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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAGCTAAAGCTGTTGAATTCATCATGTACCATGCTGAGATATCCATTGCCTTTGTCCAGGAGAGCAAGATCAAATCAgtaagcacagacatttgccccccttggaacaataatactattaccctctggttaaatgctacatgtgtttgtgatccaaaaaaattagttacatatgatt...

Basic information

species Zea mays
transcript GRMZM2G104847_T01
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G104847_T01 (Zea mays), 5'ss of exon 6
lower sequence: LOC_Os11g35400.4 (Oryza sativa), 5'ss of exon 6
GAGCTAAAGCTGTTGAATTCATCATGTACCATGCTGAGATATCCATTGCCTTTGTCCAGGAGAGCAAGATCAAATCAgtaagcacagacatttgccccccttggaacaataatactattaccctctg-gttaaatgctacatgtgtttgtgatccaaa---aaaattagttacat-atgatt--
| || || || ||||||||||| ||| | ||||||||||| || || || ||||| ||||| ||||||||  |||||||||||| ||| ||       ||||| || |||| | || ||   | |||  |||| ||  |        || |   ||||   |||  |  | | || ||||||  
GTGCAAATGCAGTTGAATTCATAATGGATCATGCTGAGATCTCTATAGCATTTGTGCAGGAAAGCAAGATACAATCAgtaagcaaagaaatga----tccttgaaa-aatatt-ctgttctgcactgtattaactggcatgc-caaatgcgcctcaaatttaaagctgatgatatgatgattga
















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|22542184|gb|BU092622.1|BU092622
EST:     ACCATGCTGAGATATCCATTGCCTTTGTCCAGGAGAGCAAGATCAAATCA                         ATACTAGCAGTTCTCCCTAAGTGCACAGCGCACCTTAGAGCCATT
genomic: ACCATGCTGAGATATCCATTGCCTTTGTCCAGGAGAGCAAGATCAAATCAgtaagcacag ... taattttcagATACTAGCAGTTCTCCCTAAGTGCACAGCGCACCTTAGAGCCATT
EST: gi|148958443|gb|EC904677.2|EC904677
EST:     ACCATGCTGAGATATCCATTGCCTTTGTCCAGGAGAGCAAGATCAAATCA                         ATACTAGCAGTTCTCCCTAAGTGCACAGCGCACCTTAGAG
genomic: ACCATGCTGAGATATCCATTGCCTTTGTCCAGGAGAGCAAGATCAAATCAgtaagcacag ... taattttcagATACTAGCAGTTCTCCCTAAGTGCACAGCGCACCTTAGAG
EST: gi|148995832|gb|EE035067.2|EE035067
EST:     ACCATGCTGAGATATCCATTGCCTTTGTCCAGGAGAGCAAGATCAAATCA                         ATACTAGCAGTTCTCCCTAAGTGCACAGCGCACCTTAGAG
genomic: ACCATGCTGAGATATCCATTGCCTTTGTCCAGGAGAGCAAGATCAAATCAgtaagcacag ... taattttcagATACTAGCAGTTCTCCCTAAGTGCACAGCGCACCTTAGAG
EST: gi|211174084|gb|FL129199.1|FL129199
EST:     ACCATGCTGAGATATCCATTGCCTTTGTCCAGGAGAGCAAGATCAAATCA                         ATACTAGCAGNTCTCCCTAAGNGCACAGCGCACCTTAGAG
genomic: ACCATGCTGAGATATCCATTGCCTTTGTCCAGGAGAGCAAGATCAAATCAgtaagcacag ... taattttcagATACTAGCAGTTCTCCCTAAGTGCACAGCGCACCTTAGAG
EST: gi|211345429|gb|FL132812.1|FL132812
EST:     ACCATGCTGAGATATCCATTGCCTTTGTCCAGGAGAGCAAGATCAAATCA                         ATACTAGCAGTTCTCCCTAAGTGCACAGCGCACCTTAGAG
genomic: ACCATGCTGAGATATCCATTGCCTTTGTCCAGGAGAGCAAGATCAAATCAgtaagcacag ... taattttcagATACTAGCAGTTCTCCCTAAGTGCACAGCGCACCTTAGAG
EST: gi|149076511|gb|EE165137.2|EE165137
EST:     ACCATGCTGAGATATCCATTGCCTTTGTCCAGGAGAGCAAGATCAAATCA                         ATACTAGCAGTTCTCCCTAAGTGCACAGCGCACCTTAGAG
genomic: ACCATGCTGAGATATCCATTGCCTTTGTCCAGGAGAGCAAGATCAAATCAgtaagcacag ... taattttcagATACTAGCAGTTCTCCCTAAGTGCACAGCGCACCTTAGAG
EST: gi|87157287|gb|DY402076.1|DY402076
EST:     ACCATGCTGAGATATCCATTGCCTTTGTCCAGGAGAGCAAGATCAAATCA                         ATACTAGCAGTTCTCCCTAAGTGCACAGCGCACCTTAGAG
genomic: ACCATGCTGAGATATCCATTGCCTTTGTCCAGGAGAGCAAGATCAAATCAgtaagcacag ... taattttcagATACTAGCAGTTCTCCCTAAGTGCACAGCGCACCTTAGAG
EST: gi|211174085|gb|FL129200.1|FL129200
EST:     ACCATGCTGAGATATCCATTGCCTTTGTCCAGGAGAGCAAGATCAAATCA                         ATACTAGCAGTTCTCCCTAAGTGCACAGCGCACCTTAGAG
genomic: ACCATGCTGAGATATCCATTGCCTTTGTCCAGGAGAGCAAGATCAAATCAgtaagcacag ... taattttcagATACTAGCAGTTCTCCCTAAGTGCACAGCGCACCTTAGAG
EST: gi|149086279|gb|EE175820.2|EE175820
EST:     ACCATGCTGAGATATCCATTGCCTTTGTCCAGGAGAGCAAGATCAAATCA                         ATACTAGCAGTTCTCCCTAAGTGCACAGCGCACCTTAGAG
genomic: ACCATGCTGAGATATCCATTGCCTTTGTCCAGGAGAGCAAGATCAAATCAgtaagcacag ... taattttcagATACTAGCAGTTCTCCCTAAGTGCACAGCGCACCTTAGAG
EST: gi|149107582|gb|EE189463.2|EE189463
EST:     ACCATGCTGAGATATCCATTGCCTTTGTCCAGGAGAGCAAGATCAAATCA                         ATACTAGCAGTTCTCCCTAAGTGCACAGCGCACCTTAGAG
genomic: ACCATGCTGAGATATCCATTGCCTTTGTCCAGGAGAGCAAGATCAAATCAgtaagcacag ... taattttcagATACTAGCAGTTCTCCCTAAGTGCACAGCGCACCTTAGAG
EST: gi|71430909|gb|DR811959.1|DR811959
EST:     ACCATGCTGAGATATCCATTGCCTTTGTCCAGGAGAGCAAGATCAAATCA                         ATACTAGCAGTTCTCCCTAAGTGCACAGCGCACCTTAGAG
genomic: ACCATGCTGAGATATCCATTGCCTTTGTCCAGGAGAGCAAGATCAAATCAgtaagcacag ... taattttcagATACTAGCAGTTCTCCCTAAGTGCACAGCGCACCTTAGAG
EST: gi|149073920|gb|EE162247.2|EE162247
EST:     ACCATGCTGAGATATCCATTGCCTTTGTCCAGGAGAGCAAGATCAAATCA                         ATACTAGCAGTTCTCCCTAAGTGCACAGCGCACCTTAGAG
genomic: ACCATGCTGAGATATCCATTGCCTTTGTCCAGGAGAGCAAGATCAAATCAgtaagcacag ... taattttcagATACTAGCAGTTCTCCCTAAGTGCACAGCGCACCTTAGAG
EST: gi|149098382|gb|EE184358.2|EE184358
EST:     ACCATGCTGAGATATCCATTGCCTTTGTCCAGGAGAGCAAGATCAAATCA                         ATACTAGCAGTTCTCCCTAAGTGCACAGCGCACCTTAGAG
genomic: ACCATGCTGAGATATCCATTGCCTTTGTCCAGGAGAGCAAGATCAAATCAgtaagcacag ... taattttcagATACTAGCAGTTCTCCCTAAGTGCACAGCGCACCTTAGAG
EST: gi|211174083|gb|FL129198.1|FL129198
EST:     ACCATGCTGAGATATCCATTGCCTTTGTCCAGGAGAGCAAGATCNAATCA                         ATACTAGCAGTTCTCCCCTAAGTGCACAGCGCACCTTANAG
genomic: ACCATGCTGAGATATCCATTGCCTTTGTCCAGGAGAGCAAGATCAAATCAgtaagcacag ... taattttcagATACTAGCAGTTCTCCC-TAAGTGCACAGCGCACCTTAGAG
EST: gi|148942583|gb|EC887602.2|EC887602
EST:     ACCATGCTGAGATATCCATTGCCTTTGTCCAGGAGAGCAAGATCAAATCA                         ATACTAGCAGTTCTCCCTAAGTGCACAGCGCACCTTAGAG
genomic: ACCATGCTGAGATATCCATTGCCTTTGTCCAGGAGAGCAAGATCAAATCAgtaagcacag ... taattttcagATACTAGCAGTTCTCCCTAAGTGCACAGCGCACCTTAGAG
EST: gi|211175752|gb|FL129203.1|FL129203
EST:     CCATGCTGAGATATCCATTGCCCTTTGTCCAGGAGAGCAAGATCAAATCC                         ATACTAGCAGTTCTCCCCTAAG
genomic: CCATGCTGAGATATCCATTGCC-TTTGTCCAGGAGAGCAAGATCAAATCAgtaagcacag ... taattttcagATACTAGCAGTTCTCCC-TAAG
EST: gi|26559314|gb|CA831549.1|CA831549
EST:     ACCATGCTGAGATATCCATTGCCTTTGTCCAGGAGAGCAAGATCAAATCA                         ATACTAGCAGTTCTCCCTAAGTGCACA
genomic: ACCATGCTGAGATATCCATTGCCTTTGTCCAGGAGAGCAAGATCAAATCAgtaagcacag ... taattttcagATACTAGCAGTTCTCCCTAAGTGCACA
EST: gi|93282461|gb|EB674725.1|EB674725
EST:     ACCATGCTGAGATATCCATTGCCTTTGTCCAGGAGAGCAAGATCAAATCA                         ATACTAGCAGTTCTCCCTAAGTGCACAGCGCACCTTAGAG
genomic: ACCATGCTGAGATATCCATTGCCTTTGTCCAGGAGAGCAAGATCAAATCAgtaagcacag ... taattttcagATACTAGCAGTTCTCCCTAAGTGCACAGCGCACCTTAGAG
EST: gi|149085816|gb|EE175338.2|EE175338
EST:     ACCATGCTGAGATATCCATTGCCTTTGTCCAGGAGAGCAAGATCAAATCA                         ATACTAGCAGTTCTCCCTAAGTGCACAGCGCACCTTAGAG
genomic: ACCATGCTGAGATATCCATTGCCTTTGTCCAGGAGAGCAAGATCAAATCAgtaagcacag ... taattttcagATACTAGCAGTTCTCCCTAAGTGCACAGCGCACCTTAGAG
EST: gi|148970227|gb|EE021164.2|EE021164
EST:     ACCATGCTGAGATATCCATTGCCTTTGTCCAGGAGAGCAAGATCAAATCA                         ATACTAGCAGTTCTCCCTAAGTGCACAGCGCACCTTAGAG
genomic: ACCATGCTGAGATATCCATTGCCTTTGTCCAGGAGAGCAAGATCAAATCAgtaagcacag ... taattttcagATACTAGCAGTTCTCCCTAAGTGCACAGCGCACCTTAGAG
EST: gi|211174082|gb|FL129197.1|FL129197
EST:     ACCATGCTGAGATATCCATTGCCTTTGTCCAGGAGAGCAAGATCAAATCA                         ATACTAGCAGTTCTCCCTAAGTGCACAGCGCACCTTAGAG
genomic: ACCATGCTGAGATATCCATTGCCTTTGTCCAGGAGAGCAAGATCAAATCAgtaagcacag ... taattttcagATACTAGCAGTTCTCCCTAAGTGCACAGCGCACCTTAGAG
EST: gi|211174078|gb|FL129193.1|FL129193
EST:     ACCATGCTGAGATATCCATTGCCTTTGTCCAGGAGAGCAAGATCAAATCA                         ATACTAGCAGTTCTCCCTAAGTGCACAGCGCACCTTAGAG
genomic: ACCATGCTGAGATATCCATTGCCTTTGTCCAGGAGAGCAAGATCAAATCAgtaagcacag ... taattttcagATACTAGCAGTTCTCCCTAAGTGCACAGCGCACCTTAGAG
EST: gi|211175750|gb|FL129201.1|FL129201
EST:     ACCATGCTGAGATATCCATTGCCTTTGTCCAGGANAGCAAGATCAAATCA                         ATACTAGCAGTTCTCCCTAAGTGCACAGCGCACCTTAGAG
genomic: ACCATGCTGAGATATCCATTGCCTTTGTCCAGGAGAGCAAGATCAAATCAgtaagcacag ... taattttcagATACTAGCAGTTCTCCCTAAGTGCACAGCGCACCTTAGAG
EST: gi|148999540|gb|EE036511.2|EE036511
EST:     ACCATGCTGAGATATCCATTGCCTTTGTCCAGGAGAGCAAGATCAAATCA                         ATACTAGCAGTTCTCCCTAAGTGCACAGCGCACCTTAGAG
genomic: ACCATGCTGAGATATCCATTGCCTTTGTCCAGGAGAGCAAGATCAAATCAgtaagcacag ... taattttcagATACTAGCAGTTCTCCCTAAGTGCACAGCGCACCTTAGAG
EST: gi|211399266|gb|FL448654.1|FL448654
EST:     ACCATGCTGAGATATCCATTGCCTTTGTCCAGGAGAGCAAGATCAAATCA                         ATAGTAGCAGTTCTCCCCTAAGTGCACAGCGCACCTTAGAG
genomic: ACCATGCTGAGATATCCATTGCCTTTGTCCAGGAGAGCAAGATCAAATCAgtaagcacag ... taattttcagATACTAGCAGTTCT-CCCTAAGTGCACAGCGCACCTTAGAG
EST: gi|211347820|gb|FL132816.1|FL132816
EST:     ACCATGCTGAGATATCCATTGCCTTTGTCCAGGAGAGCAAGATCAAATCA                         ATACTAGCAGTTCTCCCTAAGTGCACAGCGCACCT
genomic: ACCATGCTGAGATATCCATTGCCTTTGTCCAGGAGAGCAAGATCAAATCAgtaagcacag ... taattttcagATACTAGCAGTTCTCCCTAAGTGCACAGCGCACCT
EST: gi|76283292|gb|DV022860.1|DV022860
EST:     CCATGCTGAGATATCCATTGCCTTTTGTCCAGAAGAGCAAGATCAAATCA                         ATACTAGCAGTTCCTCC-TAAGTGCACAGCGCACCTTAGAGCCCTTGTTAG
genomic: CCATGCTGAGATATCCATTGCCTTT-GTCCAGGAGAGCAAGATCAAATCAgtaagcacag ... taattttcagATACTAGCAGTTC-TCCCTAAGTGCACAGCGCACCTTAGAGCCATTGTTAG
EST: gi|211175754|gb|FL129205.1|FL129205
EST:     ACCATGCTGAGATATCCATTGCCTTTGTCCAGGAGAGCAAGATCAAATCA                         ATACTAGCAGTTCTCCCTAAGTGCACAGCGCACCTTAGAG
genomic: ACCATGCTGAGATATCCATTGCCTTTGTCCAGGAGAGCAAGATCAAATCAgtaagcacag ... taattttcagATACTAGCAGTTCTCCCTAAGTGCACAGCGCACCTTAGAG

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 3 RNA-Seq libraries.


Block sizes: 49 (upstream exon), 40 (downstream exon)
Score: 180

GAGCTAAAGCTGTTGAATTCATCATGTACCATGCTGAGATATCCATTGCCTTTGTCCAGGAGAGCAAGATCAAATCAgtaagcacag ... taattttcagATACTAGCAGTTCTCCCTAAGTGCACAGCGCACCTTAGAG


Block sizes: 49 (upstream exon), 43 (downstream exon)
Score: 104

GAGCTAAAGCTGTTGAATTCATCATGTACCATGCTGAGATATCCATTGCCTTTGTCCAGGAGAGCAAGATCAAATCAgtaagcacag ... taattttcagATACTAGCAGTTCTCCCTAAGTGCACAGCGCACCTTAGAG


Block sizes: 49 (upstream exon), 40 (downstream exon)
Score: 278

GAGCTAAAGCTGTTGAATTCATCATGTACCATGCTGAGATATCCATTGCCTTTGTCCAGGAGAGCAAGATCAAATCAgtaagcacag ... taattttcagATACTAGCAGTTCTCCCTAAGTGCACAGCGCACCTTAGAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAGCTAAAGCTGTTGAATTCATCATGTACCATGCTGAGATATCCATTGCCTTTGTCCAGGAGAGCAAGATCAAATCAgtaagcacagacatttgccccccttggaacaataatactattaccctctggttaaatgctacatgtgtttgtgatccaaaaaaattagttacatatgatt

- - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cccccct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aacaataa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaaaaaat