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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...acacccctaattcacctcagtacatgtggattgagctgaatacgagagtatctaaataaagctggtttatcaacaccattctttgcccatgttttctcagGTCAAGAACCCATGGCCCAATGTTGACGCTCACAGTGGACTCTTGCTGAACCACTTTGGACTATCTGAAACACG

Basic information

species Zea mays
transcript GRMZM2G063909_T01
intron # 16
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G063909_T01 (Zea mays), 3'ss of exon 16
lower sequence: LOC_Os11g33240.2 (Oryza sativa), 3'ss of exon 17
acacccctaattcacctcagtacatgtggattgagctgaatacgagagtatctaaataaagctggtttatcaacaccattctttgcccatgttttctcagGTCAAGAACCCATGGCCCAATGTTGACGCTCACAGTGGACTCTTGCTGAACCACTTTGGACTATCTGAAACACG
           | |   || || ||   |||   | |   |||     ||| |  ||     ||| | |  |    ||  | ||| |||| ||| |  ||||||| ||||||||||| |||||||| |||||||||||| |  ||||||||||||||||| |||||||| | ||
----------gtaatgccactagatt--gatcatgattgctaccgttttatgtccatcttattggctaaaaagtgacaa-cattgtccatatttcc--agGTCAAAAACCCATGGCCTAATGTTGATGCTCACAGTGGAGTTCTGCTGAACCACTTTGGATTATCTGAAGCTCG

upper sequence: GRMZM2G063909_T01 (Zea mays), 3'ss of exon 16
lower sequence: LOC_Os02g10070.1 (Oryza sativa), 3'ss of exon 17
---acacccctaattcacctcagtacatgtggattgagctgaatacgagagtatctaaataaagctggtttatcaac-----accattctttgcccatgttttctcagGTCAAGAACCCATGGCCCAATGTTGACGCTCACAGTGGACTCTTGCTGAACCACTTTGGACTATCTGAAACACG
   |  |  |||  |    ||| ||  | | | |     | | ||||      ||    ||   |    | ||   |     |  |       ||      || ||||||||| ||||||||||| |||||||| |||||||| ||| |  | ||||||||||||||| |||||||| | ||
gtaatgctactagattga-tcaataattattgctcct-ttaattacggctccttcagtttacttccatctcattggctaagaaataagaacatccttcacattttcagGTCAAAAACCCATGGCCTAATGTTGATGCTCACAGCGGAGTTCTACTGAACCACTTTGGATTATCTGAAGCTCG

upper sequence: GRMZM2G063909_T01 (Zea mays), 3'ss of exon 16
lower sequence: AT2G44350.2 (Arabidopsis thaliana), 3'ss of exon 17
-----------------------------------------acacccctaatt-cacctcagtacatgtggattgagctgaatacgagagtatctaaataaagctggtttatcaacaccattctttgcccatg-----ttttctcagGTCAAGAACCCATGGCCCAATGTTGACGCTCACAGTGGACTCTTGCTGAACCACTTTGGACTATCTGAAACACG
                                         |  || | ||   | || ||  || |         |||     |    | ||||      |     ||| | |    | | |    || |||     || |  ||||| |||||||| ||||| |||||||| |||||||||||  ||||||||||||||| ||| ||| | ||| || |
gtagtatctctatccttcgtttaccatggtgatccttcaatattccaccaacaactccacaacaccttacctacatgctaggggcttatgaatctcttgcgaatcaattttttatttacttgcgaatccgatgatggcttgttacagGTGAAGAACCCGTGGCCAAATGTTGATGCTCACAGTGGGGTCTTGCTGAACCACTATGGTCTAACCGAAGCAAG

upper sequence: GRMZM2G063909_T01 (Zea mays), 3'ss of exon 16
lower sequence: Vv13s0156g00180.t01 (Vitis vinifera), 3'ss of exon 17
-------acacccctaattcacctcagtacatgtggattgagctgaatacgagagtatctaaataaagctggtttatcaacaccattctttgcccatgttttctcagGTCAAGAACCCATGGCCCAATGTTGACGCTCACAGTGGACTCTTGCTGAACCACTTTGGACTATCTGAAACACG
       |||  |||| |  |  || ||| |      ||  |||  |   || |       | | ||    | || |       |||     | | |||      |||| || ||||||||||||||||| || |||||||||||  ||||||||||||| |||||  ||   ||| ||||
ttctgcaacatgcctactagaattctgtaaaataaactttggcttca-gtgatacctgtggagttaacagtgattgtttttgggatttgggacacttgt------agGTTAAAAACCCATGGCCCAATGTCGATGCTCACAGTGGGGTCTTGCTGAACCATTTTGGTTTACACGAAGCACG

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|211314255|gb|FK994155.1|FK994155
EST:     TGTCCAAGTTATATGAGGTCGTGCCTCCGATCCTCACTGAGCTGGGAAAG                         GTCAAGAACCCATGGCCCAATGTTGACGCTCACAGTGGACTCTTGCTGAAC
genomic: TGTCCAAGTTATATGAGGTCGTGCCTCCGATCCTCACTGAGCTGGGAAAGgtaatgtggt ... gttttctcagGTCAAGAACCCATGGCCCAATGTTGACGCTCACAGTGGACTCTTGCTGAAC
EST: gi|60357508|gb|DN224481.1|DN224481
EST:     TGTCCAAGTTATATGAGGTCGTGCCTCCGATCCTCACTGAGCTGGGAAAG                         GTCAAGAACCCATGGCCCAATGTTGACGCTCACAGTGGACTCTTGCTGAAC
genomic: TGTCCAAGTTATATGAGGTCGTGCCTCCGATCCTCACTGAGCTGGGAAAGgtaatgtggt ... gttttctcagGTCAAGAACCCATGGCCCAATGTTGACGCTCACAGTGGACTCTTGCTGAAC
EST: gi|78076903|gb|DV505337.1|DV505337
EST:     TGTCCAAGTTATATGAGGTCGTGCCTCCGATCCTCACTGAGCTGGGAAAG                         GTCAAGAACCCATGGCCCAATGTTGACGCTCACAGTGGACTCTTGCTGAAC
genomic: TGTCCAAGTTATATGAGGTCGTGCCTCCGATCCTCACTGAGCTGGGAAAGgtaatgtggt ... gttttctcagGTCAAGAACCCATGGCCCAATGTTGACGCTCACAGTGGACTCTTGCTGAAC
EST: gi|211458206|gb|FL358448.1|FL358448
EST:     TGTCCAAGTTATATGAGGTCGTGCCTCCGATCCTCACTGAGCTGGGAAAG                         GTCAAGAACCCATGGCCCAATGTTGACGCTCACAGTGGACTCTTGCTGAAC
genomic: TGTCCAAGTTATATGAGGTCGTGCCTCCGATCCTCACTGAGCTGGGAAAGgtaatgtggt ... gttttctcagGTCAAGAACCCATGGCCCAATGTTGACGCTCACAGTGGACTCTTGCTGAAC
EST: gi|60345083|gb|DN212056.1|DN212056
EST:     TGTCCAAGTTATATGAGGTCGTGCCTCCGATCCTCACTGAGCTGGGAAAG                         GTCAAGAACCCATGGCCCAATGTTGACGCTCACAGTGGACTCTTGCTGAAC
genomic: TGTCCAAGTTATATGAGGTCGTGCCTCCGATCCTCACTGAGCTGGGAAAGgtaatgtggt ... gttttctcagGTCAAGAACCCATGGCCCAATGTTGACGCTCACAGTGGACTCTTGCTGAAC
EST: gi|50331232|gb|CO526358.1|CO526358
EST:     TGTCCAAGTTATATGAGGTCGTGCCTCCGATCCTCACTGAGCTGGGAAAG                         GTCAAGAACCCATGGCCCAATGTTGACGCTCACAGTGGACTCTTGCTGAAC
genomic: TGTCCAAGTTATATGAGGTCGTGCCTCCGATCCTCACTGAGCTGGGAAAGgtaatgtggt ... gttttctcagGTCAAGAACCCATGGCCCAATGTTGACGCTCACAGTGGACTCTTGCTGAAC
EST: gi|40334210|gb|CK368280.1|CK368280
EST:     TGTCCAAGTTATATGAGGTCGTGCCTCCGATCCTCACTGAGCTGGGAAAG                         GTCAAGAACCCATGGCCCAATGTTGACGCTCACAGTGGACTCTTGCTGAAC
genomic: TGTCCAAGTTATATGAGGTCGTGCCTCCGATCCTCACTGAGCTGGGAAAGgtaatgtggt ... gttttctcagGTCAAGAACCCATGGCCCAATGTTGACGCTCACAGTGGACTCTTGCTGAAC
EST: gi|60400601|gb|DN233408.1|DN233408
EST:     TGTCCAAGTTATATGAGGTCGTGCCTCCGATCCTCACTGAGCTGGGAAAG                         GTCAAGAACCCATGGCCCAATGTTGACGCTCACAGTGGACTCTTGCTGAAC
genomic: TGTCCAAGTTATATGAGGTCGTGCCTCCGATCCTCACTGAGCTGGGAAAGgtaatgtggt ... gttttctcagGTCAAGAACCCATGGCCCAATGTTGACGCTCACAGTGGACTCTTGCTGAAC
EST: gi|60354991|gb|DN221964.1|DN221964
EST:     TGTCCAAGTTATATGAGGTCGTGCCTCCGATCCTCACTGAGCTGGGAAAG                         GTCAAGAACCCATGGCCCAATGTTGACGCTCACAGTGGACTCTTGCTGAAC
genomic: TGTCCAAGTTATATGAGGTCGTGCCTCCGATCCTCACTGAGCTGGGAAAGgtaatgtggt ... gttttctcagGTCAAGAACCCATGGCCCAATGTTGACGCTCACAGTGGACTCTTGCTGAAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gagtatctaaataaagctggtttatcaacaccattctttgcccatgttttctcagGTCAAGAACCCATGGCCCAATGTTGACGCTCACAGTGGACTCTTGCTGAACCACTTTGGACTATCTGAAACACG
    atctaaa  putative branch site (score: 3)
                                            tgttttctc  putative PPT
     tctaaataaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
acacccctaattcacctcagtacatgtggattgagctgaatacgagagtatctaaataaagctggtttatcaacaccattctttgcccatgttttctcagGTCAAGAACCCATGGCCCAATGTTGACGCTCACAGTGGACTCTTGCTGAACCACTTTGGACTATCTGAAACACG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGTGGA
- - - - - - - - - -gtacatg
- - - - - - - - - - - - - - - -tgagctg
- - - - - - - - - - - - - - - - - - - - - - - - - - -aaataaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gctggtt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - caacacc