO517417.1|CO517417
EST:     ACTGCCTCGCCGACCGCGGCTGCGCTGTCAACACCCACCTCTTCTCCTTG                         ATTGACGACATGGATCGACTTATTGAGGTAATAAAGCAAGCAGCAAAGGAA
genomic: ACTGCCTCGCCGACCGCGGCTGCGCTGTCAACACCCACCTCTTCTCCTTGgtaaaatatc ... tgttctgtagATTGACGACATGGATCGACTTATTGAGGTAATAAAGCAAGCAGCAAAGGAA
EST: gi|50330733|gb|CO525859.1|CO525859
EST:     ACTGCCTCGCCGACCGCGGCTGCGCTGTCAACACCCACCTCTTCTCCTTG                         ATTGACGACATGGATCGACTTATT
genomic: ACTGCCTCGCCGACCGCGGCTGCGCTGTCAACACCCACCTCTTCTCCTTGgtaaaatatc ... tgttctgtagATTGACGACATGGATCGACTTATT
EST: gi|50325996|gb|CO521122.1|CO521122
EST:     ACTGCCTCGCCGACCGCGGCTGCGCTGTCAACACCCACCTCTTCTCCTTG                         ATTGACGACATGGATCGACTTATTGAGGTAATAAAGCAAGCAGCAAAGGAA
genomic: ACTGCCTCGCCGACCGCGGCTGCGCTGTCAACACCCACCTCTTCTCCTTGgtaaaatatc ... tgttctgtagATTGACGACATGGATCGACTTATTGAGGTAATAAAGCAAGCAGCAAAGGAA
EST: gi|78117840|gb|DV536227.1|DV536227
EST:     ACTGCCTCGCCGACCGCGGCTGCGCTGTCAACACCCACCTCTTCTCCTTG                         ATTGACGACATGGATCGACTTATTGAGGTAATAAAGCAAGCAGCAAAGGAA
genomic: ACTGCCTCGCCGACCGCGGCTGCGCTGTCAACACCCACCTCTTCTCCTTGgtaaaatatc ... tgttctgtagATTGACGACATGGATCGACTTATTGAGGTAATAAAGCAAGCAGCAAAGGAA
EST: gi|71425453|gb|DR806683.1|DR806683
EST:     ACTGCCTCGCCGACCGCGGCTGCGCTGTCAACACCCACCTCTTCTCCTTG                         ATTGACGACATGGATCGACTTATTGAGGTAATAAAGCAAGCAGCAAAGGAA
genomic: ACTGCCTCGCCGACCGCGGCTGCGCTGTCAACACCCACCTCTTCTCCTTGgtaaaatatc ... tgttctgtagATTGACGACATGGATCGACTTATTGAGGTAATAAAGCAAGCAGCAAAGGAA
EST: gi|148950041|gb|EC895573.2|EC895573
EST:     ACTGCCTCGCCGACCGCGGCTGCGCTGTCAACACCCACCTCTTCTCCTTG                         ATTGACGACATGGATCGACTTATTGAGGTAATAAAGCAAGCAGCAAAGGAA
genomic: ACTGCCTCGCCGACCGCGGCTGCGCTGTCAACACCCACCTCTTCTCCTTGgtaaaatatc ... tgttctgtagATTGACGACATGGATCGACTTATTGAGGTAATAAAGCAAGCAGCAAAGGAA
EST: gi|149099591|gb|EE185630.2|EE185630
EST:     ACTGCCTCGCCGACCGCGGCTGCGCTGTCAACACCCACCTCTTCTCCTTG                         ATTGACGACATGGATCGACTTATTGAGGTAATAAAGCAAGCAGCAAAGGAA
genomic: ACTGCCTCGCCGACCGCGGCTGCGCTGTCAACACCCACCTCTTCTCCTTGgtaaaatatc ... tgttctgtagATTGACGACATGGATCGACTTATTGAGGTAATAAAGCAAGCAGCAAAGGAA
EST: gi|78092492|gb|DV520866.1|DV520866
EST:     ACTGCCTCGCCGACCGCGGCTGCGCTGTCAACACCCACCTCTTCTCCTTG                         ATTGACGACATGGATCGACTTATTGAGGTAATAAAGCAAGCAGCAAAGGAA
genomic: ACTGCCTCGCCGACCGCGGCTGCGCTGTCAACACCCACCTCTTCTCCTTGgtaaaatatc ... tgttctgtagATTGACGACATGGATCGACTTATTGAGGTAATAAAGCAAGCAGCAAAGGAA
EST: gi|78117950|gb|DV536337.1|DV536337
EST:     ACTGCCTCGCCGACCGCGGCTGCGCTGTCAACACCCACCTCTTCTCCTTG                         ATTGACGACATGGATCGATTTATTGAGGTAATAAAGCAAGCAGCAAAGGAA
genomic: ACTGCCTCGCCGACCGCGGCTGCGCTGTCAACACCCACCTCTTCTCCTTGgtaaaatatc ... tgttctgtagATTGACGACATGGATCGACTTATTGAGGTAATAAAGCAAGCAGCAAAGGAA
EST: gi|71766841|gb|DR964778.1|DR964778
EST:     ACTGCCTCGCCGACCGCGGCTGCGCTGTCAACACCCACCTCTTCTCCTTG                         ATTGACGACATGGATCGACTTATTGAGGTAATAAAGCAAGCAGCAAAGGAA
genomic: ACTGCCTCGCCGACCGCGGCTGCGCTGTCAACACCCACCTCTTCTCCTTGgtaaaatatc ... tgttctgtagATTGACGACATGGATCGACTTATTGAGGTAATAAAGCAAGCAGCAAAGGAA
EST: gi|88753089|gb|DY537230.1|DY537230
EST:     ACTGCCTCGCCGACCGCGGCTGCGCTGTCAACACCCACCTCTTCTCCTTG                         ATTGACGACATGGATCGACTTATTGAGGTAATAAAGCAAGCAGCAAAAGAA
genomic: ACTGCCTCGCCGACCGCGGCTGCGCTGTCAACACCCACCTCTTCTCCTTGgtaaaatatc ... tgttctgtagATTGACGACATGGATCGACTTATTGAGGTAATAAAGCAAGCAGCAAAGGAA
EST: gi|93016697|gb|EB642217.1|EB642217
EST:     CTGCCTCGCCCGACCGCGGCTGCCCTGTCAACACCCACCTCTTCTCCTTG                         ATTGACGACATGGATCGACTTA
genomic: CTGCCTCGCC-GACCGCGGCTGCGCTGTCAACACCCACCTCTTCTCCTTGgtaaaatatc ... tgttctgtagATTGACGACATGGATCGACTTA
EST: gi|148942386|gb|EC887405.2|EC887405
EST:     CTGCCTCGCCGACCGCGGCTGCGCTGTNCA-CACCCACCTCTTCTCCTTG                         ATTGACGACATGGATCGACTTATTGAGGTAATAAAGCAAGCAGCAAAGGAA
genomic: CTGCCTCGCCGACCGCGGCTGCGCTGT-CAACACCCACCTCTTCTCCTTGgtaaaatatc ... tgttctgtagATTGACGACATGGATCGACTTATTGAGGTAATAAAGCAAGCAGCAAAGGAA
EST: gi|148996288|gb|EE035569.2|EE035569
EST:     ACTGCCTCGCCGACCGCGGCTGCGCTGTCAACACCCACCTCTTCTCCTTG                         ATTGACGACATGGATCGACTTATTGAGGTAATAAAGCAAGCAGCAAAGGAA
genomic: ACTGCCTCGCCGACCGCGGCTGCGCTGTCAACACCCACCTCTTCTCCTTGgtaaaatatc ... tgttctgtagATTGACGACATGGATCGACTTATTGAGGTAATAAAGCAAGCAGCAAAGGAA
EST: gi|71769341|gb|DR967278.1|DR967278
EST:     ACTGCCTCGCCGACCGCGGCTGCGCTGTCAACACCCACCTCTTCTCCTTG                         ATTGACGACATGGATCGACTTATTGAGGTAATAAAGCAAGCAGCAAAGGAA
genomic: ACTGCCTCGCCGACCGCGGCTGCGCTGTCAACACCCACCTCTTCTCCTTGgtaaaatatc ... tgttctgtagATTGACGACATGGATCGACTTATTGAGGTAATAAAGCAAGCAGCAAAGGAA

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: 48 (upstream exon), 48 (downstream exon)
Score: 14

CGGGTGGACCGCGGAGCACTCGGTGAACGCCGCGCTCGGACAGTTCGAGAACTGCCTCGCCGACCGCGGCTGCGCTGTCAACACCCACCTCTTCTCCTTGgtaaaatatc ... tgttctgtagATTGACGACATGGATCGACTTATTGAGGTAATAAAGCAAGCAGCAAAGGAAGGGGCACTGGTTCTCTACACCCTTGCCGATCCTTCAATGGCCGAGGCGA


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 197

CGGGTGGACCGCGGAGCACTCGGTGAACGCCGCGCTCGGACAGTTCGAGAACTGCCTCGCCGACCGCGGCTGCGCTGTCAACACCCACCTCTTCTCCTTGgtaaaatatc ... tgttctgtagATTGACGACATGGATCGACTTATTGAGGTAATAAAGCAAGCAGCAAAGGAAGGGGCACTGGTTCTCTACACCCTTGCCGATCCTTCAATGGCCGAGGCGA


Block sizes: 45 (upstream exon), 48 (downstream exon)
Score: 18

CGGGTGGACCGCGGAGCACTCGGTGAACGCCGCGCTCGGACAGTTCGAGAACTGCCTCGCCGACCGCGGCTGCGCTGTCAACACCCACCTCTTCTCCTTGgtaaaatatc ... tgttctgtagATTGACGACATGGATCGACTTATTGAGGTAATAAAGCAAGCAGCAAAGGAAGGGGCACTGGTTCTCTACACCCTTGCCGATCCTTCAATGGCCGAGGCGA


Block sizes: 46 (upstream exon), 48 (downstream exon)
Score: 114

CGGGTGGACCGCGGAGCACTCGGTGAACGCCGCGCTCGGACAGTTCGAGAACTGCCTCGCCGACCGCGGCTGCGCTGTCAACACCCACCTCTTCTCCTTGgtaaaatatc ... tgttctgtagATTGACGACATGGATCGACTTATTGAGGTAATAAAGCAAGCAGCAAAGGAAGGGGCACTGGTTCTCTACACCCTTGCCGATCCTTCAATGGCCGAGGCGA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttggtaaggggctgcatcttttgtaagtaacagcttctgctaatgttctgtagATTGACGACATGGATCGACTTATTGAGGTAATAAAGCAAGCAGCAAAGGAAGGGGCACTGGTTCTCTACACCCTTGCCGATCCTTCAATGGCCGAGGCGA
                                       tgctaat  putative branch site (score: 114)
                    ttttgtaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tacggatggaatttatatccacatttctacttgaaaaacgtcactttttggtaaggggctgcatcttttgtaagtaacagcttctgctaatgttctgtagATTGACGACATGGATCGACTTATTGAGGTAATAAAGCAAGCAGCAAAGGAAGGGGCACTGGTTCTCTACACCCTTGCCGATCCTTCAATGGCCGAGGCGA

- - - - - - - - - - - - - ctacttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -gctgcat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gcttctg