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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaacgtgtttcttctgccaatttgcccatgcactattctattctacattgagcttaccgatcagacttttgacagGCACTTATCCAGTATACTGATGCCCCAACTGCTCTTGAAGCTAAAAACTCATTGGATGGAAGAAGCATCCCAAA

Basic information

species Zea mays
transcript GRMZM2G082174_T05
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G082174_T05 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os08g33830.2 (Oryza sativa), 3'ss of exon 3
gtaacgtgtttcttctgccaatttgcccatgcactattctattctacattgagcttaccgatcagacttttgacagGCACTTATCCAGTATACTGATGCCCCAACTGCTCTTGAAGCTAAAAACTCATTGGATGGAAGAAGCATCCCAAA
||||  |  ||||| |    |  |||   |  |  |||||  | ||  || |||||| |     || ||||   ||||||||||||| ||||||||||| |||||||| || ||||| ||||| || |||||||||||||||||||| | 
gtaagatagttcttatattgagctgctactata--attct--tgtaagttcagcttatcagctggaattttcgtagGCACTTATCCAATATACTGATGCTCCAACTGCACTAGAAGCAAAAAATTCGTTGGATGGAAGAAGCATCCCGAG
















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|60401250|gb|DN234057.1|DN234057
EST:     TTGGGTTTGTTCACAAGATAGCTACTTTTGAGAAAGCAGCTGGTTTCCAG                         GCACTTATCCAGTATACTGATGCCCCAACTGCTCTTGAAGCTAAAAACTCA
genomic: TTGGGTTTGTTCACAAGATAGCTACTTTTGAGAAAGCAGCTGGTTTCCAGgtaacgtgtt ... cttttgacagGCACTTATCCAGTATACTGATGCCCCAACTGCTCTTGAAGCTAAAAACTCA
EST: gi|76922866|gb|DV169212.1|DV169212
EST:     TTGGGTTTGTTCACAAGATAGCTACTTTTGAGAAAGCAGCTGGTTTCCAG                         GCACTTATCCAGTATACTGATGCCCCAACTGCTCTTGAAGCTAAAAACTCA
genomic: TTGGGTTTGTTCACAAGATAGCTACTTTTGAGAAAGCAGCTGGTTTCCAGgtaacgtgtt ... cttttgacagGCACTTATCCAGTATACTGATGCCCCAACTGCTCTTGAAGCTAAAAACTCA
EST: gi|148949666|gb|EC895139.2|EC895139
EST:     TTGGGTTTGTTCACAAGATAGCTACTTTTGAGAAAGCAGCTGGTTTCCAG                         GCACTTATCCAGTATACTGATGCCCCAACTGCTCTTGAAGCTAAAAACTCA
genomic: TTGGGTTTGTTCACAAGATAGCTACTTTTGAGAAAGCAGCTGGTTTCCAGgtaacgtgtt ... cttttgacagGCACTTATCCAGTATACTGATGCCCCAACTGCTCTTGAAGCTAAAAACTCA
EST: gi|148967274|gb|EE018478.2|EE018478
EST:     TTGGGTTTGTTCACAAGATAGCTACTTTTGAGAAAGCAGCTGGTTTCCAG                         GCACTTATCCAGTATACTGATGCCCCAACTGCTCTTGAAGCTAAAAACTCA
genomic: TTGGGTTTGTTCACAAGATAGCTACTTTTGAGAAAGCAGCTGGTTTCCAGgtaacgtgtt ... cttttgacagGCACTTATCCAGTATACTGATGCCCCAACTGCTCTTGAAGCTAAAAACTCA
EST: gi|148942887|gb|EC887930.2|EC887930
EST:     TTGGGTTTGTTCACAAGATAGCTACTTTTGAGAAAGCAGCTGGTTTCCAG                         GCACTTATCCAGTATACTGATGCCCCAACTGCTCTTGAAGCTAAAAACTCA
genomic: TTGGGTTTGTTCACAAGATAGCTACTTTTGAGAAAGCAGCTGGTTTCCAGgtaacgtgtt ... cttttgacagGCACTTATCCAGTATACTGATGCCCCAACTGCTCTTGAAGCTAAAAACTCA
EST: gi|149098038|gb|EE183986.2|EE183986
EST:     TTGGGTTTGTTCACAAGATAGCTACTTTTGAGAAAGCAGCTGGTTTCCAG                         GCACTTATCCAGTATACTGATGCCCCAACTGCTCTTGAAGCTAAAAACTCA
genomic: TTGGGTTTGTTCACAAGATAGCTACTTTTGAGAAAGCAGCTGGTTTCCAGgtaacgtgtt ... cttttgacagGCACTTATCCAGTATACTGATGCCCCAACTGCTCTTGAAGCTAAAAACTCA
EST: gi|148944648|gb|EC889782.2|EC889782
EST:     TTGGGTTTGTTCACAAGATAGCTACTTTTGAGAAAGCAGCTGGTTTCCAG                         GCACTTATCCAGTATACTGATGCCCCAACTGCTCTTGAAGCTAAAAACTCA
genomic: TTGGGTTTGTTCACAAGATAGCTACTTTTGAGAAAGCAGCTGGTTTCCAGgtaacgtgtt ... cttttgacagGCACTTATCCAGTATACTGATGCCCCAACTGCTCTTGAAGCTAAAAACTCA
EST: gi|211283597|gb|FL006180.1|FL006180
EST:     TTGGGTTTGTTCACAAGATAGCTACTTTTGAGAAAGCAGCTGGTTTCCAG                         GCACTTATCCAGTATACTGATGCCCCA
genomic: TTGGGTTTGTTCACAAGATAGCTACTTTTGAGAAAGCAGCTGGTTTCCAGgtaacgtgtt ... cttttgacagGCACTTATCCAGTATACTGATGCCCCA
EST: gi|148982096|gb|EE028144.2|EE028144
EST:     TTGGGTTTGTTCACAAGATAGCTACTTTTGAGAAAGCAGCTGGTTTCCAG                         GCACTTATCCAGTATACTGATGCCCCAACTGCTCTTGAAGCTAAAAACTCA
genomic: TTGGGTTTGTTCACAAGATAGCTACTTTTGAGAAAGCAGCTGGTTTCCAGgtaacgtgtt ... cttttgacagGCACTTATCCAGTATACTGATGCCCCAACTGCTCTTGAAGCTAAAAACTCA
EST: gi|211285401|gb|FL006189.1|FL006189
EST:     TTGGGTTTGTTCACAAGATAGCTACTTTTGAGAAAGCAGCTGGTTTCCAG                         GCACTTATCCAGTATACTGATGCCCCAACTGCTCTTGAAGCTAAAAACTC
genomic: TTGGGTTTGTTCACAAGATAGCTACTTTTGAGAAAGCAGCTGGTTTCCAGgtaacgtgtt ... cttttgacagGCACTTATCCAGTATACTGATGCCCCAACTGCTCTTGAAGCTAAAAACTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttgcccatgcactattctattctacattgagcttaccgatcagacttttgacagGCACTTATCCAGTATACTGATGCCCCAACTGCTCTTGAAGCTAAAAACTCATTGGATGGAAGAAGCATCCCAAA
                              agcttac  putative branch site (score: 3)
                                             ctttt  putative PPT
             tattctatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaacgtgtttcttctgccaatttgcccatgcactattctattctacattgagcttaccgatcagacttttgacagGCACTTATCCAGTATACTGATGCCCCAACTGCTCTTGAAGCTAAAAACTCATTGGATGGAAGAAGCATCCCAAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC