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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...catatgtttttaaattaattagctcacattacataatgtgcgaatgtgtttttatggttaagctatagtcttgattcagattcacttctatttgattcagCTATTGGAGATGCTTCTGAATAATTGCGGAGAGCCTGTCCATAGGCAGGTCATTGATAATGGCCTTCTTCCAATACTTGTGAAGATAGTGAAGAAAAAG

Basic information

species Zea mays
transcript GRMZM5G834205_T01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G834205_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os08g01740.2 (Oryza sativa), 3'ss of exon 3
catatgtttttaaattaattagctcacattaca-taatgtgcgaatgtgtttttatggttaagctatagtcttgattcagattcact--tctatttgattcagCTATTGGAGATGCTTCTGAATAATTGCGGAGAGCCTGTCCATAGGCAGGTCATTGATAATGGCCTTCTTCCAATACTTGTGAAGATAGTGAAGAAAAAG
      |   ||    |  |   | |  |   | |  ||||   || | | | | |  |    | |||   || ||   |||| | |   ||||||| |  |||| || || |||||  ||||||| |||||||| ||| |||| | ||||||||||||||| || ||||| || |||||||||||||| ||||||||||||
---tcttccatagggaagcttattgaagtcgtaattgtgtggatatctatatcttttttgttaccatacctttaatcttgatttattgtgctatttgttgtagCTGTTAGAAATGCTCATGAATAACTGCGGAGAACCTATCCACAAGCAGGTCATTGATAACGGTCTTCTCCCGATACTTGTGAAGATTGTGAAGAAAAAG

upper sequence: GRMZM5G834205_T01 (Zea mays), 3'ss of exon 2
lower sequence: Vv07s0031g03190.t01 (Vitis vinifera), 3'ss of exon 2
catatgtttttaaattaatt--agctcacattacataatgtgcgaatgtgtttttatggttaagctatagtcttgat--tcagattcacttctatttgattcagCTATTGGAGATGCTTCTGAATAATTGCGGAGAGCCTGTCCATAGGCAGGTCATTGATAATGGCCTTCTTCCAATACTTGTGAAGATAGTGAAGAAAAAG
 ||||| |  | || |   |  |  ||  |  ||  |   |||    ||  ||      ||  ||| |     |||   |  ||||  | | |  ||  | ||| ||||||||||| |  ||||||||   ||||| ||||| || || ||||| ||||||||||| || || || ||||| ||||||||||| |||||||||
-atatggtcatgaaatggctctacatcttagcactcaccctgca---gttcttcatcacttttgctgtctatctgaccatttgattagcatttgatttttgcagTTATTGGAGATGTTGATGAATAATATTGGAGAACCTGTTCACAGACAGGTGATTGATAATGGGCTCCTCCCTATACTAGTGAAGATAGTAAAGAAAAAG
















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|89761509|gb|DY689496.1|DY689496
EST:     AGAAGTGTATAGGGAGCAGGAGCAAGACCACTCAACTCTTTGCTGTTATG                         CTATTGGAGATGCTTCTGAATAATTGCGGAGAGCCTGTCCATAGGCAGGTC
genomic: AGAAGTGTATAGGGAGCAGGAGCAAGACCACTCAACTCTTTGCTGTTATGgtgagttgtt ... tttgattcagCTATTGGAGATGCTTCTGAATAATTGCGGAGAGCCTGTCCATAGGCAGGTC
EST: gi|71421501|gb|DR805467.1|DR805467
EST:     AGAAGTGTATAGGGAGCAGGAGCAAGACCACTCAACTCTTTGCTGTTATG                         CTATTGGAGATGCTTCTGAATAATTGCGGAGAGCCTGTCCATAGGCAGGTC
genomic: AGAAGTGTATAGGGAGCAGGAGCAAGACCACTCAACTCTTTGCTGTTATGgtgagttgtt ... tttgattcagCTATTGGAGATGCTTCTGAATAATTGCGGAGAGCCTGTCCATAGGCAGGTC
EST: gi|50325447|gb|CO520573.1|CO520573
EST:     AGAAGTGTATAGGGAGCAGGAGCAAGACCACTCAACTCTTTGCTGTTATG                         CTATTGGAGATGCTTCTGAATAATTGCGGAGAGCCTGTCCATAGGCAGGTC
genomic: AGAAGTGTATAGGGAGCAGGAGCAAGACCACTCAACTCTTTGCTGTTATGgtgagttgtt ... tttgattcagCTATTGGAGATGCTTCTGAATAATTGCGGAGAGCCTGTCCATAGGCAGGTC
EST: gi|78107223|gb|DV525641.1|DV525641
EST:     AGAAGTGTATAGGGAGCAGGAGCAAGACCACTCAACTCTTTGCTGTTATG                         CTATTGGAGATGCTTCTGAATAATTGCGGAGAGCCTGTCCATAGGCAGGTC
genomic: AGAAGTGTATAGGGAGCAGGAGCAAGACCACTCAACTCTTTGCTGTTATGgtgagttgtt ... tttgattcagCTATTGGAGATGCTTCTGAATAATTGCGGAGAGCCTGTCCATAGGCAGGTC
EST: gi|93017403|gb|EB642923.1|EB642923
EST:     AGAAGTGTATAGGGAGCAGGAGCAAGACCACTCAACTCTTTGCTGTTATG                         CTATTGGAGATGCTTCTGAATAATTGCGGAGAGCCTGTCCATAGGCAGGTC
genomic: AGAAGTGTATAGGGAGCAGGAGCAAGACCACTCAACTCTTTGCTGTTATGgtgagttgtt ... tttgattcagCTATTGGAGATGCTTCTGAATAATTGCGGAGAGCCTGTCCATAGGCAGGTC
EST: gi|149059924|gb|EE157051.2|EE157051
EST:     AGAAGTGTATAGGGAGCAGGAGCAAGACCACTCAACTCTTTGCTGTTATG                         CTATTGGAGATGCTTCTGAATAATTGCGGAGAGCCTGTCCATAGGCAGGTC
genomic: AGAAGTGTATAGGGAGCAGGAGCAAGACCACTCAACTCTTTGCTGTTATGgtgagttgtt ... tttgattcagCTATTGGAGATGCTTCTGAATAATTGCGGAGAGCCTGTCCATAGGCAGGTC
EST: gi|93015305|gb|EB640825.1|EB640825
EST:     AGAACTGTATAGGGAGCAGGAGCAAGACCACTCAACTCTTTGCTGTTATG                         CTATTGGAGATGCTTCTGAATAATTGCGGAGAGCCTGTCCATAGGCAGGTC
genomic: AGAAGTGTATAGGGAGCAGGAGCAAGACCACTCAACTCTTTGCTGTTATGgtgagttgtt ... tttgattcagCTATTGGAGATGCTTCTGAATAATTGCGGAGAGCCTGTCCATAGGCAGGTC
EST: gi|149088092|gb|EE287276.2|EE287276
EST:     AGAAGTGTATAGGGAGCAGGAGCAAGACCACTCAACTCTTTGCTGTTATG                         CTATTGGAGATGCTTCTGAATAA-TGACGGAGAGCCTGTCCATAGGCAGGT
genomic: AGAAGTGTATAGGGAGCAGGAGCAAGACCACTCAACTCTTTGCTGTTATGgtgagttgtt ... tttgattcagCTATTGGAGATGCTTCTGAATAATTG-CGGAGAGCCTGTCCATAGGCAGGT
EST: gi|9953455|gb|BE640038.1|BE640038
EST:     GCAAGACCACTCAACTCTTTGCTGTTATG                         CTGTTGGAGATGCTTCTGAATAATTGCGGAGAGCCTGTCCATAGGCAGGTC
genomic: GCAAGACCACTCAACTCTTTGCTGTTATGgtgagttgtt ... tttgattcagCTATTGGAGATGCTTCTGAATAATTGCGGAGAGCCTGTCCATAGGCAGGTC
EST: gi|71421504|gb|DR805468.1|DR805468
EST:     AGAAGTGTATAGGGAGCAGGAGCAAGACCACTCAACTCTTTGCTGTTATG                         CTATTGGAGATGCTTCTGAATAATTGCGGAGAGCCTGTCCATAGGCAGGTC
genomic: AGAAGTGTATAGGGAGCAGGAGCAAGACCACTCAACTCTTTGCTGTTATGgtgagttgtt ... tttgattcagCTATTGGAGATGCTTCTGAATAATTGCGGAGAGCCTGTCCATAGGCAGGTC
EST: gi|50339160|gb|CO534286.1|CO534286
EST:     AGAAGTGTATAGGGAGCAGGAGCAAGACCACTCAACTCTTTGCTGTTATG                         CTATTGGAGATGCTTCTGAATAATTGCGGAGAGCCTGTCCATAGGCAGGTC
genomic: AGAAGTGTATAGGGAGCAGGAGCAAGACCACTCAACTCTTTGCTGTTATGgtgagttgtt ... tttgattcagCTATTGGAGATGCTTCTGAATAATTGCGGAGAGCCTGTCCATAGGCAGGTC
EST: gi|71326005|gb|DR799685.1|DR799685
EST:     AGAAGTGTATAGGGAGCAGGAGCAAGACCACTCAACTCTTTGCTGTTATG                         CTATTGGAGATGCTTCTGAATAATTGCGGAGAGCCTGTCCATAGGCAGGTC
genomic: AGAAGTGTATAGGGAGCAGGAGCAAGACCACTCAACTCTTTGCTGTTATGgtgagttgtt ... tttgattcagCTATTGGAGATGCTTCTGAATAATTGCGGAGAGCCTGTCCATAGGCAGGTC
EST: gi|71320277|gb|DR796887.1|DR796887
EST:     AGAAGTGTATAGGGAGCAGGAGCAAGACCACTCAACTCTTTGCTGTTATG                         CTATTGGAGATGCTTCTGAATAATTGCGGAGAGCCTGTCCCATAGGCA
genomic: AGAAGTGTATAGGGAGCAGGAGCAAGACCACTCAACTCTTTGCTGTTATGgtgagttgtt ... tttgattcagCTATTGGAGATGCTTCTGAATAATTGCGGAGAGCCTGTCC-ATAGGCA
EST: gi|78107222|gb|DV525640.1|DV525640
EST:     GAAGTGTATA-GGAGCAGGGAGCAAGACCACTCAACTCTTTGCTGTTATG                         CTATTGGAGATGCTTCTGAATAATTGCGGAGAGCCTGTCCATAGGCAGGTC
genomic: GAAGTGTATAGGGAGCA-GGAGCAAGACCACTCAACTCTTTGCTGTTATGgtgagttgtt ... tttgattcagCTATTGGAGATGCTTCTGAATAATTGCGGAGAGCCTGTCCATAGGCAGGTC
EST: gi|44682243|gb|CK787291.1|CK787291
EST:     AGAAGTGTATAGGGAGCAGGAGCAAGACCACTCAACTCTTTGCTGTTATG                         CTATTGGAGATGCTTCTGAATAATTGCGGAGAGCCTGTCCATAGGCAGGTC
genomic: AGAAGTGTATAGGGAGCAGGAGCAAGACCACTCAACTCTTTGCTGTTATGgtgagttgtt ... tttgattcagCTATTGGAGATGCTTCTGAATAATTGCGGAGAGCCTGTCCATAGGCAGGTC
EST: gi|148952813|gb|EC898805.2|EC898805
EST:     AGAAGTGTATAGGGAGCAGGAGCAAGACCACTCAACTCTTTGCTGTTATG                         CTATTGGAGATGCTTCTGAATAATTGCGGAGAGCCTGTCCATAGGCAGGTC
genomic: AGAAGTGTATAGGGAGCAGGAGCAAGACCACTCAACTCTTTGCTGTTATGgtgagttgtt ... tttgattcagCTATTGGAGATGCTTCTGAATAATTGCGGAGAGCCTGTCCATAGGCAGGTC
EST: gi|74245587|gb|DT653501.1|DT653501
EST:     AGAAGTGTATAGGGAGCAGGAGCAAGACCACTCAACTCTTTGCTGTTATG                         CTATTGGAGATGCTTCTGAATAATTGCGGAGAGCCTGTCCATAGGCAGGTC
genomic: AGAAGTGTATAGGGAGCAGGAGCAAGACCACTCAACTCTTTGCTGTTATGgtgagttgtt ... tttgattcagCTATTGGAGATGCTTCTGAATAATTGCGGAGAGCCTGTCCATAGGCAGGTC
EST: gi|149105965|gb|EE291598.2|EE291598
EST:     AGAAGTGTATAGGGAGCAGGAGCAAGACCACTCAACTCTTTGCTGTTATG                         CTATTGGAGATGCTTCTGAATAATTGCGGAGAGCCTGTCCATAGGCAGGTC
genomic: AGAAGTGTATAGGGAGCAGGAGCAAGACCACTCAACTCTTTGCTGTTATGgtgagttgtt ... tttgattcagCTATTGGAGATGCTTCTGAATAATTGCGGAGAGCCTGTCCATAGGCAGGTC
EST: gi|71428013|gb|DR809063.1|DR809063
EST:     GAAGTGTATAGGGAGCAGGAGCAAGACCACTCAACTC-TTGCTTGTTATG                         CTATTGGAGATGCTTCTGAATAATTGCGGAGAGCCTGTCCATAGGCAGGT
genomic: GAAGTGTATAGGGAGCAGGAGCAAGACCACTCAACTCTTTGC-TGTTATGgtgagttgtt ... tttgattcagCTATTGGAGATGCTTCTGAATAATTGCGGAGAGCCTGTCCATAGGCAGGT
EST: gi|71326004|gb|DR799684.1|DR799684
EST:     AGAAGTGTATAGGGAGCAGGAGCAAGACCACTCAACTCTTTGCTGTTATG                         CTATTAGAGATGCTTCTGAATATTTGCGGAGAGCCTGTCCATAGGCAGGTC
genomic: AGAAGTGTATAGGGAGCAGGAGCAAGACCACTCAACTCTTTGCTGTTATGgtgagttgtt ... tttgattcagCTATTGGAGATGCTTCTGAATAATTGCGGAGAGCCTGTCCATAGGCAGGTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtgtttttatggttaagctatagtcttgattcagattcacttctatttgattcagCTATTGGAGATGCTTCTGAATAATTGCGGAGAGCCTGTCCATAGGCAGGTCATTGATAATGGCCTTCTTCCAATACTTGTGAAGATAGTGAAGAAAAAG
                                       cttctattt  CT-rich tract
                                           tatttgatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
catatgtttttaaattaattagctcacattacataatgtgcgaatgtgtttttatggttaagctatagtcttgattcagattcacttctatttgattcagCTATTGGAGATGCTTCTGAATAATTGCGGAGAGCCTGTCCATAGGCAGGTCATTGATAATGGCCTTCTTCCAATACTTGTGAAGATAGTGAAGAAAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA