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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgtgtctatttttagctgacaagtactgtccggtgtactgcctactatggcttgtgtagccttctgcaaccagtcatctaatttgttttatatggatcagTGATGGAGCTGCTGCATTAGTTTTAGTGAGTGGGCAGAAGGCTCAAGAGCTTGGCCTTCAAGTCCTTGCAAGGATCAAAGGTTATGCTGATGCAGCTCAA

Basic information

species Zea mays
transcript GRMZM5G866758_T02
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G866758_T02 (Zea mays), 3'ss of exon 9
lower sequence: LOC_Os09g07830.1 (Oryza sativa), 3'ss of exon 9
---tgtgtctatttttagctgacaagtactgtccggtgtactgcctactatggcttgtgtagccttctgcaaccagtcatctaatttgttttatatggatcagTGATGGAGCTGCTGCATTAGTTTTAGTGAGTGGGCAGAAGGCTCAAGAGCTTGGCCTTCAAGTCCTTGCAAGGATCAAAGGTTATGCTGATGCAGCTCAA
     |||   | |  |  ||    |||   |||   |   ||  |  | |  |  |||      | ||   |   | | ||||||||||||| ||||| |||||| || ||||| |||||||| || ||||||||||||||||| ||||| ||||| || |||||  ||||| | |||||||| | ||| ||||||||||||
ttgactgttcttatccaattggtgcgtaaaatccccagatgtgtttgtt-tatccagtgagag--tgtgatgcttcttagctaatttgttttacatggaacagTGACGGTGCTGCCGCATTAGTATTGGTGAGTGGGCAGAAGGCACAAGAACTTGGACTGCAAGTTATTGCACGAATCAAAGGATTTGCAGATGCAGCTCAA

upper sequence: GRMZM5G866758_T02 (Zea mays), 3'ss of exon 9
lower sequence: GLYMA02G47860.1 (Glycine max), 3'ss of exon 8
tgtgtctatttttagctgacaagtactgtccggtgtactgcctactatggcttgtgtagccttctgcaaccagtcatctaatttgttttatatggatcagTGATGGAGCTGCTGCATTAGTTTTAGTGAGTGGGCAGAAGGCTCAAGAGCTTGGCCTTCAAGTCCTTGCAAGGATCAAAGGTTATGCTGATGCAGCTCAA
   ||  || | |   ||| |     ||       |  | |||| | ||   |||||     | ||  |      ||  || |  | ||      | ||||||||| || |||||| ||||||| ||||||||  ||||||| |   ||||||| ||||||||  ||||||  ||||  || ||||||||||| ||||| 
---gttaatatattattgaaa---tttgcttaacttttttcctagtgtg---tgtgtg----tgtgtga------atgaaaatgctcttgct---aacagTGATGGTGCCGCTGCACTAGTTTTGGTGAGTGGAGAGAAGGCACTGAAGCTTGGGCTTCAAGTTATTGCAAAAATCACTGGATATGCTGATGCTGCTCAG

upper sequence: GRMZM5G866758_T02 (Zea mays), 3'ss of exon 9
lower sequence: GLYMA14G00760.1 (Glycine max), 3'ss of exon 8
--tgtgtctatttttagctgacaagtactgtccggtg-tactgcctactatggcttgtgtagccttctgcaaccagtcatctaatttgttttatatggatcagTGATGGAGCTGCTGCATTAGTTTTAGTGAGTGGGCAGAAGGCTCAAGAGCTTGGCCTTCAAGTCCTTGCAAGGATCAAAGGTTATGCTGATGCAGCTCAA
  | |||   |||| | ||  ||| | || |    ||  |  |  |   ||   |  | ||||| |        |   |   ||  || | |   |  | ||||||||| ||||||||| ||||||| ||||||||  ||||||| |   ||||||| ||||||||  ||||||  ||||  || ||||||||||| ||||| 
aatatgtgggttttaaactctcaaatgctattaattgacatagtttgacattagtgat-tagccctggtttttaataaaatgaaaatgctcttgct--aacagTGATGGTGCTGCTGCACTAGTTTTGGTGAGTGGAGAGAAGGCACTGAAGCTTGGGCTTCAAGTTATTGCAAAAATCACTGGATATGCTGATGCTGCTCAG

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|30088105|gb|CB886310.1|CB886310
EST:     TTCTAGTATAAG                         TGATGGAGCTGCTGCATTAGTTTTAGTGAGTGGGCAGAAGGCTCAAGAGCT
genomic: TTCTAGTATAAGgtagctgctt ... tatggatcagTGATGGAGCTGCTGCATTAGTTTTAGTGAGTGGGCAGAAGGCTCAAGAGCT
EST: gi|101395308|gb|EB819584.1|EB819584
EST:     TTCAAGGAGAATGGTGGTACAGTTACAGCTGGAAATGCTTCTAGTATAAG                         TGATGGAGCTGCTGCATTAGTTTTAGTGAGTGGGCAGAAGGCTCAAGAGCT
genomic: TTCAAGGAGAATGGTGGTACAGTTACAGCTGGAAATGCTTCTAGTATAAGgtagctgctt ... tatggatcagTGATGGAGCTGCTGCATTAGTTTTAGTGAGTGGGCAGAAGGCTCAAGAGCT
EST: gi|211193824|gb|FL472434.1|FL472434
EST:     TTCAAGGAGAATGGTGGTACAGTTACAGCTGGAAATGCTTCTAGTATAAG                         TGATGGAGCTGCTGCATTAGTTTTGGTGAGTGGGCAGAAGGCTCAAGAGCT
genomic: TTCAAGGAGAATGGTGGTACAGTTACAGCTGGAAATGCTTCTAGTATAAGgtagctgctt ... tatggatcagTGATGGAGCTGCTGCATTAGTTTTAGTGAGTGGGCAGAAGGCTCAAGAGCT
EST: gi|31909501|gb|CD650950.1|CD650950
EST:     TTCAAGGAGAATGGTGGTACAGTTACAGCTGGAAATGCTTCTAGTATAAG                         TGATGGAGCTGCTGCATTAGTTTTAGTGAGTGGGCAGAAGGCTCAAGAGCT
genomic: TTCAAGGAGAATGGTGGTACAGTTACAGCTGGAAATGCTTCTAGTATAAGgtagctgctt ... tatggatcagTGATGGAGCTGCTGCATTAGTTTTAGTGAGTGGGCAGAAGGCTCAAGAGCT
EST: gi|18661821|gb|BM501596.1|BM501596
EST:     TTCAAGGAGAATGGTGGTACAGTTACAGCTGGAAATGCTTCTAGTATAAG                         TGATGGAGCTGCTGC-TTAGTTTT
genomic: TTCAAGGAGAATGGTGGTACAGTTACAGCTGGAAATGCTTCTAGTATAAGgtagctgctt ... tatggatcagTGATGGAGCTGCTGCATTAGTTTT
EST: gi|93281704|gb|EB673968.1|EB673968
EST:     TTCAAGGAGAATGGTGGTACAGTTACAGCTGGAAATGCTTCTAGTATAAG                         TGATGGAGCTGCTGCATTAGTTTTAGTGAGTGGGCAGAAGGCTCAAGAGCT
genomic: TTCAAGGAGAATGGTGGTACAGTTACAGCTGGAAATGCTTCTAGTATAAGgtagctgctt ... tatggatcagTGATGGAGCTGCTGCATTAGTTTTAGTGAGTGGGCAGAAGGCTCAAGAGCT
EST: gi|78087734|gb|DV516127.1|DV516127
EST:     TTCAAGGAGAATGGTGGTACAGTTACAGCTGGAAATGCTTCTAGTATAAG                         TGATGGAGCTGCTGCATTAGTTTTAGTGAGTGGGCAGAAGGCTCAAGAGCT
genomic: TTCAAGGAGAATGGTGGTACAGTTACAGCTGGAAATGCTTCTAGTATAAGgtagctgctt ... tatggatcagTGATGGAGCTGCTGCATTAGTTTTAGTGAGTGGGCAGAAGGCTCAAGAGCT
EST: gi|76921549|gb|DV168617.1|DV168617
EST:     TTCAAGGAGAATGGTGGTACAGTTACAGCTGGAAATGCTTCTAGTATAAG                         TGATGGAGCTGCTGCATTAGTTTTAGTGAGTGGGCAGAAGGCTCAAGAGCT
genomic: TTCAAGGAGAATGGTGGTACAGTTACAGCTGGAAATGCTTCTAGTATAAGgtagctgctt ... tatggatcagTGATGGAGCTGCTGCATTAGTTTTAGTGAGTGGGCAGAAGGCTCAAGAGCT
EST: gi|31909499|gb|CD650949.1|CD650949
EST:     TACAGTTACAGCTGGAAATGCTTCTAGTATAAG                         TGATGGAGCTGCTGCATTAGTTTTAGTGAGTGGGCAGAAGGCTCAAGAGCT
genomic: TACAGTTACAGCTGGAAATGCTTCTAGTATAAGgtagctgctt ... tatggatcagTGATGGAGCTGCTGCATTAGTTTTAGTGAGTGGGCAGAAGGCTCAAGAGCT
EST: gi|76284259|gb|DV023827.1|DV023827
EST:     TTCAAGGAGAATGGTGGTACAGTTACAGCTGGAAATGCTTCTAGTATAAG                         TGATGGAGCTGCTGCATTAGTTTTAGTGAGTGGGCAGAAGGCTCAAGAGCT
genomic: TTCAAGGAGAATGGTGGTACAGTTACAGCTGGAAATGCTTCTAGTATAAGgtagctgctt ... tatggatcagTGATGGAGCTGCTGCATTAGTTTTAGTGAGTGGGCAGAAGGCTCAAGAGCT
EST: gi|18654813|gb|BM499618.1|BM499618
EST:     TTCAAGGAGAATGGTGGTACAGTTACAGCTGGAAATGCTTCTAGTATAAG                         TGATGGAGCTGCTGC
genomic: TTCAAGGAGAATGGTGGTACAGTTACAGCTGGAAATGCTTCTAGTATAAGgtagctgctt ... tatggatcagTGATGGAGCTGCTGC
EST: gi|87152006|gb|DY396795.1|DY396795
EST:     TTCAAGGAGAATGGTGGTACAGTTACAGCTGGAAATGCTTCTAGTATAAG                         TGATGGAGCTGCTGCATTAGTTTTAGTGAGTGGGC
genomic: TTCAAGGAGAATGGTGGTACAGTTACAGCTGGAAATGCTTCTAGTATAAGgtagctgctt ... tatggatcagTGATGGAGCTGCTGCATTAGTTTTAGTGAGTGGGC
EST: gi|149016999|gb|EE154316.2|EE154316
EST:     TTCAAGGAGAATGGTGGTACAGTTACAGCTGGAAATGCTTCTAGTATAAG                         TGATGGAGCTGCTGCATTAGTTTTAGTGAGTGGGCAGAAGGCTCAAGAGCT
genomic: TTCAAGGAGAATGGTGGTACAGTTACAGCTGGAAATGCTTCTAGTATAAGgtagctgctt ... tatggatcagTGATGGAGCTGCTGCATTAGTTTTAGTGAGTGGGCAGAAGGCTCAAGAGCT
EST: gi|29544660|gb|CB605040.1|CB605040
EST:     TTCTAGTATAAG                         TGATGGAGCTGCTGCATTAGTTTTAGTGAGTGGGCAGAAGGCTCAAGAGCT
genomic: TTCTAGTATAAGgtagctgctt ... tatggatcagTGATGGAGCTGCTGCATTAGTTTTAGTGAGTGGGCAGAAGGCTCAAGAGCT
EST: gi|32864390|gb|CF004072.1|CF004072
EST:     TTCAAGGAGAATGGTGGTACAGTTACAGCTGGAAATGCTTCTAGTATAAG                         TGATGGAGCTGCTGCATTAGTTTTAGTGAGTGGGCAGAAGGCTCAAGAGCT
genomic: TTCAAGGAGAATGGTGGTACAGTTACAGCTGGAAATGCTTCTAGTATAAGgtagctgctt ... tatggatcagTGATGGAGCTGCTGCATTAGTTTTAGTGAGTGGGCAGAAGGCTCAAGAGCT
EST: gi|22490195|gb|BU050118.1|BU050118
EST:     TTCATTTATAATGGTGGTACAGTTACAGCTGGAAATGCTTCTAGTATAAG                         TGATGGAGCTGCTGCATTAGTTTTAGTGAGTGGGC
genomic: TTCAAGGAGAATGGTGGTACAGTTACAGCTGGAAATGCTTCTAGTATAAGgtagctgctt ... tatggatcagTGATGGAGCTGCTGCATTAGTTTTAGTGAGTGGGC
EST: gi|31353258|gb|CD437615.1|CD437615
EST:     TTCAAGGAGAATGATGGTACAGTTACAGCTGGGAATGCTTCTAGTATAAG                         TGATGGAGCTGCTGCATTAGTTTT
genomic: TTCAAGGAGAATGGTGGTACAGTTACAGCTGGAAATGCTTCTAGTATAAGgtagctgctt ... tatggatcagTGATGGAGCTGCTGCATTAGTTTT
EST: gi|76017958|gb|DT945128.1|DT945128
EST:     TCAAGGGGAAGGGTGGTACAGTTACAGCGGGAAATGCTT-TTGTATTAAG                         TGATGGAGCTGCTGCATTAGTTTTAGTGAGGGGGCAGAAGGCTCAAGAGC
genomic: TCAAGGAGAATGGTGGTACAGTTACAGCTGGAAATGCTTCTAGTA-TAAGgtagctgctt ... tatggatcagTGATGGAGCTGCTGCATTAGTTTTAGTGAGTGGGCAGAAGGCTCAAGAGC
EST: gi|32862142|gb|CF001824.1|CF001824
EST:     TTCAAGGAGAATGGTGGTACAGTTACAGCTGGAAATGCTTCTAGTATAAG                         TGATGGAGCTGCTGCATTAGTTTTAGTGAGTGGGCAGAAGGCTCAAGAGCT
genomic: TTCAAGGAGAATGGTGGTACAGTTACAGCTGGAAATGCTTCTAGTATAAGgtagctgctt ... tatggatcagTGATGGAGCTGCTGCATTAGTTTTAGTGAGTGGGCAGAAGGCTCAAGAGCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatggcttgtgtagccttctgcaaccagtcatctaatttgttttatatggatcagTGATGGAGCTGCTGCATTAGTTTTAGTGAGTGGGCAGAAGGCTCAAGAGCTTGGCCTTCAAGTCCTTGCAAGGATCAAAGGTTATGCTGATGCAGCTCAA
                              atctaat  putative branch site (score: 3)
                              atctaatttgttttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgtgtctatttttagctgacaagtactgtccggtgtactgcctactatggcttgtgtagccttctgcaaccagtcatctaatttgttttatatggatcagTGATGGAGCTGCTGCATTAGTTTTAGTGAGTGGGCAGAAGGCTCAAGAGCTTGGCCTTCAAGTCCTTGCAAGGATCAAAGGTTATGCTGATGCAGCTCAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTCA