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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtactagcataattctatgcatatataccgatctcttgtttaaggttggttaactgtatcttttgtgagtttgtctacactctacagGCAAACCCAGAAATTGTGAAAAGATGGAGCAACGAAGTTCAGGAAGCTGTGCAATCAAGAGCTCCACTTGTCCAGTTTCATGGCCTTGCTCTTCTTCACC

Basic information

species Zea mays
transcript GRMZM2G012501_T01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G012501_T03 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os03g12590.1 (Oryza sativa), 3'ss of exon 5
--gtactagcataattctatgc--atatataccgatctcttgtttaaggttggttaactgtatcttttgtgagtttgtctacactctacagGCAAACCCAGAAATTGTGAAAAGATGGAGCAACGAAGTTCAGGAAGCTGTGCAATCAAGAGCTCCACTTGTCCAGTTTCATGGCCTTGCTCTTCTTCACC
    |||   ||| |||||| |  | | | ||  |  |||| |   | ||     |||||||  | || |                | |||||||| |||||||| ||||||||||||||||||||||| ||||||||||| |||||||||  | ||||||| || ||||||||||| |||||||||||||
gtacacttctatagttctatacgaaaaaaaacataattcttttcggaagtcaaa-aactgtacttattata---------------tgcagGCAAATCCAGAAATCGTGAAAAGATGGAGCAACGAAGTGCAGGAAGCTGTTCAATCAAGATTTGCACTTGTGCAATTTCATGGCCTAGCTCTTCTTCACC

upper sequence: GRMZM2G012501_T03 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA06G01520.1 (Glycine max), 3'ss of exon 5
gtactagcataattctatgcatatataccgatctcttgtttaaggttggttaactgtatcttttgtgagtttgtctacactctacagGCAAACCCAGAAATTGTGAAAAGATGGAGCAACGAAGTTCAGGAAGCTGTGCAATCAAGAGCTCCACTTGTCCAGTTTCATGGCCTTGCTCTTCTTCACC
            |  ||  ||||  ||     || ||||      ||   || |   || ||     |   |   | |    ||||| | || || |||||||| |||||||||||||| ||||||||||||||||| |||||||||||  | ||||| || |||||||  || | | | || || |
-----------gtaatagtcatac-taatttccttttgtaattctttatatatcctcatattcatctatgcttcttgcttattacagACGAATCCTGAAATTGTAAAAAGATGGAGCAATGAAGTTCAGGAAGCTGTTCAATCAAGAGCAGCCCTTGTACAATTTCATGCACTGGGTTTGCTACATC

upper sequence: GRMZM2G012501_T03 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA12G04820.1 (Glycine max), 3'ss of exon 5
gtactagcataattctatgcatatataccgatctcttgtttaaggttggttaactgtatcttttgtgagtttgtctacactctacagGCAAACCCAGAAATTGTGAAAAGATGGAGCAACGAAGTTCAGGAAGCTGTGCAATCAAGAGCTCCACTTGTCCAGTTTCATGGCCTTGCTCTTCTTCACC
||| || || || |||||   ||  | |  ||||| | ||  |  |  |||  |||  | |||| ||      ||  | ||   ||| |||| || || ||||| ||||||||||| || || |||||||||||||| |||||||| ||  | ||||| || ||||||| ||| ||| | || || |
gtattaaca-aaatctatttgtaattccttatctcatattccatatgtgttgcctgcttattttatg------tccccccttatcagACAAATCCCGAGATTGTAAAAAGATGGAGTAATGAGGTTCAGGAAGCTGTTCAATCAAGGGCAGCTCTTGTGCAATTTCATGCCCTGGCTTTGCTGCATC

upper sequence: GRMZM2G012501_T03 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA04G01470.1 (Glycine max), 3'ss of exon 5
gtactagcataattctatgcatatataccgatctcttgtttaaggttggtta-actgtatcttttgtgagtttgtctacactctacagGCAAACCCAGAAATTGTGAAAAGATGGAGCAACGAAGTTCAGGAAGCTGTGCAATCAAGAGCTCCACTTGTCCAGTTTCATGGCCTTGCTCTTCTTCACC
               ||   |   ||||  || || | ||  |   ||  || |   |    ||  | |   ||  | |    ||||| |||| || |||||||| |||||||||||||| || |||||||||||||| |||||||||||  | ||||| || |||||||  || | | | || || |
--------------gta-atagtcatactaatttccttttgtaatctgtatatatcctcatattcattacgctgattgcttattacagACAAATCCTGAAATTGTAAAAAGATGGAGCAATGAGGTTCAGGAAGCTGTTCAATCAAGAGCAGCCCTTGTACAATTTCATGCACTGGGTTTGCTGCATC

upper sequence: GRMZM2G012501_T03 (Zea mays), 3'ss of exon 4
lower sequence: AT4G34450.1 (Arabidopsis thaliana), 3'ss of exon 4
gtactagcataattctatgcatatataccgatctcttgtttaaggttggttaactgtatcttttgtgagtttgtctacactctacagGCAAACCCAGAAATTGTGAAAAGATGGAGCAACGAAGTTCAGGAAGCTGTGCAATCAAGAGCTCCACTTGTCCAGTTTCATGGCCTTGCTCTTCTTCACC
      | |   || ||  ||   | ||   |   | | ||     | || |  |    ||| | |  || | | | |  | | ||| |||||||||||||||| |||||||||||||| |||||||| |||| | | ||||| ||| |  | ||||| ||||| |||| ||| ||| | || || |
------gtacc-ttttacacaccaaaactattaggtagcttcttaattgtaatgttatgcttatattcgtatat-tgctgttttcagACAAACCCAGAAATTGTTAAAAGATGGAGCAATGAAGTTCAAGAAGGTATTCAATCCAGATCAGCCCTTGTTCAGTTCCATGCCCTAGCTTTGCTCCATC

upper sequence: GRMZM2G012501_T03 (Zea mays), 3'ss of exon 4
lower sequence: Vv03s0063g02450.t01 (Vitis vinifera), 3'ss of exon 5
gtactagcataat-tctatgcatatataccgatct-cttgttta---aggttggttaactgtatcttttgtgagtttgtctacactct------acagGCAAACCCAGAAATTGTGAAAAGATGGAGCAACGAAGTTCAGGAAGCTGTGCAATCAAGAGCTCCACTTGTCCAGTTTCATGGCCTTGCTCTTCTTCACC
|||| |      | | | |  || | |     |||  || | ||   |  ||       |  ||  | |   | | ||  ||   | |      | || |||||||||| || |||| ||| ||||| || ||||| ||||||||||| |||||||| ||  ||||||| || ||||||| ||| ||||| || || |
gtacaattgggttgtgtgtagattttttttattctatttatatatttaaattatcctcttacatgctctaataatatgattattatttttttggatagACAAACCCAGAGATAGTGAGAAGGTGGAGTAATGAAGTACAGGAAGCTGTTCAATCAAGGGCAGCACTTGTGCAATTTCATGCCCTAGCTCTCCTGCATC

upper sequence: GRMZM2G012501_T03 (Zea mays), 3'ss of exon 4
lower sequence: PP1S276_96V6.1 (Physcomitrella patens), 3'ss of exon 5
-----gtactagcataattctatgcat-atataccgatctcttgtttaaggttg-gttaactg--tatcttttgtgagttt---gtctaca-ctctacagGCAAACCCAGAAATTGTGAAAAGATGGAGCAACGAAGTTCAGGAAGCTGTGCAATCAAGAGCTCCACTTGTCCAGTTTCATGGCCTTGCTCTTCTTCACC
     ||  |    |  || ||  | | || ||   | |   || | ||  ||  | |||| |  | |||||||    |||    |||  |  | |  ||   ||||| |||||||||||  | |||||||| ||||||||||||||||| || || | ||| || || || ||||| || ||  | ||  | ||||| |
cgaatgtttttctgttcttttaaacgttatttaaacaacaaatgatgaattttctgataacagcttctcttttgctcattttaaatctgtaattttgtagAGCAACCCCGAAATTGTGAAGCGCTGGAGCAATGAAGTTCAGGAAGCTGTCCAGTCTAAAGCACCTCTCGTTCAGTTCCACGGTTTGGCATTGCTTCATC

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|211106006|gb|FK992441.1|FK992441
EST:     ACCCAGTGGTTGCTAGTGCTTCTCTTGTTAGTGGCATCCACCTGGCCCAG                         GCAAACCCAGAAATTGTGAAAAGATGGAGCAACGAAGTTCAGGAAGCTGTG
genomic: ACCCAGTGGTTGCTAGTGCTTCTCTTGTTAGTGGCATCCACCTGGCCCAGgtactagcat ... cactctacagGCAAACCCAGAAATTGTGAAAAGATGGAGCAACGAAGTTCAGGAAGCTGTG
EST: gi|148973647|gb|EE024760.2|EE024760
EST:     ACCCAGTGGTTGCTAGTGCTTCTCTTGTTAGTGGCATCCACCTGGCCCAG                         GCAAACCCAGAAATTGTGAAAAGATGGAGCAACGAAGTTCAGGAAGCTGTG
genomic: ACCCAGTGGTTGCTAGTGCTTCTCTTGTTAGTGGCATCCACCTGGCCCAGgtactagcat ... cactctacagGCAAACCCAGAAATTGTGAAAAGATGGAGCAACGAAGTTCAGGAAGCTGTG
EST: gi|76917670|gb|DV166948.1|DV166948
EST:     ACCCAGTGGTTGCTAGTGCTTCTCTTGTTAGTGGCATCCACCTGGCCCAG                         GCAAACCCAGAAATTGTGAAAAGATGGAGCAACGAAGTTCAGGAAGCTGTG
genomic: ACCCAGTGGTTGCTAGTGCTTCTCTTGTTAGTGGCATCCACCTGGCCCAGgtactagcat ... cactctacagGCAAACCCAGAAATTGTGAAAAGATGGAGCAACGAAGTTCAGGAAGCTGTG
EST: gi|211106005|gb|FK992440.1|FK992440
EST:     ACCCAGTGGTTGCTAGTGCTTCTCTTGTTAGTGGCATCCACCTGGCCCAG                         GCAAACCCAGAAATTGTGAAAAGATGGAGCAACGAAGTTCAGGAAGCTGTG
genomic: ACCCAGTGGTTGCTAGTGCTTCTCTTGTTAGTGGCATCCACCTGGCCCAGgtactagcat ... cactctacagGCAAACCCAGAAATTGTGAAAAGATGGAGCAACGAAGTTCAGGAAGCTGTG
EST: gi|67016076|gb|CO444825.1|CO444825
EST:     ACCCAGTGGTTGCTAGTGCTTCTCTTGTTAGTGGCATCCACCTGGCCCAG                         GCAAACCCAGAAATTGTGAAAAGATGGAGCAACGAAGTTCAGGAAGCTGTG
genomic: ACCCAGTGGTTGCTAGTGCTTCTCTTGTTAGTGGCATCCACCTGGCCCAGgtactagcat ... cactctacagGCAAACCCAGAAATTGTGAAAAGATGGAGCAACGAAGTTCAGGAAGCTGTG
EST: gi|148970762|gb|EE021504.2|EE021504
EST:     ACCCAGTGGTTGCTAGTGCTTCTCTTGTTAGTGGCATCCACCTGGCCCAG                         GCAAACCCAGAAATTGTGAAAAGATGGAGCAACGAAGTTCAGGAAGCTGTG
genomic: ACCCAGTGGTTGCTAGTGCTTCTCTTGTTAGTGGCATCCACCTGGCCCAGgtactagcat ... cactctacagGCAAACCCAGAAATTGTGAAAAGATGGAGCAACGAAGTTCAGGAAGCTGTG
EST: gi|148967121|gb|EE018293.2|EE018293
EST:     ACCCAGTGGTTGCTAGTGCTTCTCTTGTTAGTGGCATCCACCTGGCCCAG                         GCAAACCCAGAAATTGTGAAAAGATGGAGCAACGAAGTTCAGGAAGCTGTG
genomic: ACCCAGTGGTTGCTAGTGCTTCTCTTGTTAGTGGCATCCACCTGGCCCAGgtactagcat ... cactctacagGCAAACCCAGAAATTGTGAAAAGATGGAGCAACGAAGTTCAGGAAGCTGTG
EST: gi|148946070|gb|EC891366.2|EC891366
EST:     ACCCAGTGGTTGCTAGTGCTTCTCTTGTTAGTGGCATCCACCTGGCCCAG                         GCAAACCCAGAAATTGTGAAAAGATGGAGCAACGAAGTTCAGGAAGCTGTG
genomic: ACCCAGTGGTTGCTAGTGCTTCTCTTGTTAGTGGCATCCACCTGGCCCAGgtactagcat ... cactctacagGCAAACCCAGAAATTGTGAAAAGATGGAGCAACGAAGTTCAGGAAGCTGTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctcttgtttaaggttggttaactgtatcttttgtgagtttgtctacactctacagGCAAACCCAGAAATTGTGAAAAGATGGAGCAACGAAGTTCAGGAAGCTGTGCAATCAAGAGCTCCACTTGTCCAGTTTCATGGCCTTGCTCTTCTTCACC
               ggttaac  putative branch site (score: 3)
                        tatctttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtactagcataattctatgcatatataccgatctcttgtttaaggttggttaactgtatcttttgtgagtttgtctacactctacagGCAAACCCAGAAATTGTGAAAAGATGGAGCAACGAAGTTCAGGAAGCTGTGCAATCAAGAGCTCCACTTGTCCAGTTTCATGGCCTTGCTCTTCTTCACC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT