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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gatattatcatcatggcttttatggggttatttgaaaaatctgacatctcactttgctgggacactgattgatgcttctgcctttgtgctgtaccaccagGGTTCAATGTTGAGAAAGTACAGTACAAGAACGTGATGTTTACAGTATGGGATGTCGGTGGCCAAGAGAAGTTGAGGCCTCTGTGGAGGCATTACTTCAA

Basic information

species Oryza sativa
transcript LOC_Os02g47110.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g47110.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G106795_T03 (Zea mays), 3'ss of exon 2
--gatattatcatcatggcttttatggggttatttgaaaaatctgacatctcactttgctgggacactgattgatgcttctgcctttgtgctg-taccaccagGGTTCAATGTTGAGAAAGTACAGTACAAGAACGTGATGTTTACAGTATGGGATGTCGGTGGCCAAGAGAAGTTGAGGCCTCTGTGGAGGCATTACTTCAA
   ||||  || | | || |||    || ||| |   ||||    |  | |||||||||  | | | | ||   || |  |  || | || || ||| || ||| |||||||| |||||||| || |||||||| ||||||||||| || |||||||| ||||||||||| |||||||||||  |||||||||| ||||||||
ccaatatgttcttaaaggttttatgaggattact---aaaaataaatgtttcactttgcctgcaaattcatgtgtgatgatatctctctgatgctactactagGTTTCAATGTCGAGAAAGTTCAATACAAGAATGTGATGTTTACTGTTTGGGATGTTGGTGGCCAAGAAAAGTTGAGGCCCTTGTGGAGGCACTACTTCAA

upper sequence: LOC_Os02g47110.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G113995_T03 (Zea mays), 3'ss of exon 2
gatattatcatcatggcttttatggggttatttgaaaaatctgacatctcactttgctgggacactgattgatgcttctgcctttgtgctg-taccaccagGGTTCAATGTTGAGAAAGTACAGTACAAGAACGTGATGTTTACAGTATGGGATGTCGGTGGCCAAGAGAAGTTGAGGCCTCTGTGGAGGCATTACTTCAA
  |  | || | || |       ||| |  |   |  |   | | | |  ||||| |  | | | |  |   ||    |   | | || || || ||| ||| ||||| || |||||||| || |||||||| ||||||||||| || |||||||| ||||||||||| |||||||||||  |||||||||| ||||||||
-ttcctgtcttaattgaaaggcagggctcctgccattacatttaaaacaaactttccctgcaaattcgtctgtgacgatatgtctctggtgctatcactagGTTTCAACGTCGAGAAAGTTCAATACAAGAATGTGATGTTTACTGTGTGGGATGTTGGTGGCCAAGAAAAGTTGAGGCCCTTGTGGAGGCACTACTTCAA

upper sequence: LOC_Os02g47110.1 (Oryza sativa), 3'ss of exon 2
lower sequence: AT3G03120.1 (Arabidopsis thaliana), 3'ss of exon 2
---gatattatcatcatggcttttatggggttatttgaaaaatctgacatctcactttgctgggacactgattgatgcttctgcctttgtgctgtaccaccagGGTTCAATGTTGAGAAAGTACAGTACAAGAACGTGATGTTTACAGTATGGGATGTCGGTGGCCAAGAGAAGTTGAGGCCTCTGTGGAGGCATTACTTCAA
   | |   ||       || ||| |    || |||      | |  ||| | |  || |   |    | | ||| | || |   ||| |  |  ||    ||| ||||||||||||||||| ||||||||||| || || || ||||| |||||||| ||||||||||||||| |||||||  |||||||||||||||||||
gtaggtcagattgctcaagcattttta---ttttttttgcgttttctcat-ttatcttacaacgg-gtttactgaggattttaaatttct--tacac----agGTTTCAATGTTGAGAAAGTTCAGTACAAGAATGTCATCTTCACAGTTTGGGATGTTGGTGGCCAAGAGAAGCTGAGGCCCTTGTGGAGGCATTACTTCAA

upper sequence: LOC_Os02g47110.1 (Oryza sativa), 3'ss of exon 2
lower sequence: AT5G17060.1 (Arabidopsis thaliana), 3'ss of exon 2
-gatattatcatcatggcttt-tatggggttatttgaaaaatctgacatctcacttt--gctgggacactgattgatgcttctgcctttgtgctgtaccac-cagGGTTCAATGTTGAGAAAGTACAGTACAAGAACGTGATGTTTACAGTATGGGATGTCGGTGGCCAAGAGAAGTTGAGGCCTCTGTGGAGGCATTACTTCAA
   |  |  ||| ||   ||| | |  | |||||       |||| ||| |  ||||  | ||      | ||   ||||      ||     | |   || |||| ||||||||||||||||| ||||||||||| |||||||| ||||| |||||||| ||||||||||||||  |||| ||||| |||||||||||||||||
ttcttgtgacattatacttttatctatgattatt-----gttctgtcattttccttttggttgtttggattatgtctgctgacaatttaaacttatgttactcagGATTCAATGTTGAGAAAGTTCAGTACAAGAATGTGATGTTCACAGTTTGGGATGTTGGTGGCCAAGAGAAACTGAGACCTCTTTGGAGGCATTACTTCAA

upper sequence: LOC_Os02g47110.1 (Oryza sativa), 3'ss of exon 2
lower sequence: Vv16s0039g02240.t01 (Vitis vinifera), 3'ss of exon 2
-gatattatcatcatggcttttatggggttatttgaaaaatctgacatctcactttgctgggacactgattgatgct--tctgcctttgtgctgtaccac-cagGGTTCAATGTTGAGAAAGTACAGTACAAGAACGTGATGTTTACAGTATGGGATGTCGGTGGCCAAGAGAAGTTGAGGCCTCTGTGGAGGCATTACTTCAA
  | | | | |||||    |  |||   |    |    |   |||  | ||   | |    |   | |||||||  |  |    | || |   |||  |   ||| |||||||| |||||||| ||||| |||||||||||||| ||||| |||||||| ||||| ||||||||  | ||||| || |||||||||||||| ||
taacagt-tgatcatattgtacatgtattatactatggatgttgatgtgtcgaatgg---agcttcagattgattttaattgatcattttctggtaatatatagGTTTCAATGTGGAGAAAGTTCAGTATAAGAACGTGATGTTCACAGTGTGGGATGTAGGTGGACAAGAGAAACTCAGGCCACTCTGGAGGCATTACTTTAA

upper sequence: LOC_Os02g47110.1 (Oryza sativa), 3'ss of exon 2
lower sequence: EDP05355 (Chlamydomonas reinhardtii), 3'ss of exon 1
---gatattatcatcatggcttttatggggttatttgaaaaatctgacatctcactttgctgggacactgattgatgcttctgcctttgtgctgta--ccaccagGGTTCAATGTTGAGAAAGTACAGTACAAGAACGTGATGTTTACAGTATGGGATGTCGGTGGCCAAGAGAAGTTGAGGCCTCTGTGGAGGCATTACTTCAA
     |||   || |      |  |||      ||   | |  | || |    |     |    ||||  ||  |  |     |||  |  ||| |  ||  |||| ||||| |||||||| || || |||||||||||  |||| || || ||||| || || ||||| |||||| || |||| |||||| |||||||||||||
cccagtatc-ccagcccatgctccatgtaccccttattacagcccga-acagaatcccccacacacac-aatccacaca--cacctgcgccctgcaaaccgacagGCTTCAACGTTGAGAAGGTGCAATACAAGAACGTTGTGTTCACGGTGTGGGACGTGGGCGGCCAGGAGAAGCTGCGGCCACTGTGGCGGCATTACTTCAA

upper sequence: LOC_Os02g47110.1 (Oryza sativa), 3'ss of exon 2
lower sequence: PP1S37_304V6.1 (Physcomitrella patens), 3'ss of exon 2
-------------------------------------------------------------------------------gatattatcatcatggcttttatggggttatttgaaaaatctg-acatctcactttgctgg-gacactgattgatgcttctgcctttgtgctgtaccaccagGGTTCAATGTTGAGAAAGTACAGTACAAGAACGTGATGTTTACAGTATGGGATGTCGGTGGCCAAGAGAAGTTGAGGCCTCTGTGGAGGCATTACTTCAA
                                                                               | | || |   ||  | |   |  |  ||   ||  || |         |   ||||  ||  |||    ||| |   |     |||    |  |    ||||||||||||| |||||||| || |||||||| ||   ||||||||| ||||| || || ||||||||||| ||| | ||||||||| |||||||||||||
gtaatttgacttatcacttgtagtcaatccttcatttttttggtagtgcgcctcttcgtttctgagtatagatggcactgttgttttatacaatgttgcaaccgtatttcctgccaagtgcatgtgagtgtttttgagggtaacatctgttgctaaattacattttccattcaattttcagGGTTCAATGTAGAGAAAGTTCAATACAAGAATGTTGAGTTTACAGTGTGGGACGTTGGAGGCCAAGAGAAATTGCGACCTCTGTGGCGGCATTACTTCAA

upper sequence: LOC_Os02g47110.1 (Oryza sativa), 3'ss of exon 2
lower sequence: PP1S47_298V6.1 (Physcomitrella patens), 3'ss of exon 2
-------------------------------------------------------------------------------gatattatcatcatggcttttatggggt--tatt---tgaaaaat-ctgacatctcactttgctgggacactgattgat--gcttctgcctttgtgctgtaccaccagGGTTCAATGTTGAGAAAGTACAGTACAAGAACGTGATGTTTACAGTATGGGATGTCGGTGGCCAAGAGAAGTTGAGGCCTCTGTGGAGGCATTACTTCAA
                                                                               | |  | | |   ||  || | ||  ||  ||||   ||   | | |||     |    || |  |||      ||| |  | |  ||   || |||  ||    ||||||||||||| |||||||| ||||||||||||||   ||||||||| |||||||| || || |||||||| ||| ||||||||||| ||||||| |||||
gtagcttgacttaacacttccagttgatccttttgtatttgaaagagcccctcttcgtttctgcttatttgatgtatttgcttatttgacggtgttttgtttgatgtattattctgtgtcgagtgctggtgaatttgctttcgaggatgtcatttgttaagttgttgtggttatgcaatat--tcagGGTTCAATGTGGAGAAAGTTCAGTACAAGAACGTCGAGTTTACAGTGTGGGATGTTGGAGGTCAAGAGAAATTGCGGCCTCTGTGGCGGCATTATTTCAA

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|88423497|gb|CI579209.1|CI579209
EST:     CCTGTACAAGCTGCACATCGGGGAGGTCCTTTCGACTGTTCCTACGATTG                         GGTTCAATGTTGAGAAAGTACAGTACAAGAACGTGATGTTTACAGTATGGG
genomic: CCTGTACAAGCTGCACATCGGGGAGGTCCTTTCGACTGTTCCTACGATTGgtatgttgct ... gtaccaccagGGTTCAATGTTGAGAAAGTACAGTACAAGAACGTGATGTTTACAGTATGGG
EST: gi|66919065|gb|CX105913.1|CX105913
EST:     CCTGTACAAGCTGCACATCGGGGAGGTCCTTTCGACTGTTCCTACGATTG                         GGTTCAATGTTGAGAAAGTACAGTACAAGAACGTGATGTTTACAGTATGGG
genomic: CCTGTACAAGCTGCACATCGGGGAGGTCCTTTCGACTGTTCCTACGATTGgtatgttgct ... gtaccaccagGGTTCAATGTTGAGAAAGTACAGTACAAGAACGTGATGTTTACAGTATGGG
EST: gi|88359999|gb|CI608513.1|CI608513
EST:     CCTGTACAAGCTGCACATCGGGGAGGTCCTTTCGACTGTTCCTACGATTG                         GGTTCAATGTTGAGAAAGTACAGTACAAGAACGTGATGTTTACAGTATGGG
genomic: CCTGTACAAGCTGCACATCGGGGAGGTCCTTTCGACTGTTCCTACGATTGgtatgttgct ... gtaccaccagGGTTCAATGTTGAGAAAGTACAGTACAAGAACGTGATGTTTACAGTATGGG
EST: gi|2310427|gb|C26582.1|C26582
EST:     CCTGTACAAGCTGCACATCGGGGAGGTCCTTTCGACTGTTCCTACGATTG                         GGTTCAATGTTGAGAAAGTACAGTACAAGAACGTGATGTTTACAGTATGGG
genomic: CCTGTACAAGCTGCACATCGGGGAGGTCCTTTCGACTGTTCCTACGATTGgtatgttgct ... gtaccaccagGGTTCAATGTTGAGAAAGTACAGTACAAGAACGTGATGTTTACAGTATGGG
EST: gi|88311186|gb|CI570260.1|CI570260
EST:     CCTGTACAAGCTGCACATCGGGGAGGTCCTTTCGACTGTTCCTACGATTG                         GGTTCAATGTTGAGAAAGTACAGTACAAGAACGTGATGTTTACAGTATGGG
genomic: CCTGTACAAGCTGCACATCGGGGAGGTCCTTTCGACTGTTCCTACGATTGgtatgttgct ... gtaccaccagGGTTCAATGTTGAGAAAGTACAGTACAAGAACGTGATGTTTACAGTATGGG
EST: gi|2310382|gb|C26537.1|C26537
EST:     CCTGTACAAGCTGCACATCGGGGAGGTCCTTTCGACTGTTCCTACGATTG                         GGTTCAATGTTGAGAAAGTACAGTACAAGAACGTGATGTTTACAGTATGGG
genomic: CCTGTACAAGCTGCACATCGGGGAGGTCCTTTCGACTGTTCCTACGATTGgtatgttgct ... gtaccaccagGGTTCAATGTTGAGAAAGTACAGTACAAGAACGTGATGTTTACAGTATGGG
EST: gi|33692402|gb|CF320641.1|CF320641
EST:     CCTGTACAAGCTGCACATCGGGGAGGTCCTTTCGACTGTTCCTACGATTG                         GGTTCAATGTTGAGAAAGTACAGTACAAGAACGTGATGTTTACAGTATGGG
genomic: CCTGTACAAGCTGCACATCGGGGAGGTCCTTTCGACTGTTCCTACGATTGgtatgttgct ... gtaccaccagGGTTCAATGTTGAGAAAGTACAGTACAAGAACGTGATGTTTACAGTATGGG
EST: gi|88405611|gb|CI588817.1|CI588817
EST:     CCTGTACAAGCTGCACATCGGGGAGGTCCTTTCGACTGTTCCTACGATTG                         GGTT-AATGTTGAGAAAGTACAGTACAAGAACGTGATGTTTACAGTATGGG
genomic: CCTGTACAAGCTGCACATCGGGGAGGTCCTTTCGACTGTTCCTACGATTGgtatgttgct ... gtaccaccagGGTTCAATGTTGAGAAAGTACAGTACAAGAACGTGATGTTTACAGTATGGG
EST: gi|88825559|gb|CI776124.1|CI776124
EST:     CCTGTACAAGCTGCACATCGGGGAGGTCCTTTCGACTGTTCCTACGATTG                         GGTTCAATGTTGAGAAAGTACAGTACAAGAACCGTGATGTTTACAGTATGG
genomic: CCTGTACAAGCTGCACATCGGGGAGGTCCTTTCGACTGTTCCTACGATTGgtatgttgct ... gtaccaccagGGTTCAATGTTGAGAAAGTACAGTACAAGAAC-GTGATGTTTACAGTATGG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gatattatcatcatggcttttatggggttatttgaaaaatctgacatctcactttgctgggacactgattgatgcttctgcctttgtgctgtaccaccagGGTTCAATGTTGAGAAAGTACAGTACAAGAACGTGATGTTTACAGTATGGGATGTCGGTGGCCAAGAGAAGTTGAGGCCTCTGTGGAGGCATTACTTCAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG