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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaagtcatttaccctcagtttcacgccttactgaatgatctgacagtggagataaattgtctcaaattagcaatcatcttatgtatgaagGTGATATCGGTGAGTGGCAACCAGACGGCACAATGAAGATCATCGACAGAAAGAAGAACATTTTCAAGCTGTCCCAAGGGGAGTATGTAGCAGTGGAGGT

Basic information

species Oryza sativa
transcript LOC_Os11g35400.2
intron # 15
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os11g35400.2 (Oryza sativa), 3'ss of exon 15
lower sequence: GRMZM2G104847_T01 (Zea mays), 3'ss of exon 15
------------gtaaagtcatttaccctcagtttca-----cgccttactgaatgatctgacagtggag--ataaattgtctca---aattagcaatcatcttatgtatgaagGTGATATCGGTGAGTGGCAACCAGACGGCACAATGAAGATCATCGACAGAAAGAAGAACATTTTCAAGCTGTCCCAAGGGGAGTATGTAGCAGTGGAGGT
              ||| ||||||  |     ||| |     | ||| |||||| |||| | ||||| ||       | |  ||    || | |  |||| | ||||| || |||||||||||| ||||||||| |  | ||||| ||||||||||||||||||||||||||||| |||||||||||||| ||||||||||| ||||| |||||
gtgaaagaataaaaaaaatcatttctcacttcttttaatttgcacctaactgaaggatcagtcagtgaagcagctggtcgattcgtggaacttgtcatcaccctatgtgtgcagGTGATATCGGGGAGTGGCAATCCAATGGCACGATGAAGATCATCGACAGAAAGAAGAACATCTTCAAGCTGTCCCAGGGGGAGTATGTGGCAGTTGAGGT

upper sequence: LOC_Os11g35400.2 (Oryza sativa), 3'ss of exon 15
lower sequence: AT1G49430.1 (Arabidopsis thaliana), 3'ss of exon 15
gtaaagtcatttaccctcagtttcacgccttactgaatgatctgacagt---ggagataaattgtctcaaatta----gcaatc--atcttatgtat----gaagGTGATATCGGTGAGTGGCAACCAGACGGCACAATGAAGATCATCGACAGAAAGAAGAACATTTTCAAGCTGTCCCAAGGGGAGTATGTAGCAGTGGAGGT
    || |  | |  || ||| | |    |||   | |    ||  |||     |   || |||| |   || |    | |||   || | || |||    | ||| ||||| || || ||||||  ||| ||  |||||||||||||||| || ||||||||||| |||||| |||| ||||| || ||||| || || ||   
----agactctaaaacttagtct-atattttaaccattagattgttagttacaaaagcaacttgtattggataatgttgaaatttgatttcatttatatgagtagGAGATATTGGAGAATGGCAAGAAGATGGATCAATGAAGATCATCGATAGGAAGAAGAACATCTTCAAGTTGTCTCAAGGTGAATATGTTGCTGTTGAAAA

upper sequence: LOC_Os11g35400.2 (Oryza sativa), 3'ss of exon 15
lower sequence: PP1S218_19V6.1 (Physcomitrella patens), 3'ss of exon 16
----------------------------------------------------------------gtaaagtcatttaccctcagtttcacgccttac-tgaatgatctgacagtggagataaattgtct-caaattagcaatcatcttatgtatgaagGTGATATCGGTGAGTGGCAACCAGACGGCACAATGAAGATCATCGACAGAAAGAAGAACATTTTCAAGCTGTCCCAAGGGGAGTATGTAGCAGTGGAGGT
                                                                  |  ||| |||    ||  |   |    |||  | ||   | ||  | ||  |  | || |||| ||   |     || || ||    || |||||||||||| |||||| |   ||| ||  |  |||||||||||||||| ||||||||||| |||||| |||| || || || || || || || |||  
gtaatgtcttctctttaattgacgttttctttttaaataatttggatcttgctttttccctcagagagtgtctttttgtttcgttggaattgtttatattaacactgtggaactgctg-catatggtctacattctgattctcttcgtaaaactgcagGTGATATCGGGGAGTGGAAGAAAGATGGATCCTTGAAGATCATCGACAGGAAGAAGAACATCTTCAAGTTGTCACAGGGTGAATACGTTGCTGTCGAGAA

upper sequence: LOC_Os11g35400.2 (Oryza sativa), 3'ss of exon 15
lower sequence: EFJ23443 (Selaginella moellendorffii), 3'ss of exon 15
gtaaagtcatttaccctcagtttcacgccttactgaatgatctgacagtggagataaattgtctcaaattagcaatcatcttatgtatgaagGTGATATCGGTGAGTGGCAACCAGACGGCACAATGAAGATCATCGACAGAAAGAAGAACATTTTCAAGCTGTCCCAAGGGGAGTATGTAGCAGTGGAGGT
                              ||  || | |   || | | |   ||  | ||    | | | | |   | ||||      ||| |||||||| ||||||| |||| ||||  |  |||| ||||| ||||| ||||||||||||||||| || || ||||| || || || || || |||  
-----------------------------gtagggactcaaaagaaacttgc--tacgtggttcttactgaacgaggtttttat------agGAGATATCGGAGAGTGGCTACCAAACGGAGCCTTGAAAATCATAGACAGGAAGAAGAACATTTTCAAACTCTCGCAAGGCGAATACGTCGCTGTAGAGAA

upper sequence: LOC_Os11g35400.2 (Oryza sativa), 3'ss of exon 15
lower sequence: EFJ25426 (Selaginella moellendorffii), 3'ss of exon 15
gtaaagtcatttaccctcagtttcacgccttactgaatgatctgacagtggagataaattgtctca-aattagcaatcatctta-tgtatgaagGTGATATCGGTGAGTGGCAACCAGACGGCACAATGAAGATCATCGACAGAAAGAAGAACATTTTCAAGCTGTCCCAAGGGGAGTATGTAGCAGTGGAGGT
                                        |  |       |   || |||   |    || | | | | |    | | |  ||| |||||||| ||||||| |||| ||||  |  |||| ||||| ||||| ||||||||||||||||| || || ||||| || || || || || |||  
---------------------------------------gtagggactcaaaagaaacttgctacgtggttcgtactgaacgaggtttttacagGAGATATCGGAGAGTGGCTACCAAACGGAGCCTTGAAAATCATAGACAGGAAGAAGAACATTTTCAAACTCTCGCAAGGCGAATACGTCGCTGTAGAGAA

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|58668934|gb|CK057620.1|CK057620
EST:     GCGCCCTGACCTCACCGAGGAAGTATTCTCAGATGGTTGGTTCCATACAG                         GTGATATCGGTGAGTGG
genomic: GCGCCCTGACCTCACCGAGGAAGTATTCTCAGATGGTTGGTTCCATACAGgtaaagtcat ... atgtatgaagGTGATATCGGTGAGTGG
EST: gi|66947111|gb|AU311955.1|AU311955
EST:     GCGCCCTGACCTCACCGAGGAAGTATTCTCAGATGGTTGGTTCCATACAG                         GTGATATCGGTGAGTGGCAACCAGACGGCACAATGAAGATCATCGACAGAA
genomic: GCGCCCTGACCTCACCGAGGAAGTATTCTCAGATGGTTGGTTCCATACAGgtaaagtcat ... atgtatgaagGTGATATCGGTGAGTGGCAACCAGACGGCACAATGAAGATCATCGACAGAA
EST: gi|86501867|gb|CI144500.1|CI144500
EST:     GAAGTATTCTCAGATGGTTGGTTCCATACAG                         GTGATATCGGTGAGTGGCAACCAGACGGCACAATGAAGATCATCGACAGAA
genomic: GAAGTATTCTCAGATGGTTGGTTCCATACAGgtaaagtcat ... atgtatgaagGTGATATCGGTGAGTGGCAACCAGACGGCACAATGAAGATCATCGACAGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgatctgacagtggagataaattgtctcaaattagcaatcatcttatgtatgaagGTGATATCGGTGAGTGGCAACCAGACGGCACAATGAAGATCATCGACAGAAAGAAGAACATTTTCAAGCTGTCCCAAGGGGAGTATGTAGCAGTGGAGGT
  atctgac  putative branch site (score: 3)
              agataaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaagtcatttaccctcagtttcacgccttactgaatgatctgacagtggagataaattgtctcaaattagcaatcatcttatgtatgaagGTGATATCGGTGAGTGGCAACCAGACGGCACAATGAAGATCATCGACAGAAAGAAGAACATTTTCAAGCTGTCCCAAGGGGAGTATGTAGCAGTGGAGGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG