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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagttgttgtttgtaatgtaaccaccattttgtgatgcgcacacgtcattatgataaatttctttttcagATAAAATATGTCAGTGGTTCCTATGACAGCGGAGAAGGATTTGAGAAATTGAACAAGGAAATTTCAGAGTATGAGAAGTCAAACAAATCAGAAAGCCCTC

Basic information

species Oryza sativa
transcript LOC_Os04g40874.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g40874.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G130230_T03 (Zea mays), 3'ss of exon 4
gtgagttgttgtttgtaatgtaaccaccattttgtgat---gcgcacacgtcattatgataaatttctttttcagATAAAATATGTCAGTGGTTCCTATGACAGCGGAGAAGGATTTGAGAAATTGAACAAGGAAATTTCAGAGTATGAGAAGTCAAACAAATCAGAAAGCCCTC
|| ||||||| |   ||   |||      | | ||  |   |  || || |||||||||||  ||| | | |||||||||||||||||||||||||||||| |  |||||||||||||||||| |||||| || ||| ||||||||||||  |||||| |  |||| ||||  ||
gtaagttgttataactacaataattgtattctagttctagggtacagacatcattatgatatttttgtgtctcagATAAAATATGTCAGTGGTTCCTATGATACTGGAGAAGGATTTGAGAAACTGAACAGGGCAATATCAGAGTATGAGGTGTCAAAGAGTTCAGGAAGCTATC
















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|88421242|gb|CI569087.1|CI569087
EST:     ATACCTCAAAGGAGCCCTCAGAAGAACATCTCTCAGACTTTTTGCAACAT                         ATAAAATATGTCAGTGGTTC-TATGACAGCGGAGAAGGATTTGAGAAATTG
genomic: ATACCTCAAAGGAGCC-TCAGAAGAACATCTCTCAGACTTTTTGCAACATgtgagttgtt ... tctttttcagATAAAATATGTCAGTGGTTCCTATGACAGCGGAGAAGGATTTGAGAAATTG
EST: gi|29663317|gb|CB659592.1|CB659592
EST:     ATACCTCAAAGGAGCCTCAGAAGAACATCTCTCAGACTTTTTGCAACAT                         ATAAAATATGTCAGTGGTTCCTATGACAGCGGAGAAGGATTTGAGAAATTG
genomic: ATACCTCAAAGGAGCCTCAGAAGAACATCTCTCAGACTTTTTGCAACATgtgagttgtt ... tctttttcagATAAAATATGTCAGTGGTTCCTATGACAGCGGAGAAGGATTTGAGAAATTG
EST: gi|88313812|gb|CI597443.1|CI597443
EST:     ATACCTCAAAGGAGCCTCAGAAGAACATCTCTCAGACTTTTTGCAACAT                         ATAAAATATGTCAGTGGTTC-TATGACAGCGGAGAAGGATTTGAG
genomic: ATACCTCAAAGGAGCCTCAGAAGAACATCTCTCAGACTTTTTGCAACATgtgagttgtt ... tctttttcagATAAAATATGTCAGTGGTTCCTATGACAGCGGAGAAGGATTTGAG
EST: gi|88449978|gb|CI572109.1|CI572109
EST:     ATACCTCAAAGGAGCCTCAGAAGAACATCTCTCAGACTTTTTGCAACAT                         ATAAAATATGTCAGTGGTTCCTATGACAGCG
genomic: ATACCTCAAAGGAGCCTCAGAAGAACATCTCTCAGACTTTTTGCAACATgtgagttgtt ... tctttttcagATAAAATATGTCAGTGGTTCCTATGACAGCG
EST: gi|58654814|gb|CK043494.1|CK043494
EST:     ATACCTCAAAGGAGCCTCAGAAGAACATCTCTCAGACTTTTTGCAACAT                         ATAAAATATGTCAGTGGTTCCTATGACAGCGGAGAAGGATTTGAGAAATTG
genomic: ATACCTCAAAGGAGCCTCAGAAGAACATCTCTCAGACTTTTTGCAACATgtgagttgtt ... tctttttcagATAAAATATGTCAGTGGTTCCTATGACAGCGGAGAAGGATTTGAGAAATTG
EST: gi|88719764|gb|CI743274.1|CI743274
EST:     ATACCTCAAAGGAGCCTCAGAAGAACATCTCTCAGACTTTTTGCAACAT                         ATAAAATATGTCAGTGGTTCCTATGA
genomic: ATACCTCAAAGGAGCCTCAGAAGAACATCTCTCAGACTTTTTGCAACATgtgagttgtt ... tctttttcagATAAAATATGTCAGTGGTTCCTATGA
EST: gi|58611861|gb|CK039573.1|CK039573
EST:     ATACCTCAAAGGAGCCTCAGAAGAACATCTCTCAGACTTTTTGCAACAT                         ATAAAATATGTCAGTGGTTCCTATGACAGCGGAGAAGGATTTGAGAAATTG
genomic: ATACCTCAAAGGAGCCTCAGAAGAACATCTCTCAGACTTTTTGCAACATgtgagttgtt ... tctttttcagATAAAATATGTCAGTGGTTCCTATGACAGCGGAGAAGGATTTGAGAAATTG
EST: gi|88388045|gb|CI590321.1|CI590321
EST:     ATACCTCAAAGGAGCCTCAGAAGAACATCTCTCAGACTTTTTGCAACAT                         ATAAAATATGTCAGT
genomic: ATACCTCAAAGGAGCCTCAGAAGAACATCTCTCAGACTTTTTGCAACATgtgagttgtt ... tctttttcagATAAAATATGTCAGT
EST: gi|88407965|gb|CI588994.1|CI588994
EST:     ATACCTCAAAGGAGCCTCAGAAGAACATCTCTCAGACTTTTTGCAACAT                         ATAAAATATGTCAGTGGTTCCTATG
genomic: ATACCTCAAAGGAGCCTCAGAAGAACATCTCTCAGACTTTTTGCAACATgtgagttgtt ... tctttttcagATAAAATATGTCAGTGGTTCCTATG
EST: gi|88430411|gb|CI567430.1|CI567430
EST:     ATACC-CAAAGGAGCCTCAGAAGAACATCTCTCAGACTTTTTGCAACAT                         ATAAAATATGTCAGTGGTTCCTATGACAGCGGAGAAGGATTTGAGAAATTG
genomic: ATACCTCAAAGGAGCCTCAGAAGAACATCTCTCAGACTTTTTGCAACATgtgagttgtt ... tctttttcagATAAAATATGTCAGTGGTTCCTATGACAGCGGAGAAGGATTTGAGAAATTG
EST: gi|88409948|gb|CI571205.1|CI571205
EST:     ATACCTCAAAGGAGCCTCAGAAGAACATCTCTCAGACTTTTTGCAACAT                         ATAAAATATGTCAGTGGTTCCTATGA
genomic: ATACCTCAAAGGAGCCTCAGAAGAACATCTCTCAGACTTTTTGCAACATgtgagttgtt ... tctttttcagATAAAATATGTCAGTGGTTCCTATGA
EST: gi|29634314|gb|CB639323.1|CB639323
EST:     ATACCTCAAAGGAGCCTCAGAAGAACATCTCTCAGACTTTTTGCAACAT                         ATAAAATATGTCAGTGGTTCCTATGACAGCGGAGAAGGATTTGAGAAATTG
genomic: ATACCTCAAAGGAGCCTCAGAAGAACATCTCTCAGACTTTTTGCAACATgtgagttgtt ... tctttttcagATAAAATATGTCAGTGGTTCCTATGACAGCGGAGAAGGATTTGAGAAATTG
EST: gi|29614696|gb|CB619709.1|CB619709
EST:     ATACCTCAAAGGAGCCTCAGAAGAACATCTCTCAGACTTTTTGCAACAT                         ATAAAATATGTCAGTGGTTCCTATGACAGCGGAGAAGGATTTGAGAAATTG
genomic: ATACCTCAAAGGAGCCTCAGAAGAACATCTCTCAGACTTTTTGCAACATgtgagttgtt ... tctttttcagATAAAATATGTCAGTGGTTCCTATGACAGCGGAGAAGGATTTGAGAAATTG
EST: gi|88396043|gb|CI595591.1|CI595591
EST:     ATAC-TCAAAGGAGCCTCAGAAGAACATCTCTCAGACTTTTTGGAACAT                         ATAAAATATGT
genomic: ATACCTCAAAGGAGCCTCAGAAGAACATCTCTCAGACTTTTTGCAACATgtgagttgtt ... tctttttcagATAAAATATGT
EST: gi|88421686|gb|CI569067.1|CI569067
EST:     ATACCTCAAAGGAGCCTCAGAAGAACATCTCTCAGACTTTTTGCAACAT                         ATAAAATATGTCAGTGGTTCCTATGAGAGCGGAGAAGGATTTGAGAAATTG
genomic: ATACCTCAAAGGAGCCTCAGAAGAACATCTCTCAGACTTTTTGCAACATgtgagttgtt ... tctttttcagATAAAATATGTCAGTGGTTCCTATGACAGCGGAGAAGGATTTGAGAAATTG
EST: gi|58608815|gb|CK036848.1|CK036848
EST:     ATACCTCAAAGGAGCCTCAGAAGAACATCTCTCAGACTTTTTGCAACAT                         ATAAAATATGTCAGTGGTTCCTATGACAGCGGAGAAGGATTTGAGAAATTG
genomic: ATACCTCAAAGGAGCCTCAGAAGAACATCTCTCAGACTTTTTGCAACATgtgagttgtt ... tctttttcagATAAAATATGTCAGTGGTTCCTATGACAGCGGAGAAGGATTTGAGAAATTG
EST: gi|58670061|gb|CK058747.1|CK058747
EST:     ATACCTCAAAGGAGCCTCAGAAGAACATCTCTCAGACTTTTTGCAACAT                         ATAAAATATGTCAGTGGTTCCTATGACAGCGGAGAAGGATTTGAGAAATTG
genomic: ATACCTCAAAGGAGCCTCAGAAGAACATCTCTCAGACTTTTTGCAACATgtgagttgtt ... tctttttcagATAAAATATGTCAGTGGTTCCTATGACAGCGGAGAAGGATTTGAGAAATTG
EST: gi|29680803|gb|CB677078.1|CB677078
EST:     ATACCTCAAAGGAGCCTCAGAAGAACATCTCTCAGACTTTTTGCAACAT                         ATAAAATATGTCAGTGGTTCCTATGACAGCGGAGAAGGATTTGAGAAATTG
genomic: ATACCTCAAAGGAGCCTCAGAAGAACATCTCTCAGACTTTTTGCAACATgtgagttgtt ... tctttttcagATAAAATATGTCAGTGGTTCCTATGACAGCGGAGAAGGATTTGAGAAATTG
EST: gi|29635386|gb|CB640395.1|CB640395
EST:     ATACCTCAAAGGAGCCTCAGAAGAACATCTCTCAGACTTTTTGCAACAT                         ATAAAATATGTTAGTGGTTCCTATGACAGCGGAGAAGGATTTGAGAAATTG
genomic: ATACCTCAAAGGAGCCTCAGAAGAACATCTCTCAGACTTTTTGCAACATgtgagttgtt ... tctttttcagATAAAATATGTCAGTGGTTCCTATGACAGCGGAGAAGGATTTGAGAAATTG
EST: gi|88363865|gb|CI607175.1|CI607175
EST:     ATACCTCAAAGGAGCCTCAGAAGAACATCTCTCAGACTTTTTGCAAAAT                         ATAAAATATGTCAGTGGTTCCTATGAGAGCGGAGAAGGATTTGA
genomic: ATACCTCAAAGGAGCCTCAGAAGAACATCTCTCAGACTTTTTGCAACATgtgagttgtt ... tctttttcagATAAAATATGTCAGTGGTTCCTATGACAGCGGAGAAGGATTTGA
EST: gi|163920079|gb|EG712021.1|EG712021
EST:     ATACCTCAAAGGAGCCTCAGAAGAACATCTCTCAGACTTTTTGCAACAT                         ATAAAATATGTCAGTGGTTCCTAT
genomic: ATACCTCAAAGGAGCCTCAGAAGAACATCTCTCAGACTTTTTGCAACATgtgagttgtt ... tctttttcagATAAAATATGTCAGTGGTTCCTAT
EST: gi|117243651|gb|CT843162.1|CT843162
EST:     ATACCTCAAAGGAGCCTCAGAAGAACATCTCTCAGACTTTTTGCAACAT                         ATAAAATATGTCAGTGGTTCCTATGACAGCGGAGAAGGATTTGAGAAATTG
genomic: ATACCTCAAAGGAGCCTCAGAAGAACATCTCTCAGACTTTTTGCAACATgtgagttgtt ... tctttttcagATAAAATATGTCAGTGGTTCCTATGACAGCGGAGAAGGATTTGAGAAATTG

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: 49 (upstream exon), 75 (downstream exon)
Score: 75

ATACCTCAAAGGAGCCTCAGAAGAACATCTCTCAGACTTTTTGCAACATgtgagttgtt ... tctttttcagATAAAATATGTCAGTGGTTCCTATGACAGCGGAGAAGGATTTGAGAAATTGAACAAGGAAATTTCAGAGTATGAGAAGTCAAACAAATCAGAAAGCCCTC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atgtaaccaccattttgtgatgcgcacacgtcattatgataaatttctttttcagATAAAATATGTCAGTGGTTCCTATGACAGCGGAGAAGGATTTGAGAAATTGAACAAGGAAATTTCAGAGTATGAGAAGTCAAACAAATCAGAAAGCCCTC
 atgtaac  putative branch site (score: 75)
                                           tttctttttc  putative PPT
                              tcattatgataaattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagttgttgtttgtaatgtaaccaccattttgtgatgcgcacacgtcattatgataaatttctttttcagATAAAATATGTCAGTGGTTCCTATGACAGCGGAGAAGGATTTGAGAAATTGAACAAGGAAATTTCAGAGTATGAGAAGTCAAACAAATCAGAAAGCCCTC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGT