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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gttttacatccatcaatctggataccgattatttgcctgcgcaacacatttctctcactgtaaacttattcctctcatctccttgtattgcttttgacagGGGGTTCCTGTAAGAATAGAGATAGGTCCACGTGATGTCACAAATAAGAGTGTTGTGGTTTCTAGGCGTGATGTCCCTGGAAAGCAAGGAAAGGAGTTTG

Basic information

species Zea mays
transcript GRMZM2G107089_T01
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G107089_T02 (Zea mays), 3'ss of exon 7
lower sequence: LOC_Os07g07060.1 (Oryza sativa), 3'ss of exon 6
gttttacatccatcaatctggataccgattatttgcctgcgcaacacatttctctcactgtaaacttattcctctcatctccttgtattgcttttgacagGGGGTTCCTGTAAGAATAGAGATAGGTCCACGTGATGTCACAAATAAGAGTGTTGTGGTTTCTAGGCGTGATGTCCCTGGAAAGCAAGGAAAGGAGTTTG
        |  | |    | | |  |  || | ||  |  |||      |||| ||  || |  || |  | ||| | |    | ||   ||||  |||||| |||||| ||||| |||| || ||||| |||||||||||||| || ||||||||  |||||||||| ||| |||||||||| ||||||||||||||||
-------gtatagctcatttgctctctgtt-tctgtttatgcag---gcttctttc--tgaattctgacacttct-accattgtttacaactttcaacagGGAGTTCCTATAAGACTAGAAATTGGTCCCCGTGATGTCACAAACAAAAGTGTTGTTATTTCTAGGCGAGATATCCCTGGAAAACAAGGAAAGGAGTTTG
















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|32832964|gb|CD972642.1|CD972642
EST:     ACTCAGAGCTGCGAACTCCTGGATGGAAATTCAATCACTATGAGATGAAA                         GGGGTTCCTGTAAGAATAGAGATAGGTCCACGTGATGTCACAAATAAGAGT
genomic: ACTCAGAGCTGCGAACTCCTGGATGGAAATTCAATCACTATGAGATGAAAgtaattgttt ... cttttgacagGGGGTTCCTGTAAGAATAGAGATAGGTCCACGTGATGTCACAAATAAGAGT
EST: gi|32833724|gb|CD973402.1|CD973402
EST:     ACTCAGAGCTGCGAACTCCTGGATGGAAATTCAATCACTATGAGATGAAA                         GGGGTTCCTGTAAGAATAGAGATAGGTCCACGTGATGTCACAAATAAGAGT
genomic: ACTCAGAGCTGCGAACTCCTGGATGGAAATTCAATCACTATGAGATGAAAgtaattgttt ... cttttgacagGGGGTTCCTGTAAGAATAGAGATAGGTCCACGTGATGTCACAAATAAGAGT
EST: gi|32834986|gb|CD974664.1|CD974664
EST:     ACTCAGAGCTGCGAACTCCTGGATGGAAATTCAATCACTATGAGATGAAA                         GGGGTTCCTGTAAGAATAGAGATAGGTCCACGTGATGTCACAAATAAGAGT
genomic: ACTCAGAGCTGCGAACTCCTGGATGGAAATTCAATCACTATGAGATGAAAgtaattgttt ... cttttgacagGGGGTTCCTGTAAGAATAGAGATAGGTCCACGTGATGTCACAAATAAGAGT
EST: gi|32833500|gb|CD973178.1|CD973178
EST:     ACTCAGAGCTGCGAACTCCTGGATGGAAATTCAATCACTATGAGATGAAA                         GGGGTTCCTGTAAGAATAGAGATAGGTCCACGTGATGTCACAAATAAGAGT
genomic: ACTCAGAGCTGCGAACTCCTGGATGGAAATTCAATCACTATGAGATGAAAgtaattgttt ... cttttgacagGGGGTTCCTGTAAGAATAGAGATAGGTCCACGTGATGTCACAAATAAGAGT
EST: gi|60397373|gb|DN230189.1|DN230189
EST:     ACTCAGAGCTGCGAACTCCTGGATGGAAATTCAATCACTATGAGATGAAA                         GGGGTTCCTGTAAGAATAGAGATAGGTCCACGTGATGTCACAAATAAGAGT
genomic: ACTCAGAGCTGCGAACTCCTGGATGGAAATTCAATCACTATGAGATGAAAgtaattgttt ... cttttgacagGGGGTTCCTGTAAGAATAGAGATAGGTCCACGTGATGTCACAAATAAGAGT
EST: gi|83279137|gb|DV943145.1|DV943145
EST:     ACTCAGAGCTGCGAACTCCTGGATGGAAATTCAATCACTATGAGATGAAA                         GGGGTTCCTGTAAGAATAGAGATAGGTCCACGTGATGTCACAAATAAGAGT
genomic: ACTCAGAGCTGCGAACTCCTGGATGGAAATTCAATCACTATGAGATGAAAgtaattgttt ... cttttgacagGGGGTTCCTGTAAGAATAGAGATAGGTCCACGTGATGTCACAAATAAGAGT
EST: gi|32835396|gb|CD975074.1|CD975074
EST:     ACTCAGAGCTGCGAACTCCTGGATGGAAATTCAATCACTATGAGATGAAA                         GGGGTTCCTGTAAGAATAGAGATAGGTCCACGTGATGTCACAAATAAGAGT
genomic: ACTCAGAGCTGCGAACTCCTGGATGGAAATTCAATCACTATGAGATGAAAgtaattgttt ... cttttgacagGGGGTTCCTGTAAGAATAGAGATAGGTCCACGTGATGTCACAAATAAGAGT
EST: gi|148954704|gb|EC900156.2|EC900156
EST:     ACTCAGAGCTGCGAACTCCTGGATGGAAATTCAATCACTATGAGATGAAA                         GGGGTTCCTGTAAGAATAGAGATAGGTCCACGTGATGTCACAAATAAGAGT
genomic: ACTCAGAGCTGCGAACTCCTGGATGGAAATTCAATCACTATGAGATGAAAgtaattgttt ... cttttgacagGGGGTTCCTGTAAGAATAGAGATAGGTCCACGTGATGTCACAAATAAGAGT
EST: gi|33091118|gb|CF051112.1|CF051112
EST:     ACTCAGAGCTGCGAACTCCTGGATGGAAATTCAATCGCTATGAGATGAAA                         GGGGTTCCTGTAAGAATAGAGATAGGTCCACGTGATGTCACAAATAAGAGT
genomic: ACTCAGAGCTGCGAACTCCTGGATGGAAATTCAATCACTATGAGATGAAAgtaattgttt ... cttttgacagGGGGTTCCTGTAAGAATAGAGATAGGTCCACGTGATGTCACAAATAAGAGT
EST: gi|149110508|gb|EE190454.2|EE190454
EST:     ACTCAGAGCTGCGAACTCCTGGATGGAAATTCAATCACTATGAGATGAAA                         GGGGTTCCTGTAAGAATAGAGATAGGTCCACGTGATGTCACAAATAAGAGT
genomic: ACTCAGAGCTGCGAACTCCTGGATGGAAATTCAATCACTATGAGATGAAAgtaattgttt ... cttttgacagGGGGTTCCTGTAAGAATAGAGATAGGTCCACGTGATGTCACAAATAAGAGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acatttctctcactgtaaacttattcctctcatctccttgtattgcttttgacagGGGGTTCCTGTAAGAATAGAGATAGGTCCACGTGATGTCACAAATAAGAGTGTTGTGGTTTCTAGGCGTGATGTCCCTGGAAAGCAAGGAAAGGAGTTTG
      ctctcac  putative branch site (score: 3)
                       ttcctctcatctcctt  putative PPT
               taaacttatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttttacatccatcaatctggataccgattatttgcctgcgcaacacatttctctcactgtaaacttattcctctcatctccttgtattgcttttgacagGGGGTTCCTGTAAGAATAGAGATAGGTCCACGTGATGTCACAAATAAGAGTGTTGTGGTTTCTAGGCGTGATGTCCCTGGAAAGCAAGGAAAGGAGTTTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG