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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtttctgattttccttctatcttagatatttaactaatcttgtaataaacataattgttgcttgatgatgtattgatatttcctattaaaaatagctgttgaaagttgctaatcacattcacgtatatcttttcttttatgttcacttgaacagCACTGAGGCGGATAGTTATGGTCAGGCTACCTCAAACCTAGTTGCTGGCAGCAACTTGGAAGGAACAATTAAATCCATTCTTGAAATGGGTGGCGGGACA

Basic information

species Zea mays
transcript GRMZM2G061620_T02
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G061620_T05 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os09g24200.1 (Oryza sativa), 3'ss of exon 5
gtaagtttctgattttccttctatcttagatatttaactaatcttgtaataaacataattgttgcttgatgatgtattgatatttcctattaaaaatagctgttgaaagttgctaatcacattcacgtatatcttttcttttatgttcacttgaacagCACTGAGGCGGATAGTTATGGTCAGGCTACCTCAAACCTAGTTGCTGGCAGCAACTTGGAAGGAACAATTAAATCCATTCTTGAAATGGGTGGCGGGACA
|| |||| ||||| |||| || ||  || | |||| | || |||  |  | ||  || ||  ||||||| |||||  ||  |||| ||         | |  ||   | |||                  |||||||||| | ||  || |||| |||| |||| || ||||  || |||||||| ||||||||||| ||||||||||||||  | || | ||||||| |||| ||||||||||||||||| || | |
gtgagttcctgatgttccatccattctataaatttgattattctcatg-tgaatgtagtttctgcttgaggatgtgctgtaatttactga-------acccattttgacttg------------------atcttttcttct-tgc-catttgagcagCTCTGAAGCTGATAACTACGGTCAGGCCACCTCAAACCTTGTTGCTGGCAGCAATCTAGAGGCAACAATTCAATCAATTCTTGAAATGGGTGGTGGAATA
















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|211500818|gb|FL228127.1|FL228127
EST:     GCACCGGCTGCAACTGCTACAGCCTCAGCAGCTCCTGCTGTTGCTGTCTC                         CACTGAGGCGGATAGTTATGGTCAGGCTACCTC
genomic: GCACCGGCTGCAACTGCTACAGCCTCAGCAGCTCCTGCTGTTGCTGTCTCgtaagtttct ... acttgaacagCACTGAGGCGGATAGTTATGGTCAGGCTACCTC
EST: gi|76012358|gb|DT939528.1|DT939528
EST:     GCACCGGCTGCAACTGCTACAGCCTCAGCAGCTCCTGCTGTTGCTGTCTC                         CACTGAGGCGGATAGTTATGGTCAGGCTACCTCAAACCTAGTTGCTGGCAG
genomic: GCACCGGCTGCAACTGCTACAGCCTCAGCAGCTCCTGCTGTTGCTGTCTCgtaagtttct ... acttgaacagCACTGAGGCGGATAGTTATGGTCAGGCTACCTCAAACCTAGTTGCTGGCAG
EST: gi|5296098|gb|AI782973.1|AI782973
EST:     GCACCGGCTGCAACTGCTACAGCCTCAGCAGCTCCTGCTGTTGCTGTCTC                         CACTGAGGCGGATAGTTATGGTCAGGCTACCTCAAACCTAGTTGCTGGCAG
genomic: GCACCGGCTGCAACTGCTACAGCCTCAGCAGCTCCTGCTGTTGCTGTCTCgtaagtttct ... acttgaacagCACTGAGGCGGATAGTTATGGTCAGGCTACCTCAAACCTAGTTGCTGGCAG
EST: gi|7216451|gb|AW562573.1|AW562573
EST:     GCACCGGCTGCAACTGCTACAGCCTCAGCAGCTCCTGCTGTTGCTGTCTC                         CACTGAGGCGGATAGTTATGGTCAGGCTACCTCAAACCTAGTTGCTGGCAG
genomic: GCACCGGCTGCAACTGCTACAGCCTCAGCAGCTCCTGCTGTTGCTGTCTCgtaagtttct ... acttgaacagCACTGAGGCGGATAGTTATGGTCAGGCTACCTCAAACCTAGTTGCTGGCAG
EST: gi|4314922|gb|AI444722.2|AI444722
EST:     GCACCGGCTGCAACTGCTACAGCCTCAGCAGCTCCTGCTGTTGCTGTCTC                         CACTGAGGCGGATAGTTATGGTCAGGCTACCTCAAACCTAGTTGCTGGCAG
genomic: GCACCGGCTGCAACTGCTACAGCCTCAGCAGCTCCTGCTGTTGCTGTCTCgtaagtttct ... acttgaacagCACTGAGGCGGATAGTTATGGTCAGGCTACCTCAAACCTAGTTGCTGGCAG
EST: gi|211500823|gb|FL228132.1|FL228132
EST:     GCACCGGCTGCAACTGCTACAGCCTCAGCAGCTCCTGCTGTTGCTGTCTC                         CACTGAGGCGGATAGTTATGGTCAGGCTACCTCAAACCTAGTTGCTGGCAG
genomic: GCACCGGCTGCAACTGCTACAGCCTCAGCAGCTCCTGCTGTTGCTGTCTCgtaagtttct ... acttgaacagCACTGAGGCGGATAGTTATGGTCAGGCTACCTCAAACCTAGTTGCTGGCAG
EST: gi|211500820|gb|FL228129.1|FL228129
EST:     GCACCGGCWGCAACTGCTACAGCCTCAGCAGCTCCTGCTGTTGCTGTCTC                         CACTGGAGGCGGATAGT-ATGGTCAGGCTACCTCAAACCTAGT
genomic: GCACCGGCTGCAACTGCTACAGCCTCAGCAGCTCCTGCTGTTGCTGTCTCgtaagtttct ... acttgaacagCACTG-AGGCGGATAGTTATGGTCAGGCTACCTCAAACCTAGT
EST: gi|101401583|gb|EB822467.1|EB822467
EST:     GCACCGGCTGCAACTGCTACAGCCTCAGCAGCTCCTGCTGTTGCTGTCTC                         CACTGAGGCGGATAGTTATGGTCAGGCTACCTCAAACCTAGTTGCTGGCAG
genomic: GCACCGGCTGCAACTGCTACAGCCTCAGCAGCTCCTGCTGTTGCTGTCTCgtaagtttct ... acttgaacagCACTGAGGCGGATAGTTATGGTCAGGCTACCTCAAACCTAGTTGCTGGCAG
EST: gi|32915276|gb|CF020088.1|CF020088
EST:     GCACCGGCTGCAACTGCTACAGCCTCAGCAGCTCCTGCTGTTGCTGTCTC                         CACTGAGGCGGATAGTTATGGTCAGGCTACCTCAAACCTAGTTGCTGGCAG
genomic: GCACCGGCTGCAACTGCTACAGCCTCAGCAGCTCCTGCTGTTGCTGTCTCgtaagtttct ... acttgaacagCACTGAGGCGGATAGTTATGGTCAGGCTACCTCAAACCTAGTTGCTGGCAG
EST: gi|76280698|gb|DV020266.1|DV020266
EST:     GCACCGGCTGCAACTGCTACAGCCTCAGCAGCTCCTGCTGTTGCTGTCTC                         CACTGAGGCGGATAGTTATGGTCAGGCTACCTCAAACCTAGTTGCTGGCAG
genomic: GCACCGGCTGCAACTGCTACAGCCTCAGCAGCTCCTGCTGTTGCTGTCTCgtaagtttct ... acttgaacagCACTGAGGCGGATAGTTATGGTCAGGCTACCTCAAACCTAGTTGCTGGCAG
EST: gi|211500822|gb|FL228131.1|FL228131
EST:     GCACCGGCTGCAACTGCTACAGCCTCAGCAGCTCCTGCTGTTGCTGTCTC                         CACTGAGGCGGATAGTTATGGTCAGGCTACCTCAAACCTAGTTGCTGGCAG
genomic: GCACCGGCTGCAACTGCTACAGCCTCAGCAGCTCCTGCTGTTGCTGTCTCgtaagtttct ... acttgaacagCACTGAGGCGGATAGTTATGGTCAGGCTACCTCAAACCTAGTTGCTGGCAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgaaagttgctaatcacattcacgtatatcttttcttttatgttcacttgaacagCACTGAGGCGGATAGTTATGGTCAGGCTACCTCAAACCTAGTTGCTGGCAGCAACTTGGAAGGAACAATTAAATCCATTCTTGAAATGGGTGGCGGGACA
       tgctaat  putative branch site (score: 2)
                            tcttttcttttatgtt  putative PPT
                        tatatcttttctttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtttctgattttccttctatcttagatatttaactaatcttgtaataaacataattgttgcttgatgatgtattgatatttcctattaaaaatagctgttgaaagttgctaatcacattcacgtatatcttttcttttatgttcacttgaacagCACTGAGGCGGATAGTTATGGTCAGGCTACCTCAAACCTAGTTGCTGGCAGCAACTTGGAAGGAACAATTAAATCCATTCTTGAAATGGGTGGCGGGACA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA