Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aaattacctccttatttcagacaattcgatttcctgcgcagtattcttatttgtctggagcattcttctaattatctggagctatatgctctgtttacagGACGATGGTTATATTCCCAGACATTCAGTGATGGAGCTCCAGAAGGCATGGCCAGGCTCAGAGGTCCGGTGGGTAACAGGTGGCCATGTCTCCTCTTTCT

Basic information

species Zea mays
transcript GRMZM2G331374_T01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G331374_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os02g10160.1 (Oryza sativa), 3'ss of exon 5
aaattacctccttatttcagacaattcgatttcctgcgcagtattcttatttgtctggagcattcttctaa---ttatctggagc---tatatgctctgtttacagGACGATGGTTATATTCCCAGACATTCAGTGATGGAGCTCCAGAAGGCATGGCCAGGCTCAGAGGTCCGGTGGGTAACAGGTGGCCATGTCTCCTCTTTCT
       || |||| ||| |    |||   |  |       | || |  ||    |  |  |||      |   |  |||| |||   | |   || | ||| ||||| || || || || |||| ||||||  | ||||||||||| |||||||||||||| |||||||||||||||||||| || || || || || || || |
------tctgcttaattctgtactttcagatatcaatatgcttttttcgttatcatataatatttaatggagcttggtctgaagcaaatgttctctttattttcagGATGACGGCTACATCCCCAAACATTCGATAATGGAGCTCCAAAAGGCATGGCCAGGTTCAGAGGTCCGGTGGGTAACCGGAGGGCACGTATCGTCGTTTT

upper sequence: GRMZM2G331374_T01 (Zea mays), 3'ss of exon 2
lower sequence: PP1S376_2V6.1 (Physcomitrella patens), 3'ss of exon 5
--aaattacctcct-tatttcagacaattcgatttcctgcgc--------agtattcttatttgtctggagcatt--cttctaattatctggagctatatgct-------ctgtttacagGACGATGGTTATATTCCCAGACATTCAGTGATGGAGCTCCAGAAGGCATGGCCAGGCTCAGAGGTCCGGTGGGTAACAGGTGGCCATGTCTCCTCTTTCT
  |||||  ||  | |  |     |||||   |  ||| |||          ||||||| |    | |   || |  |  |||||    |  |  ||||  ||          | | ||||| ||||| ||| | ||    || || ||| || |  | ||| |||| |||||||| ||||| ||  ||||||||| |||||||||||||||||| ||| 
gtaaattctcttgtctgctcttatcaattttgtacccttcgcctctttgagatattcttttcctccagttccactaccacctaatccgtttaatttataccctggcttgctaatcttcagGATGATGGATATGTGCCGGACCACTCGGTGCTGAAATTACAGCAGGCTTGGCCAGGGTCAGAAGTTAGGTGGGTAAGAGGTGGCCATGTCTCCTCCTTCA
















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|5325141|gb|AI783332.1|AI783332
EST:     GATTTCCAGTCCCAAAGAACCCACAGGCGGTCATCTTTGTTGGTGCAACG                         GACGATGGTTATATTCCCAGACATTCAGTGATGGAGCTCCAGAAGGCATGG
genomic: GATTTCCAGTCCCAAAGAACCCACAGGCGGTCATCTTTGTTGGTGCAACGgttagtgatg ... ctgtttacagGACGATGGTTATATTCCCAGACATTCAGTGATGGAGCTCCAGAAGGCATGG
EST: gi|24765478|gb|CA400637.1|CA400637
EST:     GATTTCCAGTCCCAAAGAACCCACAGGCGGTCATTTTTGTTGGTGCAACG                         GACGATGGTTATATTCCCAGACATTCAGTGATGGAGCTCCAGAAGGCATGG
genomic: GATTTCCAGTCCCAAAGAACCCACAGGCGGTCATCTTTGTTGGTGCAACGgttagtgatg ... ctgtttacagGACGATGGTTATATTCCCAGACATTCAGTGATGGAGCTCCAGAAGGCATGG
EST: gi|211411443|gb|FL197908.1|FL197908
EST:     TCCCAAAGAACCCACAGGCGGTCATCTTTCTTTGTGCAACG                         GACGATGGTTATATTCCCAGACATTCAGTGATGGAGCTCCAGAAGGCATGG
genomic: TCCCAAAGAACCCACAGGCGGTCATCTTTGTTGGTGCAACGgttagtgatg ... ctgtttacagGACGATGGTTATATTCCCAGACATTCAGTGATGGAGCTCCAGAAGGCATGG
EST: gi|32907912|gb|CF012725.1|CF012725
EST:     GATTTCCAGTCCCAAAGAACCCACAGGCGGTCATCTTTGTTGGTGCAACG                         GACGATGGTTATATTCCCAGACATTCAGTGATGGAGCTCCAGAAGGCATGG
genomic: GATTTCCAGTCCCAAAGAACCCACAGGCGGTCATCTTTGTTGGTGCAACGgttagtgatg ... ctgtttacagGACGATGGTTATATTCCCAGACATTCAGTGATGGAGCTCCAGAAGGCATGG
EST: gi|71764524|gb|DR962461.1|DR962461
EST:     GATTTCCAGTCCCAAAGAACCCACAGGCGGTCATCTTTGTTGGTGCAACG                         GACGATGGTTATATTCCCAGACATTCAGTGATGGAGCTCCAGAAGGCATGG
genomic: GATTTCCAGTCCCAAAGAACCCACAGGCGGTCATCTTTGTTGGTGCAACGgttagtgatg ... ctgtttacagGACGATGGTTATATTCCCAGACATTCAGTGATGGAGCTCCAGAAGGCATGG
EST: gi|31909965|gb|CD651184.1|CD651184
EST:     GATTTCCAGTCCCAAAGAACCCACAGGCGGTCATCTTTGTTGGTGCAACG                         GACGATGGTTATATTCCCAGACATTCAGTGATGGAGCTCCAGAAGGCATGG
genomic: GATTTCCAGTCCCAAAGAACCCACAGGCGGTCATCTTTGTTGGTGCAACGgttagtgatg ... ctgtttacagGACGATGGTTATATTCCCAGACATTCAGTGATGGAGCTCCAGAAGGCATGG
EST: gi|211532436|gb|FL471828.1|FL471828
EST:     GATTTCCAGTCCCAAAGAACCCACAGGCGGTCATCTTTGTTGGTGCAACG                         GACGATGGTTATATTCCCAGACATTCAGTGATGGAGCTCCAGAAGGCATGG
genomic: GATTTCCAGTCCCAAAGAACCCACAGGCGGTCATCTTTGTTGGTGCAACGgttagtgatg ... ctgtttacagGACGATGGTTATATTCCCAGACATTCAGTGATGGAGCTCCAGAAGGCATGG
EST: gi|24768193|gb|CA403322.1|CA403322
EST:     GATTTCCAGTCCCAAAGAACCCACAGGCGGTCATCTTTGTTGGTGCAACG                         GACGATGGTTATATTCCCAGACATTCAGTGATGGAGCTCCAGAAGGCATGG
genomic: GATTTCCAGTCCCAAAGAACCCACAGGCGGTCATCTTTGTTGGTGCAACGgttagtgatg ... ctgtttacagGACGATGGTTATATTCCCAGACATTCAGTGATGGAGCTCCAGAAGGCATGG
EST: gi|24768628|gb|CA403757.1|CA403757
EST:     GATTTCCAGTCCCAAAGAACCCACAGGCGGTCATCTTTGTTGGTGCAACG                         GACGATGGTTATATTCCCAGACATTCAGTGATGGAGCTCCAGAAGGCATGG
genomic: GATTTCCAGTCCCAAAGAACCCACAGGCGGTCATCTTTGTTGGTGCAACGgttagtgatg ... ctgtttacagGACGATGGTTATATTCCCAGACATTCAGTGATGGAGCTCCAGAAGGCATGG
EST: gi|108953195|gb|EC364631.1|EC364631
EST:     GATTTCCAGTCCCAAAGAACCCACAGGCGGTCATCTTTGTTGGTGCAACG                         GACGATGGTTATATTCCCAGACATTCAGTGATGGAGCTCCAGAAGGCATGG
genomic: GATTTCCAGTCCCAAAGAACCCACAGGCGGTCATCTTTGTTGGTGCAACGgttagtgatg ... ctgtttacagGACGATGGTTATATTCCCAGACATTCAGTGATGGAGCTCCAGAAGGCATGG
EST: gi|76011385|gb|DT938555.1|DT938555
EST:     GATTTCCAGTCCCAAAGAACCCACAGGCGGTCATCTTTGTTGGTGCAACG                         GACGATGGTTATATTCCCAGACATTCAGTGATGGAGCTCCAGAAGGCATGG
genomic: GATTTCCAGTCCCAAAGAACCCACAGGCGGTCATCTTTGTTGGTGCAACGgttagtgatg ... ctgtttacagGACGATGGTTATATTCCCAGACATTCAGTGATGGAGCTCCAGAAGGCATGG
EST: gi|111193190|gb|EE291326.1|EE291326
EST:     GATTTCCAGTCCCAAAGAACCCACAGGCGGTCATCTTTGTTGGTGCAACG                         GACGATGGTTATATTCCCAGACATTCAGTGATGGAGCTCCAGAAGGCATGG
genomic: GATTTCCAGTCCCAAAGAACCCACAGGCGGTCATCTTTGTTGGTGCAACGgttagtgatg ... ctgtttacagGACGATGGTTATATTCCCAGACATTCAGTGATGGAGCTCCAGAAGGCATGG
EST: gi|4298693|gb|AI438798.1|AI438798
EST:     GATTTCCAGTCCCAAAGAACCCACAGGCGGTCATCTTTGTTGGTGCAACG                         GACGATGGTTATATTCCCAGACATTCAGTGATGGAGCTCCAGAAGGCATGG
genomic: GATTTCCAGTCCCAAAGAACCCACAGGCGGTCATCTTTGTTGGTGCAACGgttagtgatg ... ctgtttacagGACGATGGTTATATTCCCAGACATTCAGTGATGGAGCTCCAGAAGGCATGG
EST: gi|76292451|gb|DV032019.1|DV032019
EST:     GATTTCCAGTCCCAAAGAACCCACAGGCGGTCATCTTTGTTGGTGCAACG                         GACGATGGTTATATTCCCAGACATTCAGTGATGGAGCTCCAGAAGGCATGG
genomic: GATTTCCAGTCCCAAAGAACCCACAGGCGGTCATCTTTGTTGGTGCAACGgttagtgatg ... ctgtttacagGACGATGGTTATATTCCCAGACATTCAGTGATGGAGCTCCAGAAGGCATGG
EST: gi|29544684|gb|CB605064.1|CB605064
EST:     GATTTCCAGTCCCAAAGAACCCACAGGCGGTCATCTTTGTTGGTGCAACG                         GACGATNGGTTATATTCCCAGGACATTCAGTGATGGAGCTCCAGAAGGCAT
genomic: GATTTCCAGTCCCAAAGAACCCACAGGCGGTCATCTTTGTTGGTGCAACGgttagtgatg ... ctgtttacagGACGAT-GGTTATATTCCCA-GACATTCAGTGATGGAGCTCCAGAAGGCAT
EST: gi|24769949|gb|CA405078.1|CA405078
EST:     GATTTCCAGTCCCAAAGAACCCACAGGCGGTCATCTTTGTTGGTGCAACG                         GACGATGGTTATATTCCCAGACATTCAGTGATGGAGCTCCAGAAGGCATGG
genomic: GATTTCCAGTCCCAAAGAACCCACAGGCGGTCATCTTTGTTGGTGCAACGgttagtgatg ... ctgtttacagGACGATGGTTATATTCCCAGACATTCAGTGATGGAGCTCCAGAAGGCATGG
EST: gi|78083285|gb|DV511678.1|DV511678
EST:     GATTTCCAGTCCCAAAGAACCCACAGGCGGTCATCTTTGTTGGTGCAACG                         GACGATGGTTATATTCCCAGACATTCAGTGATGGAGCTCCAGAAGGCATGG
genomic: GATTTCCAGTCCCAAAGAACCCACAGGCGGTCATCTTTGTTGGTGCAACGgttagtgatg ... ctgtttacagGACGATGGTTATATTCCCAGACATTCAGTGATGGAGCTCCAGAAGGCATGG
EST: gi|32943520|gb|CF048339.1|CF048339
EST:     GATTTCCAGTCCCAAAGAACCCACAGGCGGTCATCTTTGTTGGTGCAACG                         GACGATGGTTATATTCCCAGACATTCAGTGATGGGGCTCCAGAAGGCATGG
genomic: GATTTCCAGTCCCAAAGAACCCACAGGCGGTCATCTTTGTTGGTGCAACGgttagtgatg ... ctgtttacagGACGATGGTTATATTCCCAGACATTCAGTGATGGAGCTCCAGAAGGCATGG
EST: gi|78106399|gb|DV524817.1|DV524817
EST:     GATTTCCAGTCCCAAAGAACCCACAGGCGGTCATCTTTGTTGGTGCAACG                         GACGATGGTTATATTCCCAGACATTCAGTGATGGAGCTCCAGAAGGCATGG
genomic: GATTTCCAGTCCCAAAGAACCCACAGGCGGTCATCTTTGTTGGTGCAACGgttagtgatg ... ctgtttacagGACGATGGTTATATTCCCAGACATTCAGTGATGGAGCTCCAGAAGGCATGG
EST: gi|33096590|gb|CF056584.1|CF056584
EST:     GATTTCCAGTCCCAAAGAACCCACAGGCGGTCATCTTTGTTGGTGCAACG                         GACGATGGTTATATTCCCAGACATTCAGTGATGGAGCTCCAGAAGGCATGG
genomic: GATTTCCAGTCCCAAAGAACCCACAGGCGGTCATCTTTGTTGGTGCAACGgttagtgatg ... ctgtttacagGACGATGGTTATATTCCCAGACATTCAGTGATGGAGCTCCAGAAGGCATGG
EST: gi|211119586|gb|FL439090.1|FL439090
EST:     GATTTCCAGTCCCAAAGAACCCACAGGCGGTCATCTTTGTTGGTGCAACG                         GACGATGGTTATATTCCCAGACATTCAGTGATGGAGCTCCAGAAGGCATGG
genomic: GATTTCCAGTCCCAAAGAACCCACAGGCGGTCATCTTTGTTGGTGCAACGgttagtgatg ... ctgtttacagGACGATGGTTATATTCCCAGACATTCAGTGATGGAGCTCCAGAAGGCATGG
EST: gi|5847236|gb|AW000315.1|AW000315
EST:     GATTTCCAGTCCCAAAGAACCCACAGGCGGTCATCTTTGTTGGTGCAACG                         GACGATGGTTATATTCCCAGACATTCAGTGATGGAGCTCCAGAAGGCATGG
genomic: GATTTCCAGTCCCAAAGAACCCACAGGCGGTCATCTTTGTTGGTGCAACGgttagtgatg ... ctgtttacagGACGATGGTTATATTCCCAGACATTCAGTGATGGAGCTCCAGAAGGCATGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttatttgtctggagcattcttctaattatctggagctatatgctctgtttacagGACGATGGTTATATTCCCAGACATTCAGTGATGGAGCTCCAGAAGGCATGGCCAGGCTCAGAGGTCCGGTGGGTAACAGGTGGCCATGTCTCCTCTTTCT
                    ttctaat  putative branch site (score: 2)
                                           ctctgttt  putative PPT
                attcttctaattat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aaattacctccttatttcagacaattcgatttcctgcgcagtattcttatttgtctggagcattcttctaattatctggagctatatgctctgtttacagGACGATGGTTATATTCCCAGACATTCAGTGATGGAGCTCCAGAAGGCATGGCCAGGCTCAGAGGTCCGGTGGGTAACAGGTGGCCATGTCTCCTCTTTCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTCCTC
- - - - - - - - - - - - - - - ttcctgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - ctggagc