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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctctgtgtttgttatttgttggatgggattgttgacaatgaaccatagtgttctgaagttttgcaaccacagcaagctaacctgtttgcttccttttcagGCAAGAAGGTGAGCAAGGCACCTAAGATCCAGCGGCTTGTGACCCCCTTGACCCTCCAGAGGAAGCGTGCTAGAATTGCTGACAAGAAGAAGAGGATCGC

Basic information

species Zea mays
transcript GRMZM5G851698_T01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G851698_T02 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os07g42950.1 (Oryza sativa), 3'ss of exon 5
ctctgtgtt-tgttatttgt-tggatgggattgttgacaatgaaccatagtgttctgaagttttgcaaccacagcaagctaacctgtttgcttccttttcagGCAAGAAGGTGAGCAAGGCACCTAAGATCCAGCGGCTTGTGACCCCCTTGACCCTCCAGAGGAAGCGTGCTAGAATTGCTGACAAGAAGAAGAGGATCGC
| |  | || | || | ||  ||  ||  | | || |     ||  |||   | | |     || |  |   | | | ||||     ||| ||   || |||||||||||||||||||||| |||||||||||||| |||||||| ||| | |||||||||||||||||||| ||||| |||||||||||||||||||||||
caccatattatattgtctgcatgtttgtcagttttcaagtcaaaatatatcttccaggtagctttctgct-tacctacctaatggtgttg-ttgtgttgcagGCAAGAAGGTGAGCAAGGCTCCTAAGATCCAGCGTCTTGTGACTCCCCTCACCCTCCAGAGGAAGCGTGCCAGAATCGCTGACAAGAAGAAGAGGATCGC

upper sequence: GRMZM5G851698_T02 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA16G09330.1 (Glycine max), 3'ss of exon 3
ctctgtgtttgttatttgttggatgggattgttgacaatgaaccatagtgttctgaagttttgcaaccacagcaagctaacctgtttgcttcct--tttcagGCAAGAAGGTGAGCAAGGCACCTAAGATCCAGCGGCTTGTGACCCCCTTGACCCTCCAGAGGAAGCGTGCTAGAATTGCTGACAAGAAGAAGAGGATCGC
  || |  |   ||| |||    |    |  |  | |   ||  | | |    | |  |  |   |  |   | ||      |  | | ||  |  || |||| || ||||| ||||| || || ||||| ||||| || || || ||  |||| || || |||||||| || ||||||||||| ||||||||||| |||||
--ctttaatcaatatatgtgatgtttcctcttcaatatccaattaaaatcggatcagttcatattatgaattctagtctcagtaatggatttttggttgcagGGAAAAAGGTAAGCAAAGCTCCAAAGATTCAGCGACTCGTCACTCCACTGACACTGCAAAGGAAGCGGGCAAGAATTGCTGATAAGAAGAAGAGAATCGC

upper sequence: GRMZM5G851698_T02 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA15G08210.1 (Glycine max), 3'ss of exon 5
-ctctgtgtttgttatttgttggatgggattgttgacaatgaaccatagtgttctgaagttttgcaaccacagcaag-ctaacctgtttgc-ttccttttcagGCAAGAAGGTGAGCAAGGCACCTAAGATCCAGCGGCTTGTGACCCCCTTGACCCTCCAGAGGAAGCGTGCTAGAATTGCTGACAAGAAGAAGAGGATCGC
  | | || | ||| |||| ||| | |||    |   |    |  ||  | ||    |   |||  |  |   | || || |  |   |   ||   ||  ||| || ||||||||||| || |||||||| || ||||| || || ||| |||||||||| || ||| | || || ||||| || ||||||||||| || ||
tatttatgct-gttgtttgatgggtaggacccattgaaggagattat--ttttggacatgattgtgatgatttctagtctgagttacatatgtttggttgtagGGAAAAAGGTGAGCAAAGCTCCTAAGATACAACGGCTGGTCACTCCCCTGACCCTCCAAAGAAAGAGGGCAAGGATTGCAGATAAGAAGAAGAGAATTGC

upper sequence: GRMZM5G851698_T02 (Zea mays), 3'ss of exon 5
lower sequence: AT4G31700.1 (Arabidopsis thaliana), 3'ss of exon 5
ctctgtgtttgttatttgttggatgggattgttgacaatgaaccatagtgttctgaagttttgcaaccacagcaagctaacctgtttgcttccttttcagGCAAGAAGGTGAGCAAGGCACCTAAGATCCAGCGGCTTGTGACCCCCTTGACCCTCCAGAGGAAGCGTGCTAGAATTGCTGACAAGAAGAAGAGGATCGC
      ||  |  | |        |  || || |    |||| || | |      |   | |      | |      |   |||||||  |  ||  |||||||| | || ||||| || |||||||||||| ||||||||||||| ||||| || ||||||||| | |||||||||||||||||||||||||  || ||
------gtgagacactgaacttgagaaatagtggtttctgaatcacacttgagaaataatgttttctgaaacttgtttcttctgtttggatttttgacagGCAAGGAAGTTAGCAAAGCCCCTAAGATCCAGAGGCTTGTGACCCCATTGACTCTTCAGAGGAAGAGAGCTAGAATTGCTGACAAGAAGAAGAAAATTGC

upper sequence: GRMZM5G851698_T02 (Zea mays), 3'ss of exon 5
lower sequence: AT5G10360.2 (Arabidopsis thaliana), 3'ss of exon 5
-------------ctctgtgtttgttatttgttggatgggattgttgacaatgaaccatagtgttctgaagttttgcaaccacagcaagctaacctgtttgcttccttttcagGCAAGAAGGTGAGCAAGGCACCTAAGATCCAGCGGCTTGTGACCCCCTTGACCCTCCAGAGGAAGCGTGCTAGAATTGCTGACAAGAAGAAGAGGATCGC
              |  |    |   |||   |  | | |||  |||| ||      |||   |  ||| | ||| | |  | |  | |||           | | | | ||||||||||||| |||||||| |||||||||||| |||||||||| || |||||||||||||||||| | |||||||||||||||||||||||||| |||||
acaaacaagaagggtaagaaaattagattcacttaaagagataattgaaaactgtttatacgat--tgatgatttactaatatatgaggct-----------tccatgtgcagGCAAGAAGGTTAGCAAGGCTCCTAAGATCCAGAGGCTTGTGACTCCATTGACCCTCCAGAGGAAGAGAGCTAGAATTGCTGACAAGAAGAAGAGAATCGC

upper sequence: GRMZM5G851698_T02 (Zea mays), 3'ss of exon 5
lower sequence: AT5G10360.1 (Arabidopsis thaliana), 3'ss of exon 5
ctctgtgtttgttatttgttggatgggattgttgacaatgaaccatagtgttctgaagttttgcaaccacagcaagctaacctgtttgcttccttttcagGCAAGAAGGTGAGCAAGGCACCTAAGATCCAGCGGCTTGTGACCCCCTTGACCCTCCAGAGGAAGCGTGCTAGAATTGCTGACAAGAAGAAGAGGATCGC
 |  |    |   |||   |  | | |||  |||| ||      |||   |  ||| | ||| | |  | |  | |||           | | | | ||||||||||||| |||||||| |||||||||||| |||||||||| || |||||||||||||||||| | |||||||||||||||||||||||||| |||||
gtaagaaaattagattcacttaaagagataattgaaaactgtttatacgat--tgatgatttactaatatatgaggct-----------tccatgtgcagGCAAGAAGGTTAGCAAGGCTCCTAAGATCCAGAGGCTTGTGACTCCATTGACCCTCCAGAGGAAGAGAGCTAGAATTGCTGACAAGAAGAAGAGAATCGC

upper sequence: GRMZM5G851698_T02 (Zea mays), 3'ss of exon 5
lower sequence: Vv03s0017g01350.t01 (Vitis vinifera), 3'ss of exon 5
ctctgtgtttgttatttgttggatgggattgttgacaatgaaccatagtgttctgaagttttgcaaccacag--caagctaacctgtttgct-tccttttcagGCAAGAAGGTGAGCAAGGCACCTAAGATCCAGCGGCTTGTGACCCCCTTGACCCTCCAGAGGAAGCGTGCTAGAATTGCTGACAAGAAGAAGAGGATCGC
  |||   ||   || || ||  |   | | ||      | |   |  | ||   |||  |    ||   ||    |  |    |  |  || |  |  ||||| |||||    || || || |||||||| ||| |||| |||||||| ||||| || |||||||||||||| || ||||| || ||||||||||| || ||
-actgaaatt--catgtgatgcttaaaagtattatttcagtattttgctttttaaaagactaaagacagaagattgatatggtttcatcactgtgatcctcagGGAAGAAATGCAGTAAAGCCCCTAAGATTCAGAGGCTGGTGACCCCATTGACTCTGCAGAGGAAGCGTGCAAGGATTGCAGAGAAGAAGAAGAGAATTGC

upper sequence: GRMZM5G851698_T02 (Zea mays), 3'ss of exon 5
lower sequence: PP1S3195_1V6.1 (Physcomitrella patens), 3'ss of exon 2
-------------------------ctctgtgttt-gttatttgttggatgggattgttgacaatgaaccatagtgttctgaagttttgcaaccacagcaagctaacctgtttgcttccttttcagGCAAGAAGGTGAGCAAGGCACCTAAGATCCAGCGGCTTGTGACCCCCTTGACCCTCCAGAGGAAGCGTGCTAGAATTGCTGACAAGAAGAAGAGGATCGC
                             || ||| |  ||   |    | |    || | | ||| |     | |  |     |      | | |   |       |||  ||| | |||| |||||||||||  |||||||||||| ||||||||| |||||||||| || |||||  | |||||||||||   |||| | ||   |||||||  | |  ||||
gtacagtcatggctcctgatgtgggtgtcgtattttgccatgcttcctttcgtgcagtcgccgatgtagagcgggggccattgttgcgaggagccctctactgacgtctgcgtgcgtgcttt-cagGCAAGAAGAGGAGCAAGGCACCGAAGATCCAGAGGCTTGTGACTCCTTTGACTTTGCAGAGGAAGCGCCGTAGAGTGGCAATCAAGAAGGCGCGTGTCGC

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|149077415|gb|EE166104.2|EE166104
EST:     CGTGCGCAAGTACGTGAACACGTTCCGCAGGACATTCACTTCCAAGAATG                         GCAAGAAGGTGAGCAAGGCACCTAAGATCCAGCGGCTTGTGACCCCCTTGA
genomic: CGTGCGCAAGTACGTGAACACGTACCGCAGGACATTCACTACCAAGAATGgtgagctttc ... tccttttcagGCAAGAAGGTGAGCAAGGCACCTAAGATCCAGCGGCTTGTGACCCCCTTGA
EST: gi|60338176|gb|DN205149.1|DN205149
EST:     CGTGCGCAAGTACGTGAACACGTACCGCAGGACATTCACTACCAAGAATG                         GCAAGAAGGTGAGCAAGGCACCTAAGATCCAGCGGCTTGTGACCCCCTTGA
genomic: CGTGCGCAAGTACGTGAACACGTACCGCAGGACATTCACTACCAAGAATGgtgagctttc ... tccttttcagGCAAGAAGGTGAGCAAGGCACCTAAGATCCAGCGGCTTGTGACCCCCTTGA
EST: gi|149097337|gb|EE183170.2|EE183170
EST:     CGTGCGCAAGTACGTGAACACGTACCGCAGGACATTCACTACCAAGAATG                         GCAAGAAGGTGAGCAAGGCACCTAAGATCCAGCGGCTTGTGACCCCCTTGA
genomic: CGTGCGCAAGTACGTGAACACGTACCGCAGGACATTCACTACCAAGAATGgtgagctttc ... tccttttcagGCAAGAAGGTGAGCAAGGCACCTAAGATCCAGCGGCTTGTGACCCCCTTGA
EST: gi|33102879|gb|CF062839.1|CF062839
EST:     GTACCGCAGGACATTCACTACCAAGAATG                         GCAAGAAGGTGAGCAAGGCACCTAAGATCCAGCGGCTTGTGACCCCCTTGA
genomic: GTACCGCAGGACATTCACTACCAAGAATGgtgagctttc ... tccttttcagGCAAGAAGGTGAGCAAGGCACCTAAGATCCAGCGGCTTGTGACCCCCTTGA
EST: gi|32944070|gb|CF048889.1|CF048889
EST:     ACGTGAACACATACCGCAGGACATTCACTACCAAGAACG                         GCAAGAAGGTCAGCAAGGCACCTAAGATCCAACGGCTTGTGACACCCTTGA
genomic: ACGTGAACACGTACCGCAGGACATTCACTACCAAGAATGgtgagctttc ... tccttttcagGCAAGAAGGTGAGCAAGGCACCTAAGATCCAGCGGCTTGTGACCCCCTTGA
EST: gi|211523896|gb|FL150680.1|FL150680
EST:     CGTGCGCAAGTACGTGAACACGTACCGCAGGACATTCACTACCAAGAATG                         GCGAAGAAGGTGAGCAAGGCACCTAAGATCCAGCGGCTTGTGACCCCCTTG
genomic: CGTGCGCAAGTACGTGAACACGTACCGCAGGACATTCACTACCAAGAATGgtgagctttc ... tccttttcagGC-AAGAAGGTGAGCAAGGCACCTAAGATCCAGCGGCTTGTGACCCCCTTG
EST: gi|31406382|gb|CD485114.1|CD485114
EST:     CGTGCGCAAGTACGTGAACACGTACCGCAGGACATTCACTACCAAGAATG                         GCAAGAAGGTGAGCAAGGCACCTAAGATCCAGCGGCTTGTGACCCCCTTGA
genomic: CGTGCGCAAGTACGTGAACACGTACCGCAGGACATTCACTACCAAGAATGgtgagctttc ... tccttttcagGCAAGAAGGTGAGCAAGGCACCTAAGATCCAGCGGCTTGTGACCCCCTTGA
EST: gi|149081498|gb|EE170633.2|EE170633
EST:     CGTGCGCAAGTACGTGAACACGTACCGCAGGACATTCACTACCAAGAATG                         GCAAGAAGGTGAGCAAGGCACCTAAGATCCAGCGGCTTGTGACCCCCTTGA
genomic: CGTGCGCAAGTACGTGAACACGTACCGCAGGACATTCACTACCAAGAATGgtgagctttc ... tccttttcagGCAAGAAGGTGAGCAAGGCACCTAAGATCCAGCGGCTTGTGACCCCCTTGA
EST: gi|148954012|gb|EC899409.2|EC899409
EST:     CGTGCGCAAGTACGTGAACACGTACCGCAGGACATTCACTACCAAGAATG                         GCAAGAAGGTGAGCAAGGCACCTAAGATCCAGCGGCTTGTGACCCCCTTGA
genomic: CGTGCGCAAGTACGTGAACACGTACCGCAGGACATTCACTACCAAGAATGgtgagctttc ... tccttttcagGCAAGAAGGTGAGCAAGGCACCTAAGATCCAGCGGCTTGTGACCCCCTTGA
EST: gi|5740271|gb|AI947961.1|AI947961
EST:     CGTGCCCAAGTACGTGAACACGTACCCCAGGACATTCACTACCAAGAATG                         GCAAGAAGGTGAGCAAGGCACCTAAGATCCAGCGGCTTGTGACCCCCTTGA
genomic: CGTGCGCAAGTACGTGAACACGTACCGCAGGACATTCACTACCAAGAATGgtgagctttc ... tccttttcagGCAAGAAGGTGAGCAAGGCACCTAAGATCCAGCGGCTTGTGACCCCCTTGA
EST: gi|29945711|gb|CB815780.1|CB815780
EST:     CGTGCGCAAGTACGTGAACACGTACCGCAGGACATTCACTACCAAGAATG                         GCAAGAAGGTGAGCAAGGCACCTAAGATCCAGCGGCTTGTGACCCCCTTGA
genomic: CGTGCGCAAGTACGTGAACACGTACCGCAGGACATTCACTACCAAGAATGgtgagctttc ... tccttttcagGCAAGAAGGTGAGCAAGGCACCTAAGATCCAGCGGCTTGTGACCCCCTTGA
EST: gi|101383670|gb|EB813890.1|EB813890
EST:     CGTGCGCAAGTACGTGAACACGTACCGCAGGACATTCACTACCAAGAATG                         GCAAGAAGGTGAGCAAGGCACCTAAGATCCAGCGGCTTGTGACCCCCTTGA
genomic: CGTGCGCAAGTACGTGAACACGTACCGCAGGACATTCACTACCAAGAATGgtgagctttc ... tccttttcagGCAAGAAGGTGAGCAAGGCACCTAAGATCCAGCGGCTTGTGACCCCCTTGA
EST: gi|211025728|gb|FL435836.1|FL435836
EST:     CGTGCGCAAGTACGTGAACACGTACCGCAGGACATTCACTACCAAGAATG                         GCAAGAAGGTGAGCAAGGCACCTAAGATCCAGCGGCTTGTGACCCCCTTGA
genomic: CGTGCGCAAGTACGTGAACACGTACCGCAGGACATTCACTACCAAGAATGgtgagctttc ... tccttttcagGCAAGAAGGTGAGCAAGGCACCTAAGATCCAGCGGCTTGTGACCCCCTTGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tagtgttctgaagttttgcaaccacagcaagctaacctgtttgcttccttttcagGCAAGAAGGTGAGCAAGGCACCTAAGATCCAGCGGCTTGTGACCCCCTTGACCCTCCAGAGGAAGCGTGCTAGAATTGCTGACAAGAAGAAGAGGATCGC
                             agctaac  putative branch site (score: 2)
                                   cctgtttgcttccttt  CT-rich tract
          aagtttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ctctgtgtttgttatttgttggatgggattgttgacaatgaaccatagtgttctgaagttttgcaaccacagcaagctaacctgtttgcttccttttcagGCAAGAAGGTGAGCAAGGCACCTAAGATCCAGCGGCTTGTGACCCCCTTGACCCTCCAGAGGAAGCGTGCTAGAATTGCTGACAAGAAGAAGAGGATCGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAT