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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCCTTCAGAGCAAGGTTGTCTCTCCATTGTTGTACTTGGGGCTTCTGGTGACCTTGCTAAGAAGAAAACATTCCCAGCCCTCTACCACCTCTTTGAGCAGgtatgaactattctctatacaattttacaacttagagtataacttcaactgtaatgcacatttttttctcaaatacacaggagagttgcacatcattaca...

Basic information

species Zea mays
transcript GRMZM2G130230_T02
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G130230_T03 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os04g40874.1 (Oryza sativa), 5'ss of exon 2
TCCTTCAGAGCAAGGTTGTCTCTCCATTGTTGTACTTGGGGCTTCTGGTGACCTTGCTAAGAAGAAAACATTCCCAGCCCTCTACCACCTCTTTGAGCAGgta--tgaact----attctctatacaattttacaacttagagtataacttcaactgtaatgcacatttttttctcaaatacacaggagagttgcaca-tcattaca--
 |||||||||||||||||||||||  || |||| || ||||||||||| ||||| || ||||||||||| ||||| || |||| ||| || ||||  ||||||  |  |||    | ||   | |  |  |  |   ||   ||| || ||| |    |||  ||| |        |||   |||    ||| ||||| |||||  |  
CCCTTCAGAGCAAGGTTGTCTCTCTGTTATTGTCCTCGGGGCTTCTGGAGACCTAGCCAAGAAGAAAACTTTCCCGGCACTCTTCCATCTTTTTGCACAGgtaatttgactcctgagtcctgacaataactagctgtttcatgtacaatttccaa---aatctacactacg-----aaaggaacaatctagt-gcacagtcatttgagg

upper sequence: GRMZM2G130230_T03 (Zea mays), 5'ss of exon 2
lower sequence: GLYMA19G24250.1 (Glycine max), 5'ss of exon 2
TCCTTCAGAGCAAGGTTGTCTCTCCATTGTTGTACTTGGGGCTTCTGGTGACCTTGCTAAGAAGAAAACATTCCCAGCCCTCTACCACCTCTTTGAGCAGgtatgaactattctctatacaattttacaacttagagtataacttc-aactgtaatgcacatttttttctcaaatacacaggagagttgcacatcattaca--
|    | ||    || |  ||||| |||||||| ||||| |||||||| || |||||||||||||| ||||| || || || | ||| || |    |||||||   |  | |||   |   ||  |     |||| || |||  |  ||||||  |  |  |          ||| |  || |  | ||   |||||   |  
TGTGCCTGAAACTGGGTCACTCTCTATTGTTGTGCTTGGCGCTTCTGGGGATCTTGCTAAGAAGAAGACATTTCCTGCACTTTTCCATCTATACCGGCAGgtaaagaagaatcttggtg-gatcatgttgattagtgtgtaatgtagaactgttgtaaaagtgagaaatattaatgc--agaattgctgatgatcatgcaact

upper sequence: GRMZM2G130230_T03 (Zea mays), 5'ss of exon 2
lower sequence: GLYMA16G06850.1 (Glycine max), 5'ss of exon 2
TCCTTCAGAGCAAGGTTGTCTCTCCATTGTTGTACTTGGGGCTTCTGGTGACCTTGCTAAGAAGAAAACATTCCCAGCCCTCTACCACCTCTTTGAGCAGgtatgaactattctctatacaattttacaacttagagtataacttc-aactgtaatgcacatttttttctcaaatacacaggagagttgcacatcattaca-
|    | ||    || |  ||||| ||||| || ||||| ||||||||||| |||||||||||||| ||||| || || || | |||||| |    |||||||      | |||   |   ||  |     |||| || | |  |  ||| ||  |  | ||          ||| || | ||   | |||  | || |   
TGTGCCTGAAACTGGGTCACTCTCTATTGTGGTGCTTGGTGCTTCTGGTGATCTTGCTAAGAAGAAGACATTTCCTGCACTTTTCCACCTATACCTGCAGgtaaagcagaatcttggtg-gatcatgttgattagtgtgtgatgtagaacagttgtaaaaatgagaaatattaatgcagatgatcat-gcaactaatgatgg

upper sequence: GRMZM2G130230_T03 (Zea mays), 5'ss of exon 2
lower sequence: GLYMA19G22690.1 (Glycine max), 5'ss of exon 2
TCCTTCAGAGCAAGGTTGTCTCTCCATTGTTGTACTTGGGGCTTCTGGTGACCTTGCTAAGAAGAAAACATTCCCAGCCCTCTACCACCTCTTTGAGCAGgtatgaactattctctatacaattttacaacttagagtataacttc----aactgtaatgcacatttttttctcaaatacacaggagagttgcacatcattaca
| |  | ||    || |  |||||||||||||| ||||| |||||||||||||||||||||||||| ||||| ||||| || | | |||| |     ||||| |||   ||     ||     || |     || || ||||| |     |||  |  |    | |   || |    |    | || |     | |  | |   
TGCAACTGAAACTGGGTCACTCTCCATTGTTGTGCTTGGTGCTTCTGGTGACCTTGCTAAGAAGAAGACATTTCCAGCACTTTTCAACCTATACCGTCAGgtttga-taatctaagatttgtgttaaaggaataaaggataacctttgtgaaccatgttatttagtggcttttttgttgttgaagaaaacacaaaaagaat---

upper sequence: GRMZM2G130230_T03 (Zea mays), 5'ss of exon 2
lower sequence: AT3G27300.2 (Arabidopsis thaliana), 5'ss of exon 3
TCCTTCAGAGCAAGGTTGTCTCTCCATTGTTGTACTTGGGGCTTCTGGTGACCTTGCTAAGAAGAAAACATTCCCAGCCCTCTACCACCTCTTTGAGCAGgtatgaactattctctatacaattttacaacttagagtataacttcaactgtaatgcacatttttttctcaaatacacaggagagttgcacatcattaca-
     | ||    ||  ||||||| ||  |||| ||||| ||||||||||| |||||||||||||| || || || || || | | | || ||| | ||||| |     |      |   |  |||   |  |    |||   ||  | ||| |      ||| ||| |   ||          |||  |||| |  ||| 
AGTCACGGAAACTGGGAGTCTCTCTATCATTGTTCTTGGTGCTTCTGGTGATCTTGCTAAGAAGAAGACTTTTCCTGCACTTTTCAATCTATTTCATCAGgtttttttaaacaaacaagaatcttttttatcttt--tattgttttcaatgtcacttgtttttatttatttgatgtgtttattggttttacatgagcacag

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|211003557|gb|FK956136.1|FK956136
EST:     ACCTTGCTAAGAAGAAAACATTCCCAGCCCTCTACCACCTCTTTGAGCAG                         GGATTCATACAATCTGGAGAAGTCCATATATTTGGTTATGCTAGATCAAAT
genomic: ACCTTGCTAAGAAGAAAACATTCCCAGCCCTCTACCACCTCTTTGAGCAGgtatgaacta ... attgttacagGGATTCATACAATCTGGAGAAGTCCATATATTTGGTTATGCTAGATCAAAT
EST: gi|74237092|gb|DT645006.1|DT645006
EST:     ACCTTGCTAAGAAGAAAACATTCCCAGCCCTCTACCACCTCTTTGAGCAG                         GGATTCATACAATCTGGAGAAGTCCATATATTTGGTTATGCTAGATCAAAT
genomic: ACCTTGCTAAGAAGAAAACATTCCCAGCCCTCTACCACCTCTTTGAGCAGgtatgaacta ... attgttacagGGATTCATACAATCTGGAGAAGTCCATATATTTGGTTATGCTAGATCAAAT
EST: gi|71449499|gb|DR830549.1|DR830549
EST:     ACCTTGCTAAGAAGAAAACATTCCCAGCCCTCTACCACCTCTTTGAGCAG                         GGATTCATACAATCTGGAGAAGTCCATATATTTGGTTATGCTAGATCAAAT
genomic: ACCTTGCTAAGAAGAAAACATTCCCAGCCCTCTACCACCTCTTTGAGCAGgtatgaacta ... attgttacagGGATTCATACAATCTGGAGAAGTCCATATATTTGGTTATGCTAGATCAAAT
EST: gi|211398371|gb|FK956119.1|FK956119
EST:     ACCTTGCTAAGAAGAAAACATTCCCAGCCCTCTACCACCTCTTTGAGCAG                         GGATTCATACAATCTGGAGAAGTCCATATATTTGGTTATGCTAGATCAAAT
genomic: ACCTTGCTAAGAAGAAAACATTCCCAGCCCTCTACCACCTCTTTGAGCAGgtatgaacta ... attgttacagGGATTCATACAATCTGGAGAAGTCCATATATTTGGTTATGCTAGATCAAAT
EST: gi|50339442|gb|CO534568.1|CO534568
EST:     ACCTTGCTAAGAAGAAAACATTCCCAGCCCTCTACCACCTCTTTGAGCAG                         GGATTCATACAATCTGTATAAGTCCATATATTTGGTTATGCTAGATCAAAT
genomic: ACCTTGCTAAGAAGAAAACATTCCCAGCCCTCTACCACCTCTTTGAGCAGgtatgaacta ... attgttacagGGATTCATACAATCTGGAGAAGTCCATATATTTGGTTATGCTAGATCAAAT
EST: gi|71447340|gb|DR828390.1|DR828390
EST:     ACCTTGCTAAGAAGAAAACATTCCCAGCCCTCTACCACCTCTTTGAGCAG                         GGATTCATACAATCTGGAGAAGTCCATATATTTGGTTATGCTAGATCAAAT
genomic: ACCTTGCTAAGAAGAAAACATTCCCAGCCCTCTACCACCTCTTTGAGCAGgtatgaacta ... attgttacagGGATTCATACAATCTGGAGAAGTCCATATATTTGGTTATGCTAGATCAAAT
EST: gi|89759526|gb|DY688327.1|DY688327
EST:     ACCTTGCTAAGAAGAAAACATTCCCAGCCCTCTACCACCTCTTTGAGCAG                         GGATTCATACAATCTGGAGAAGTCCATATATTTGGTTATGCTAGATCAAAT
genomic: ACCTTGCTAAGAAGAAAACATTCCCAGCCCTCTACCACCTCTTTGAGCAGgtatgaacta ... attgttacagGGATTCATACAATCTGGAGAAGTCCATATATTTGGTTATGCTAGATCAAAT
EST: gi|211003554|gb|FK956133.1|FK956133
EST:     ACCTTGCTAAGAAGAAAACATTCCCAGCCCTCTACCACCTCTTTGAGCAG                         GGATTCATACAATCTGGAGAAGTCCATATATTTGGTTATGCTAGATCAAAT
genomic: ACCTTGCTAAGAAGAAAACATTCCCAGCCCTCTACCACCTCTTTGAGCAGgtatgaacta ... attgttacagGGATTCATACAATCTGGAGAAGTCCATATATTTGGTTATGCTAGATCAAAT
EST: gi|78083439|gb|DV511832.1|DV511832
EST:     ACCTTGCTAAGAAGAAAACATTCCCAGCCCTCTACCACCTCTTTGAGCAG                         GGATTCATACAATCTGGAGAAGTCCATATATTTGGTTATGCTAGATCAAAT
genomic: ACCTTGCTAAGAAGAAAACATTCCCAGCCCTCTACCACCTCTTTGAGCAGgtatgaacta ... attgttacagGGATTCATACAATCTGGAGAAGTCCATATATTTGGTTATGCTAGATCAAAT
EST: gi|211398372|gb|FK956120.1|FK956120
EST:     ACCTTGCTAAGAAGAAAACATTCCCAGCCCTCTACCACCTCTTTGAGCAG                         GGATTCATACAATCTGGAGAAGTCCATATATTTGGTTATGCTAGATCAAAT
genomic: ACCTTGCTAAGAAGAAAACATTCCCAGCCCTCTACCACCTCTTTGAGCAGgtatgaacta ... attgttacagGGATTCATACAATCTGGAGAAGTCCATATATTTGGTTATGCTAGATCAAAT
EST: gi|211398375|gb|FK956123.1|FK956123
EST:     ACCTTGCTAAGAAGAAAACATTCCCAGCCCTCTACCACCTCTTTGAGCAG                         GGATTCATACAATCTGGAGAAGTCCATATATTTGGTTATGCTAGATCAAAT
genomic: ACCTTGCTAAGAAGAAAACATTCCCAGCCCTCTACCACCTCTTTGAGCAGgtatgaacta ... attgttacagGGATTCATACAATCTGGAGAAGTCCATATATTTGGTTATGCTAGATCAAAT
EST: gi|211398373|gb|FK956121.1|FK956121
EST:     ACCTTGCTAAGAAGAAAACATTCCCAGCCCTCTACCACCTCTTTGAGCAG                         GGATTCATACAATCTGGAGAAGTCCATATATTTGGTTATGCTAGATCAAAT
genomic: ACCTTGCTAAGAAGAAAACATTCCCAGCCCTCTACCACCTCTTTGAGCAGgtatgaacta ... attgttacagGGATTCATACAATCTGGAGAAGTCCATATATTTGGTTATGCTAGATCAAAT
EST: gi|211003558|gb|FK956137.1|FK956137
EST:     ACCTTGCTAAGAAGAAAACATTCCCAGCCCTCTACCACCTCTTTGAGCAG                         GGATTCATACAATCTGGAGAAGTCCATATATTTGGTTATGCTAGATCAAAT
genomic: ACCTTGCTAAGAAGAAAACATTCCCAGCCCTCTACCACCTCTTTGAGCAGgtatgaacta ... attgttacagGGATTCATACAATCTGGAGAAGTCCATATATTTGGTTATGCTAGATCAAAT
EST: gi|211003549|gb|FK956128.1|FK956128
EST:     ACCTTGCTAAGAAGAAAACATTCCCAGCCCTCTACCACCTCTTTGAGCAG                         GGATTCATACAATCTGGAGAAGTCCATATATTTGGTTATGCTAGATCAAAT
genomic: ACCTTGCTAAGAAGAAAACATTCCCAGCCCTCTACCACCTCTTTGAGCAGgtatgaacta ... attgttacagGGATTCATACAATCTGGAGAAGTCCATATATTTGGTTATGCTAGATCAAAT
EST: gi|211398378|gb|FK956126.1|FK956126
EST:     ACCTTGCTAAGAAGAAAACATTCCCAGCCCTCTACCACCTCTTTGAGCAG                         GGATTCATACAATCTGGAGAAGTCCATATATTTGGTTATGCTAGATCAAAT
genomic: ACCTTGCTAAGAAGAAAACATTCCCAGCCCTCTACCACCTCTTTGAGCAGgtatgaacta ... attgttacagGGATTCATACAATCTGGAGAAGTCCATATATTTGGTTATGCTAGATCAAAT
EST: gi|211003552|gb|FK956131.1|FK956131
EST:     CCTTGCTAAGAAGAAAACATTCCCAGCCCTCTACCACCTCTTTGAAGCAG                         GGATTCATACAATCTGGAGAAGTCCATATATTTGGTTATGCTAGATCAAA
genomic: CCTTGCTAAGAAGAAAACATTCCCAGCCCTCTACCACCTCTTTGA-GCAGgtatgaacta ... attgttacagGGATTCATACAATCTGGAGAAGTCCATATATTTGGTTATGCTAGATCAAA
EST: gi|211003559|gb|FK956138.1|FK956138
EST:     ACCTTGCTAAGAAGAAAACATTCCCAGCCCTCTACCACCTCTTTGAGCAG                         GGATTCATACAATCTGGAGAAGTCCATATATTTGGTTATGCTAGATCAAAT
genomic: ACCTTGCTAAGAAGAAAACATTCCCAGCCCTCTACCACCTCTTTGAGCAGgtatgaacta ... attgttacagGGATTCATACAATCTGGAGAAGTCCATATATTTGGTTATGCTAGATCAAAT
EST: gi|71436592|gb|DR817642.1|DR817642
EST:     ACCTTGCTAAGAAGAAAACATTCCCAGCCCTCTACCACCTCTTTGAGCAG                         GGATTCATACAATCTGGAGAAGTCCATATATTTGGTTATGCTAGATCAAAT
genomic: ACCTTGCTAAGAAGAAAACATTCCCAGCCCTCTACCACCTCTTTGAGCAGgtatgaacta ... attgttacagGGATTCATACAATCTGGAGAAGTCCATATATTTGGTTATGCTAGATCAAAT
EST: gi|211003548|gb|FK956127.1|FK956127
EST:     ACCTTGCTAAGAAGAAAACATTCCCAGCCCTCTACCACCTCTTTGAGCAG                         GGATTCATACAATCTGGAGAAGTCCATATATTTGGTTATGCTAGATCAAAT
genomic: ACCTTGCTAAGAAGAAAACATTCCCAGCCCTCTACCACCTCTTTGAGCAGgtatgaacta ... attgttacagGGATTCATACAATCTGGAGAAGTCCATATATTTGGTTATGCTAGATCAAAT
EST: gi|211003556|gb|FK956135.1|FK956135
EST:     ACCTTGCTAAGNNNNNNNCATTCCCAGCCCTCTACCACCTCTTTGAGCAG                         GGATTCATACAATCTGGAGAAGTCCATATATTTGGTTATGCTAGATCAAAT
genomic: ACCTTGCTAAGAAGAAAACATTCCCAGCCCTCTACCACCTCTTTGAGCAGgtatgaacta ... attgttacagGGATTCATACAATCTGGAGAAGTCCATATATTTGGTTATGCTAGATCAAAT
EST: gi|211003560|gb|FK956139.1|FK956139
EST:     ACCTTGCTAAGAAGAAAACATTCCCAGCCCTCTACCACCTCTTTGAGCAG                         GGATTCATACAATCTGGAGAAGTCCATATATTTGGTTATGCTAGATCAAAT
genomic: ACCTTGCTAAGAAGAAAACATTCCCAGCCCTCTACCACCTCTTTGAGCAGgtatgaacta ... attgttacagGGATTCATACAATCTGGAGAAGTCCATATATTTGGTTATGCTAGATCAAAT
EST: gi|211398377|gb|FK956125.1|FK956125
EST:     ACCTTGCTAAGAAGAAAACATTCCCAGCCCTCTACCACCTCTTTGAGCAG                         GGATTCATACAATCTGGAGAAGTCCATATATTTGGTTATGCTAGATCAAAT
genomic: ACCTTGCTAAGAAGAAAACATTCCCAGCCCTCTACCACCTCTTTGAGCAGgtatgaacta ... attgttacagGGATTCATACAATCTGGAGAAGTCCATATATTTGGTTATGCTAGATCAAAT
EST: gi|211398376|gb|FK956124.1|FK956124
EST:     ACCTTGCTAAGAAGAAAACATTCCCAGCCCTCTACCACCTCTTTGAGCAG                         GGATTCATACAATCTGGAGAAGTCCATATATTTGGTTATGCTAGATCAAAT
genomic: ACCTTGCTAAGAAGAAAACATTCCCAGCCCTCTACCACCTCTTTGAGCAGgtatgaacta ... attgttacagGGATTCATACAATCTGGAGAAGTCCATATATTTGGTTATGCTAGATCAAAT
EST: gi|211003553|gb|FK956132.1|FK956132
EST:     ACCTTGCTAAGAAGAAAACATTCCCAGCCCTCTACCACCTCTTTGAGCAG                         GGATTCATACAATCTGGAGAAGTCCATATATTTGGTTATGCTAGATCAAAT
genomic: ACCTTGCTAAGAAGAAAACATTCCCAGCCCTCTACCACCTCTTTGAGCAGgtatgaacta ... attgttacagGGATTCATACAATCTGGAGAAGTCCATATATTTGGTTATGCTAGATCAAAT
EST: gi|93283386|gb|EB675650.1|EB675650
EST:     ACCTTGCTAAGAAGAAAACATTCCCAGCCCTCTACCACCTCTTTGAGCAG                         GGATTCATACAATCTGGAGAAGTCCATATATTTGGTTATGCTAGATCAAAT
genomic: ACCTTGCTAAGAAGAAAACATTCCCAGCCCTCTACCACCTCTTTGAGCAGgtatgaacta ... attgttacagGGATTCATACAATCTGGAGAAGTCCATATATTTGGTTATGCTAGATCAAAT
EST: gi|78109778|gb|DV528194.1|DV528194
EST:     ACCTTGCTAAGAAGAAAACATTCCCAGCCCTCTACCACCTCTTTGAGCAG                         GGATTCATACAATCTGGAGAAGTCCATATATTTGGTTATGCTAGATCAAAT
genomic: ACCTTGCTAAGAAGAAAACATTCCCAGCCCTCTACCACCTCTTTGAGCAGgtatgaacta ... attgttacagGGATTCATACAATCTGGAGAAGTCCATATATTTGGTTATGCTAGATCAAAT
EST: gi|71449885|gb|DR830935.1|DR830935
EST:     ACCTTGCTAAGAAGAAAACATTCCCAGCCCTCTACCACCTCTTTGAGCAG                         GGATTCATACAATCTGGAGAAGTCCATATATTTGGTTATGCTAGATCAAAT
genomic: ACCTTGCTAAGAAGAAAACATTCCCAGCCCTCTACCACCTCTTTGAGCAGgtatgaacta ... attgttacagGGATTCATACAATCTGGAGAAGTCCATATATTTGGTTATGCTAGATCAAAT
EST: gi|211398374|gb|FK956122.1|FK956122
EST:     ACCTTGCTAAGNNNNNNNCATTCCCAGCCCTCTACCACCTCTTTGAGCAG                         GGATTCATACAATCTGGAGAAGTCCATATATTTGGTTATGCTAGATCAAAT
genomic: ACCTTGCTAAGAAGAAAACATTCCCAGCCCTCTACCACCTCTTTGAGCAGgtatgaacta ... attgttacagGGATTCATACAATCTGGAGAAGTCCATATATTTGGTTATGCTAGATCAAAT
EST: gi|211003555|gb|FK956134.1|FK956134
EST:     ACCTTGCTAAGAAGAAAACATTCCCAGCCCTCTACCACCTCTTTGAGCAG                         GGATTCATACAATCTGGAGAAGTCCATATATTTGGTTATGCTAGATCAAAT
genomic: ACCTTGCTAAGAAGAAAACATTCCCAGCCCTCTACCACCTCTTTGAGCAGgtatgaacta ... attgttacagGGATTCATACAATCTGGAGAAGTCCATATATTTGGTTATGCTAGATCAAAT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TCCTTCAGAGCAAGGTTGTCTCTCCATTGTTGTACTTGGGGCTTCTGGTGACCTTGCTAAGAAGAAAACATTCCCAGCCCTCTACCACCTCTTTGAGCAGgtatgaactattctctatacaattttacaacttagagtataacttcaactgtaatgcacatttttttctcaaatacacaggagagttgcacatcattaca

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG