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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cagatctgtcagttttctgtgtgattattttttttggtcagtgcaacactccaatgcatgtacatctgcagactcaaccaaatttattgttcatattcagATATACCATGGAGCGCCCTCGATTTAGTGATCATCTTGAAGCAATCAAGTTTATCTGCAAAGATTTTTGGTCAGAGCTGTTCAAGAAGCAGATTGACAAT

Basic information

species Zea mays
transcript GRMZM5G886989_T03
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G886989_T03 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os09g06970.3 (Oryza sativa), 3'ss of exon 1
----cagatctgtcagttttctgtgt-gattattttttttggtcagtgcaacactccaatgcatgtacatctgcagactcaaccaaatttattgttcatattcagATATACCATGGAGCGCCCTCGATTTAGTGATCATCTTGAAGCAATCAAGTTTATCTGCAAAGATTTTTGGTCAGAGCTGTTCAAGAAGCAGATTGACAAT
    || || |  | | | ||||  | |  ||| | | ||||   || |    ||||| | | ||||   ||||    | ||||| | ||  |||||| | |||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||| |||||||||||||| |||||||||||||||||||||
agcacaaatgtaactgctgtctgaattgcatatgtgtattgg---gttcttacctccactccttgtagtgctgcga--ttaaccataatttctgttcaaaatcagATATACCATGGAGCGCCCTCGATTTAGTGATCATCTTGAAGCAATCAAATTTATCTGCAAAGACTTTTGGTCAGAGCTATTCAAGAAGCAGATTGACAAT

upper sequence: GRMZM5G886989_T03 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os07g19060.2 (Oryza sativa), 3'ss of exon 1
-cagatctgtcagttttctgtg-tgattattttttttg-gtcagtgcaacactccaatgcatgtacatctgcagactcaaccaaatttattgttcatattcagATATACCATGGAGCGCCCTCGATTTAGTGATCATCTTGAAGCAATCAAGTTTATCTGCAAAGATTTTTGGTCAGAGCTGTTCAAGAAGCAGATTGACAAT
 || || |  |   |  |||   |  ||   || |||   |  || |   ||  | | ||  || |   |||| | | ||||||| ||  |||||| | |||||||||| ||||||||||||||||||||||||||||||||||||||||| |||||||||||||| |||||||||||| | ||||||||||| |||||||||
acaaatataactactcactgaaatatttgcattctttatattggttccttacctccaggccagtgc---tgcaaagttaaccaaagtttctgttcaaaatcagATATACTATGGAGCGCCCTCGATTTAGTGATCATCTTGAAGCAATCAAATTTATCTGCAAAGACTTTTGGTCAGAGTTATTCAAGAAGCAAATTGACAAT

upper sequence: GRMZM5G886989_T03 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA19G42850.1 (Glycine max), 3'ss of exon 1
--cagatctgtcagttttctgtgtgattattttttttggtcagtgcaacactccaatgcatgtacatctgcagactcaaccaaatttattgttcatattcagATATACCATGGAGCGCCCTCGATTTAGTGATCATCTTGAAGCAATCAAGTTTATCTGCAAAGATTTTTGGTCAGAGCTGTTCAAGAAGCAGATTGACAAT
   |  | ||| |   |    |||  || |   |  ||        ||       || |||| |  |     || | |   ||| || | |||  |  | || |||||||||||||| ||||| || |  |||||||| || || |||||||| |||||||| ||||||||||| ||||| |||||||||||||||||||| 
gttaactttgtaatgatgtaatgtagttctacatgatgactctctaaagggaattat-catgaaatttgattgaattagt-aaaattgtggtttgttgttagGTATACCATGGAGCGGCCTCGGTTCACGGATCATCTCGAGGCCATCAAGTTCATCTGCAAGGATTTTTGGTCTGAGCTCTTCAAGAAGCAGATTGACAAC

upper sequence: GRMZM5G886989_T03 (Zea mays), 3'ss of exon 2
lower sequence: AT3G05000.1 (Arabidopsis thaliana), 3'ss of exon 1
cagatctgtcagtttt----ctgtgtgattattttttttggtcagtgcaacactccaatgcatgtacatctgcagactcaaccaaatttattgttcatattcagATATACCATGGAGCGCCCTCGATTTAGTGATCATCTTGAAGCAATCAAGTTTATCTGCAAAGATTTTTGGTCAGAGCTGTTCAAGAAGCAGATTGACAAT
    | || |    |     |||| | |   | || | || |    |  |     || |  |  |   | |||| |   |    |   | || |   |  | || || || |||||  | ||  | || ||||| ||||| || ||||||||||||||||||||||| || ||||| ||| | ||||||||||||||||| |||
-gtgtttgcctacataaaaactgttttacagtgttgtatgatggcagatatttagcattttacttgattgtgcata---acttcagccttttttatgtcgttagGTACACTATGGAAAGACCAAGGTTCAGTGACCATCTAGAGGCAATCAAGTTTATCTGCAAAGACTTCTGGTCTGAGGTCTTCAAGAAGCAGATTGATAAT

upper sequence: GRMZM5G886989_T03 (Zea mays), 3'ss of exon 2
lower sequence: Vv14s0030g00700.t01 (Vitis vinifera), 3'ss of exon 1
-cagatctgtcagttttctgtgtgattattttttttggtcagtgcaacactccaatgcatgtacatctgcagactcaaccaaatttattgttcatattcagATATACCATGGAGCGCCCTCGATTTAGTGATCATCTTGAAGCAATCAAGTTTATCTGCAAAGATTTTTGGTCAGAGCTGTTCAAGAAGCAGATTGACAAT
   ||    |||  | | |       || |  ||    |   |       |    |   |||  |     |     ||  |  | | || ||  | || |||||||| |||||| | || || |||||||||||||| || |||||||||||||||||||| || || ||||| ||||| ||||||||||| || ||||| 
agggagtgatcatatatatagccccataatccttagacttccttttttctttttttttttgtgtagtcataataataaaaaggtat-ttttttttttttagATATACTATGGAGAGGCCCCGGTTTAGTGATCATCTAGAGGCAATCAAGTTTATCTGCAAGGACTTCTGGTCTGAGCTCTTCAAGAAGCAAATAGACAAC

upper sequence: GRMZM5G886989_T03 (Zea mays), 3'ss of exon 2
lower sequence: EFJ32385 (Selaginella moellendorffii), 3'ss of exon 1
---------------------------------------------------------------------------------cagatctgtcagttttct-gtgtgattattttttttggtcag----tgcaacactccaatgcatgtacatctgcaga-------ctcaaccaaatttattgttcatattcagATATACCATGGAGCGCCCTCGATTTAGTGATCATCTTGAAGCAATCAAGTTTATCTGCAAAGATTTTTGGTCAGAGCTGTTCAAGAAGCAGATTGACAAT
                                                                                 |   |   || | || || | |||| | ||  ||||||   |    || ||    | |||| ||  |  ||   |          |    | |  || ||     | | |||||| || |  || || || ||||| |  || ||  | ||||  |||||||| || ||||| ||||| ||| | ||| | |||||||||||||||||||||
gtaaaattttcttacattgccgtggagctcaaatgcttgcgaggaatgtggcttgcattccttgatctgcttagattggttccagtggatctgcttgcttgcgtgaattttccttttggattgatcttgtaagttccaaatgtataaatctcaagaaggtggttttttcttcgatcttttttcctctttccagATACACAAGAGATCGTCCGCGATTCACAGACCACTTGGAAGTCATCAAGTTCATATGCAAGGATTTCTGGGCGGAGGTTTTCAAGAAGCAGATTGACAAT

upper sequence: GRMZM5G886989_T03 (Zea mays), 3'ss of exon 2
lower sequence: EFJ20859 (Selaginella moellendorffii), 3'ss of exon 1
----------------------------------------------------------cagatctgtcagttttct-gtgtgattattttttttggtcag----tgcaacactccaatgcatgtacatctgcaga-------ctcaaccaaatttattgttcatattcagATATACCATGGAGCGCCCTCGATTTAGTGATCATCTTGAAGCAATCAAGTTTATCTGCAAAGATTTTTGGTCAGAGCTGTTCAAGAAGCAGATTGACAAT
                                                          |   |   || | || || | |||| | ||  ||||||   |    || ||    | |||| ||  |  ||   |          |    | |  || ||     | | |||||| || |  || || || ||||| |  |||||  | ||||  |||||||| || ||||| ||||| ||| | ||| | |||||||||||||||||||||
gtaaaattttctgctcaaatgcttgcgaggaatgtggcttgatctgcttagattggttccagtggatctgcttgcttgcgtgaattttccttttggattgatcttgtaagttccaaatgtataaatctcaagaaggtggttttttcttctatcttttttcctctttccagATACACAAGAGATCGTCCGCGATTCACAGATCACTTGGAAGTCATCAAGTTCATATGCAAGGATTTCTGGGCGGAGGTTTTCAAGAAGCAGATTGACAAT

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|50334363|gb|CO529489.1|CO529489
EST:     CGCCGCATCGAGGCCATCGGCTTCCAAGTCGGGCACCAGCTCTCTGAGAG                         ATATACCATGGAGCGCCCTCGATTTAGTGATCATCTTGAAGCAATCAAGTT
genomic: CGCCGCATCGAGGCCATCGGCTTCCAAGTCGGGCACCAGCTCTCTGAGAGgtacaaccag ... tcatattcagATATACCATGGAGCGCCCTCGATTTAGTGATCATCTTGAAGCAATCAAGTT
EST: gi|60343078|gb|DN210051.1|DN210051
EST:     CGCCGCATCGAGGCCATCGGCTTCCAAGTCGGGCACCAGCTCTCTGAGAG                         ATATACCATGGAGCGCCCTCGATTTAGTGATCATCTTGAAGCAATCAAGTT
genomic: CGCCGCATCGAGGCCATCGGCTTCCAAGTCGGGCACCAGCTCTCTGAGAGgtacaaccag ... tcatattcagATATACCATGGAGCGCCCTCGATTTAGTGATCATCTTGAAGCAATCAAGTT
EST: gi|60350952|gb|DN217925.1|DN217925
EST:     CGCCGCATCGAGGCCATCGGCTTCCAAGTCGGGCACCAGCTCTCTGAGAG                         ATATACCATGGAGCGCCCTCGATTTAGTGATCATCTTGAAGCAATCAAGTT
genomic: CGCCGCATCGAGGCCATCGGCTTCCAAGTCGGGCACCAGCTCTCTGAGAGgtacaaccag ... tcatattcagATATACCATGGAGCGCCCTCGATTTAGTGATCATCTTGAAGCAATCAAGTT
EST: gi|60355961|gb|DN222934.1|DN222934
EST:     CGCCGCATCGAGGCCATCGGCTTCCAAGTCGGGCACCAGCTCTCTGAGAG                         ATATACCATGGAGCGCCCTCGATTTAGTGATCATCTTGAAGCAATCAAGTT
genomic: CGCCGCATCGAGGCCATCGGCTTCCAAGTCGGGCACCAGCTCTCTGAGAGgtacaaccag ... tcatattcagATATACCATGGAGCGCCCTCGATTTAGTGATCATCTTGAAGCAATCAAGTT
EST: gi|78075052|gb|DV503486.1|DV503486
EST:     CGGGCACCAGCTCTCTGAGAG                         ATATACCATGGAGCGCCCTCGATTTAGTGATCATCTTGAAGCAATCAAGTT
genomic: CGGGCACCAGCTCTCTGAGAGgtacaaccag ... tcatattcagATATACCATGGAGCGCCCTCGATTTAGTGATCATCTTGAAGCAATCAAGTT
EST: gi|211101165|gb|FL105401.1|FL105401
EST:     CGCCGCATCGAGGCCATCGGCTTCCAAGTCGGGCACCAGCTCTCTGAGAG                         ATATACCATGGAGCGCCCTCGATTTAGTGATCATCTTGAAGCAATCAAGTT
genomic: CGCCGCATCGAGGCCATCGGCTTCCAAGTCGGGCACCAGCTCTCTGAGAGgtacaaccag ... tcatattcagATATACCATGGAGCGCCCTCGATTTAGTGATCATCTTGAAGCAATCAAGTT
EST: gi|60343072|gb|DN210045.1|DN210045
EST:     CGCCGCATCGAGGCCATCGGCTTCCAAGTCGGGCACCAGCTCTCTGAGAG                         ATATACCATGGAGCGCCCTCGATTTAGTGATCATCTTGAAGCAATCAAGTT
genomic: CGCCGCATCGAGGCCATCGGCTTCCAAGTCGGGCACCAGCTCTCTGAGAGgtacaaccag ... tcatattcagATATACCATGGAGCGCCCTCGATTTAGTGATCATCTTGAAGCAATCAAGTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acactccaatgcatgtacatctgcagactcaaccaaatttattgttcatattcagATATACCATGGAGCGCCCTCGATTTAGTGATCATCTTGAAGCAATCAAGTTTATCTGCAAAGATTTTTGGTCAGAGCTGTTCAAGAAGCAGATTGACAAT
                                  aaatttattgttcata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cagatctgtcagttttctgtgtgattattttttttggtcagtgcaacactccaatgcatgtacatctgcagactcaaccaaatttattgttcatattcagATATACCATGGAGCGCCCTCGATTTAGTGATCATCTTGAAGCAATCAAGTTTATCTGCAAAGATTTTTGGTCAGAGCTGTTCAAGAAGCAGATTGACAAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGAT