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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgtttgatggaaaatttcttatgactcatcttatattcgttcttgccttcaaagttaactcctgcactgcacatgaaggcttttcgttaacttttcatgtatttttattagGTCATGTGTGCTATTATTTCGCTGGTTCTGGAGCTATATTTACAGGTGACACCTTGTTCAATCTATCATGCGGAAAGCTTTTTGAAGGGACTCCACAGCA

Basic information

species Zea mays
transcript GRMZM2G120300_T01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G120300_T01 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os09g34100.1 (Oryza sativa), 3'ss of exon 4
gtgtttgatggaaaatttcttatgactcatcttatattcgttcttgccttcaaagttaactcctgcactgcacatgaaggcttttcgttaacttttcatgtatttttattagGTCATGTGTGCTATTATTTCGCTGGTTCTGGAGCTATATTTACAGGTGACACCTTGTTCAATCTATCATGCGGAAAGCTTTTTGAAGGGACTCCACAGCA
            | ||| |   |    |||||||| ||  ||       |  | || ||  |   |  |     | ||      ||   || ||  | | || || |||||||||||||||||||  | ||| |||| |||||||| ||||||||||| ||||| ||||| | | | ||||| |||||||||||||||||||||||||| ||
----------ttatattgcgatttttgcatcttatgtttatttacaagat--atgtcaatactatctttttttttaaaaaaaaatcaccaatttcccttctacttatattagGTCATGTGTGCTACCACTTCCCTGGATCTGGAGCAATATTTACAGGGGACACATTGTTTAGTTTGTCATGTGGAAAGCTTTTTGAAGGGACTCCACAACA
















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|5325053|gb|AI783244.1|AI783244
EST:     GTTCGCTGGCCATCAAGTTCTTGTACTGGAAACTCCTGGGCATACAACAG                         GTCATGTGTGCTATTATTTCGCTGGTTCTGGAGCTATATTTACAGGTGACA
genomic: GTTCGCTGGCCATCAAGTTCTTGTACTGGAAACTCCTGGGCATACAACAGgtgtttgatg ... tttttattagGTCATGTGTGCTATTATTTCGCTGGTTCTGGAGCTATATTTACAGGTGACA
EST: gi|76286960|gb|DV026528.1|DV026528
EST:     TGGCCATCAAGTTCTTGTACTGGAAACTCCTGGGCATACAACAG                         GTCATGTGTGCTATTATTTCGCTGGTTCTGGAGCTATATTTACAGGTGACA
genomic: TGGCCATCAAGTTCTTGTACTGGAAACTCCTGGGCATACAACAGgtgtttgatg ... tttttattagGTCATGTGTGCTATTATTTCGCTGGTTCTGGAGCTATATTTACAGGTGACA
EST: gi|111991062|gb|EE331971.1|EE331971
EST:     GTTCGCTGGCCATCAAGTTCTTGTACTGGAAACTCCTGGGCATACAACAG                         GTCATGTGTGCTATTATTTCGCTGGTTCTGGAGCTATATTTACAGGTGACA
genomic: GTTCGCTGGCCATCAAGTTCTTGTACTGGAAACTCCTGGGCATACAACAGgtgtttgatg ... tttttattagGTCATGTGTGCTATTATTTCGCTGGTTCTGGAGCTATATTTACAGGTGACA
EST: gi|32925422|gb|CF030234.1|CF030234
EST:     TACTGGAAACTCCTGGGCATACAACAG                         GTCATGTGTGCTATTATTTCGCTGGTTCTGGAGCTATATTTACAGGTGATA
genomic: TACTGGAAACTCCTGGGCATACAACAGgtgtttgatg ... tttttattagGTCATGTGTGCTATTATTTCGCTGGTTCTGGAGCTATATTTACAGGTGACA
EST: gi|149112938|gb|EE295731.2|EE295731
EST:     GTTCGCTGGCCATCAAGTTCTTGTACTGGAAACTCCTGGGCATACAACAG                         GTCATGTGTGCTATTATTTCGCTGGTTCTGGAGCTATATTTA
genomic: GTTCGCTGGCCATCAAGTTCTTGTACTGGAAACTCCTGGGCATACAACAGgtgtttgatg ... tttttattagGTCATGTGTGCTATTATTTCGCTGGTTCTGGAGCTATATTTA
EST: gi|32831167|gb|CD970845.1|CD970845
EST:     ACTGGAAACTCCTGGGCATACAACAG                         GTCATGTGTGCTATTATTTCGCTGGTTCTGGAGCTATATTTACAGGTGATA
genomic: ACTGGAAACTCCTGGGCATACAACAGgtgtttgatg ... tttttattagGTCATGTGTGCTATTATTTCGCTGGTTCTGGAGCTATATTTACAGGTGACA
EST: gi|32926516|gb|CF031328.1|CF031328
EST:     TACTGGAAACTCCTGGGCATACAACAG                         GTCATGTGTGCTATTATTTCGCTGGTTCTGGAGCTATATTTACAGGTGATA
genomic: TACTGGAAACTCCTGGGCATACAACAGgtgtttgatg ... tttttattagGTCATGTGTGCTATTATTTCGCTGGTTCTGGAGCTATATTTACAGGTGACA
EST: gi|32925540|gb|CF030352.1|CF030352
EST:     ACTGGAAACTCCTGGGCATACAACAG                         GTCATGTGTGCTATTATTTCGCTGGTTCTGGAGCTATATTTACAGGTGATA
genomic: ACTGGAAACTCCTGGGCATACAACAGgtgtttgatg ... tttttattagGTCATGTGTGCTATTATTTCGCTGGTTCTGGAGCTATATTTACAGGTGACA
EST: gi|78113025|gb|DV531419.1|DV531419
EST:     GTTCGCTGGCCATCAAGTTCTTGTACTGGAAACTCCTGGGCATACAACAG                         GTCATGTGTGCTATTATTTCGCTGGTTCTGGAGCTATATTTACAGGTGACA
genomic: GTTCGCTGGCCATCAAGTTCTTGTACTGGAAACTCCTGGGCATACAACAGgtgtttgatg ... tttttattagGTCATGTGTGCTATTATTTCGCTGGTTCTGGAGCTATATTTACAGGTGACA
EST: gi|148939665|gb|EC884322.2|EC884322
EST:     GTTCGCTGGCCATCAAGTTCTTGTACTGGAAACTCCTGGGCATACAACAG                         GTCATGTGTGCTATTATTTCGCTGGTTCTGGAGCTATATTTACAGGTGACA
genomic: GTTCGCTGGCCATCAAGTTCTTGTACTGGAAACTCCTGGGCATACAACAGgtgtttgatg ... tttttattagGTCATGTGTGCTATTATTTCGCTGGTTCTGGAGCTATATTTACAGGTGACA
EST: gi|148957405|gb|EC903461.2|EC903461
EST:     GTTCGCTGGCCATCAAGTTCTTGTACTGGAAACTCCTGGGCATACAACAG                         GTCATGTGTGCTATTATTTCGCTGGTTCTGGAGCTATATTTACAGGTGACA
genomic: GTTCGCTGGCCATCAAGTTCTTGTACTGGAAACTCCTGGGCATACAACAGgtgtttgatg ... tttttattagGTCATGTGTGCTATTATTTCGCTGGTTCTGGAGCTATATTTACAGGTGACA
EST: gi|32831772|gb|CD971450.1|CD971450
EST:     ACTGGAAACTCCTGGGCATACAACAG                         GTCATGTGTGCTATTATTTCGCTGGTTCTGGAGCTATATTTACAGGTGATA
genomic: ACTGGAAACTCCTGGGCATACAACAGgtgtttgatg ... tttttattagGTCATGTGTGCTATTATTTCGCTGGTTCTGGAGCTATATTTACAGGTGACA
EST: gi|149075909|gb|EE164468.2|EE164468
EST:     GTTCGCTGGCCATCAAGTTCTTGTACTGGAAACTCCTGGGCATACAACAG                         GTCATGTGTGCTATTATTTCGCTGGTTCTGGAGCTATATTTACAGGTGACA
genomic: GTTCGCTGGCCATCAAGTTCTTGTACTGGAAACTCCTGGGCATACAACAGgtgtttgatg ... tttttattagGTCATGTGTGCTATTATTTCGCTGGTTCTGGAGCTATATTTACAGGTGACA
EST: gi|5846865|gb|AI999948.1|AI999948
EST:     GTTCGCTGGCCATCAAGTTCTTGTACTGGAAACTCCTGGGCATACAACAG                         GTCATGTGTGCTATTATTTCGCTGGTTCTGGAGCTATATTTACAGGTGACA
genomic: GTTCGCTGGCCATCAAGTTCTTGTACTGGAAACTCCTGGGCATACAACAGgtgtttgatg ... tttttattagGTCATGTGTGCTATTATTTCGCTGGTTCTGGAGCTATATTTACAGGTGACA
EST: gi|60400379|gb|DN233186.1|DN233186
EST:     GTTCGCTGGCCATCAAGTTCTTGTACTGGAAACTCCTGGGCATACAACAG                         GTCATGTGTGCTATTATTTCGCT-GTTCTGGAGCTATATTTACAGGTGACA
genomic: GTTCGCTGGCCATCAAGTTCTTGTACTGGAAACTCCTGGGCATACAACAGgtgtttgatg ... tttttattagGTCATGTGTGCTATTATTTCGCTGGTTCTGGAGCTATATTTACAGGTGACA
EST: gi|76286961|gb|DV026529.1|DV026529
EST:     GTTCGCTGGCCATCAAGTTCTTGTACTGGNAACTCCTGGGCATACAACAG                         GTCATGTGTGCTATTATTTCGCTGGTTCTGGAGCTATATTTACAGGTGACA
genomic: GTTCGCTGGCCATCAAGTTCTTGTACTGGAAACTCCTGGGCATACAACAGgtgtttgatg ... tttttattagGTCATGTGTGCTATTATTTCGCTGGTTCTGGAGCTATATTTACAGGTGACA
EST: gi|89758697|gb|DY687784.1|DY687784
EST:     GTTCGCTGGCCATCAAGTTCTTGTACTGGAAACTCCTGGGCATACAACAG                         GTCATGTGTGCTATTATTTCGCTGGTTCTGGAGCTATATTTACAGGTGACA
genomic: GTTCGCTGGCCATCAAGTTCTTGTACTGGAAACTCCTGGGCATACAACAGgtgtttgatg ... tttttattagGTCATGTGTGCTATTATTTCGCTGGTTCTGGAGCTATATTTACAGGTGACA
EST: gi|76912679|gb|DV164844.1|DV164844
EST:     GTTCGCTGGCCATCAAGTTCTTGTACTGGAAACTCCTGGGCATACTACAG                         GTCATGTGTGCTATTATTTCGCTGGTTCTGGAGCTATATTTACAGGTGACA
genomic: GTTCGCTGGCCATCAAGTTCTTGTACTGGAAACTCCTGGGCATACAACAGgtgtttgatg ... tttttattagGTCATGTGTGCTATTATTTCGCTGGTTCTGGAGCTATATTTACAGGTGACA
EST: gi|78113024|gb|DV531418.1|DV531418
EST:     GTTCGCTGGCCATCAAGTTCTTGTACTGGAAACTCCTGGGCATACAACAG                         GTCATGTGTGCTATTATTTCGCTGGTTCTGGAGCTATATTTACAGGTGACA
genomic: GTTCGCTGGCCATCAAGTTCTTGTACTGGAAACTCCTGGGCATACAACAGgtgtttgatg ... tttttattagGTCATGTGTGCTATTATTTCGCTGGTTCTGGAGCTATATTTACAGGTGACA
EST: gi|32926815|gb|CF031627.1|CF031627
EST:     TACTGGAAACTCCTGGGCATACAACAG                         GTCATGTGTGCTATTATTTCGCTGGTTCTGGAGCTATATTTACAGGTGATA
genomic: TACTGGAAACTCCTGGGCATACAACAGgtgtttgatg ... tttttattagGTCATGTGTGCTATTATTTCGCTGGTTCTGGAGCTATATTTACAGGTGACA
EST: gi|93282109|gb|EB674373.1|EB674373
EST:     GTTCGCTGGCCATCAAGTTCTTGTACTGGAAACTCCTGGGCATACAACAG                         GTCATGTGTGCTATTATTTCGCTGGTTCTGGAGCTATATTTACAGGTGACA
genomic: GTTCGCTGGCCATCAAGTTCTTGTACTGGAAACTCCTGGGCATACAACAGgtgtttgatg ... tttttattagGTCATGTGTGCTATTATTTCGCTGGTTCTGGAGCTATATTTACAGGTGACA
EST: gi|149112937|gb|EE295730.2|EE295730
EST:     GTTCTTGTACTGGAAACTCCTGGGCATACAACAG                         GTCATGTGTGCTATTATTTCGCTGGTTCTGGAGCTATATTTACAGGTGACA
genomic: GTTCTTGTACTGGAAACTCCTGGGCATACAACAGgtgtttgatg ... tttttattagGTCATGTGTGCTATTATTTCGCTGGTTCTGGAGCTATATTTACAGGTGACA
EST: gi|211480476|gb|FL101272.1|FL101272
EST:     GTTCGCTGGCCATCAAGTTCTTGTACTGGAAACTCCTGGACATACAACAG                         GTCATGTGTGCTATTATTTCGCTGGTTCTGGAGCTATATTTACAGGTGACA
genomic: GTTCGCTGGCCATCAAGTTCTTGTACTGGAAACTCCTGGGCATACAACAGgtgtttgatg ... tttttattagGTCATGTGTGCTATTATTTCGCTGGTTCTGGAGCTATATTTACAGGTGACA
EST: gi|6445407|gb|AW179475.1|AW179475
EST:     GTTCGCTGGCCATCAAGTTCTTGTACTGGAAACTCCTGTACATACAACAG                         GTCATGTGTGCTATTATTTCGCTGGTTCTGGAGCTATATTTACAGGTGACA
genomic: GTTCGCTGGCCATCAAGTTCTTGTACTGGAAACTCCTGGGCATACAACAGgtgtttgatg ... tttttattagGTCATGTGTGCTATTATTTCGCTGGTTCTGGAGCTATATTTACAGGTGACA
EST: gi|149103112|gb|EE288479.2|EE288479
EST:     GTTCGCTGGCCATCAAGTTCTTGTACTGGAAACTCCTGGGCATACAACAG                         GTCATGTGTGCTATTATTTCGCTGGTTCTGGAGCTATATTTA
genomic: GTTCGCTGGCCATCAAGTTCTTGTACTGGAAACTCCTGGGCATACAACAGgtgtttgatg ... tttttattagGTCATGTGTGCTATTATTTCGCTGGTTCTGGAGCTATATTTA
EST: gi|148947425|gb|EC892845.2|EC892845
EST:     AACTCCTGGGCATACAACAG                         GTCATGTGTGCTATTATTTCGCTGGTTCTGGAGCTATATTTACAGGTGACA
genomic: AACTCCTGGGCATACAACAGgtgtttgatg ... tttttattagGTCATGTGTGCTATTATTTCGCTGGTTCTGGAGCTATATTTACAGGTGACA
EST: gi|60352578|gb|DN219551.1|DN219551
EST:     GTTCGCTGGCCATCAAGTTCTTGTACTGGAAACTCCTGGGCATACAACAG                         GTCATGTGTGCTATTATTTCGCTGGTTCTGGAGCTATATTTACAGGTGACA
genomic: GTTCGCTGGCCATCAAGTTCTTGTACTGGAAACTCCTGGGCATACAACAGgtgtttgatg ... tttttattagGTCATGTGTGCTATTATTTCGCTGGTTCTGGAGCTATATTTACAGGTGACA
EST: gi|149026716|gb|EE046118.2|EE046118
EST:     GTTCGCTGGCCATCAAGTTCTTGTACTGGAAACTCCTGGGCATACAACAG                         GTCATGTGTGCTATTATTTCGCTGGTTCTGGAGCTATATTTACAGGTGACA
genomic: GTTCGCTGGCCATCAAGTTCTTGTACTGGAAACTCCTGGGCATACAACAGgtgtttgatg ... tttttattagGTCATGTGTGCTATTATTTCGCTGGTTCTGGAGCTATATTTACAGGTGACA
EST: gi|91048227|gb|EB158645.1|EB158645
EST:     GTTCGCTGGCCATCAAGTTCTTGTACTGGAAACTCCTGGGCATACAACAG                         GTCATGTGTGCTATTATTTCGCTGGTTCTGGAGCTATATTTACAGGTGACA
genomic: GTTCGCTGGCCATCAAGTTCTTGTACTGGAAACTCCTGGGCATACAACAGgtgtttgatg ... tttttattagGTCATGTGTGCTATTATTTCGCTGGTTCTGGAGCTATATTTACAGGTGACA
EST: gi|67017612|gb|CO446361.1|CO446361
EST:     GTTCGCTGGCCATCAAGTTCTTGTACTGGAAACTCCTGGGCATACAACAG                         GTCATGTGTGCTATTATTTCGCTGGTTCTGGAGCTATATTTACAGGTGACA
genomic: GTTCGCTGGCCATCAAGTTCTTGTACTGGAAACTCCTGGGCATACAACAGgtgtttgatg ... tttttattagGTCATGTGTGCTATTATTTCGCTGGTTCTGGAGCTATATTTACAGGTGACA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aactcctgcactgcacatgaaggcttttcgttaacttttcatgtatttttattagGTCATGTGTGCTATTATTTCGCTGGTTCTGGAGCTATATTTACAGGTGACACCTTGTTCAATCTATCATGCGGAAAGCTTTTTGAAGGGACTCCACAGCA
                            cgttaac  putative branch site (score: 3)
                                             tttttatt  putative PPT
                              ttaacttttcatgtat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgtttgatggaaaatttcttatgactcatcttatattcgttcttgccttcaaagttaactcctgcactgcacatgaaggcttttcgttaacttttcatgtatttttattagGTCATGTGTGCTATTATTTCGCTGGTTCTGGAGCTATATTTACAGGTGACACCTTGTTCAATCTATCATGCGGAAAGCTTTTTGAAGGGACTCCACAGCA

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