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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttctatgtttgtgctggcgttagatttcttatcttgtatttgcacattttaggtttatctgattctgtttgtatctatggtcactgttgaagGGTGCTAGGTACACCGAATGAACAAGGTTGGCCTGGAGTCAGTTGTTTGCCTGACTTCAAGACTGCTTTCCCCAGGTGGCAAGCTCAG

Basic information

species Zea mays
transcript GRMZM2G143213_T01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G143213_T02 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os03g02680.1 (Oryza sativa), 3'ss of exon 4
gttctatgtttgtgctggcgttagatttctta--tcttgtatttgcacattttaggtttatctgattc-tgt-ttgtatctatggtcactgttgaagGGTGCTAGGTACACCGAATGAACAAGGTTGGCCTGGAGTCAGTTGTTTGCCTGACTTCAAGACTGCTTTCCCCAGGTGGCAAGCTCAG
|||||||  |||| |||   |||  ||| ||   |||  || |||    |||      | | |||||  ||| |||| |   |||| ||| ||||||||| ||||| || || ||||||||| ||||||| ||||| || |  || ||||||| |||| |||||||||||| ||||||||| |||
gttctattattgtactgagattacctttttttgttctgttaattgtgtttttgccaactctatgatttatgtgttgtgttc-tggttacttttgaagGGTACTAGGAACTCCAAATGAACAAAGTTGGCCAGGAGTTAGCTCATTACCTGACTACAAGTCTGCTTTCCCCAAGTGGCAAGCACAG

upper sequence: GRMZM2G143213_T02 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os03g01850.2 (Oryza sativa), 3'ss of exon 5
gttctatgtttgtgctggcgttagatttctta--tcttgtatttgcacattttaggtttatctgattctgtttgtat-ctatggtcactgttgaagGGTGCTAGGTACACCGAATGAACAAGGTTGGCCTGGAGTCAGTTGTTTGCCTGACTTCAAGACTGCTTTCCCCAGGTGGCAAGCTCAG
|||||||  | || |||   |||  ||| ||   |||  ||||||    |||      | |||||||    | || |  | |||| ||| ||||||||| ||||| || || ||||||||| ||||||| ||||| || |  || ||||||| |||| |||||||||||| |||||| || |||
gttctattatcgtactgagattacctttttttgttctgttatttgtgtttttgccaactctctgatttatgtggtgtgttctggttacttttgaagGGTACTAGGAACTCCAAATGAACAAAGTTGGCCAGGAGTTAGCTCATTACCTGACTACAAGTCTGCTTTCCCCAAGTGGCAGGCACAG
















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|18166338|gb|BM336177.1|BM336177
EST:     GGTGATTCTGAGATCGACGAACTGTTCAAGATATTCAG                         GGTGCTAGGTACACCGAATGAACAAGGTTGGCCTGGAGTCAGTTGTTTGCC
genomic: GGTGATTCTGAGATCGACGAACTGTTCAAGATATTCAGgttctatgtt ... actgttgaagGGTGCTAGGTACACCGAATGAACAAGGTTGGCCTGGAGTCAGTTGTTTGCC
EST: gi|78093070|gb|DV521444.1|DV521444
EST:     CCACTATTCCCTGGTGATTCTGAGATCGACGAACTGTTCAAGATATTCAG                         GGTGCTAGGTACACCGAATGAACAAGGTTGGCCTGGAGTCAGTTGTTTGCC
genomic: CCACTATTCCCTGGTGATTCTGAGATCGACGAACTGTTCAAGATATTCAGgttctatgtt ... actgttgaagGGTGCTAGGTACACCGAATGAACAAGGTTGGCCTGGAGTCAGTTGTTTGCC
EST: gi|60397283|gb|DN230099.1|DN230099
EST:     CCACTATTCCCTGGTGATTCTGAGATCGACGAACTGTTCAAGATATTCAG                         GGTGCTAGGTACACCGAATGAACAAGGTTGGCCTGGAGTCAGTTGTTTGCC
genomic: CCACTATTCCCTGGTGATTCTGAGATCGACGAACTGTTCAAGATATTCAGgttctatgtt ... actgttgaagGGTGCTAGGTACACCGAATGAACAAGGTTGGCCTGGAGTCAGTTGTTTGCC
EST: gi|27575994|gb|CA998688.1|CA998688
EST:     CCACTATTCCCTGGTGATTCTGAGATCGACGAACTGTTCAAGATATTCAG                         GGTGCTAGGTACACCGAATGAACAAGGTTGGCCTGGAGTCAGTTGTTTGCC
genomic: CCACTATTCCCTGGTGATTCTGAGATCGACGAACTGTTCAAGATATTCAGgttctatgtt ... actgttgaagGGTGCTAGGTACACCGAATGAACAAGGTTGGCCTGGAGTCAGTTGTTTGCC
EST: gi|5847313|gb|AW000392.1|AW000392
EST:     CCACTATTCCCTGGTGATTCTGAGATTGACGAACTGTTCAAGATATTCAG                         GGTGCTAGGTACACCGAATGAACAAAGTTGGCCTGGAGTCAGTTGTTTGCC
genomic: CCACTATTCCCTGGTGATTCTGAGATCGACGAACTGTTCAAGATATTCAGgttctatgtt ... actgttgaagGGTGCTAGGTACACCGAATGAACAAGGTTGGCCTGGAGTCAGTTGTTTGCC
EST: gi|91051178|gb|EB161596.1|EB161596
EST:     CCACTATTCCCTGGTGATTCTGAGATGGACGAACTGTTCAAGATATTCAG                         GGTGCTAGGTACACCGAATGAACAAGGTTGGCCTGGAGTCAGTTGTTTGCC
genomic: CCACTATTCCCTGGTGATTCTGAGATCGACGAACTGTTCAAGATATTCAGgttctatgtt ... actgttgaagGGTGCTAGGTACACCGAATGAACAAGGTTGGCCTGGAGTCAGTTGTTTGCC
EST: gi|32916297|gb|CF021109.1|CF021109
EST:     CCACTATTCCCTGGTGATTCTGAGATCGACGAACTGTTCAAGATATTCAG                         GGTGCTAGGTACACCGAATGAACAAGGTTGGCCTGGAGTCAGTTGTTTGCC
genomic: CCACTATTCCCTGGTGATTCTGAGATCGACGAACTGTTCAAGATATTCAGgttctatgtt ... actgttgaagGGTGCTAGGTACACCGAATGAACAAGGTTGGCCTGGAGTCAGTTGTTTGCC
EST: gi|31910663|gb|CD651537.1|CD651537
EST:     CCACTATTCCCTGGTGATTCTGAGATCGACGAACTGTTCAAGATATTCAG                         GGTGCTAGGTACACCGAATGAACAAGGTTGGCCTGGAGTCAGTTGTTTGCC
genomic: CCACTATTCCCTGGTGATTCTGAGATCGACGAACTGTTCAAGATATTCAGgttctatgtt ... actgttgaagGGTGCTAGGTACACCGAATGAACAAGGTTGGCCTGGAGTCAGTTGTTTGCC
EST: gi|60394332|gb|DN227202.1|DN227202
EST:     CCACTATTCCCTGGTGATTCTGAGATCGACGAACTGTTCAAGATATTCAG                         GGTGCTAGGTACACCGAATGAACAAGGTTGGCCTGGAGTCAGTTGTTTGCC
genomic: CCACTATTCCCTGGTGATTCTGAGATCGACGAACTGTTCAAGATATTCAGgttctatgtt ... actgttgaagGGTGCTAGGTACACCGAATGAACAAGGTTGGCCTGGAGTCAGTTGTTTGCC
EST: gi|110194217|gb|EC876115.1|EC876115
EST:     CCACTATTCCCTGGTGATTCTGAGATCGACGAACTGTTCAAGATATTCAG                         GGTGCTAGGTACACCGAATGAACAAGGTTGGCCTGGAGTCAGTTGTTTGCC
genomic: CCACTATTCCCTGGTGATTCTGAGATCGACGAACTGTTCAAGATATTCAGgttctatgtt ... actgttgaagGGTGCTAGGTACACCGAATGAACAAGGTTGGCCTGGAGTCAGTTGTTTGCC
EST: gi|60344999|gb|DN211972.1|DN211972
EST:     CCACTATTCCCTGGTGATTCTGAGATTGACGAACTGTTCAAGATATTCAG                         GGTGCTAGGTACACCGAATGAACAAAGTTGGCCTGGAGTCAGTTGTTTGCC
genomic: CCACTATTCCCTGGTGATTCTGAGATCGACGAACTGTTCAAGATATTCAGgttctatgtt ... actgttgaagGGTGCTAGGTACACCGAATGAACAAGGTTGGCCTGGAGTCAGTTGTTTGCC
EST: gi|60394730|gb|DN227600.1|DN227600
EST:     CCACTATTCCCTGGTGATTCTGAGATCGACGAACTGTTCAAGATATTCAG                         GGTGCTAGGTACACCGAATGAACAAGGTTGGCCTGGAGTCAGTTGTTTGCC
genomic: CCACTATTCCCTGGTGATTCTGAGATCGACGAACTGTTCAAGATATTCAGgttctatgtt ... actgttgaagGGTGCTAGGTACACCGAATGAACAAGGTTGGCCTGGAGTCAGTTGTTTGCC
EST: gi|78074515|gb|DV502949.1|DV502949
EST:     CCACTATTCCCTGGTGATTCTGAGATCGACGAACTGTTCAAGATATTCAG                         GGTGCTAGGTACACCGAATGAACAAGGTTGGCCTGGAGTCAGTTGTTTGCC
genomic: CCACTATTCCCTGGTGATTCTGAGATCGACGAACTGTTCAAGATATTCAGgttctatgtt ... actgttgaagGGTGCTAGGTACACCGAATGAACAAGGTTGGCCTGGAGTCAGTTGTTTGCC
EST: gi|60398759|gb|DN231575.1|DN231575
EST:     CCACTATTCCCTGGTGATTCTGAGATCGACGAACTGTTCAAGATATTCAG                         GGTGCTAGGTACACCGAATGAACAAGGTTGGCCTGGAGTCAGTTGTTTGCC
genomic: CCACTATTCCCTGGTGATTCTGAGATCGACGAACTGTTCAAGATATTCAGgttctatgtt ... actgttgaagGGTGCTAGGTACACCGAATGAACAAGGTTGGCCTGGAGTCAGTTGTTTGCC
EST: gi|67024512|gb|CO453261.1|CO453261
EST:     CCACTATTCCCTGGTGATTCTGAGATTGACGAACTGTTCAAGATATTCAG                         GGTGCTAGGTACACCGAATGAACAAAGTTGGCCTGGAGTCAGTTGTTTGCC
genomic: CCACTATTCCCTGGTGATTCTGAGATCGACGAACTGTTCAAGATATTCAGgttctatgtt ... actgttgaagGGTGCTAGGTACACCGAATGAACAAGGTTGGCCTGGAGTCAGTTGTTTGCC
EST: gi|31909621|gb|CD651010.1|CD651010
EST:     CCACTATTCCCTGGTGATTCTGAGATCGACGAACTGTTCAAGATATTCAG                         GGTGCTAGGTACACCGAATGAACAAGGTTGGCCTGGAGTCAGTTGTTTGCC
genomic: CCACTATTCCCTGGTGATTCTGAGATCGACGAACTGTTCAAGATATTCAGgttctatgtt ... actgttgaagGGTGCTAGGTACACCGAATGAACAAGGTTGGCCTGGAGTCAGTTGTTTGCC
EST: gi|18166704|gb|BM336543.1|BM336543
EST:     CCACTATTCCCTGGTGATTCTGAGATCGACGAACTGTTCAAGATATTCAG                         GGTGCTAGGTACACCGAATGAACAAGGTTGGCCTGGAGTCAGTTGTTTGCC
genomic: CCACTATTCCCTGGTGATTCTGAGATCGACGAACTGTTCAAGATATTCAGgttctatgtt ... actgttgaagGGTGCTAGGTACACCGAATGAACAAGGTTGGCCTGGAGTCAGTTGTTTGCC
EST: gi|18650116|gb|BM498935.1|BM498935
EST:     TATTCCCTGGTGATTCTGAGATCGACGAACTGTTCAAGATATTCAG                         GGTGCTAGGTACACCGAATGAACAAAGTTGGCCTGGAGTCAGTTGTTTGCC
genomic: TATTCCCTGGTGATTCTGAGATCGACGAACTGTTCAAGATATTCAGgttctatgtt ... actgttgaagGGTGCTAGGTACACCGAATGAACAAGGTTGGCCTGGAGTCAGTTGTTTGCC
EST: gi|4967063|gb|AI692029.1|AI692029
EST:     CCACTATTCCCTGGTGATTCTGAGATCGACGAACTGTTCAAGATATTCAG                         GGTGCTAGGTACACCGAATGAACAAAGTTGGCCTGGAGTCAGTTGTTTGCC
genomic: CCACTATTCCCTGGTGATTCTGAGATCGACGAACTGTTCAAGATATTCAGgttctatgtt ... actgttgaagGGTGCTAGGTACACCGAATGAACAAGGTTGGCCTGGAGTCAGTTGTTTGCC
EST: gi|37384260|gb|CF629190.1|CF629190
EST:     CCACTATTCCCTGGTGATTCTGAGATCGACGAACTGTTCAAGATATTCAG                         GGTGCTAGGTACACCGAATGAACAAAGTTGGCCTGGAGTCAGTTGTTTGCC
genomic: CCACTATTCCCTGGTGATTCTGAGATCGACGAACTGTTCAAGATATTCAGgttctatgtt ... actgttgaagGGTGCTAGGTACACCGAATGAACAAGGTTGGCCTGGAGTCAGTTGTTTGCC
EST: gi|17929629|gb|BM266589.1|BM266589
EST:     CCACTATTCCCTGGTGATTCTGAGATCGACGAACTGTTCAAGATATTCAG                         GGTGCTAGGTACACCGAATGAACAAGGTTGGCCTGGAGTCAGTTGTTTGCC
genomic: CCACTATTCCCTGGTGATTCTGAGATCGACGAACTGTTCAAGATATTCAGgttctatgtt ... actgttgaagGGTGCTAGGTACACCGAATGAACAAGGTTGGCCTGGAGTCAGTTGTTTGCC
EST: gi|18162372|gb|BM332211.1|BM332211
EST:     CCACTATTCCCTGGTGATTCTGAGATCGACGAACTGTTCAAGATATTCAG                         GGTGCTAGGTACACCGAATGAACAAGGTTGGCCTGGAGTCAGTTGTTTGCC
genomic: CCACTATTCCCTGGTGATTCTGAGATCGACGAACTGTTCAAGATATTCAGgttctatgtt ... actgttgaagGGTGCTAGGTACACCGAATGAACAAGGTTGGCCTGGAGTCAGTTGTTTGCC
EST: gi|18167215|gb|BM337054.1|BM337054
EST:     CCACTATTCCCTGGTGATTCTGAGATCGACGAACTGTTCAAGATATTCAG                         GGTGCTAGGTACACCGAATGAACAAGGTTGGCCTGGAGTCAGTTGTTTGCC
genomic: CCACTATTCCCTGGTGATTCTGAGATCGACGAACTGTTCAAGATATTCAGgttctatgtt ... actgttgaagGGTGCTAGGTACACCGAATGAACAAGGTTGGCCTGGAGTCAGTTGTTTGCC
EST: gi|60398446|gb|DN231262.1|DN231262
EST:     CCACTATTCCCTGGTGATTCTGAGATCGACGAACTGTTCAAGATATTCAG                         GGTGCTAGGTACACCGAATGAACAAAGTTGGCCTGGAGTCAGTTGTTTGCC
genomic: CCACTATTCCCTGGTGATTCTGAGATCGACGAACTGTTCAAGATATTCAGgttctatgtt ... actgttgaagGGTGCTAGGTACACCGAATGAACAAGGTTGGCCTGGAGTCAGTTGTTTGCC
EST: gi|12968998|gb|BG265943.1|BG265943
EST:     CCACTATTCCCTGGTGATTCTGAGATCGACGAACTGTTCAAGATATTCAG                         GGTGCTAGGTACACCGAATGAACAAAGTTGGCCTGGAGTCAGTTGTTTGCC
genomic: CCACTATTCCCTGGTGATTCTGAGATCGACGAACTGTTCAAGATATTCAGgttctatgtt ... actgttgaagGGTGCTAGGTACACCGAATGAACAAGGTTGGCCTGGAGTCAGTTGTTTGCC
EST: gi|78025082|gb|DV493469.1|DV493469
EST:     CCACTATTCCCTGGTGATTCTGAGATCGACGAACTGTTCAAGATATTCAG                         GGTGCTAGGTACACCGAATGAACAAAGTTGGCCTGGAGTCAGTTGTTTGCC
genomic: CCACTATTCCCTGGTGATTCTGAGATCGACGAACTGTTCAAGATATTCAGgttctatgtt ... actgttgaagGGTGCTAGGTACACCGAATGAACAAGGTTGGCCTGGAGTCAGTTGTTTGCC
EST: gi|18163570|gb|BM333409.1|BM333409
EST:     CCACTATTCCCTGGTGATTCTGAGATCGACGAACTGTTCAAGATATTCAG                         GGTGCTAGGTACACCGAATGAACAAGGTTGGCCTGGAGTCAGTTGTTTGCC
genomic: CCACTATTCCCTGGTGATTCTGAGATCGACGAACTGTTCAAGATATTCAGgttctatgtt ... actgttgaagGGTGCTAGGTACACCGAATGAACAAGGTTGGCCTGGAGTCAGTTGTTTGCC
EST: gi|5525594|gb|AI861487.1|AI861487
EST:     CCACTATTCCCTGGTGATTCTGAGATTGACGAACTGTTCAAGATATTCAG                         GGTGCTAGGTACACCGAATGAACAAAGTTGGCCTGGAGTCAGTTGTTTGCC
genomic: CCACTATTCCCTGGTGATTCTGAGATCGACGAACTGTTCAAGATATTCAGgttctatgtt ... actgttgaagGGTGCTAGGTACACCGAATGAACAAGGTTGGCCTGGAGTCAGTTGTTTGCC
EST: gi|5819371|gb|AI987577.1|AI987577
EST:     CCACTATTCCCTGGTGATTCTGAGATTGACGAACTGTTCAAGATATTCAG                         GGTGCTAGGTACACCGAATGAACAAAGTTGGCCTGGAGTCAGTTGTTTGCC
genomic: CCACTATTCCCTGGTGATTCTGAGATCGACGAACTGTTCAAGATATTCAGgttctatgtt ... actgttgaagGGTGCTAGGTACACCGAATGAACAAGGTTGGCCTGGAGTCAGTTGTTTGCC
EST: gi|211268426|gb|FL478582.1|FL478582
EST:     CCACTATTCCCTGGTGATTCTGAGATCGACGAACTGTTCAAGATATTCAG                         GGTGCTAGGTACACCGAATGAACAAGGTTGGCCTGGAGTCAGTTGTTTGCC
genomic: CCACTATTCCCTGGTGATTCTGAGATCGACGAACTGTTCAAGATATTCAGgttctatgtt ... actgttgaagGGTGCTAGGTACACCGAATGAACAAGGTTGGCCTGGAGTCAGTTGTTTGCC

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 4 RNA-Seq libraries.


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 223

TGACGTATGGTCTGTGTGGCTGTATCTTTGCGGAAATGGTGAACCAAAAGCCACTATTCCCTGGTGATTCTGAGATCGACGAACTGTTCAAGATATTCAGgttctatgtt ... actgttgaagGGTGCTAGGTACACCGAATGAACAAGGTTGGCCTGGAGTCAGTTGTTTGCCTGACTTCAAGACTGCTTTCCCCAGGTGGCAAGCTCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 112

TGACGTATGGTCTGTGTGGCTGTATCTTTGCGGAAATGGTGAACCAAAAGCCACTATTCCCTGGTGATTCTGAGATCGACGAACTGTTCAAGATATTCAGgttctatgtt ... actgttgaagGGTGCTAGGTACACCGAATGAACAAGGTTGGCCTGGAGTCAGTTGTTTGCCTGACTTCAAGACTGCTTTCCCCAGGTGGCAAGCTCAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 101

TGACGTATGGTCTGTGTGGCTGTATCTTTGCGGAAATGGTGAACCAAAAGCCACTATTCCCTGGTGATTCTGAGATCGACGAACTGTTCAAGATATTCAGgttctatgtt ... actgttgaagGGTGCTAGGTACACCGAATGAACAAGGTTGGCCTGGAGTCAGTTGTTTGCCTGACTTCAAGACTGCTTTCCCCAGGTGGCAAGCTCAG


Block sizes: 39 (upstream exon), 49 (downstream exon)
Score: 107

TGACGTATGGTCTGTGTGGCTGTATCTTTGCGGAAATGGTGAACCAAAAGCCACTATTCCCTGGTGATTCTGAGATCGACGAACTGTTCAAGATATTCAGgttctatgtt ... actgttgaagGGTGCTAGGTACACCGAATGAACAAGGTTGGCCTGGAGTCAGTTGTTTGCCTGACTTCAAGACTGCTTTCCCCAGGTGGCAAGCTCAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atttgcacattttaggtttatctgattctgtttgtatctatggtcactgttgaagGGTGCTAGGTACACCGAATGAACAAGGTTGGCCTGGAGTCAGTTGTTTGCCTGACTTCAAGACTGCTTTCCCCAGGTGGCAAGCTCAG
                   atctgat  putative branch site (score: 107)
      acatttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttctatgtttgtgctggcgttagatttcttatcttgtatttgcacattttaggtttatctgattctgtttgtatctatggtcactgttgaagGGTGCTAGGTACACCGAATGAACAAGGTTGGCCTGGAGTCAGTTGTTTGCCTGACTTCAAGACTGCTTTCCCCAGGTGGCAAGCTCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA