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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cattgatgattatttgataatttggccatctttggaagcaagtcaatgtgaattatatgatcttgtttaaaacttaacaattcttttcccttgtatgcagGTCTGGCCCGTTGATATAGATATGAAGTTCCTAGAGCCATTTGGACGGGAACTACATTCAATGAAAAAA

Basic information

species Zea mays
transcript GRMZM2G127453_T03
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G127453_T03 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os01g56890.2 (Oryza sativa), 3'ss of exon 2
cattgatgattatttgataatttggccatctttggaagcaagtcaatgtgaattatatgatctt----gtttaaaacttaacaattcttttcccttgtatgcagGTCTGGCCCGTTGATATAGATATGAAGTTCCTAGAGCCATTTGGACGGGAACTACATTCAATGAAAAAA-------------------------------
     |           |||  |||| |   |   |        | ||||||  |    |  ||    || | ||| ||| |  || || ||  || |||| |||| |||||| |||||||||| ||||||||||| |||||||||||||||||||||||||| ||||||||                                
---aaaccccagccaattaacatggctagtatgaaatattgtgaactgtgaaacacccaaatttttcagtcttaaatttatcc-tttttgtcatttctatgtagGTTTGGCCCCTTGATATAGAGATGAAGTTCCTGGAGCCATTTGGACGGGAACTACATTCCATGAAAAAGGTAATGCAAGCTTGAGGCTTTCCATCTGTTG

upper sequence: GRMZM2G127453_T03 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os01g56890.1 (Oryza sativa), 3'ss of exon 2
cattgatgattatttgataatttggccatctttggaagcaagtcaatgtgaattatatgatctt----gtttaaaacttaacaattcttttcccttgtatgcagGTCTGGCCCGTTGATATAGATATGAAGTTCCTAGAGCCATTTGGACGGGAACTACATTCAATGAAAAAA
     |           |||  |||| |   |   |        | ||||||  |    |  ||    || | ||| ||| |  || || ||  || |||| |||| |||||| |||||||||| ||||||||||| |||||||||||||||||||||||||| |||||||| 
---aaaccccagccaattaacatggctagtatgaaatattgtgaactgtgaaacacccaaatttttcagtcttaaatttatcc-tttttgtcatttctatgtagGTTTGGCCCCTTGATATAGAGATGAAGTTCCTGGAGCCATTTGGACGGGAACTACATTCCATGAAAAAG
















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|211045913|gb|FK963041.1|FK963041
EST:     AGTGCATCGTGCCCGGACAGCAAGCGCCTCTAAGGCTTATGGGGCTCAAG                         GTCTGGCCCGTTGATATAGATATGAAGTTC-TAGAGCCATTTGGACG
genomic: AGTGCATCGTGCCCGGACAGCAAGCGCCTCTAAGGCTTATGGGGCTCAAGgtacgaatcc ... ttgtatgcagGTCTGGCCCGTTGATATAGATATGAAGTTCCTAGAGCCATTTGGACG
EST: gi|31909649|gb|CD651024.1|CD651024
EST:     AGTGCATCGTGCCCGGACAGCAAGCGCCTCTAAGGCTTATGGGGCTCAAG                         GTCTGGCCCGTTGATATAGATATGAAGTTCCTAGAGCCATTTGGACGGGAA
genomic: AGTGCATCGTGCCCGGACAGCAAGCGCCTCTAAGGCTTATGGGGCTCAAGgtacgaatcc ... ttgtatgcagGTCTGGCCCGTTGATATAGATATGAAGTTCCTAGAGCCATTTGGACGGGAA
EST: gi|211042955|gb|FK963033.1|FK963033
EST:     AGTGCATCGTGCCCGGACAGCAAGCGCCTCTAAGGCTTATGGGGCTCAAG                         GTCTGGCCCGTTGATATAGATATGAAGTTCCTAGAGCCATTTGGACGGGAA
genomic: AGTGCATCGTGCCCGGACAGCAAGCGCCTCTAAGGCTTATGGGGCTCAAGgtacgaatcc ... ttgtatgcagGTCTGGCCCGTTGATATAGATATGAAGTTCCTAGAGCCATTTGGACGGGAA
EST: gi|211042961|gb|FK963039.1|FK963039
EST:     AGTGCATCGTGCCCGGACAGCAAGCGCCTCTAAGGCTTATGGGGCTCAAG                         GTCTGGCCCGTTGATATAGATATGAAGTTCCTAGAGCCATTTGGACGGGAA
genomic: AGTGCATCGTGCCCGGACAGCAAGCGCCTCTAAGGCTTATGGGGCTCAAGgtacgaatcc ... ttgtatgcagGTCTGGCCCGTTGATATAGATATGAAGTTCCTAGAGCCATTTGGACGGGAA
EST: gi|211167601|gb|FL258650.1|FL258650
EST:     GTTGCATCGTGCCCGGACAGCAAGCGCCTCTAAGGCTTATGGGGCTCAAG                         GTCTGGCCCGTTGATATAGATATGAAGTTCCTAGAGCCATTTGGACGGGAA
genomic: GT-GCATCGTGCCCGGACAGCAAGCGCCTCTAAGGCTTATGGGGCTCAAGgtacgaatcc ... ttgtatgcagGTCTGGCCCGTTGATATAGATATGAAGTTCCTAGAGCCATTTGGACGGGAA
EST: gi|211245830|gb|FL313150.1|FL313150
EST:     AGTGCATCGTGCCCGGACAGCAAGCGCCTCTAAGGCTTATGGGGCTCAAG                         GTCTGGCCCGTTGATATAGATATGAAGTTCCTAGAGCCATTTGGACGGGAA
genomic: AGTGCATCGTGCCCGGACAGCAAGCGCCTCTAAGGCTTATGGGGCTCAAGgtacgaatcc ... ttgtatgcagGTCTGGCCCGTTGATATAGATATGAAGTTCCTAGAGCCATTTGGACGGGAA
EST: gi|31353639|gb|CD437996.1|CD437996
EST:     AGTGCATCGTGCCCGGACAGCAAGCGCCTCTAAGGCTTATGGGGCTCAAG                         GTCTGGCCCGTTGATATAGATATGAAGTTCCTAGAGCCATTTGGACGGGAA
genomic: AGTGCATCGTGCCCGGACAGCAAGCGCCTCTAAGGCTTATGGGGCTCAAGgtacgaatcc ... ttgtatgcagGTCTGGCCCGTTGATATAGATATGAAGTTCCTAGAGCCATTTGGACGGGAA
EST: gi|211042950|gb|FK963028.1|FK963028
EST:     AGTGCATCGTGCCCGGACAGCAAGCGCCTCTAAGGCTTATGGGGCTCAAG                         GTCTGGCCCGTTGATATAGATATGAAGTTCCTAGAGCCATTTGGACGGGAA
genomic: AGTGCATCGTGCCCGGACAGCAAGCGCCTCTAAGGCTTATGGGGCTCAAGgtacgaatcc ... ttgtatgcagGTCTGGCCCGTTGATATAGATATGAAGTTCCTAGAGCCATTTGGACGGGAA
EST: gi|211156223|gb|FL476869.1|FL476869
EST:     AGTGCATCGTGCCCGGACAGCAAGCGCCTCTAAGGCTTATGGGGCTCAAG                         GTCTGGCCCGTTGATATAGATATGAAGTTCCTAGAGCCATTTGGACGGGAA
genomic: AGTGCATCGTGCCCGGACAGCAAGCGCCTCTAAGGCTTATGGGGCTCAAGgtacgaatcc ... ttgtatgcagGTCTGGCCCGTTGATATAGATATGAAGTTCCTAGAGCCATTTGGACGGGAA
EST: gi|211167597|gb|FL258646.1|FL258646
EST:     AGTGCATCGTGCCCGGACAGCAAGCGCCTCTAAGGCTTATGGGGCTCAAG                         GTCTGGCCCGTTGATATAGATATGAAGTTCCTAGAGCCATTTGGACGGGAA
genomic: AGTGCATCGTGCCCGGACAGCAAGCGCCTCTAAGGCTTATGGGGCTCAAGgtacgaatcc ... ttgtatgcagGTCTGGCCCGTTGATATAGATATGAAGTTCCTAGAGCCATTTGGACGGGAA
EST: gi|78180798|gb|DV551171.1|DV551171
EST:     AGTGCATCGTGCCCGGACAGCAAGCGCCTCTAAGGCTTATGGGGCTCAAG                         GTCTGGCCCGTTGATATAGATATGAAGTTCCTAGAGCCATTTGGACGGGAA
genomic: AGTGCATCGTGCCCGGACAGCAAGCGCCTCTAAGGCTTATGGGGCTCAAGgtacgaatcc ... ttgtatgcagGTCTGGCCCGTTGATATAGATATGAAGTTCCTAGAGCCATTTGGACGGGAA
EST: gi|8665358|gb|BE186174.1|BE186174
EST:     AGTGCATCGTGCCCGGACAGCAAGCGCCTCTAAGGCTTATGGGGCTCAAG                         GTCTGGCCCGTTGATATAGATATGAAGTTCCTAGAGCCATTTGGACGGGAA
genomic: AGTGCATCGTGCCCGGACAGCAAGCGCCTCTAAGGCTTATGGGGCTCAAGgtacgaatcc ... ttgtatgcagGTCTGGCCCGTTGATATAGATATGAAGTTCCTAGAGCCATTTGGACGGGAA
EST: gi|211167599|gb|FL258648.1|FL258648
EST:     AGTGCATCGTGCCCGGACAGCAAGCGCCTCTAAGGCTTATGGGGCTCAAG                         GTCTGGCCCGTTGATATAGATATGAAGTTCCTAGATCCATTTGGACGGGAA
genomic: AGTGCATCGTGCCCGGACAGCAAGCGCCTCTAAGGCTTATGGGGCTCAAGgtacgaatcc ... ttgtatgcagGTCTGGCCCGTTGATATAGATATGAAGTTCCTAGAGCCATTTGGACGGGAA
EST: gi|211045919|gb|FK963047.1|FK963047
EST:     AGTGCATCGTGCCCGGACAGCAAGCGCCTCTAAGGCTTATGGGGCTCAAG                         GTCTGGCCCGTTGATATAGATATGAAGTTCCTAGAGCCATTTGGACGGGAA
genomic: AGTGCATCGTGCCCGGACAGCAAGCGCCTCTAAGGCTTATGGGGCTCAAGgtacgaatcc ... ttgtatgcagGTCTGGCCCGTTGATATAGATATGAAGTTCCTAGAGCCATTTGGACGGGAA
EST: gi|8401369|gb|BE057003.1|BE057003
EST:     AGTGCATCGTGCCCGGACAGCAAGCGCCTCTAAGGCTTATGGGGCTCAAG                         GTCTGGCCCGTTGATATAGATATGAAGTTCCTAGAGCCATTTGGACGGGAA
genomic: AGTGCATCGTGCCCGGACAGCAAGCGCCTCTAAGGCTTATGGGGCTCAAGgtacgaatcc ... ttgtatgcagGTCTGGCCCGTTGATATAGATATGAAGTTCCTAGAGCCATTTGGACGGGAA
EST: gi|5525193|gb|AI861191.1|AI861191
EST:     AGTGCATCGTGCCCGGACAGCAAGCGCCTCTAAGGCTTATGGGGCTCAAG                         GTCTGGCCCGTTGATATAGATATGAAGTTCCTAGAGCCATTTGGACGGGAA
genomic: AGTGCATCGTGCCCGGACAGCAAGCGCCTCTAAGGCTTATGGGGCTCAAGgtacgaatcc ... ttgtatgcagGTCTGGCCCGTTGATATAGATATGAAGTTCCTAGAGCCATTTGGACGGGAA
EST: gi|211104453|gb|FL478968.1|FL478968
EST:     AGTGCATCGTGCCCGGACAGCAAGCGCCTCTAAGGCTTATGGGGCTCAAG                         GTCTGGCCCGTTGATATAGATATGAAGTTCCTAGATCCATTTGGACGGGAA
genomic: AGTGCATCGTGCCCGGACAGCAAGCGCCTCTAAGGCTTATGGGGCTCAAGgtacgaatcc ... ttgtatgcagGTCTGGCCCGTTGATATAGATATGAAGTTCCTAGAGCCATTTGGACGGGAA
EST: gi|88755570|gb|DY539711.1|DY539711
EST:     AGTGCATCGTGCCCGGACAGCAAGCGCCTCTAAGGCTTATGGGGCTCAAG                         GTCTGGCCCGTTGATATAGATATGAAGTTCCTAGAGCCATTTGGACGGGAA
genomic: AGTGCATCGTGCCCGGACAGCAAGCGCCTCTAAGGCTTATGGGGCTCAAGgtacgaatcc ... ttgtatgcagGTCTGGCCCGTTGATATAGATATGAAGTTCCTAGAGCCATTTGGACGGGAA
EST: gi|211115674|gb|FL110115.1|FL110115
EST:     AGTGCATCGTGCCCGGACAGCAAGCGCCTCTAAGGCTTATGGGGCTCAAG                         GTCTGGCCCGTTGATATAGATATGAAGTTCCTA
genomic: AGTGCATCGTGCCCGGACAGCAAGCGCCTCTAAGGCTTATGGGGCTCAAGgtacgaatcc ... ttgtatgcagGTCTGGCCCGTTGATATAGATATGAAGTTCCTA
EST: gi|31909179|gb|CD650789.1|CD650789
EST:     AGTGCATCGTGCCCGGACAGCAAGCGCCTCTAAGGCTTATGGGGCTCAAG                         GTCTGGCCCGTTGATATAGATATGAAGTTCCTAGAGCCATTTGGACGGGAA
genomic: AGTGCATCGTGCCCGGACAGCAAGCGCCTCTAAGGCTTATGGGGCTCAAGgtacgaatcc ... ttgtatgcagGTCTGGCCCGTTGATATAGATATGAAGTTCCTAGAGCCATTTGGACGGGAA
EST: gi|211167596|gb|FL258645.1|FL258645
EST:     AGTGCATCGTGCCCGGACAGCAAGCGCCTCTAAGGCTTATGGGGCTCAAG                         GTCTGGCCCGTTGATATAGATATGAAGTTCCTAGATCCATTTGGACGGGAA
genomic: AGTGCATCGTGCCCGGACAGCAAGCGCCTCTAAGGCTTATGGGGCTCAAGgtacgaatcc ... ttgtatgcagGTCTGGCCCGTTGATATAGATATGAAGTTCCTAGAGCCATTTGGACGGGAA
EST: gi|161590278|gb|EY957950.1|EY957950
EST:     CGGACAGCAAGCGCCTCTAAGGCTTATGGGGCTCAAG                         GTCTGGCCCGTTGATATAGATATGAAGTTCCTAGAGCCATTTGGACGGGAA
genomic: CGGACAGCAAGCGCCTCTAAGGCTTATGGGGCTCAAGgtacgaatcc ... ttgtatgcagGTCTGGCCCGTTGATATAGATATGAAGTTCCTAGAGCCATTTGGACGGGAA
EST: gi|31360970|gb|CD445327.1|CD445327
EST:     AGTGCATCGTGCCCGGACAGCAAGCGCCTCTAAGGCTTATGGGGCTCAAG                         GTCTGGCCCGTTGATATAGATATGAAGTTCCTAGAGCCATTTGGACGGGAA
genomic: AGTGCATCGTGCCCGGACAGCAAGCGCCTCTAAGGCTTATGGGGCTCAAGgtacgaatcc ... ttgtatgcagGTCTGGCCCGTTGATATAGATATGAAGTTCCTAGAGCCATTTGGACGGGAA

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: 49 (upstream exon), 46 (downstream exon)
Score: 44

GATTGGCGAGGGGCTGGCTATGGAGGCGTTCGCGGAGGCAGCCGGGCCGGAGTGCATCGTGCCCGGACAGCAAGCGCCTCTAAGGCTTATGGGGCTCAAGgtacgaatcc ... ttgtatgcagGTCTGGCCCGTTGATATAGATATGAAGTTCCTAGAGCCATTTGGACGGGAACTACATTCAATGAAAAAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 431

GATTGGCGAGGGGCTGGCTATGGAGGCGTTCGCGGAGGCAGCCGGGCCGGAGTGCATCGTGCCCGGACAGCAAGCGCCTCTAAGGCTTATGGGGCTCAAGgtacgaatcc ... ttgtatgcagGTCTGGCCCGTTGATATAGATATGAAGTTCCTAGAGCCATTTGGACGGGAACTACATTCAATGAAAAAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 242

GATTGGCGAGGGGCTGGCTATGGAGGCGTTCGCGGAGGCAGCCGGGCCGGAGTGCATCGTGCCCGGACAGCAAGCGCCTCTAAGGCTTATGGGGCTCAAGgtacgaatcc ... ttgtatgcagGTCTGGCCCGTTGATATAGATATGAAGTTCCTAGAGCCATTTGGACGGGAACTACATTCAATGAAAAAA


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 167

GATTGGCGAGGGGCTGGCTATGGAGGCGTTCGCGGAGGCAGCCGGGCCGGAGTGCATCGTGCCCGGACAGCAAGCGCCTCTAAGGCTTATGGGGCTCAAGgtacgaatcc ... ttgtatgcagGTCTGGCCCGTTGATATAGATATGAAGTTCCTAGAGCCATTTGGACGGGAACTACATTCAATGAAAAAA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atgtgaattatatgatcttgtttaaaacttaacaattcttttcccttgtatgcagGTCTGGCCCGTTGATATAGATATGAAGTTCCTAGAGCCATTTGGACGGGAACTACATTCAATGAAAAAA
                          acttaac  putative branch site (score: 167)
                                   ttcttttcccttgtat  putative PPT
     aattatatgatcttgt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cattgatgattatttgataatttggccatctttggaagcaagtcaatgtgaattatatgatcttgtttaaaacttaacaattcttttcccttgtatgcagGTCTGGCCCGTTGATATAGATATGAAGTTCCTAGAGCCATTTGGACGGGAACTACATTCAATGAAAAAA

- -tgatgat
- - - - - - - - - - - - - - - - - - - - - -caatgtg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cttgttt