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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatcttttgttaattgccggacatggtttttcttctttcttttccatataatgccagcctactttgcaaaagctcgtcatgtgcctgtagattaagttcacttaggattattttgcttcttgattagctttcagcagtttcaccgtccagctgctcatcacatgcgtttctgaaatttccatagGCTTTGCACGAGGCTCTTATCAGGCAAGAGGAACTGCTTGCGTACATCGACCGCAAAGAGATTGCCAAGGCTCAG

Basic information

species Zea mays
transcript GRMZM2G171354_T04
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G171354_T01 (Zea mays), 3'ss of exon 13
lower sequence: LOC_Os02g04020.1 (Oryza sativa), 3'ss of exon 13
gtaatcttttgttaattgccggacatggtttttcttctttcttttccatataatgccagcctactttgcaaaagctcgtcatgtgcctgtagattaagttcacttaggattattt--tgcttcttgattagctttcagcagtttcaccgtccagctgctcatcacatgcgtttctgaaatttccatagGCTTTGCACGAGGCTCTTATCAGGCAAGAGGAACTGCTTGCGTACATCGACCGCAAAGAGATTGCCAAGGCTCAG-------------------------
                                                                   | |||   |  | |  |||  | |  || |  | |  ||| ||  |||    || ||| |||||  |     |     ||    |||||| ||||    |||       || ||||   ||||  | || |||||||||||||||||||||||||| || || ||||||||| | || ||| ||||||||||||||                         
-------------------------------------------------------------------gtaaacaattctgaactgc--gaaactttacatta--tagtatcgtttatcactactttattagggtatgtgaa----acatgtcagctgatcatt---tgcaa----aaattttctcaagGCCCTACATGAGGCTCTTATCAGGCAAGAGGAACTACTAGCCTACATCGACAGTAAGGAGGTTGCCAAGGCTCAGAAAAAGAAGAAGGCGATGTTTTGCT
















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|40303122|gb|CK347509.1|CK347509
EST:     CTGTGCGTCGTGTCGATGCATTGGAAGCCGAACTAATTGTAACAAAGAAG                         GCTTTGCACGAGGCTCTTATCAGGCAAGAGGAACTGCTTGCGTACATCGAC
genomic: CTGTGCGTCGTGTCGATGCATTGGAAGCCGAACTAATTGTAACAAAGAAGgtaatctttt ... atttccatagGCTTTGCACGAGGCTCTTATCAGGCAAGAGGAACTGCTTGCGTACATCGAC
EST: gi|113702635|gb|EE680139.1|EE680139
EST:     CTGTGCGTCGTGTCGATGCATTGGAAGCCGAACTAATTGTAACAAAGAAG                         GCTTTGCACGAGGCTCTTATCAGGCAAGAGGAACTGCTTGCGTACATCGAC
genomic: CTGTGCGTCGTGTCGATGCATTGGAAGCCGAACTAATTGTAACAAAGAAGgtaatctttt ... atttccatagGCTTTGCACGAGGCTCTTATCAGGCAAGAGGAACTGCTTGCGTACATCGAC
EST: gi|71762206|gb|DR960143.1|DR960143
EST:     CTGTGCGTCGTGTCGATGCATTGGAAGCCGAACTAATTGTAACAAAGAAG                         GCTTTGCACGAGGCTTTTATCAGGCAAGAGGAACTGCTTGCGTACATCGAC
genomic: CTGTGCGTCGTGTCGATGCATTGGAAGCCGAACTAATTGTAACAAAGAAGgtaatctttt ... atttccatagGCTTTGCACGAGGCTCTTATCAGGCAAGAGGAACTGCTTGCGTACATCGAC
EST: gi|211399534|gb|FL455814.1|FL455814
EST:     CTGTGCGTCGTGTCGATGCATTGGAAGCCGAACTAATTGTAACAAAGAAG                         GCTTTGCACGAGGCTCTTATCAGGCAAGAGGAACTGCTTGCGTACATCGAC
genomic: CTGTGCGTCGTGTCGATGCATTGGAAGCCGAACTAATTGTAACAAAGAAGgtaatctttt ... atttccatagGCTTTGCACGAGGCTCTTATCAGGCAAGAGGAACTGCTTGCGTACATCGAC
EST: gi|113702380|gb|EE679884.1|EE679884
EST:     CTGTGCGTCGTGTCGATGCATTGGAAGCCGAACTAATTGTAACAAAGAAG                         GCTTTGCACGAGGCTCTTATCAGGCAAGAGGAACTGCTTGCGTACATCGAC
genomic: CTGTGCGTCGTGTCGATGCATTGGAAGCCGAACTAATTGTAACAAAGAAGgtaatctttt ... atttccatagGCTTTGCACGAGGCTCTTATCAGGCAAGAGGAACTGCTTGCGTACATCGAC
EST: gi|28983565|gb|BQ538689.2|BQ538689
EST:     CTGTGCGTCGTGTCGATGCATTGGAAGCCGAACTAATTGTAACAAAGAAG                         GCTTTGCACGAGGCTCTTATCAGGCAAGAGGAACTGCTTGCGTACATCGAC
genomic: CTGTGCGTCGTGTCGATGCATTGGAAGCCGAACTAATTGTAACAAAGAAGgtaatctttt ... atttccatagGCTTTGCACGAGGCTCTTATCAGGCAAGAGGAACTGCTTGCGTACATCGAC
EST: gi|211130597|gb|FL448938.1|FL448938
EST:     CTGTGCGTCGTGTCGATGCATTGGAAGCCGAACTAATTGTAACAAAGAAG                         GCTTTGCACGAGGCTCTTATCAGGCAAGAGGAACTGCTTGCGTACATCGAC
genomic: CTGTGCGTCGTGTCGATGCATTGGAAGCCGAACTAATTGTAACAAAGAAGgtaatctttt ... atttccatagGCTTTGCACGAGGCTCTTATCAGGCAAGAGGAACTGCTTGCGTACATCGAC
EST: gi|16920005|gb|BM074460.1|BM074460
EST:     CTGTGCGTCGTGTCGATGCATTGGAAGCCGAACTAATTGTAACAAAGAAG                         GCTTTGCACGAGGCTCTTATCAGGCAAGAGGAACTGCTTGCGTACATCGAC
genomic: CTGTGCGTCGTGTCGATGCATTGGAAGCCGAACTAATTGTAACAAAGAAGgtaatctttt ... atttccatagGCTTTGCACGAGGCTCTTATCAGGCAAGAGGAACTGCTTGCGTACATCGAC
EST: gi|33100072|gb|CF060032.1|CF060032
EST:     CTGTGCGTCGTGTCGATGCATTGGAAGCCGAACTAATTGTAACAAAGAAG                         GCTTTGCACGAGGCTCTTATCAGGCAAGAGGAACTGCTTGCGT
genomic: CTGTGCGTCGTGTCGATGCATTGGAAGCCGAACTAATTGTAACAAAGAAGgtaatctttt ... atttccatagGCTTTGCACGAGGCTCTTATCAGGCAAGAGGAACTGCTTGCGT
EST: gi|40337029|gb|CK371099.1|CK371099
EST:     CTGTGCGTCGTGTCGATGCATTGGAAGCCGAACTAATTGTAACAAAGAAG                         GCTTTGCACGAGGCTCTTATCAGGCAAGAGGAACTGCTTGCGTACATCGAC
genomic: CTGTGCGTCGTGTCGATGCATTGGAAGCCGAACTAATTGTAACAAAGAAGgtaatctttt ... atttccatagGCTTTGCACGAGGCTCTTATCAGGCAAGAGGAACTGCTTGCGTACATCGAC
EST: gi|211361627|gb|FL314636.1|FL314636
EST:     CTGTGCGTCGKGTCGATGCATTGGAAGCCGAACYAATTGTAACAAAGAAG                         GCTTTGCACGAGGCTCTTATCAGGCAAGAGGAACTGCTTGCGTACATCGAC
genomic: CTGTGCGTCGTGTCGATGCATTGGAAGCCGAACTAATTGTAACAAAGAAGgtaatctttt ... atttccatagGCTTTGCACGAGGCTCTTATCAGGCAAGAGGAACTGCTTGCGTACATCGAC
EST: gi|32936966|gb|CF041785.1|CF041785
EST:     TGCGTCGTGTCGATGCATTGGAAGCCGAACTAATTGTAACAAAGAAG                         GCTTTGCACGAGGCTCTTATCAGGCAAGAGGAACTGCTTGCGTACATCGAC
genomic: TGCGTCGTGTCGATGCATTGGAAGCCGAACTAATTGTAACAAAGAAGgtaatctttt ... atttccatagGCTTTGCACGAGGCTCTTATCAGGCAAGAGGAACTGCTTGCGTACATCGAC
EST: gi|5124115|gb|AI745739.1|AI745739
EST:     CTGTGCGTCGTGTCGATGCATTGGAAGCCGAACTAATTGTAACAAAGAAG                         GCTTTGCACGAGGCTCTTATCAGGCAAGAGGAACTGCTTGCGTACATCGGC
genomic: CTGTGCGTCGTGTCGATGCATTGGAAGCCGAACTAATTGTAACAAAGAAGgtaatctttt ... atttccatagGCTTTGCACGAGGCTCTTATCAGGCAAGAGGAACTGCTTGCGTACATCGAC
EST: gi|211399535|gb|FL455815.1|FL455815
EST:     CTGTGCGTCGTGTCGATGCATTGGAAGCCGAACTAATTGTAACAAAGAAG                         GCTTTGCACGAGGCTCTTATCAGGCAAGAGGAACTGCTTGCGTACATCGAC
genomic: CTGTGCGTCGTGTCGATGCATTGGAAGCCGAACTAATTGTAACAAAGAAGgtaatctttt ... atttccatagGCTTTGCACGAGGCTCTTATCAGGCAAGAGGAACTGCTTGCGTACATCGAC
EST: gi|6563798|gb|AW231330.1|AW231330
EST:     CTGTGCGTCGTGTCGATGCATTGGAAGCCGAACTAATTGTAACAAAGAAG                         GCTTTGCACGAGGCTCTTATCAGGCAAGAGGAACTGCTTGCGTACATCGAC
genomic: CTGTGCGTCGTGTCGATGCATTGGAAGCCGAACTAATTGTAACAAAGAAGgtaatctttt ... atttccatagGCTTTGCACGAGGCTCTTATCAGGCAAGAGGAACTGCTTGCGTACATCGAC
EST: gi|37397469|gb|CF636033.1|CF636033
EST:     CTGTGCGTCGTGTCGATGCATTGGAAGCCGAACTAATTGTAACAAAGAAG                         GCTTTGCACGAGGCTCTTATCAGGCAAGAGGAACTGCTTGCGTACATCGAC
genomic: CTGTGCGTCGTGTCGATGCATTGGAAGCCGAACTAATTGTAACAAAGAAGgtaatctttt ... atttccatagGCTTTGCACGAGGCTCTTATCAGGCAAGAGGAACTGCTTGCGTACATCGAC
EST: gi|45568449|gb|CK986069.1|CK986069
EST:     CTGTGCGTCGTGTCGATGCATTGGAAGCCGAACTAATTGTAACAAAGAAG                         GCTTTGCACGAGGCTCTTATCAGGCAAGAGGAACTGCTTGCGTACATCGAC
genomic: CTGTGCGTCGTGTCGATGCATTGGAAGCCGAACTAATTGTAACAAAGAAGgtaatctttt ... atttccatagGCTTTGCACGAGGCTCTTATCAGGCAAGAGGAACTGCTTGCGTACATCGAC
EST: gi|37379233|gb|CF626352.1|CF626352
EST:     CTGTGCGTCGTGTCGATGCATTGGAAGCCGAACTAATTGTAACAAAGAAG                         GCTTTGCACGAGGCTCTTATCAGGCAAGAGGAACTGCTTGCGTACATCGAC
genomic: CTGTGCGTCGTGTCGATGCATTGGAAGCCGAACTAATTGTAACAAAGAAGgtaatctttt ... atttccatagGCTTTGCACGAGGCTCTTATCAGGCAAGAGGAACTGCTTGCGTACATCGAC
EST: gi|44900735|gb|CK827280.1|CK827280
EST:     CTGTGCGTCGTGTCGATGCATTGGAAGCCGAACTAATTGTAACAAAGAAG                         GCTTTGCACGAGGCTCTTATCAGGCAAGAGGAACTGCTTGCGTACATCGAC
genomic: CTGTGCGTCGTGTCGATGCATTGGAAGCCGAACTAATTGTAACAAAGAAGgtaatctttt ... atttccatagGCTTTGCACGAGGCTCTTATCAGGCAAGAGGAACTGCTTGCGTACATCGAC
EST: gi|6539003|gb|AW225142.1|AW225142
EST:     CTGTGCGTCGTGTCGATGCATTGGAAGCCGAACTAATTGTAACAAAGAAG                         GCTTTGCACGAGGCTCTTATCAGGCAAGAGGAACTGCTTGCGTACATCGAC
genomic: CTGTGCGTCGTGTCGATGCATTGGAAGCCGAACTAATTGTAACAAAGAAGgtaatctttt ... atttccatagGCTTTGCACGAGGCTCTTATCAGGCAAGAGGAACTGCTTGCGTACATCGAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcagcagtttcaccgtccagctgctcatcacatgcgtttctgaaatttccatagGCTTTGCACGAGGCTCTTATCAGGCAAGAGGAACTGCTTGCGTACATCGACCGCAAAGAGATTGCCAAGGCTCAG
                                              tttccat  CT-rich tract
                                         tgaaattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaatcttttgttaattgccggacatggtttttcttctttcttttccatataatgccagcctactttgcaaaagctcgtcatgtgcctgtagattaagttcacttaggattattttgcttcttgattagctttcagcagtttcaccgtccagctgctcatcacatgcgtttctgaaatttccatagGCTTTGCACGAGGCTCTTATCAGGCAAGAGGAACTGCTTGCGTACATCGACCGCAAAGAGATTGCCAAGGCTCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGA