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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatctgaaaaatctgtgccaaatgctactcccaagtattttggagcttgcaatttttaactagtagtgggtatgattactacatggtagtgattgcacatctgtgagtgcagGGGGAGCTTCAATACTTCATTGGTGTGCAACTTGATGGAAGTGATCATGTTGAACCCCTCAGGAACCGCCTTTCGGAGAATACTGAGATACAGAGTGCCA

Basic information

species Oryza sativa
transcript LOC_Os04g23890.4
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g23890.4 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G032351_T01 (Zea mays), 3'ss of exon 7
gtatctgaaaaatctgtgccaaatgctactcccaagtattttggagcttgcaatttttaactagtagtgggtatgattactacatggtagtgattgcac-atctgtgagtgcagGGGGAGCTTCAATACTTCATTGGTGTGCAACTTGATGGAAGTGATCATGTTGAACCCCTCAGGAACCGCCTTTCGGAGAATACTGAGATACAGAGTGCCA
                          ||||| |  |   | |      |  | || ||    | | ||   | || | ||        | | |||  |  || || |  || |||| |||||||||||||||||||| || ||| | |||||||| || |||||||||||||| ||||| || || || ||||| |||||  |||| ||||| |
-------------------------gtactcactggctatatctcttgtcaacttgttgcacacttgttcatgtggt-accgtgca-cactcattttattatttgggtatgtagGGAGAGCTTCAATACTTCATTGGAGTTCAATTGGATGGAAGCGACCATGTTGAACCCCTTAGGAATCGTCTCTCTGAGAACACTGAACTACAAAGTGCTA

upper sequence: LOC_Os04g23890.4 (Oryza sativa), 3'ss of exon 8
lower sequence: GLYMA08G33560.1 (Glycine max), 3'ss of exon 8
--gtatctgaaaaatctgtgccaaatgctactcccaagtattttggagcttgcaatttttaactagtagtgggt-atgattactacatggtagtgattg-cacatctgtgagtg---------cagGGGGAGCTTCAATACTTCATTGGTGTGCAACTTGATGGAAGTGATCATGTTGAACCCCTCAGGAACCGCCTTTCGGAGAATACTGAGATACAGAGTGCCA
  | || ||| |    | ||  | |    | |       | |   || | | |||| | ||   |  | |   |  || |  |  | |  ||||   |      | | | | ||          |||| || |||||||||||||||||||| ||||| ||||||||||||||||| |||||| | |  |||||||| || ||||  ||||||  ||| ||||| |
gtgaatgtgatactgttatggtagaaaacaattaatctgaatcatgaacattcaatatctattaaacaatacattgtgttcccccctttttagtttctaatgtttttctcaatgatttgtatttagGGTGAACTTCAATACTTCATTGGTGTTCAACTAGATGGAAGTGATCATGTAGAACCCTTAAAAAACCGCCTGTCTGAGACAACTGAGCAACAAAGTGCTA

upper sequence: LOC_Os04g23890.4 (Oryza sativa), 3'ss of exon 8
lower sequence: GLYMA16G19560.1 (Glycine max), 3'ss of exon 10
---------gtatctgaaaaatctgtgccaaatg--ctactcccaagtattttggagcttgcaatttttaactagtagtgggtatgat-tactacatggtagtgattgcacatctgtgagtgcagGGGGAGCTTCAATACTTCATTGGTGTGCAACTTGATGGAAGTGATCATGTTGAACCCCTCAGGAACCGCCTTTCGGAGAATACTGAGATACAGAGTGCCA
          ||     |   |      |||||    |   |  ||  |||    | ||   ||  | ||  | ||  |        | || |   |  |  |  |  ||    | ||  |  |||| || |||||||||||||||||||| ||||| ||||||||||||||||| |||||| | |  |||||||| || ||||  ||||||  ||| ||||| |
gtgaaagtgatactgttatgctagaaaacaaataatttgaacataaacattcaatatctattaaactatatattgtcttcccccctttctagtttctaatgttattctcaatgatttgtatttagGGTGAACTTCAATACTTCATTGGTGTTCAACTAGATGGAAGTGATCATGTAGAACCCTTAAAAAACCGCCTGTCTGAGACAACTGAGCAACAAAGTGCTA

upper sequence: LOC_Os04g23890.4 (Oryza sativa), 3'ss of exon 8
lower sequence: AT5G58140.2 (Arabidopsis thaliana), 3'ss of exon 9
gtatctgaaaaatctgtgccaaatgctactcccaagtattttggagcttgcaatttttaactagtagtgggtatgattactacatggtagtgattgcacatctgtgagtgcagGGGGAGCTTCAATACTTCATTGGTGTGCAACTTGATGGAAGTGATCATGTTGAACCCCTCAGGAACCGCCTTTCGGAGAATACTGAGATACAGAGTGCCA
            |||  |  | ||  || |   |     | ||||  || | ||| || |  |  |  | | ||  || ||   |    |   ||   ||||| |      |||| ||||||||||||||||| |||||||| |||||||||||||||||||| || ||||||   || ||  | || ||||  || ||||| |||||| | |
-----------gtcttcgtgagat--tattgttata---tctgga--ttccgattcttgaagaaaaccgtgcattgttgctgattacatgactttattcatctat-----tagGGAGAGCTTCAATACTTCATCGGTGTGCAGCTTGATGGAAGTGATCATGTAGAGCCCCTCCAAAATCGTTTGTCTGAGAGAACAGAGATGCAGAGTTCGA

upper sequence: LOC_Os04g23890.4 (Oryza sativa), 3'ss of exon 8
lower sequence: Vv03s0038g04210.t01 (Vitis vinifera), 3'ss of exon 8
gtatctgaaaaatctgtgccaaatgctactcccaagtattttggagcttgcaatttttaactagtagtgggtatgattactacatggtagt--gattgcacatctgtgagtgcagGGGGAGCTTCAATACTTCATTGGTGTGCAACTTGATGGAAGTGATCATGTTGAACCCCTCAGGAACCGCCTTTCGGAGAATACTGAGATACAGAGTGCCA
||  ||   | ||   |     ||   ||||  || |   ||   | |    |   |  | |  |  ||     | || || ||||    |   | |   |   | |    | |||| || |||||||||||||||||||| ||| | ||||||||||||||| | ||||||||| | |||||||| || ||| | ||||||  ||| ||||| |
gtggctatgagatacttattctatataactcttaatttggttttggatgaagagaatgtatttatgctgca---gcttccttcatgactttccaagtctcctgttatattcgtagGGTGAACTTCAATACTTCATTGGTGTCCAATTAGATGGAAGTGATCATCTGGAACCCCTCCGAAACCGCCTGTCAGAGCAAACTGAGCAACAAAGTGCTA

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|29612810|gb|CB617823.1|CB617823
EST:     GGAAGAAGTTCTGGAACTTGTTCCACCTTCAACCCATGCGCGACCAGAAG                         GGGGAGCTTCAATACTTCATTGGTGTGCAACTTGATGGAAGTGATCATGTT
genomic: GGAAGAAGTTCTGGAACTTGTTCCACCTTCAACCCATGCGCGACCAGAAGgtatctgaaa ... gtgagtgcagGGGGAGCTTCAATACTTCATTGGTGTGCAACTTGATGGAAGTGATCATGTT
EST: gi|14571435|gb|BI118803.1|BI118803
EST:     GGAAGAAGTTCTGGAACTTGTTCCACCTTCAACCCATGCGCGACCAGAAG                         GGGGAGCTTCAATACTTCATTGGTGTGCAACTTGATGGAAGTGATCATGTT
genomic: GGAAGAAGTTCTGGAACTTGTTCCACCTTCAACCCATGCGCGACCAGAAGgtatctgaaa ... gtgagtgcagGGGGAGCTTCAATACTTCATTGGTGTGCAACTTGATGGAAGTGATCATGTT
EST: gi|29666947|gb|CB663222.1|CB663222
EST:     GGAAGAAGTTCTGGAACTTGTTCCACCTTCAACCCATGCGCGACCAGAAG                         GGGGAGCTTCAATACTTCATTGGTGTGCAACTTGATGGAAGTGATCATGTT
genomic: GGAAGAAGTTCTGGAACTTGTTCCACCTTCAACCCATGCGCGACCAGAAGgtatctgaaa ... gtgagtgcagGGGGAGCTTCAATACTTCATTGGTGTGCAACTTGATGGAAGTGATCATGTT
EST: gi|58587914|gb|CF986222.1|CF986222
EST:     GGAAGAAGTTCTGGAACTGGTGCCACCTTCAACCCATGCGCGACCAGAAG                         GGGGAGCTTCAATACTTCATTGGTGTGCAACTTGATGGAAGTGATCATGTT
genomic: GGAAGAAGTTCTGGAACTTGTTCCACCTTCAACCCATGCGCGACCAGAAGgtatctgaaa ... gtgagtgcagGGGGAGCTTCAATACTTCATTGGTGTGCAACTTGATGGAAGTGATCATGTT
EST: gi|29615865|gb|CB620877.1|CB620877
EST:     GGAAGAAGTTCTGGAACTTGTTCCACCTTCAACCCATGCGCGACCAGAAG                         GGGGAGCTTCAATACTTCATTGGTGTGCAACTTGATGGAAGTGATCATGTT
genomic: GGAAGAAGTTCTGGAACTTGTTCCACCTTCAACCCATGCGCGACCAGAAGgtatctgaaa ... gtgagtgcagGGGGAGCTTCAATACTTCATTGGTGTGCAACTTGATGGAAGTGATCATGTT
EST: gi|29686409|gb|CB682684.1|CB682684
EST:     GGAAGAAGTTCTGGAACTTGTTCCACCTTCAACCCATGCGCGACCAGAAG                         GGGGAGCTTCAATACTTCATTGGTGTGCAACTTGATGGAAGTGATCATGTT
genomic: GGAAGAAGTTCTGGAACTTGTTCCACCTTCAACCCATGCGCGACCAGAAGgtatctgaaa ... gtgagtgcagGGGGAGCTTCAATACTTCATTGGTGTGCAACTTGATGGAAGTGATCATGTT
EST: gi|29680789|gb|CB677064.1|CB677064
EST:     GGAAGAAGTTCTGGAACTTGTTCCACCTTCAACCCATGCGCGACCAGAAG                         GGGGAGCTTCAATACTTCATTGGTGTGCAACTTGATGGAAGTGATCATGTT
genomic: GGAAGAAGTTCTGGAACTTGTTCCACCTTCAACCCATGCGCGACCAGAAGgtatctgaaa ... gtgagtgcagGGGGAGCTTCAATACTTCATTGGTGTGCAACTTGATGGAAGTGATCATGTT
EST: gi|29613843|gb|CB618856.1|CB618856
EST:     GGAAGAAGTTCTGGAACTTGTTCCACCTTCAACCCATGCGCGACCAGAAG                         GGGGAGCTTCAATACTTCATTGGTGTGCAACTTGATGGAAGTGATCATGTT
genomic: GGAAGAAGTTCTGGAACTTGTTCCACCTTCAACCCATGCGCGACCAGAAGgtatctgaaa ... gtgagtgcagGGGGAGCTTCAATACTTCATTGGTGTGCAACTTGATGGAAGTGATCATGTT
EST: gi|29646469|gb|CB651476.1|CB651476
EST:     GGAAGAAGTTCTGGAACTTGTTCCACCTTCAACCCATGCGCGACCAGAAG                         GGGGAGCTTCAATACTTCATTGGTGTGCAACTTGATGGAAGTGATCATGTT
genomic: GGAAGAAGTTCTGGAACTTGTTCCACCTTCAACCCATGCGCGACCAGAAGgtatctgaaa ... gtgagtgcagGGGGAGCTTCAATACTTCATTGGTGTGCAACTTGATGGAAGTGATCATGTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aactagtagtgggtatgattactacatggtagtgattgcacatctgtgagtgcagGGGGAGCTTCAATACTTCATTGGTGTGCAACTTGATGGAAGTGATCATGTTGAACCCCTCAGGAACCGCCTTTCGGAGAATACTGAGATACAGAGTGCCA
 ttttaac  putative branch site (score: 2)
             tatgatta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatctgaaaaatctgtgccaaatgctactcccaagtattttggagcttgcaatttttaactagtagtgggtatgattactacatggtagtgattgcacatctgtgagtgcagGGGGAGCTTCAATACTTCATTGGTGTGCAACTTGATGGAAGTGATCATGTTGAACCCCTCAGGAACCGCCTTTCGGAGAATACTGAGATACAGAGTGCCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA