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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtcaccgccgtatatctgggttaactgtttcttggagaggctgtctcaagtgctataataccttgtcaattgtggttgcagGACAACAGTGTATTGTGGTGCATTGGTTGGCAAAGGAACCAGGGCCAAGAAATAACTATACTCGGAG

Basic information

species Zea mays
transcript GRMZM2G133029_T01
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G133029_T01 (Zea mays), 3'ss of exon 7
lower sequence: LOC_Os01g56930.1 (Oryza sativa), 3'ss of exon 7
--------------------------------------gtaagtcaccgccgtatatctgggttaactgtttcttggagaggctgtctcaagtgctat-aataccttgtcaattgtggttgcagGACAACAGTGTATTGTGGTGCATTGGTTGGCAAAGGAACCAGGGCCAAGAAATAACTATACTCGGAG
                                       |  || || |  |||||||||   |||| ||||||   |     |||  |      ||| |||||| | |||  ||   || |||||||||| |||||||||||| ||||||||||||||||||||||| ||| ||||||| ||||||||||
gtaagcctgcattttttttaatatatttggtttctggccttggtaacagttgtatatctgc-ctaaccgtttctgaaaagacttgttcctgcccatattaataccatatca--tgctttt-cagGACAACAATGTATTGTGGTGTATTGGTTGGCAAAGGAACCAGGGTCAACAAATAACCATACTCGGAG
















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|14203670|gb|BG837347.1|BG837347
EST:     TTGCGATGTCGGTGAAGCCAGAGAACTATYTTTTACAGCAGGCTTCTGTT                         GACAACAGTGTATTGTGGTGCATTGGTTGGCAAAGGAACCAGGGCCAAGAA
genomic: TTGCGATGTCGGTGAAGCCAGAGAACTATCTTTTACAGCAGGCTTCTGTTgtaagtcacc ... gtggttgcagGACAACAGTGTATTGTGGTGCATTGGTTGGCAAAGGAACCAGGGCCAAGAA
EST: gi|32928510|gb|CF033322.1|CF033322
EST:     TTGCGATGTCGGTGAAGCCAGAGAACTATCTTTTGCAGCAGGCTTCTGTT                         GACAACAGTGTATTGTGGTGCATTGGTTGGCAAAGGAACCAGGGCCAAGAA
genomic: TTGCGATGTCGGTGAAGCCAGAGAACTATCTTTTACAGCAGGCTTCTGTTgtaagtcacc ... gtggttgcagGACAACAGTGTATTGTGGTGCATTGGTTGGCAAAGGAACCAGGGCCAAGAA
EST: gi|32919740|gb|CF024552.1|CF024552
EST:     TTGCGATGTCGGTGAAGCCAGAGAACTATCTTTTGCAGCAGGCTTCTGTT                         GACAGCAGTGTATTGTGGTGCATTGGTTGGCAAAGGAACCAGGGCCAAGAA
genomic: TTGCGATGTCGGTGAAGCCAGAGAACTATCTTTTACAGCAGGCTTCTGTTgtaagtcacc ... gtggttgcagGACAACAGTGTATTGTGGTGCATTGGTTGGCAAAGGAACCAGGGCCAAGAA
EST: gi|88749541|gb|DY533682.1|DY533682
EST:     GAGAACTAT-TTTTACAGCAGGCTTCTGTT                         GACAACAGTGTATTGTGGTGCATTGGTTGGCAAAGGAACCAGGGCCAAGAA
genomic: GAGAACTATCTTTTACAGCAGGCTTCTGTTgtaagtcacc ... gtggttgcagGACAACAGTGTATTGTGGTGCATTGGTTGGCAAAGGAACCAGGGCCAAGAA
EST: gi|84976772|gb|DW475194.1|DW475194
EST:     TGCGATGTCCGGTGAAGCCAGAGAACTATCTTTTGCAGCAGGCTTCTGCT                         GACAATAGTGTATTGTGGTGCATTGGTTGGCAAAGGAACCAGGGCCAAGAA
genomic: TGCGATGTC-GGTGAAGCCAGAGAACTATCTTTTACAGCAGGCTTCTGTTgtaagtcacc ... gtggttgcagGACAACAGTGTATTGTGGTGCATTGGTTGGCAAAGGAACCAGGGCCAAGAA
EST: gi|211449625|gb|FL035069.1|FL035069
EST:     TTGCGATGTCAGTGAAGCCAGAGAACTATCTTTTGCAGCAGGCTTCTGTT                         GATAACAGTGTATTGTGGGTGCATTGGTTGGCAAAGGAACCAGGGCCAAGA
genomic: TTGCGATGTCGGTGAAGCCAGAGAACTATCTTTTACAGCAGGCTTCTGTTgtaagtcacc ... gtggttgcagGACAACAGTGTATTGTGG-TGCATTGGTTGGCAAAGGAACCAGGGCCAAGA
EST: gi|74234970|gb|DT642884.1|DT642884
EST:     TTGCGATGTCGGTGAAGCCAGAGAACTATCTTTTACAGCAGGCTTCTGTT                         GACAACAGTGTATTGTGGTGCATTGGTTGGCAAAGGAAACAGGGCCAAGAA
genomic: TTGCGATGTCGGTGAAGCCAGAGAACTATCTTTTACAGCAGGCTTCTGTTgtaagtcacc ... gtggttgcagGACAACAGTGTATTGTGGTGCATTGGTTGGCAAAGGAACCAGGGCCAAGAA
EST: gi|148940876|gb|EC885709.2|EC885709
EST:     TTGCGATGTCGGTGAAGCCAGAGAACTATCTTTTACAGCAGGCTTCTGTT                         GACAACAGTGTATTGTGGTGCATTGGTTGGCAAAGGAACCAGGGCCAAGAA
genomic: TTGCGATGTCGGTGAAGCCAGAGAACTATCTTTTACAGCAGGCTTCTGTTgtaagtcacc ... gtggttgcagGACAACAGTGTATTGTGGTGCATTGGTTGGCAAAGGAACCAGGGCCAAGAA
EST: gi|32928535|gb|CF033347.1|CF033347
EST:     TTGCGATGTCGGTGAAGCCAGAGAACTATCTTTTGCAGCAGGCTTCTGTT                         GACAACAGTGTATTGTGGTGCATTGGTTGGCAAAGGAACCAGGGCCAAGAA
genomic: TTGCGATGTCGGTGAAGCCAGAGAACTATCTTTTACAGCAGGCTTCTGTTgtaagtcacc ... gtggttgcagGACAACAGTGTATTGTGGTGCATTGGTTGGCAAAGGAACCAGGGCCAAGAA
EST: gi|19350596|gb|BM895128.1|BM895128
EST:     TTGCGATGTCGGTGAAGCCAGAGAACTATCTTTTGCAGCAGGCTTCTGTT                         GACAACAGTGTATTGTGGTGCATTGGTTGGCAAAGGAACCAGGGCCAAGAA
genomic: TTGCGATGTCGGTGAAGCCAGAGAACTATCTTTTACAGCAGGCTTCTGTTgtaagtcacc ... gtggttgcagGACAACAGTGTATTGTGGTGCATTGGTTGGCAAAGGAACCAGGGCCAAGAA
EST: gi|32929051|gb|CF033863.1|CF033863
EST:     TTGCGATGTCGGTGAAGCCAGAGAACTATCTTTTGCAGCAGGCTTCTGTT                         GACAACAGTGTATTGTGGTGCATTGGTTGGCAAAGGAACCAGGGCCAAGAA
genomic: TTGCGATGTCGGTGAAGCCAGAGAACTATCTTTTACAGCAGGCTTCTGTTgtaagtcacc ... gtggttgcagGACAACAGTGTATTGTGGTGCATTGGTTGGCAAAGGAACCAGGGCCAAGAA
EST: gi|74234969|gb|DT642883.1|DT642883
EST:     TTGCGATGTCGGTGAAGCCAGAGAACTATCTTTTACAGCAGGCTTCTGTT                         GACAACAGTGTATTGTGGTGCATTGGTTGGCAAAGGAACCAGGGCCAAGAA
genomic: TTGCGATGTCGGTGAAGCCAGAGAACTATCTTTTACAGCAGGCTTCTGTTgtaagtcacc ... gtggttgcagGACAACAGTGTATTGTGGTGCATTGGTTGGCAAAGGAACCAGGGCCAAGAA
EST: gi|113702354|gb|EE679858.1|EE679858
EST:     TTGCGATGTCGGTGAAGCCAGAGAACTATCTTTTGCAGCAGGCTTCTGTT                         GACAATAGTGTATTGTGGTGCATTGGTTGGCAAAGGAACCAGGGCCAAGAA
genomic: TTGCGATGTCGGTGAAGCCAGAGAACTATCTTTTACAGCAGGCTTCTGTTgtaagtcacc ... gtggttgcagGACAACAGTGTATTGTGGTGCATTGGTTGGCAAAGGAACCAGGGCCAAGAA
EST: gi|32931524|gb|CF036336.1|CF036336
EST:     TTGCGATGTCGGTGAAGCCAGAGAACTATCTTTTGCAGCAGGCTTCTGTT                         GACAACAGTGTATTGTGGTGCATTGGTTGGCAAAGGAACCAGGGCCAAGAA
genomic: TTGCGATGTCGGTGAAGCCAGAGAACTATCTTTTACAGCAGGCTTCTGTTgtaagtcacc ... gtggttgcagGACAACAGTGTATTGTGGTGCATTGGTTGGCAAAGGAACCAGGGCCAAGAA
EST: gi|33100162|gb|CF060122.1|CF060122
EST:     TTGCGATGTCGGTGAAGCCAGAGAACTATCTTTTGCAGCAGGCTTCTGTT                         GACAACAGTGTATTGTGGTGCATTGGTTGGCAAAGGAACCAGGGCCAAGAA
genomic: TTGCGATGTCGGTGAAGCCAGAGAACTATCTTTTACAGCAGGCTTCTGTTgtaagtcacc ... gtggttgcagGACAACAGTGTATTGTGGTGCATTGGTTGGCAAAGGAACCAGGGCCAAGAA
EST: gi|33095406|gb|CF055400.1|CF055400
EST:     TTGCGATGTCGGTGAAGCCAGAGAACTATCTTTTGCAGCAGGCTTCTGTT                         GACAACAGTGTATTGTGGTGCATTGGTTGGCAAAGGAACCAGGGCCAAGAA
genomic: TTGCGATGTCGGTGAAGCCAGAGAACTATCTTTTACAGCAGGCTTCTGTTgtaagtcacc ... gtggttgcagGACAACAGTGTATTGTGGTGCATTGGTTGGCAAAGGAACCAGGGCCAAGAA
EST: gi|211451752|gb|FL035074.1|FL035074
EST:     TTGCGATGTCGGTGAAGCCAGAGAACTATCTTTTGCAGCAGGCTTCTGTT                         GACAACAGTGTATTGTGGTGCATTGGTTGGCAAAGGAACCAGGGCCAAGAA
genomic: TTGCGATGTCGGTGAAGCCAGAGAACTATCTTTTACAGCAGGCTTCTGTTgtaagtcacc ... gtggttgcagGACAACAGTGTATTGTGGTGCATTGGTTGGCAAAGGAACCAGGGCCAAGAA
EST: gi|148983004|gb|EE028899.2|EE028899
EST:     TTGCGATGTCGGTGAAGCCAGAGAACTATCTTTTACAGCAGGCTTCTGTT                         GACAACAGTGTATTGTGGTGCATTGGTTGGCAAAGGAACCAGGGCCAAGAA
genomic: TTGCGATGTCGGTGAAGCCAGAGAACTATCTTTTACAGCAGGCTTCTGTTgtaagtcacc ... gtggttgcagGACAACAGTGTATTGTGGTGCATTGGTTGGCAAAGGAACCAGGGCCAAGAA
EST: gi|33099546|gb|CF059506.1|CF059506
EST:     TTGCGATGTCGGTGAAGCCAGAGAACTATCTTTTGCAGCAGGCTTCTGTT                         GACAACAGTGTATTGTGGTGCATTGGTTGGCAAAGGAACCAGGGCCAAGAA
genomic: TTGCGATGTCGGTGAAGCCAGAGAACTATCTTTTACAGCAGGCTTCTGTTgtaagtcacc ... gtggttgcagGACAACAGTGTATTGTGGTGCATTGGTTGGCAAAGGAACCAGGGCCAAGAA
EST: gi|148941418|gb|EC886337.2|EC886337
EST:     TTTTACAGCAGGCTTCTGTT                         GACAACAGTGTATTGTGGTGCATTGGTTGGCAAAGGAACCAGGGCCAAGAA
genomic: TTTTACAGCAGGCTTCTGTTgtaagtcacc ... gtggttgcagGACAACAGTGTATTGTGGTGCATTGGTTGGCAAAGGAACCAGGGCCAAGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtttcttggagaggctgtctcaagtgctataataccttgtcaattgtggttgcagGACAACAGTGTATTGTGGTGCATTGGTTGGCAAAGGAACCAGGGCCAAGAAATAACTATACTCGGAG
                           tataata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtcaccgccgtatatctgggttaactgtttcttggagaggctgtctcaagtgctataataccttgtcaattgtggttgcagGACAACAGTGTATTGTGGTGCATTGGTTGGCAAAGGAACCAGGGCCAAGAAATAACTATACTCGGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA