Skip to another splice site:
1  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCCGCCTACCACGCCGAGGCGAAAAGCTCTGCAACCGCGCGTACGAGCTCCAGATTTGGCAGGACAGGGGACAGGCTCGCTCAAGGCATCAAAGAACATGgtacgttcttctccagtccatcttggaccatactacttttgatcttggatgagttcgatttttcatggttgcgaattggagaattggtactgaacaatcttttcttgatgatttgcag

Basic information

species Oryza sativa
transcript LOC_Os04g44510.1
intron # 1
splice site 5'
intron type U2

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|86906816|gb|CI291216.1|CI291216
EST:     CAGATTTGGCAGGACAGGGGACAGGCTCGCTCAAGGCATCAAAGAACATG                         TGACTCTAGGACCAAAACTGTACGAGACCATGAAAGGCAAGCTGACGCTGG
genomic: CAGATTTGGCAGGACAGGGGACAGGCTCGCTCAAGGCATCAAAGAACATGgtacgttctt ... tgatttgcagTGACTCTAGGACCAAAACTGTACGAGACCATGAAAGGCAAGCTGACGCTGG
EST: gi|33690626|gb|CF318865.1|CF318865
EST:     CAGATTTGGCAGGACAGGGGACAGGCTCGCTCAAGGCATCAAAGAACATG                         TGACTCTAGGACCAAAACTGTACGAGACCATGAAAGGCAAGCTGACGCTGG
genomic: CAGATTTGGCAGGACAGGGGACAGGCTCGCTCAAGGCATCAAAGAACATGgtacgttctt ... tgatttgcagTGACTCTAGGACCAAAACTGTACGAGACCATGAAAGGCAAGCTGACGCTGG
EST: gi|88736139|gb|CI759647.1|CI759647
EST:     CAGATTTGGCAGGACAGGGGACAGGCTCGCTCAAGGCATCAAAGAACATG                         TGACTCTAGGACCAAAACTGTACGAGACCATGAAAGGCAAGCTGACGCTGG
genomic: CAGATTTGGCAGGACAGGGGACAGGCTCGCTCAAGGCATCAAAGAACATGgtacgttctt ... tgatttgcagTGACTCTAGGACCAAAACTGTACGAGACCATGAAAGGCAAGCTGACGCTGG
EST: gi|88760148|gb|CI769704.1|CI769704
EST:     CAGATTTGGCAGGACAGGGGACAGGCTCGCTCAAGGCATCAAAGAACATG                         TGACTCTAGGACCAAAACTGTACGAGACCATGAAAGGCAAGCTGACGCTGG
genomic: CAGATTTGGCAGGACAGGGGACAGGCTCGCTCAAGGCATCAAAGAACATGgtacgttctt ... tgatttgcagTGACTCTAGGACCAAAACTGTACGAGACCATGAAAGGCAAGCTGACGCTGG
EST: gi|27547474|gb|CA765642.2|CA765642
EST:     CAGGCTCGCTCAAGGCATCAAAGAACATG                         TGACTCTAGGACCAAAACTGTACGAGACCATGAAAGGCAAGCTGACGCTGG
genomic: CAGGCTCGCTCAAGGCATCAAAGAACATGgtacgttctt ... tgatttgcagTGACTCTAGGACCAAAACTGTACGAGACCATGAAAGGCAAGCTGACGCTGG
EST: gi|58587720|gb|CF986028.1|CF986028
EST:     AGGCTCGCTCAAGGCATCAAAGAACATG                         TGACTCTAGGACCAAAACTGTACGAGACCATGAAAGGCAAGCTGACGCTTG
genomic: AGGCTCGCTCAAGGCATCAAAGAACATGgtacgttctt ... tgatttgcagTGACTCTAGGACCAAAACTGTACGAGACCATGAAAGGCAAGCTGACGCTGG
EST: gi|86847416|gb|CI286996.1|CI286996
EST:     CAGATTTGGCAGGACAGGGGACAGGCTCGCTCAAGGCATCAAAGAACATG                         TGACTCTAGGACCAAAACTGTACGAGACCATGAAAGGCAAGCTGACGCTGG
genomic: CAGATTTGGCAGGACAGGGGACAGGCTCGCTCAAGGCATCAAAGAACATGgtacgttctt ... tgatttgcagTGACTCTAGGACCAAAACTGTACGAGACCATGAAAGGCAAGCTGACGCTGG
EST: gi|58602988|gb|CK013516.1|CK013516
EST:     CAGATTTGGCAGGACAGGGGACAGGCTCGCTCAAGGCATCAAAGAACATG                         TGACTCTAGGACCAAAACTGTACGAGACCATGAAAGGCAAGCTGACGCTGG
genomic: CAGATTTGGCAGGACAGGGGACAGGCTCGCTCAAGGCATCAAAGAACATGgtacgttctt ... tgatttgcagTGACTCTAGGACCAAAACTGTACGAGACCATGAAAGGCAAGCTGACGCTGG
EST: gi|33813671|gb|CF332725.1|CF332725
EST:     CAGGTTTGGCAGGACAGGGGACAGGCTCGCTCAAGGCATCAAAGAACATG                         TGACTCTAGGACCAAAACTGTACGAGACCATGAAAGGCAAGCTGACGCTGG
genomic: CAGATTTGGCAGGACAGGGGACAGGCTCGCTCAAGGCATCAAAGAACATGgtacgttctt ... tgatttgcagTGACTCTAGGACCAAAACTGTACGAGACCATGAAAGGCAAGCTGACGCTGG
EST: gi|88328215|gb|CI651221.1|CI651221
EST:     CAGATTTGGCAGGACAGGGGACAGGCTCGCTCAAGGCATCAAAGAACATG                         TGACTCTAGGACCAAAACTGTACGAGACCATGAAAGGCAAGCTGACGCTGG
genomic: CAGATTTGGCAGGACAGGGGACAGGCTCGCTCAAGGCATCAAAGAACATGgtacgttctt ... tgatttgcagTGACTCTAGGACCAAAACTGTACGAGACCATGAAAGGCAAGCTGACGCTGG
EST: gi|86595822|gb|CI290096.1|CI290096
EST:     CAGATTTGGCAGGACAGGGGACAGGCTCGCTCAAGGCATCAAAGAACATG                         TGACTCTAGGACCAAAACTGTACGAGACCATGAAAGGCAAGCTGACGCTGG
genomic: CAGATTTGGCAGGACAGGGGACAGGCTCGCTCAAGGCATCAAAGAACATGgtacgttctt ... tgatttgcagTGACTCTAGGACCAAAACTGTACGAGACCATGAAAGGCAAGCTGACGCTGG
EST: gi|88298739|gb|CI565936.1|CI565936
EST:     CAGATTTGGCAGGACAGGGGACAGGCTCGCTCAAGGCATCAAAGAACATG                         TGACTCTAGGACCAAAACTGTACGAGACCATGAAAGGCAAGCTGACGCTGG
genomic: CAGATTTGGCAGGACAGGGGACAGGCTCGCTCAAGGCATCAAAGAACATGgtacgttctt ... tgatttgcagTGACTCTAGGACCAAAACTGTACGAGACCATGAAAGGCAAGCTGACGCTGG
EST: gi|569049|gb|D39898.1|D39898
EST:     CAGATTTGGCAGGACAGGGGACAGGCTCGNTCAAGGCATCAAAGGACATG                         TGACTCTAGGACCAAAACTGTACGAGACCATGAAAGGCAAG
genomic: CAGATTTGGCAGGACAGGGGACAGGCTCGCTCAAGGCATCAAAGAACATGgtacgttctt ... tgatttgcagTGACTCTAGGACCAAAACTGTACGAGACCATGAAAGGCAAG
EST: gi|87035215|gb|CI189837.1|CI189837
EST:     GGGGACAGGCTCGCTCAAGGCATCAAAGAACATG                         TGACTCTAGGACCAAAACTGTACGAGACCATGAAAGGCAAGCTGACGCTGG
genomic: GGGGACAGGCTCGCTCAAGGCATCAAAGAACATGgtacgttctt ... tgatttgcagTGACTCTAGGACCAAAACTGTACGAGACCATGAAAGGCAAGCTGACGCTGG
EST: gi|86905613|gb|CI287178.1|CI287178
EST:     CAGATTTGGCAGGACAGGGGACAGGCTCGCTCAAGGCATCAAAGAACATG                         TGACTCTAGGACCA
genomic: CAGATTTGGCAGGACAGGGGACAGGCTCGCTCAAGGCATCAAAGAACATGgtacgttctt ... tgatttgcagTGACTCTAGGACCA
EST: gi|4878785|gb|AU063084.1|AU063084
EST:     CAGATTTGGCAGGACAGGGGACAGGCTCGCTCAAGGCATCAAAGAACATG                         TGACTCTAGGACCAAAACTGTACGAGACCATGAAAGGCAAGCTGACGCT
genomic: CAGATTTGGCAGGACAGGGGACAGGCTCGCTCAAGGCATCAAAGAACATGgtacgttctt ... tgatttgcagTGACTCTAGGACCAAAACTGTACGAGACCATGAAAGGCAAGCTGACGCT

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: 74 (upstream exon), 67 (downstream exon)
Score: 56

GCCGCCTACCACGCCGAGGCGAAAAGCTCTGCAACCGCGCGTACGAGCTCCAGATTTGGCAGGACAGGGGACAGGCTCGCTCAAGGCATCAAAGAACATGgtacgttctt ... tgatttgcagTGACTCTAGGACCAAAACTGTACGAGACCATGAAAGGCAAGCTGACGCTGGGCGCGAGAATCCTCCAGGCAGGCGGCGTGGAGAAGGTCTTCCGCCGGTG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCCGCCTACCACGCCGAGGCGAAAAGCTCTGCAACCGCGCGTACGAGCTCCAGATTTGGCAGGACAGGGGACAGGCTCGCTCAAGGCATCAAAGAACATGgtacgttcttctccagtccatcttggaccatactacttttgatcttggatgagttcgatttttcatggttgcgaattggagaattggtactgaacaatcttttcttgatgatttgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAC