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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...acaaacactgcctttatttattaaaaaacagaactacaaatagagctccttacatccgcattgcctgcttatgttatgatcttccctttctaacctacagTACGAGGATTTAAGACAGCTATGCGCTGATACAAGGGCAAGAGCTGCTGTCCTGGCTGACATGGACTCTATTGGAAAGGAGGCACAG

Basic information

species Oryza sativa
transcript LOC_Os11g04980.2
intron # 20
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os11g04980.2 (Oryza sativa), 3'ss of exon 20
lower sequence: GRMZM2G176546_T01 (Zea mays), 3'ss of exon 11
--acaaacactgcctttatttattaaaaaacagaactacaaatagagctccttacatccgcattgcctgcttatgttatgatct-tccctttctaacctacagTACGAGGATTTAAGACAGCTATGCGCTGATACAAGGGCAAGAGCTGCTGTCCTGGCTGACATGGACTCTATTGGAAAGGAGGCACAG
   | | ||| |  |  | ||    | | | ||  || |||  |   || |  ||||| |||  |  |  ||||| | | | || | | ||| |||| |  ||| ||| || || || ||||| || |||||  | || ||||||||||| |||||||| |||||||| ||| |||| ||||| ||||||
tgtccatcacag--taaaattcagcacagataggccttcaagcaactcttca-acatctgcacaggttctttatgctctaaactgttcttttgtaacatgtagTGCGAAGACTTGAGGCAGCTTTGTGCTGACCCTAGAGCAAGAGCTGCAGTCCTGGCCGACATGGATTCTGTTGGGAAGGAAGCACAG
















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|33800033|gb|CF325882.1|CF325882
EST:     TGTTGAAGGCTTGGGCTGCATCGGAAGGAATCCAG                         TACGAGGATTTAAGACAGCTATGCGCTGATACAAGGGCAAGAGCTGCTGTC
genomic: TGTTGAAGGCTTGGGCTGCATCGGAAGGAATCCAGgtaaatgtgc ... taacctacagTACGAGGATTTAAGACAGCTATGCGCTGATACAAGGGCAAGAGCTGCTGTC
EST: gi|29671404|gb|CB667679.1|CB667679
EST:     CAGTTGAACCAGAGGTGTTGAAGGCTTGGGCTGCATCGGAAGGAATCCAG                         TACGAGGATTTAAGACAGCTATGCGCTGATACAAGGGCAAGAGCTGCTGTC
genomic: CAGTTGAACCAGAGGTGTTGAAGGCTTGGGCTGCATCGGAAGGAATCCAGgtaaatgtgc ... taacctacagTACGAGGATTTAAGACAGCTATGCGCTGATACAAGGGCAAGAGCTGCTGTC
EST: gi|58590451|gb|CF988759.1|CF988759
EST:     CAGTTGAACCAGAGGTGTTGAAGGCTTGGGCTGCATCGGAAGGAATCCAG                         TACGAGGATTTAAGACAGCTATGCGCTGATACAAGGGCAAGAGCTGCTGTC
genomic: CAGTTGAACCAGAGGTGTTGAAGGCTTGGGCTGCATCGGAAGGAATCCAGgtaaatgtgc ... taacctacagTACGAGGATTTAAGACAGCTATGCGCTGATACAAGGGCAAGAGCTGCTGTC
EST: gi|58595336|gb|CF993644.1|CF993644
EST:     CAGTTGAACCAGAGGTGTTGAAGGCTTGGGCTGCATCGGAAGGAATCCAG                         TACGAGGATTTAAGACCAGCTATGCGCTGATACAAGGGCAAGAGCT
genomic: CAGTTGAACCAGAGGTGTTGAAGGCTTGGGCTGCATCGGAAGGAATCCAGgtaaatgtgc ... taacctacagTACGAGGATTTAAGAC-AGCTATGCGCTGATACAAGGGCAAGAGCT
EST: gi|29618419|gb|CB623431.1|CB623431
EST:     CAGTTGAACCAGAGGTGTTGAAGGCTTGGGCTGCATCGGAAGGAATCCAG                         TACGAGGATTTAAGACAGCTATGCGCTGATACAAGGGCAAGAGCTGCTGTC
genomic: CAGTTGAACCAGAGGTGTTGAAGGCTTGGGCTGCATCGGAAGGAATCCAGgtaaatgtgc ... taacctacagTACGAGGATTTAAGACAGCTATGCGCTGATACAAGGGCAAGAGCTGCTGTC
EST: gi|29679208|gb|CB675483.1|CB675483
EST:     CAGTTGAACCAGAGGTGTTGAAGGCTTGGGCTGCATCGGAAGGAATCCAG                         TACGAGGATTTAAGACAGCTATGCGCTGATACAAGGGCAAGAGCTGCTGTC
genomic: CAGTTGAACCAGAGGTGTTGAAGGCTTGGGCTGCATCGGAAGGAATCCAGgtaaatgtgc ... taacctacagTACGAGGATTTAAGACAGCTATGCGCTGATACAAGGGCAAGAGCTGCTGTC
EST: gi|29679210|gb|CB675485.1|CB675485
EST:     CAGTTGAACCAGAGGTGTTGAAGGCTTGGGCTGCATCGGAAGGAATCCAG                         TACGAGGATTTAAGACAGCTATGCGCTGATACAAGGGCAAGAGCTGCTGTC
genomic: CAGTTGAACCAGAGGTGTTGAAGGCTTGGGCTGCATCGGAAGGAATCCAGgtaaatgtgc ... taacctacagTACGAGGATTTAAGACAGCTATGCGCTGATACAAGGGCAAGAGCTGCTGTC
EST: gi|29665943|gb|CB662218.1|CB662218
EST:     CAGTTGAACCAGAGGTGTTGAAGGCTTGGGCTGCATCGGAAGGAATCCAG                         TACGAGGATTTAAGACAGCTATGCGCTGATACAAGGGCAAGAGCTGCTGTC
genomic: CAGTTGAACCAGAGGTGTTGAAGGCTTGGGCTGCATCGGAAGGAATCCAGgtaaatgtgc ... taacctacagTACGAGGATTTAAGACAGCTATGCGCTGATACAAGGGCAAGAGCTGCTGTC
EST: gi|25806438|gb|CA762399.1|CA762399
EST:     AGTTG-ACCAGAGGGTGTTGAAGGCTTGGGCTGCCTCGTAAGGAATCCAG                         TACGAGGATTTAAGACAGCTATGCGCTGATACAAGGGCAAGAG-TGGCTGT
genomic: AGTTGAACCAGA-GGTGTTGAAGGCTTGGGCTGCATCGGAAGGAATCCAGgtaaatgtgc ... taacctacagTACGAGGATTTAAGACAGCTATGCGCTGATACAAGGGCAAGAGCT-GCTGT
EST: gi|29665942|gb|CB662217.1|CB662217
EST:     CAGTTGAACCAGAGGTGTTGAAGGCTTGGGCTGCATCGGAAGGAATCCAG                         TACGAGGATTTAAGACAGCTATGCGCTGATACAAGGGCAAGAGCTGCTGTC
genomic: CAGTTGAACCAGAGGTGTTGAAGGCTTGGGCTGCATCGGAAGGAATCCAGgtaaatgtgc ... taacctacagTACGAGGATTTAAGACAGCTATGCGCTGATACAAGGGCAAGAGCTGCTGTC
EST: gi|29674249|gb|CB670524.1|CB670524
EST:     CAGTTGAACCAGAGGTGTTGAAGGCTTGGGCTGCATCGGAAGGAATCCAG                         TACGAGGATTTAAGACAGCTATGCGCTGATACAAGGGCAAGAGCTGCTGTC
genomic: CAGTTGAACCAGAGGTGTTGAAGGCTTGGGCTGCATCGGAAGGAATCCAGgtaaatgtgc ... taacctacagTACGAGGATTTAAGACAGCTATGCGCTGATACAAGGGCAAGAGCTGCTGTC
EST: gi|29670549|gb|CB666824.1|CB666824
EST:     CAGTTGAACCAGAGGTGTTGAAGGCTTGGGCTGCATCGGAAGGAATCCAG                         TACGAGGATTTAAGACAGCTATGCGCTGATACAAGGGCAAGAGCTGCTGTC
genomic: CAGTTGAACCAGAGGTGTTGAAGGCTTGGGCTGCATCGGAAGGAATCCAGgtaaatgtgc ... taacctacagTACGAGGATTTAAGACAGCTATGCGCTGATACAAGGGCAAGAGCTGCTGTC
EST: gi|29622335|gb|CB627346.1|CB627346
EST:     CAGTTGAACCAGAGGTGTTGAAGGCTTGGGCTGCATCGGAAGGAATCCAG                         TACGAGGATTTAAGACAGCTATGCGCTGATACAAGGGCAAGAGCTGCTGTC
genomic: CAGTTGAACCAGAGGTGTTGAAGGCTTGGGCTGCATCGGAAGGAATCCAGgtaaatgtgc ... taacctacagTACGAGGATTTAAGACAGCTATGCGCTGATACAAGGGCAAGAGCTGCTGTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctccttacatccgcattgcctgcttatgttatgatcttccctttctaacctacagTACGAGGATTTAAGACAGCTATGCGCTGATACAAGGGCAAGAGCTGCTGTCCTGGCTGACATGGACTCTATTGGAAAGGAGGCACAG
                                          ttctaac  putative branch site (score: 1)
                                  tcttccctttctaacc  CT-rich tract
                       ttatgttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
acaaacactgcctttatttattaaaaaacagaactacaaatagagctccttacatccgcattgcctgcttatgttatgatcttccctttctaacctacagTACGAGGATTTAAGACAGCTATGCGCTGATACAAGGGCAAGAGCTGCTGTCCTGGCTGACATGGACTCTATTGGAAAGGAGGCACAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG