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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCAAGAAGCAGCTGAGAAAGAAGCCGCTCTTGCAAGGAGGAGACAAGAGAAGGCCATGGCTCTTGGAGCAGAACCTGAGAAAGGACCAGATGTTACTCGAgtatgttcacattctttgtccatcttccttatcaacctgttatgatcttattctaggataatgtgctgacaagttacaaccacatttgtctacttttgat...

Basic information

species Oryza sativa
transcript LOC_Os10g37630.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os10g37630.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G159538_T01 (Zea mays), 5'ss of exon 3
CCAAGAAGCAGCTGAGAAAGAAGCCGCTCTTGCAAGGAGGAGACAAGAGAAGGCCATGGCTCTTGGAGCAGAACCTGAGAAAGGACCAGATGTTACTCGAgtatgttcacat-tctttg-tccatcttccttatcaacctgttatgatcttattctaggataatgtgctgacaagttacaaccacatttgtctacttttgat--
||||||||||||||| || ||||| ||||||||||||||||| |||||||||||||||||||||||||| ||||||||||||||||||| ||||||||| |||||| | ||| || | | | | | | |||| || | ||| | | | | | ||| ||| || || ||| ||| ||
CCAAGAAGCAGCTGAAAAGGAAGCTGCTCTTGCAAGGAGGAGGCAAGAGAAGGCCATGGCTCTTGGAGCTGAACCTGAGAAAGGACCAGGTGTTACTCGGgtatgtctaagcctctatgctttgtgtctttaaactacctttttttttctccaattcttactacaagataacatgtt----tcatgttgttctgatttggaagt

upper sequence: LOC_Os10g37630.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G343688_T02 (Zea mays), 5'ss of exon 3
CCAAGAAGCAGCTGAGAAAGAAGCCGCTCTTGCAAGGAGGAGACAAGAGAAGGCCATGGCTCTTGGAGCAGAACCTGAGAAAGGACCAGATGTTACTCGAgtatgt------tcacattctttgtccatcttccttatcaacctgttatga--tcttattctaggataatgtgctgacaagttacaaccacatttgtctacttttgat
|||||||||||||||||| ||||| ||||||||||||||||| |||||||||||||||||||||||||| ||||||||||||||||||| ||||||||| |||||| | || ||| || | | | | | |||| || | ||||| | | |||| |||| || ||| | | ||| |
CCAAGAAGCAGCTGAGAAGGAAGCTGCTCTTGCAAGGAGGAGGCAAGAGAAGGCCATGGCTCTTGGAGCTGAACCTGAGAAAGGACCAGGTGTTACTCGGgtatgtgatgtctaaccctctatgcttgtgtctttaaactacctttttccaattcttactgcaagatagcatgctt-catgttgtgccgatttttaaggat-------

upper sequence: LOC_Os10g37630.1 (Oryza sativa), 5'ss of exon 3
lower sequence: AT4G10790.1 (Arabidopsis thaliana), 5'ss of exon 3
CCAAGAAGCAGCTGAGAAAGAAGCCGCTCTTGCAAGGAGGAGACAAGAGAAGGCCATGGCTCTTGGAGCAGAACCTGAGAAAGGACCAGATGTTACTCGAgtatgttcacattctttgtccatc-ttccttatcaacctgttatgatcttattcta-ggataatgtgctgacaagttacaaccacatttgtctacttttgat--
| ||||| | |||| | |||| ||| | | | |||||||||||| || | |||||||||| ||||||||||||||| || |||||||| | |||| |||| | ||||| | | || ||| | || || | | || | ||| | ||| | ||| | || ||| | |||||
GCGTGAAGCTGAAGAGAGACAAGCTGCTAGAGTGCGAATGAGACAAGAGAAAGCTCTTGCTCTTGGAGAAGAACCTGAGAAAGGCCCTGATGTTACACAAgtaagttcgccttcttccttagccatttattacttatcttttctcacacagtttcgtagcctatgcaattgcaa---agaacattaattatct-ttattgatat

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|88828550|gb|CI073420.1|CI073420
EST:     AGGCCATGGCTCTTGGAGCAGAACCTGAGAAAGGACCAGATGTTACTCGA                         GTTCTTATAAGATTTCCAACTGGAGAGCGCAAAGAAAGGAGATTCAACAGT
genomic: AGGCCATGGCTCTTGGAGCAGAACCTGAGAAAGGACCAGATGTTACTCGAgtatgttcac ... gattttgtagGTTCTTATAAGATTTCCAACTGGAGAGCGCAAAGAAAGGAGATTCAACAGT
EST: gi|88955777|gb|CI092066.1|CI092066
EST:     AGGCCATGGCTCTTGGAGCAGAACCTGAGAAAGGACCAGATGTTACTCGA                         GTTCTTATAAGATTTCCAACTGGAGAGCGCAAAGAAAGGAGATTCAACAGT
genomic: AGGCCATGGCTCTTGGAGCAGAACCTGAGAAAGGACCAGATGTTACTCGAgtatgttcac ... gattttgtagGTTCTTATAAGATTTCCAACTGGAGAGCGCAAAGAAAGGAGATTCAACAGT
EST: gi|89161732|gb|CI100892.1|CI100892
EST:     AGGCCATGGCTCTTGGAGCAGAACCTGAGAAAGGACCAGATGTTACTCGA                         GTTCTTATAAGATTTCCAACTGGAGAGCGCAAAGAAAGGAGATTCAACAGT
genomic: AGGCCATGGCTCTTGGAGCAGAACCTGAGAAAGGACCAGATGTTACTCGAgtatgttcac ... gattttgtagGTTCTTATAAGATTTCCAACTGGAGAGCGCAAAGAAAGGAGATTCAACAGT
EST: gi|86536892|gb|CI177098.1|CI177098
EST:     AGGCCATGGCTCTTGGAGCAGAACCTGAGAAAGGACCAGATGTTACTCGA                         GTTCTTATAAGATTTCCAACTGGAGAGCGCAAGGAAAGGAGATTCAACAGT
genomic: AGGCCATGGCTCTTGGAGCAGAACCTGAGAAAGGACCAGATGTTACTCGAgtatgttcac ... gattttgtagGTTCTTATAAGATTTCCAACTGGAGAGCGCAAAGAAAGGAGATTCAACAGT
EST: gi|88978113|gb|CI384595.1|CI384595
EST:     AGGCCATGGCTCTTGGAGCAGAACCTGAGAAAGGACCAGATGTTACTCGA                         GTTCTTATAAGATTTCCAACTGGAGAGCGCAAAGAAAGGAGATTCAACATT
genomic: AGGCCATGGCTCTTGGAGCAGAACCTGAGAAAGGACCAGATGTTACTCGAgtatgttcac ... gattttgtagGTTCTTATAAGATTTCCAACTGGAGAGCGCAAAGAAAGGAGATTCAACAGT
EST: gi|86536571|gb|CI176777.1|CI176777
EST:     AGGCCATGGCTCTTGGAGCAGAACCTGAGAAAGGACCAGATGTTACTCGA                         GTTCTTATAAGATTTCCAACTGGAGAGCGCAAGGAAAGGAGATTCAACAGT
genomic: AGGCCATGGCTCTTGGAGCAGAACCTGAGAAAGGACCAGATGTTACTCGAgtatgttcac ... gattttgtagGTTCTTATAAGATTTCCAACTGGAGAGCGCAAAGAAAGGAGATTCAACAGT
EST: gi|88967571|gb|CI014922.1|CI014922
EST:     AGGCCATGGCTCTTGGAGCAGAACCTGAGAAAGGACCAGATGTTACTCGA                         GTTCTTATAAGATTTCCAACTGGAGAGCGCAAAGAAAGGAGATTCAACAGT
genomic: AGGCCATGGCTCTTGGAGCAGAACCTGAGAAAGGACCAGATGTTACTCGAgtatgttcac ... gattttgtagGTTCTTATAAGATTTCCAACTGGAGAGCGCAAAGAAAGGAGATTCAACAGT
EST: gi|88263286|gb|CI367060.1|CI367060
EST:     AGGCCATGGCTCTTGGAGCAGAACCTGAGAAAGGACCAGATGTTACTCGA                         GTTCTTATAAGATTTCCAACTGGAGAGCGCAAAGAAAGGAGATTCAACAGT
genomic: AGGCCATGGCTCTTGGAGCAGAACCTGAGAAAGGACCAGATGTTACTCGAgtatgttcac ... gattttgtagGTTCTTATAAGATTTCCAACTGGAGAGCGCAAAGAAAGGAGATTCAACAGT
EST: gi|89188189|gb|CI115438.1|CI115438
EST:     AGGCCATGGCTCTTGGAGCAGAACCTGAGAAAGGACCAGATGTTACTCGA                         GTTCTGATAAGATTTCCAACTGGAGAGCGCAAAGAAAGGAGATTCAACAGT
genomic: AGGCCATGGCTCTTGGAGCAGAACCTGAGAAAGGACCAGATGTTACTCGAgtatgttcac ... gattttgtagGTTCTTATAAGATTTCCAACTGGAGAGCGCAAAGAAAGGAGATTCAACAGT
EST: gi|89180514|gb|CI044793.1|CI044793
EST:     AGGCCATGGCTCTTGGAGCAGAACCTGAGAAAGGACCAGATGTTACTCGA                         GTTCTTATAAGATTTCCAACTGGAGAGCGCAAAGAAAGGAGATTCAACAGT
genomic: AGGCCATGGCTCTTGGAGCAGAACCTGAGAAAGGACCAGATGTTACTCGAgtatgttcac ... gattttgtagGTTCTTATAAGATTTCCAACTGGAGAGCGCAAAGAAAGGAGATTCAACAGT
EST: gi|86490064|gb|CI132697.1|CI132697
EST:     AGGCCATGGCTCTTGGAGCAGAACCTGAGAAAGGACCAGATGTTACTCGA                         GTTCTTATAAGATTTCCAACTGGAGAGCGCAAAGAAAGGAGATTCAACAGT
genomic: AGGCCATGGCTCTTGGAGCAGAACCTGAGAAAGGACCAGATGTTACTCGAgtatgttcac ... gattttgtagGTTCTTATAAGATTTCCAACTGGAGAGCGCAAAGAAAGGAGATTCAACAGT
EST: gi|89173517|gb|CI041410.1|CI041410
EST:     AGGCCATGGCTCTTGGAGCAGAACCTGAGAAAGGACCAGATGTTACTCGA                         GTTCTTATAAGATTTCCAACTGGAGAGCGCAAAGAAAGGAGATTCAACAGT
genomic: AGGCCATGGCTCTTGGAGCAGAACCTGAGAAAGGACCAGATGTTACTCGAgtatgttcac ... gattttgtagGTTCTTATAAGATTTCCAACTGGAGAGCGCAAAGAAAGGAGATTCAACAGT
EST: gi|24468678|gb|CA305627.1|CA305627
EST:     AGGCCATGGCTCTTGGAGCAGAACCTGAGAAAGGACCAGATGTTACTCGA                         GTTCTTATAAGATTTCCAACTGGAGAGCGCAAAGAAAGGAGATTCAACAGT
genomic: AGGCCATGGCTCTTGGAGCAGAACCTGAGAAAGGACCAGATGTTACTCGAgtatgttcac ... gattttgtagGTTCTTATAAGATTTCCAACTGGAGAGCGCAAAGAAAGGAGATTCAACAGT
EST: gi|86860794|gb|CI325023.1|CI325023
EST:     AGGCCATGGCTCTTGGAGCAGAACCTGAGAAAGGACCAGATGTTACTCGA                         GTTCTTATAAGATTTCCAAGTGGAGAGCGCAAAGAAAGGAGATTCAACAGT
genomic: AGGCCATGGCTCTTGGAGCAGAACCTGAGAAAGGACCAGATGTTACTCGAgtatgttcac ... gattttgtagGTTCTTATAAGATTTCCAACTGGAGAGCGCAAAGAAAGGAGATTCAACAGT
EST: gi|86428400|gb|CI075081.1|CI075081
EST:     AGGCCATGGCTCTTGGAGCAGAACCTGAGAAAGGACCAGATGTTACTCGA                         GTTCTTATAAGATTTCCAACTGGAGAGCGCAAAGAAAGGAGATTCAACAGT
genomic: AGGCCATGGCTCTTGGAGCAGAACCTGAGAAAGGACCAGATGTTACTCGAgtatgttcac ... gattttgtagGTTCTTATAAGATTTCCAACTGGAGAGCGCAAAGAAAGGAGATTCAACAGT
EST: gi|4715368|gb|AU056485.1|AU056485
EST:     AGGCCATGGCTCTTGGAGCAGAACCTGAGAAAGGACCAGATGTNACTCGA                         GTTCTTATAAGATTTCCAACTGGAGAGCGCAAAGAAAGGAGATTCAACAGT
genomic: AGGCCATGGCTCTTGGAGCAGAACCTGAGAAAGGACCAGATGTTACTCGAgtatgttcac ... gattttgtagGTTCTTATAAGATTTCCAACTGGAGAGCGCAAAGAAAGGAGATTCAACAGT
EST: gi|86825459|gb|CI360083.1|CI360083
EST:     CTCTTGGAGCAGAACCTGAGAAAGGACCAGATGTTACTCGA                         GTTCTTATAAGATTTCCAACTGGAGAGCGCAAAGAAAGGAGATTCAACAGT
genomic: CTCTTGGAGCAGAACCTGAGAAAGGACCAGATGTTACTCGAgtatgttcac ... gattttgtagGTTCTTATAAGATTTCCAACTGGAGAGCGCAAAGAAAGGAGATTCAACAGT
EST: gi|88246185|gb|CI246034.1|CI246034
EST:     AGGCCATGGCTCTTGGAGCAGAACCTGAGAAAGGACCAGATGTTACTCGA                         GTTCTTATAAGATTTCCAACTGGAGAGCGCAAAGAAAGGAGATTCAACAGT
genomic: AGGCCATGGCTCTTGGAGCAGAACCTGAGAAAGGACCAGATGTTACTCGAgtatgttcac ... gattttgtagGTTCTTATAAGATTTCCAACTGGAGAGCGCAAAGAAAGGAGATTCAACAGT
EST: gi|86842718|gb|CI341841.1|CI341841
EST:     CATGGCTCTTGGAGCAGAACCTGAGAAAGGACCAGATGTTACTCGA                         GTTCTTATAAGATTTCCAACTGGAGAGCGCAAAGAAAGGAGATTCAACAGT
genomic: CATGGCTCTTGGAGCAGAACCTGAGAAAGGACCAGATGTTACTCGAgtatgttcac ... gattttgtagGTTCTTATAAGATTTCCAACTGGAGAGCGCAAAGAAAGGAGATTCAACAGT

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 1 RNA-Seqlibrary.


Block sizes: 65 (upstream exon), 72 (downstream exon)
Score: 12

CCAAGAAGCAGCTGAGAAAGAAGCCGCTCTTGCAAGGAGGAGACAAGAGAAGGCCATGGCTCTTGGAGCAGAACCTGAGAAAGGACCAGATGTTACTCGAgtatgttcac ... gattttgtagGTTCTTATAAGATTTCCAACTGGAGAGCGCAAAGAAAGGAGATTCAACAGTTCCACTACCATCACTTCACTGTATGACTATGTTGATTCTTTGGACTGCT




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CCAAGAAGCAGCTGAGAAAGAAGCCGCTCTTGCAAGGAGGAGACAAGAGAAGGCCATGGCTCTTGGAGCAGAACCTGAGAAAGGACCAGATGTTACTCGAgtatgttcacattctttgtccatcttccttatcaacctgttatgatcttattctaggataatgtgctgacaagttacaaccacatttgtctacttttgat

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG