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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agtctggaagtaaaaaacaaatctctctcaagcaacaacacttcttagcttgcacagtggcctcgctgctgtaaattatgctaatgcgcgccgaacgcagTGACCTTATCGAAGACCAAGAAGAAGCCAGGTTTAGAGCGCAAGGGCAAAGTAGTCGCCGAGATAAAAGATGCTGTCGACAAATACAGCAGCGCCTATGT

Basic information

species Zea mays
transcript GRMZM2G467086_T01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G467086_T01 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os12g01430.1 (Oryza sativa), 3'ss of exon 1
---------agtctggaagtaaaaaacaaatctctctcaagcaacaacacttcttagcttgcacagtggcctcgctgctgtaaattatgctaatgcgcgccgaacgcagTGACCTTATCGAAGACCAAGAAGAAGCCAGGTTTAGAGCGCAAGGGCAAAGTAGTCGCCGAGATAAAAGATGCTGTCGACAAATACAGCAGCGCCTATGT
         |  ||| |  |     ||| ||| ||||        ||      |||| | |   |   ||  |   ||| ||| || |||   ||     ||| |||||| |||||||| ||||||||||||||||| || |||||||||||||||||||| ||  |||| || |||||||| |||||  | |||   |  ||||||||
tttttttctatcctgcatattctgcacagatcgctcttgttttgtaa------ttagttagt-tatcagcaccaaagctctaatttgtgcccctgatt--cgagcgcagTAACCTTATCCAAGACCAAGAAGAAGCCTGGATTAGAGCGCAAGGGCAAAGTTGTTACCGATATCAAAGATGCCGTCGAGCACTACGCTAATGCCTATGT

upper sequence: GRMZM2G467086_T01 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os11g01420.1 (Oryza sativa), 3'ss of exon 1
---------agtctggaagtaaaaaacaaatctctctcaagcaacaacacttcttagcttgcacagtggcctcgctgctgtaaattatgctaatgcgcgccgaacgcagTGACCTTATCGAAGACCAAGAAGAAGCCAGGTTTAGAGCGCAAGGGCAAAGTAGTCGCCGAGATAAAAGATGCTGTCGACAAATACAGCAGCGCCTATGT
         |  ||| |  |     ||| ||| ||||        ||      |||| | |   |   ||  |    || ||| || |||   ||     ||| |||||| |||||||| ||||||||||||||||| || |||||||||||||||||||| ||  |||| || |||||||| |||||  | |||   |  ||||||||
tttttttctatcctgcatattctgcacagatcgctcttgttttgtaa------ttagttagt-tatcagcaccaaatctctaatttgtgcccctgatt--cgagcgcagTAACCTTATCCAAGACCAAGAAGAAGCCTGGATTAGAGCGCAAGGGCAAAGTGGTTACCGATATCAAAGATGCCGTCGAGCACTACGCTAATGCCTATGT
















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|21891514|gb|BQ744727.1|BQ744727
EST:     AGAGGAAGGAAGCAGGAACGCGATGCCGAAGTCGAAGCGCAACCGCCCAG                         TGACCTTATCGAAGACCAAGAAGAAGCCAGGTTTAGAGCGCAAGGGCAAAG
genomic: CGAGGAAGGAAGCAGGAACGCGATGCCGAAGTCGAAGCGCAACCGCCCAGgtgatcatca ... ccgaacgcagTGACCTTATCGAAGACCAAGAAGAAGCCAGGTTTAGAGCGCAAGGGCAAAG
EST: gi|149010282|gb|EE042111.2|EE042111
EST:     CGAGGAAGGAAGCAGGAACGCGATGCCGAAGTCGAAGCGCAACCGCCCAG                         TGACCTTATCGAAGACCAAGAAGAAGCCAGGTTTAGAGCGCAAGGGCAAAG
genomic: CGAGGAAGGAAGCAGGAACGCGATGCCGAAGTCGAAGCGCAACCGCCCAGgtgatcatca ... ccgaacgcagTGACCTTATCGAAGACCAAGAAGAAGCCAGGTTTAGAGCGCAAGGGCAAAG
EST: gi|22133771|gb|BQ833893.1|BQ833893
EST:     GAGGAAGGAAGCAGGAACGCGATGCCGAAGTCGAAGCGCAACCGCCCAG                         TGACCTTATCGAAGACCAAGAAGAAGCCAGGTTTAGAGCGCAAGGGCAAAG
genomic: GAGGAAGGAAGCAGGAACGCGATGCCGAAGTCGAAGCGCAACCGCCCAGgtgatcatca ... ccgaacgcagTGACCTTATCGAAGACCAAGAAGAAGCCAGGTTTAGAGCGCAAGGGCAAAG
EST: gi|67015514|gb|CO444263.1|CO444263
EST:     AGAGGAAGGAAGCAGGAACGCGATGCCGAAGTCGAAGCGCAACCGCCCAG                         TGACCTTATCGAAGACCAAGAAGAAGCCAGGTTTAGAGCGCAAGGGCAAAG
genomic: CGAGGAAGGAAGCAGGAACGCGATGCCGAAGTCGAAGCGCAACCGCCCAGgtgatcatca ... ccgaacgcagTGACCTTATCGAAGACCAAGAAGAAGCCAGGTTTAGAGCGCAAGGGCAAAG
EST: gi|20802773|gb|BQ293823.1|BQ293823
EST:     GAGGAAGGAAGCAGGAACGCGATGCCGAAGTCGAAGCGCAACCGCCCAG                         TGACCTTATCGAAGACCAAGAAGAAGCCAGGTTTAGAGCGCAAGGGCAAAG
genomic: GAGGAAGGAAGCAGGAACGCGATGCCGAAGTCGAAGCGCAACCGCCCAGgtgatcatca ... ccgaacgcagTGACCTTATCGAAGACCAAGAAGAAGCCAGGTTTAGAGCGCAAGGGCAAAG
EST: gi|71441332|gb|DR822382.1|DR822382
EST:     CGAGGAAGGAAGCAGGAACGCGATGCCGAAGTCGAAGCGCAACCGCCCAG                         TGACCTTATCGAAGACCAAGAAGAAGCCAGGTTTAGAGCGCAAGGGCAAAG
genomic: CGAGGAAGGAAGCAGGAACGCGATGCCGAAGTCGAAGCGCAACCGCCCAGgtgatcatca ... ccgaacgcagTGACCTTATCGAAGACCAAGAAGAAGCCAGGTTTAGAGCGCAAGGGCAAAG
EST: gi|40337158|gb|CK371228.1|CK371228
EST:     GAGGAAGGAAGCAGGAACGCGATGCCGAAGTCGAAGCGCAACCGCCCAG                         TGACCTTATCGAAGACCAAGAAGAAGCCAGGTTTAGAGCGCAAGGGCAAAG
genomic: GAGGAAGGAAGCAGGAACGCGATGCCGAAGTCGAAGCGCAACCGCCCAGgtgatcatca ... ccgaacgcagTGACCTTATCGAAGACCAAGAAGAAGCCAGGTTTAGAGCGCAAGGGCAAAG
EST: gi|5499042|gb|AI854909.1|AI854909
EST:     CGCGATGCCGAAGTCGAAGCGCAACCGCCCAG                         TGACCTTATCGAAGACCAAGAAGAAGCCAGGTTTAGAGCGCAAGGGCAAAG
genomic: CGCGATGCCGAAGTCGAAGCGCAACCGCCCAGgtgatcatca ... ccgaacgcagTGACCTTATCGAAGACCAAGAAGAAGCCAGGTTTAGAGCGCAAGGGCAAAG
EST: gi|71434423|gb|DR815473.1|DR815473
EST:     CGAGGAAGGAAGCAGGAACGCGATGCCGAAGTCGAAGCGCAACCGCCCAG                         TGACCTTATCGAAGACCAAGAAGAAGCCAGGTTTAGAGCGCAAGGGCAAAG
genomic: CGAGGAAGGAAGCAGGAACGCGATGCCGAAGTCGAAGCGCAACCGCCCAGgtgatcatca ... ccgaacgcagTGACCTTATCGAAGACCAAGAAGAAGCCAGGTTTAGAGCGCAAGGGCAAAG
EST: gi|71447892|gb|DR828942.1|DR828942
EST:     CGAGGAAGGAAGCAGGAACGCGATGCCGAAGTCGAAGCGCAACCGCCCAG                         TGACCTTATCGAAGACCAAGAAGAAGCCAGGTTTAGAGCGCAAGGGCAAAG
genomic: CGAGGAAGGAAGCAGGAACGCGATGCCGAAGTCGAAGCGCAACCGCCCAGgtgatcatca ... ccgaacgcagTGACCTTATCGAAGACCAAGAAGAAGCCAGGTTTAGAGCGCAAGGGCAAAG
EST: gi|71322698|gb|DR798027.1|DR798027
EST:     CGAGGAAGGAAGCAGGAACGCGATGCCGAAGTCGAAGCGCAACCGCCCAG                         TGACCTTATCGAAGACCAAGAAGAAGCCAGGTTTAGAGCGCAAGGGCAAAG
genomic: CGAGGAAGGAAGCAGGAACGCGATGCCGAAGTCGAAGCGCAACCGCCCAGgtgatcatca ... ccgaacgcagTGACCTTATCGAAGACCAAGAAGAAGCCAGGTTTAGAGCGCAAGGGCAAAG
EST: gi|211520202|gb|FL010171.1|FL010171
EST:     CGAGGAAGGAAGCAGGAACGCGATGCCGAAGTCGAAGCGCAACCGCCCAG                         TGACCTTATCGAAGACCAAGAAGAAGCCAGGTTTAGAGCGCAAGGGCAAAG
genomic: CGAGGAAGGAAGCAGGAACGCGATGCCGAAGTCGAAGCGCAACCGCCCAGgtgatcatca ... ccgaacgcagTGACCTTATCGAAGACCAAGAAGAAGCCAGGTTTAGAGCGCAAGGGCAAAG
EST: gi|21088993|gb|BQ401306.1|BQ401306
EST:     AGAGGAAGGAAGCAGGAACGCGATGCCGAAGTCGAAGCGCAACCGCCCAG                         TGACCTTATCGAAGACCAAGAAGAAGCCAGGTTTAGAGCGCAAGGGCAAAG
genomic: CGAGGAAGGAAGCAGGAACGCGATGCCGAAGTCGAAGCGCAACCGCCCAGgtgatcatca ... ccgaacgcagTGACCTTATCGAAGACCAAGAAGAAGCCAGGTTTAGAGCGCAAGGGCAAAG
EST: gi|29130506|gb|CB381210.1|CB381210
EST:     CGAGGAAGGAAGCAGGAACGCGATGCCGAAGTCGAAGCGCAACCGCCCAG                         -GACCTTATCGAAGACCAAGAAGAAGCCAGGTTTAGAGCGCAAGGGCAAAG
genomic: CGAGGAAGGAAGCAGGAACGCGATGCCGAAGTCGAAGCGCAACCGCCCAGgtgatcatca ... ccgaacgcagTGACCTTATCGAAGACCAAGAAGAAGCCAGGTTTAGAGCGCAAGGGCAAAG
EST: gi|22819557|gb|BU499647.1|BU499647
EST:     GAGGAAGGAAGCAGGAACGCGATGCCGAAGTCGAAGCGCAACCGCCCAG                         -GACCTTATCGAAGACCAAGAAGAAGCCAGGTTTAGAGCGCAAGGGCAAAG
genomic: GAGGAAGGAAGCAGGAACGCGATGCCGAAGTCGAAGCGCAACCGCCCAGgtgatcatca ... ccgaacgcagTGACCTTATCGAAGACCAAGAAGAAGCCAGGTTTAGAGCGCAAGGGCAAAG
EST: gi|67020213|gb|CO448962.1|CO448962
EST:     AGAGGGAGGAAGCAGGAACGCGATGCCGAAGTCGAAGCGCAACCGCCCAG                         TGACCTTATCGAAGACCAAGAAGAAGCCAGGTTTAGAGCGCAAGGGCAAAG
genomic: CGAGGAAGGAAGCAGGAACGCGATGCCGAAGTCGAAGCGCAACCGCCCAGgtgatcatca ... ccgaacgcagTGACCTTATCGAAGACCAAGAAGAAGCCAGGTTTAGAGCGCAAGGGCAAAG
EST: gi|120480859|gb|EH211066.1|EH211066
EST:     CGAGGAAGGAAGCAGGAACGCGATGCCGAAGTCGAAGCGCAACCGCCCAG                         TGACCTTATCGAAGACCAAGAAGAAGCCAGGTTTAGAGCGCAAGGGCAAAG
genomic: CGAGGAAGGAAGCAGGAACGCGATGCCGAAGTCGAAGCGCAACCGCCCAGgtgatcatca ... ccgaacgcagTGACCTTATCGAAGACCAAGAAGAAGCCAGGTTTAGAGCGCAAGGGCAAAG
EST: gi|101383868|gb|EB813989.1|EB813989
EST:     CGAGGAAGGAAGCAGGAACGCGATGCCGAAGTCGAAGCGCAACCGCCCAG                         TGACCTTATCGAAGACCAAGAAGAAGCCAGGTTTAGAGCGCAAGGGCAAAG
genomic: CGAGGAAGGAAGCAGGAACGCGATGCCGAAGTCGAAGCGCAACCGCCCAGgtgatcatca ... ccgaacgcagTGACCTTATCGAAGACCAAGAAGAAGCCAGGTTTAGAGCGCAAGGGCAAAG
EST: gi|20301485|gb|BQ164428.1|BQ164428
EST:     AGAGGAAGGAAGCAGGAACGCGATGCCTATGTCGAAGCGCAACCGCCCAG                         TGACCTTATCGAAGACCAAGAAGAAGCCAGGTTTAGAGCGCAAGGGCAAAG
genomic: CGAGGAAGGAAGCAGGAACGCGATGCCGAAGTCGAAGCGCAACCGCCCAGgtgatcatca ... ccgaacgcagTGACCTTATCGAAGACCAAGAAGAAGCCAGGTTTAGAGCGCAAGGGCAAAG
EST: gi|148969444|gb|EE020248.2|EE020248
EST:     CGAGGAAGGAAGCAGGAACGCGATGCCGAAGTCGAAGCGCAACCGCCCAG                         TGACCTTATCGAAGACCAAGAAGAAGCCAGGTTTAGAGCGCAAGGGCAAAG
genomic: CGAGGAAGGAAGCAGGAACGCGATGCCGAAGTCGAAGCGCAACCGCCCAGgtgatcatca ... ccgaacgcagTGACCTTATCGAAGACCAAGAAGAAGCCAGGTTTAGAGCGCAAGGGCAAAG
EST: gi|5398724|gb|AI812189.1|AI812189
EST:     GAGGAAGGAAGCAGGAACGCGATGCCGAAGTCGAAGCGCAACCGCCCAG                         TGACCTTATCGAAGACCAAGAAGAAGCCAGGTTTAGAGCGCAAGGGCAAAG
genomic: GAGGAAGGAAGCAGGAACGCGATGCCGAAGTCGAAGCGCAACCGCCCAGgtgatcatca ... ccgaacgcagTGACCTTATCGAAGACCAAGAAGAAGCCAGGTTTAGAGCGCAAGGGCAAAG
EST: gi|28987333|gb|CB351581.1|CB351581
EST:     CGAGGAAGGAAGCAGGAACGCGATGCCGAAGTCGAAGCGCAACCGCCCAG                         TGACCTTATCGAAGACCAAGAAGAAGCCAGGTTTAGAGCGCAAGGGCAAAG
genomic: CGAGGAAGGAAGCAGGAACGCGATGCCGAAGTCGAAGCGCAACCGCCCAGgtgatcatca ... ccgaacgcagTGACCTTATCGAAGACCAAGAAGAAGCCAGGTTTAGAGCGCAAGGGCAAAG
EST: gi|149015123|gb|EE044887.2|EE044887
EST:     CGAGGAAGGAAGCAGGAACGCGATGCCGAAGTCGAAGCGCAACCGCCCAG                         TGACCTTATCGAAGACCAAGAAGAAGCCAGGTTTAGAGCGCAAGGGCAAAG
genomic: CGAGGAAGGAAGCAGGAACGCGATGCCGAAGTCGAAGCGCAACCGCCCAGgtgatcatca ... ccgaacgcagTGACCTTATCGAAGACCAAGAAGAAGCCAGGTTTAGAGCGCAAGGGCAAAG
EST: gi|87156128|gb|DY400917.1|DY400917
EST:     GAGGAAGGAAGCAGGAACGCGATGCCGAAGTCGAAGCGCAACCGCCCAG                         TGACCTTATCGAAGACCAAGAAGAAGCCAGGTTTAGAGCGCAAGGGCAAAG
genomic: GAGGAAGGAAGCAGGAACGCGATGCCGAAGTCGAAGCGCAACCGCCCAGgtgatcatca ... ccgaacgcagTGACCTTATCGAAGACCAAGAAGAAGCCAGGTTTAGAGCGCAAGGGCAAAG
EST: gi|22549184|gb|BU101385.1|BU101385
EST:     GAGGAAGGAAGCAGGAACGCGATGCCGAAGTCGAAGCGCAACCGCCCAG                         -GACCTTATCGAAGACCAAGAAGAAGCCAGGTTTAGAGCGCAAGGGCAAAG
genomic: GAGGAAGGAAGCAGGAACGCGATGCCGAAGTCGAAGCGCAACCGCCCAGgtgatcatca ... ccgaacgcagTGACCTTATCGAAGACCAAGAAGAAGCCAGGTTTAGAGCGCAAGGGCAAAG
EST: gi|89761969|gb|DY689774.1|DY689774
EST:     CGAGGAAGGAAGCAGGAACGCGATGCCGAAGTCGAAGCGCAACCGCCCAG                         TGACCTTATCGAAGACCAAGAAGAAGCCAGGTTTAGAGCGCAAGGGCAAAG
genomic: CGAGGAAGGAAGCAGGAACGCGATGCCGAAGTCGAAGCGCAACCGCCCAGgtgatcatca ... ccgaacgcagTGACCTTATCGAAGACCAAGAAGAAGCCAGGTTTAGAGCGCAAGGGCAAAG
EST: gi|21810013|gb|BQ668331.1|BQ668331
EST:     AGAGGAAGGAAGCAGGAACGCGATGCCGAAGTCGAAGCGCAACCGCCCAG                         TGACCTTATCGAAGACCAAGAAGAAGCCAGGTTTAGAGCGCAAGGGCAAAG
genomic: CGAGGAAGGAAGCAGGAACGCGATGCCGAAGTCGAAGCGCAACCGCCCAGgtgatcatca ... ccgaacgcagTGACCTTATCGAAGACCAAGAAGAAGCCAGGTTTAGAGCGCAAGGGCAAAG
EST: gi|78119879|gb|DV538263.1|DV538263
EST:     CGAGGAAGGAAGCAGGAACGCGATGCCGAAGTCGAAGCGCAACCGCCCAG                         TGACCTTATCGAAGACCAAGAAGAAGCCAGGTTTAGAGCGCAAGGGCAAAG
genomic: CGAGGAAGGAAGCAGGAACGCGATGCCGAAGTCGAAGCGCAACCGCCCAGgtgatcatca ... ccgaacgcagTGACCTTATCGAAGACCAAGAAGAAGCCAGGTTTAGAGCGCAAGGGCAAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tagcttgcacagtggcctcgctgctgtaaattatgctaatgcgcgccgaacgcagTGACCTTATCGAAGACCAAGAAGAAGCCAGGTTTAGAGCGCAAGGGCAAAGTAGTCGCCGAGATAAAAGATGCTGTCGACAAATACAGCAGCGCCTATGT
                                 tgctaat  putative branch site (score: 2)
                          taaattatgctaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
agtctggaagtaaaaaacaaatctctctcaagcaacaacacttcttagcttgcacagtggcctcgctgctgtaaattatgctaatgcgcgccgaacgcagTGACCTTATCGAAGACCAAGAAGAAGCCAGGTTTAGAGCGCAAGGGCAAAGTAGTCGCCGAGATAAAAGATGCTGTCGACAAATACAGCAGCGCCTATGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG
- - - - - taaaaaa
- - - - - - - - - - - - - - - - caacaac
- - - - - - - - - - - - - - - - - - - - - - - -gcttgca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gctgctg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gctaatg