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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTATGACTACCTTCCATACTTCTACTCGAGGGTTTTTGAGTACGAGGGAAGTTCGAGGAAAGTCTGGTGGCAGTTTTATGGCGACAATGgtgagtaccatgacatccattttatacatcacaagttgatccttgtgattaagcttaagcatgcatattcatgagactaatgcccttggtttgtgctctgagcag

Basic information

species Zea mays
transcript GRMZM5G828229_T01
intron # 12
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G828229_T02 (Zea mays), 5'ss of exon 14
lower sequence: LOC_Os08g05570.3 (Oryza sativa), 5'ss of exon 14
GTATGACTACCTTCCATACTTCTACTCGAGGGTTTTTGAGTACGAGGGAAGTTCGAGGAAAGTCTGGTGGCAGTTTTATGGCGACAATGgtgagtaccatgacatccattttatacatcacaagttgatccttgtgattaagcttaagcatgcatattcatgagactaatgcccttggtttgtgctctgagcag
|||||||||||||||||| ||||| || || |||||||||||||| |||||||| |||||| | |||||||| ||||| || || ||||||       || ||||   |  |    |  |||    |    |  || |||  |||       || | |||  |    ||| ||||   | | ||  ||||||||
GTATGACTACCTTCCATATTTCTATTCAAGAGTTTTTGAGTACGAAGGAAGTTCAAGGAAAATTTGGTGGCAATTTTACGGTGATAATGgtacagtatataacataagtaattcctactacataacgcatgtcctg-ttagactt-------caaaatcacaaactcaataccctctctgt-tgtgctgagcag

upper sequence: GRMZM5G828229_T02 (Zea mays), 5'ss of exon 14
lower sequence: GLYMA05G37430.1 (Glycine max), 5'ss of exon 13
GTATGACTACCTTCCATACTTCTACTCGAGGGTTTTTGAGTACGAGGGAAGTTCGAGGAAAGTCTGGTGGCAGTTTTATGGCGACAATGgtgagtacca--tgacatccattttatacatcacaagttgatccttgtgattaagcttaagcatgcatattcatgagactaatgcccttggtttgtgctctgagcag
||||||||| |||||||||||||| || ||| ||||||| || || |||||  | || ||||| ||||||||||| | | | ||||| ||  ||||  |  | | |   |  |   |   |   |  |  || ||    ||||  ||     | |    || |    ||  | |   |  ||| | || ||  |||
GTATGACTATCTTCCATACTTCTATTCAAGGATTTTTGAATATGAAGGAAGCCCTAGAAAAGTGTGGTGGCAGTTCTTTAGAGACAAGGGCAAgtattagttaaaaaataaatagcattgccttaccttttcttttcttttaatttttgaatttctc--tcctattgctcttactgcttattt-ttctttggacag

upper sequence: GRMZM5G828229_T02 (Zea mays), 5'ss of exon 14
lower sequence: GLYMA08G02100.2 (Glycine max), 5'ss of exon 13
GTATGACTACCTTCCATACTTCTACTCGAGGGTTTTTGAGTACGAGGGAAGTTCGAGGAAAGTCTGGTGGCAGTTTTATGGCGACAATGgtgagtacca--tgacatccattttatacatcacaagttgatccttgtgattaagcttaagcatgcatattcatgagactaatgcccttggtttgtgctctgagcag
|||||| || ||||||||||||||||||||| ||||||| || || |||||  | || ||||| ||||||||||| | ||| ||||||||| ||||  |  | | |   |  |   |   |   |  |  || ||    ||||  ||    |       || |    ||  | || ||  ||| | || ||  |||
GTATGATTATCTTCCATACTTCTACTCGAGGATTTTTGAATATGAAGGAAGCCCTAGAAAAGTGTGGTGGCAGTTCTTTGGAGACAATGgtaagtattagttaaaaaataaatagcattgccttaccttttcttttcttttaattttt--taatttctctcctattgctcttaccgtttattt-ttctttggacag

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|211009192|gb|FL302293.1|FL302293
EST:     GTACGAGGGAAGTTCGAGGAAAGTCTGGTGGCAGTTTTATGGCGACAATG                         TCGGCGAAGCAGTCGAAGTAGGGAACTTTGATCCAAAGGTTGCGACTTTCT
genomic: GTACGAGGGAAGTTCGAGGAAAGTCTGGTGGCAGTTTTATGGCGACAATGgtgagtacca ... ctctgagcagTCGGCGAAGCAGTCGAAGTAGGGAACTTTGATCCAAAGGTTGCGACTTTCT
EST: gi|86466009|gb|DY232382.1|DY232382
EST:     GTACGAGGGAAGTTCGAGGAAAGTCTGGTGGCAGTTTTATGGCGACAATG                         TCGGCGAAGCAGTCGAAGTAGGGAACTTTGATCCAAAGGTTGCGACTTTCT
genomic: GTACGAGGGAAGTTCGAGGAAAGTCTGGTGGCAGTTTTATGGCGACAATGgtgagtacca ... ctctgagcagTCGGCGAAGCAGTCGAAGTAGGGAACTTTGATCCAAAGGTTGCGACTTTCT
EST: gi|86471329|gb|DY237699.1|DY237699
EST:     GTACGAGGGAAGTTCGAGGAAAGTCTGGTGGCAGTTTTATGGCGACAATG                         TCGGCGAAGCAGTCGAAGTAGGGAACTTTGATCCAAAGGTTGCGACTTTCT
genomic: GTACGAGGGAAGTTCGAGGAAAGTCTGGTGGCAGTTTTATGGCGACAATGgtgagtacca ... ctctgagcagTCGGCGAAGCAGTCGAAGTAGGGAACTTTGATCCAAAGGTTGCGACTTTCT
EST: gi|60340056|gb|DN207029.1|DN207029
EST:     GTACGAGGGAAGTTCGAGGAAAGTCTGGTGGCAGTTTTATGGCGACAATG                         TCGGCGAAGCAGTCGAAGTAGGGAACTTTGATCCAAAGGTTGCGACTTTCT
genomic: GTACGAGGGAAGTTCGAGGAAAGTCTGGTGGCAGTTTTATGGCGACAATGgtgagtacca ... ctctgagcagTCGGCGAAGCAGTCGAAGTAGGGAACTTTGATCCAAAGGTTGCGACTTTCT
EST: gi|87152588|gb|DY397377.1|DY397377
EST:     GTACGAGGGAAGTTCGAGGAAAGTCTGGTGGCAGTTTTATGGCGACAATG                         TCGGCGAAGCAGTCGAAGTAGGGAACTTTGATCCAAAGGTTGCGACTTTCT
genomic: GTACGAGGGAAGTTCGAGGAAAGTCTGGTGGCAGTTTTATGGCGACAATGgtgagtacca ... ctctgagcagTCGGCGAAGCAGTCGAAGTAGGGAACTTTGATCCAAAGGTTGCGACTTTCT
EST: gi|60342475|gb|DN209448.1|DN209448
EST:     GTACGAGGGAAGTTCGAGGAAAGTCTGGTGGCAGTTTTATGGCGACAATG                         TCGGCGAAGCAGTCGAAGTAGGGAACTTTGATCCAAAGGTTGCGACTTTCT
genomic: GTACGAGGGAAGTTCGAGGAAAGTCTGGTGGCAGTTTTATGGCGACAATGgtgagtacca ... ctctgagcagTCGGCGAAGCAGTCGAAGTAGGGAACTTTGATCCAAAGGTTGCGACTTTCT
EST: gi|18655110|gb|BM499915.1|BM499915
EST:     GGGAAGTTCGAGGAAAGTCTGGTGGCAGTTTTATGGCGACAATG                         TCGGCGAAGCAGTCG-AGTAGGGAACTTTGATCCAAAGGTTGCGACTTTCT
genomic: GGGAAGTTCGAGGAAAGTCTGGTGGCAGTTTTATGGCGACAATGgtgagtacca ... ctctgagcagTCGGCGAAGCAGTCGAAGTAGGGAACTTTGATCCAAAGGTTGCGACTTTCT
EST: gi|211009193|gb|FL302294.1|FL302294
EST:     TTTTATGGCGACAATG                         TCGGCGNAGCAGTCGAAGTAGGGAACTYTGATCCAAAGGTTGCGACTTTCT
genomic: TTTTATGGCGACAATGgtgagtacca ... ctctgagcagTCGGCGAAGCAGTCGAAGTAGGGAACTTTGATCCAAAGGTTGCGACTTTCT
EST: gi|211410389|gb|FL480482.1|FL480482
EST:     GTACGAGGGAAGTTCGAGGAAAGTCTGGTGGCAGTTTTATGGCGACAATG                         TCGGCGAAGCAGTCGAAGTAGGGAACTTTGATCCAAAGGTTGCGACTTTCT
genomic: GTACGAGGGAAGTTCGAGGAAAGTCTGGTGGCAGTTTTATGGCGACAATGgtgagtacca ... ctctgagcagTCGGCGAAGCAGTCGAAGTAGGGAACTTTGATCCAAAGGTTGCGACTTTCT
EST: gi|110943981|gb|EE164138.1|EE164138
EST:     GTACGAGGGAAGTTCGAGGAAAGTCTGGTGGCAGTTTTATGGCGACAATG                         TCGGCGAAGCAGTCGAAGTAGGGAACTTTGATCCAAAGGTTGCGACTTTCT
genomic: GTACGAGGGAAGTTCGAGGAAAGTCTGGTGGCAGTTTTATGGCGACAATGgtgagtacca ... ctctgagcagTCGGCGAAGCAGTCGAAGTAGGGAACTTTGATCCAAAGGTTGCGACTTTCT
EST: gi|60355749|gb|DN222722.1|DN222722
EST:     GTACGAGGGAAGTTCGAGGAAAGTCTGGTGGCAGTTTTATGGCGACAATG                         TCGGCGAAGCAGTCGAAGTAGGGAACTTTGATCCAAAGGTTGCGACTTTCT
genomic: GTACGAGGGAAGTTCGAGGAAAGTCTGGTGGCAGTTTTATGGCGACAATGgtgagtacca ... ctctgagcagTCGGCGAAGCAGTCGAAGTAGGGAACTTTGATCCAAAGGTTGCGACTTTCT
EST: gi|32848350|gb|CD988031.1|CD988031
EST:     ACGAGGGGAGTTCGAGGAAAGTCTGGTGGCAGTTTTATGGCGACAATG                         TCGGCGAAGCAGTCGAAGTAGGGAACTTTGATCCAAAGGTTGCGACTTTCT
genomic: ACGAGGGAAGTTCGAGGAAAGTCTGGTGGCAGTTTTATGGCGACAATGgtgagtacca ... ctctgagcagTCGGCGAAGCAGTCGAAGTAGGGAACTTTGATCCAAAGGTTGCGACTTTCT
EST: gi|86467590|gb|DY233960.1|DY233960
EST:     GTACGAGGGAAGTTCGAGGAAAGTCTGGTGGCAGTTTTATGGCGACAATG                         TCGGCGAAGCAGTCGAAGTAGGGAACTTTGATCCAAAGGTTGCGACTTTCT
genomic: GTACGAGGGAAGTTCGAGGAAAGTCTGGTGGCAGTTTTATGGCGACAATGgtgagtacca ... ctctgagcagTCGGCGAAGCAGTCGAAGTAGGGAACTTTGATCCAAAGGTTGCGACTTTCT
EST: gi|40303824|gb|CK348211.1|CK348211
EST:     GTACGAGGGAAGTTCGAGGAAAGTCTGGTGGCAGTTTTATGGCGACAATG                         TCGGCGAAGCAGTCGAAGTAGGGAACTTTGATCCAAAGGTTGCGACTTTCT
genomic: GTACGAGGGAAGTTCGAGGAAAGTCTGGTGGCAGTTTTATGGCGACAATGgtgagtacca ... ctctgagcagTCGGCGAAGCAGTCGAAGTAGGGAACTTTGATCCAAAGGTTGCGACTTTCT
EST: gi|148929039|gb|EC874295.2|EC874295
EST:     GTACGAGGGAAGTTCGAGGAAAGTCTGGTGGCAGTTTTATGGCGACAATG                         TCGGCGAAGCAGTCGAAGTAGGGAACTTTGATCCAAAGGTTGCGACTTTCT
genomic: GTACGAGGGAAGTTCGAGGAAAGTCTGGTGGCAGTTTTATGGCGACAATGgtgagtacca ... ctctgagcagTCGGCGAAGCAGTCGAAGTAGGGAACTTTGATCCAAAGGTTGCGACTTTCT
EST: gi|211520540|gb|FL475907.1|FL475907
EST:     GTACGAGGGAAGTTCGAGGAAAGTCTGGTGGCAGTTTTATGGCGACAATG                         TCGGCGAAGCAGTCGAAGTAGGGAACTTTGATCCAAAGGTTGCGACTTTCT
genomic: GTACGAGGGAAGTTCGAGGAAAGTCTGGTGGCAGTTTTATGGCGACAATGgtgagtacca ... ctctgagcagTCGGCGAAGCAGTCGAAGTAGGGAACTTTGATCCAAAGGTTGCGACTTTCT
EST: gi|71760295|gb|DR958232.1|DR958232
EST:     TTTTATGGCGCCAATG                         TCGGCGAAGCAGTCGAAGTAGGGAACTCTGATCCAAAGGTTGGGACTTTCT
genomic: TTTTATGGCGACAATGgtgagtacca ... ctctgagcagTCGGCGAAGCAGTCGAAGTAGGGAACTTTGATCCAAAGGTTGCGACTTTCT
EST: gi|22490231|gb|BU050154.1|BU050154
EST:     GGGAAGTTCGAGGAAAGTCTGGTGGCAGTTTTATGGCGACAATG                         TCGGCGAAGCAGTCGAAGTAGGGAACTTTGATCCAAAGGTTGCGACTTTCT
genomic: GGGAAGTTCGAGGAAAGTCTGGTGGCAGTTTTATGGCGACAATGgtgagtacca ... ctctgagcagTCGGCGAAGCAGTCGAAGTAGGGAACTTTGATCCAAAGGTTGCGACTTTCT
EST: gi|148990926|gb|EE032349.2|EE032349
EST:     AAGTCTGGTGGCAGTTTTATGGCGACAAAG                         TCGGCGAAGCAGTCGAAGTAGGGAACTTTGATCCAAAGGTTGCGACTTTCT
genomic: AAGTCTGGTGGCAGTTTTATGGCGACAATGgtgagtacca ... ctctgagcagTCGGCGAAGCAGTCGAAGTAGGGAACTTTGATCCAAAGGTTGCGACTTTCT
EST: gi|78103955|gb|DV522373.1|DV522373
EST:     GTACGAGGGAAGTTCGAGGAAAGTCTGGTGGCAGTTTTATGGCGACAATG                         TCGGCGAAGCAGTCGAAGTAGGGAACTTTGATCCAAAGGTTGCGACTTTCT
genomic: GTACGAGGGAAGTTCGAGGAAAGTCTGGTGGCAGTTTTATGGCGACAATGgtgagtacca ... ctctgagcagTCGGCGAAGCAGTCGAAGTAGGGAACTTTGATCCAAAGGTTGCGACTTTCT
EST: gi|87153578|gb|DY398367.1|DY398367
EST:     GGGAAGTTCGAGGAAAGTCTGGTGGCAGTTTTATGGCGACAATG                         TCGGCGAAGCAGTCGAAGTAGGGAACTTTGATCCAAAGGTTGCGACTTTCT
genomic: GGGAAGTTCGAGGAAAGTCTGGTGGCAGTTTTATGGCGACAATGgtgagtacca ... ctctgagcagTCGGCGAAGCAGTCGAAGTAGGGAACTTTGATCCAAAGGTTGCGACTTTCT
EST: gi|60341998|gb|DN208971.1|DN208971
EST:     GTACGAGGGAAGTTCGAGGAAAGTCTGGTGGCAGTTTTATGGCGACAATG                         TCGGCGAAGCAGTCGAAGTAGGGAACTTTGATCCAAAGGTTGCGACTTTCT
genomic: GTACGAGGGAAGTTCGAGGAAAGTCTGGTGGCAGTTTTATGGCGACAATGgtgagtacca ... ctctgagcagTCGGCGAAGCAGTCGAAGTAGGGAACTTTGATCCAAAGGTTGCGACTTTCT
EST: gi|33101850|gb|CF061810.1|CF061810
EST:     GTACGAGGGAAGTTCGAGGAAAGTCTGGTGGCAGTTTTATGGCGACAATG                         TCGGCGAAGCAGTCGAAGTAGGGAACTTTGATCTAAAGGTTGCGACTTTCT
genomic: GTACGAGGGAAGTTCGAGGAAAGTCTGGTGGCAGTTTTATGGCGACAATGgtgagtacca ... ctctgagcagTCGGCGAAGCAGTCGAAGTAGGGAACTTTGATCCAAAGGTTGCGACTTTCT
EST: gi|148933345|gb|EC877007.2|EC877007
EST:     GTACGAGGGAAGTTCGAGGAAAGTCTGGTGGCAGTTTTATGGCGACAATG                         TCGGCGAAGCAGTCGAAGTAGGGAACTTTGATCCAAAGGTTGCGACTTTCT
genomic: GTACGAGGGAAGTTCGAGGAAAGTCTGGTGGCAGTTTTATGGCGACAATGgtgagtacca ... ctctgagcagTCGGCGAAGCAGTCGAAGTAGGGAACTTTGATCCAAAGGTTGCGACTTTCT
EST: gi|33102180|gb|CF062140.1|CF062140
EST:     GTACGAGGGAAGTTCGAGGAAAGTCTGGTGGCAGTTTTATGGCGACAATG                         TCGGCGAAGCAGTCGAAGTAGGGAACTTTGATCTAAAGGTTGCGACTTTCT
genomic: GTACGAGGGAAGTTCGAGGAAAGTCTGGTGGCAGTTTTATGGCGACAATGgtgagtacca ... ctctgagcagTCGGCGAAGCAGTCGAAGTAGGGAACTTTGATCCAAAGGTTGCGACTTTCT
EST: gi|33090861|gb|CF050855.1|CF050855
EST:     ACGAGGGAAGTTCGAGGAAAGTCTGGTGGCAGTTTTATGGCGACAATG                         TCGGCGAAGCAGTCGAAGTAGGGAACTTTGATCCAAAGGTTGCGACTTTCT
genomic: ACGAGGGAAGTTCGAGGAAAGTCTGGTGGCAGTTTTATGGCGACAATGgtgagtacca ... ctctgagcagTCGGCGAAGCAGTCGAAGTAGGGAACTTTGATCCAAAGGTTGCGACTTTCT
EST: gi|32831851|gb|CD971529.1|CD971529
EST:     ACGAGGGAAGTTCGAGGAAAGTCTGGTGGCAGTTTTATGGCGACAATG                         TCGGCGAAGCAGTCGAAGTAGGGAACCTTTGATCCAAAGGTTGCGACTTTC
genomic: ACGAGGGAAGTTCGAGGAAAGTCTGGTGGCAGTTTTATGGCGACAATGgtgagtacca ... ctctgagcagTCGGCGAAGCAGTCGAAGTAGGGAA-CTTTGATCCAAAGGTTGCGACTTTC
EST: gi|14190977|gb|BG833207.1|BG833207
EST:     GTACGAGGGAAGTTCGAGGAAAGTCTGGTGGCAGTTTTATGGCGACAATG                         TCGGCGAAGCAGTCGAAGTAGGGAACTTTGATCCAAAGGTTGCGACTTTCT
genomic: GTACGAGGGAAGTTCGAGGAAAGTCTGGTGGCAGTTTTATGGCGACAATGgtgagtacca ... ctctgagcagTCGGCGAAGCAGTCGAAGTAGGGAACTTTGATCCAAAGGTTGCGACTTTCT

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), 49 (downstream exon)
Score: 274

GTATGACTACCTTCCATACTTCTACTCGAGGGTTTTTGAGTACGAGGGAAGTTCGAGGAAAGTCTGGTGGCAGTTTTATGGCGACAATGgtgagtacca ... ctctgagcagTCGGCGAAGCAGTCGAAGTAGGGAACTTTGATCCAAAGGTTGCGACTTTCTGGATCGACTCTG


Block sizes: 46 (upstream exon), 46 (downstream exon)
Score: 178

GTATGACTACCTTCCATACTTCTACTCGAGGGTTTTTGAGTACGAGGGAAGTTCGAGGAAAGTCTGGTGGCAGTTTTATGGCGACAATGgtgagtacca ... ctctgagcagTCGGCGAAGCAGTCGAAGTAGGGAACTTTGATCCAAAGGTTGCGACTTTCTGGATCGACTCTG


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 137

GTATGACTACCTTCCATACTTCTACTCGAGGGTTTTTGAGTACGAGGGAAGTTCGAGGAAAGTCTGGTGGCAGTTTTATGGCGACAATGgtgagtacca ... ctctgagcagTCGGCGAAGCAGTCGAAGTAGGGAACTTTGATCCAAAGGTTGCGACTTTCTGGATCGACTCTG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 208

GTATGACTACCTTCCATACTTCTACTCGAGGGTTTTTGAGTACGAGGGAAGTTCGAGGAAAGTCTGGTGGCAGTTTTATGGCGACAATGgtgagtacca ... ctctgagcagTCGGCGAAGCAGTCGAAGTAGGGAACTTTGATCCAAAGGTTGCGACTTTCTGGATCGACTCTG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTATGACTACCTTCCATACTTCTACTCGAGGGTTTTTGAGTACGAGGGAAGTTCGAGGAAAGTCTGGTGGCAGTTTTATGGCGACAATGgtgagtaccatgacatccattttatacatcacaagttgatccttgtgattaagcttaagcatgcatattcatgagactaatgcccttggtttgtgctctgagcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG