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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tttttgtgtggtttaccgtttctttgagatgaactgacaacaaagtcaataaagcctgaagcttagctgacttttcttgttcctgatgggcatggttcagGTAGCATTTGTTGCGATTGGAGCAACCATGGTAGGAAGCATCACGTTCTTGAAAAAAGAGGGTGACTACGTCCGCAAAGGAGATGAG

Basic information

species Zea mays
transcript GRMZM2G133885_T02
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G133885_T02 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os01g72940.1 (Oryza sativa), 3'ss of exon 16
tttttgtgtggtttaccgtttctttgagatgaactgacaacaaagtcaataaagcctgaagcttagctgacttttcttgttc-ctgatgggc-------atggttcagGTAGCATTTGTTGCGATTGGAGCAACCATGGTAGGAAGCATCACGTTCTTGAAAAAAGAGGGTGACTACGTCCGCAAAGGAGATGAG
   ||||    |||||  || |  |   ||   || |  |||    ||| |  ||||  | ||| || | |  |   ||| | ||| |  ||       ||||||||||| ||||| || || ||||||||||| ||||| |||||||||  |||||||||| |||||||||||||||||| |||||||||||||
--cttgtcatatttacatttccaatataatc--cttattaca----caacactgcctttaactttgccgccgctcactgtgcactgctttgcttataacatggttcagGTGGCATTCGTGGCCATTGGAGCAACAATGGTTGGAAGCATCGAGTTCTTGAAAGAAGAGGGTGACTACGTCCACAAAGGAGATGAG

upper sequence: GRMZM2G133885_T02 (Zea mays), 3'ss of exon 3
lower sequence: AT4G25970.1 (Arabidopsis thaliana), 3'ss of exon 18
---------------------------------------------------------------------tttttgtgtggtttaccgtttctttgagatgaactgaca--------acaaagt----caataaagcctgaagct-tagctgacttttcttgttcctgatgggcatggttcagGTAGCATTTGTTGCGATTGGAGCAACCATGGTAGGAAGCATCACGTTCTTGAAAAAAGAGGGTGACTACGTCCGCAAAGGAGATGAG
                                                                      | |||||     | |  |    |  |  ||||     |        || |||     |||| ||  ||||   | | || ||  ||  |     || |     |||   ||||| ||||||||||||||||||||||| ||||| || || ||||  ||  | |   ||||||| ||| | ||    ||||| || |||
gtatgtcatcttgtataagtcataaacatcttttttctcggtctgctgatgaaaatatttctcagttgcctcttgtgcttgatgctttgaactcaaattgaagcagtattttataaacgaaggtgtacaatgaaatctgatcttatcgcagaacttgatctcagctta-atatatgtaacagGTCGCATTTGTTGCGATTGGAGCAACAATGGTTGGTAGTATCAGCTTTGTTAGGCAAGAGGGAGACCATGTGAAGAAAGGGGACGAG
















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|5922429|gb|AW055718.1|AW055718
EST:     CTGAGAATAAAAGAGTTGTATCAATGATATCAACTTCAGAGTTTGGAAAG                         GTAGCATTTGTTGCGATTGGAGCAACAATGGTAGGAAGCATCACGTTCTTG
genomic: CTGAGAATAAAAGAGTTGTATCAATGATATCAACTTCAGAGTTTGGAAAGgtttgcattt ... catggttcagGTAGCATTTGTTGCGATTGGAGCAACCATGGTAGGAAGCATCACGTTCTTG
EST: gi|32844513|gb|CD984194.1|CD984194
EST:     CTGAGAATAAAAGAGTTGTATCAATGATATCAACTTCAGAGTTTGGAAAG                         GTAGCATTTGTTGCGATTGGAGCAACCATGGTAGGAAGCATCACGTTCTTG
genomic: CTGAGAATAAAAGAGTTGTATCAATGATATCAACTTCAGAGTTTGGAAAGgtttgcattt ... catggttcagGTAGCATTTGTTGCGATTGGAGCAACCATGGTAGGAAGCATCACGTTCTTG
EST: gi|6021540|gb|AW066468.1|AW066468
EST:     CTGAGAATAAAAGAGTTGTATCAATGATATCAACTTCAGAGTTTGGAAAG                         GTAGCATTTGTTGCGATTGGAGCAACAATGGTAGGAAGCATCACGTTCTTG
genomic: CTGAGAATAAAAGAGTTGTATCAATGATATCAACTTCAGAGTTTGGAAAGgtttgcattt ... catggttcagGTAGCATTTGTTGCGATTGGAGCAACCATGGTAGGAAGCATCACGTTCTTG
EST: gi|32912653|gb|CF017465.1|CF017465
EST:     CTGAGAATAAAAGAGTTGTATCAATGATATCAACTTCAGAGTTTGGAAAG                         GTAGCATTTGTTGCGATTGGAGCAACCATGGTAGGAAGCATCACGTTCTTG
genomic: CTGAGAATAAAAGAGTTGTATCAATGATATCAACTTCAGAGTTTGGAAAGgtttgcattt ... catggttcagGTAGCATTTGTTGCGATTGGAGCAACCATGGTAGGAAGCATCACGTTCTTG
EST: gi|32913231|gb|CF018043.1|CF018043
EST:     CTGAGAATAAAAGAGTTGTATCAATGATATCAACTTCAGAGTTTGGAAAG                         GTAGCATTTGTTGCGATTGGAGCAACCATGGTAGGAAGCATCACGTTCTTG
genomic: CTGAGAATAAAAGAGTTGTATCAATGATATCAACTTCAGAGTTTGGAAAGgtttgcattt ... catggttcagGTAGCATTTGTTGCGATTGGAGCAACCATGGTAGGAAGCATCACGTTCTTG
EST: gi|211196234|gb|FL472452.1|FL472452
EST:     CTGAGAATAAAAGAGTTGTATCAATGATATCAACTTCAGAGTTTGGAAAG                         GTAGCATTTGTTGCGATTGGAGCAACCATGGTAGGAAGCATCACGTTCTTG
genomic: CTGAGAATAAAAGAGTTGTATCAATGATATCAACTTCAGAGTTTGGAAAGgtttgcattt ... catggttcagGTAGCATTTGTTGCGATTGGAGCAACCATGGTAGGAAGCATCACGTTCTTG
EST: gi|78103985|gb|DV522403.1|DV522403
EST:     CTGAGAATAAAAGAGTTGTATCAATGATATCAACTTCAGAGTTTGGAAAG                         GTAGCATTTGTTGCGATTGGAGCAACCATGGTAGGAAGCATCACGTTCTTG
genomic: CTGAGAATAAAAGAGTTGTATCAATGATATCAACTTCAGAGTTTGGAAAGgtttgcattt ... catggttcagGTAGCATTTGTTGCGATTGGAGCAACCATGGTAGGAAGCATCACGTTCTTG
EST: gi|40302877|gb|CK347264.1|CK347264
EST:     CTGAGAATAAAAGAGTTGTATCAATGATATCAACTTCAGAGTTTGGAAAG                         GTAGCATTTGTTGCGATTGGAGCAACCATGGTAGGAAGCATCACGTTCTTG
genomic: CTGAGAATAAAAGAGTTGTATCAATGATATCAACTTCAGAGTTTGGAAAGgtttgcattt ... catggttcagGTAGCATTTGTTGCGATTGGAGCAACCATGGTAGGAAGCATCACGTTCTTG
EST: gi|60396723|gb|DN229588.1|DN229588
EST:     CTGAGAATAAAAGAGTTGTATCAATGATATCAACTTCAGAGTTTGGAAAG                         GTAGCATTTGTTGCGATTGGAGCAACCATGGTAGGAAGCATCACGTTCTTG
genomic: CTGAGAATAAAAGAGTTGTATCAATGATATCAACTTCAGAGTTTGGAAAGgtttgcattt ... catggttcagGTAGCATTTGTTGCGATTGGAGCAACCATGGTAGGAAGCATCACGTTCTTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcaataaagcctgaagcttagctgacttttcttgttcctgatgggcatggttcagGTAGCATTTGTTGCGATTGGAGCAACCATGGTAGGAAGCATCACGTTCTTGAAAAAAGAGGGTGACTACGTCCGCAAAGGAGATGAG
                                   tcctgat  putative branch site (score: 3)
                          ttttctt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tttttgtgtggtttaccgtttctttgagatgaactgacaacaaagtcaataaagcctgaagcttagctgacttttcttgttcctgatgggcatggttcagGTAGCATTTGTTGCGATTGGAGCAACCATGGTAGGAAGCATCACGTTCTTGAAAAAAGAGGGTGACTACGTCCGCAAAGGAGATGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATG
- - - - - - - - - - - - - - -tgaactg
- - - - - - - - - - - - - - - - - - -caacaaa
- - - - - - - - - - - - - - - - - - - - - - - caataaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - -ctgaagc