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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagttaccaaattgttgttggttacataataaatgttttttggtcaagttgtttgctaactcccttttgctttccctctgtgaaagGGTTTCTGGAAAGATCATCTGCGAGGAAGACCATACCACATCAG

Basic information

species Oryza sativa
transcript LOC_Os02g44510.1
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g44510.1 (Oryza sativa), 3'ss of exon 13
lower sequence: GRMZM5G846198_T02 (Zea mays), 3'ss of exon 6
-----------------------gtaagttacca-------aattgttgttggttacataataaatgt-----tttttggtcaagttgtttgctaactcccttttgctttccctctgtgaaagGGTTTCTGGAAAGATCATCTGCGAGGAAGACCATACCACATCAG
                         | ||||| |       |||||||  || | | |  ||||| ||     | |||  ||||||| || | | || |  | ||  ||  ||||||   |||||||| |||||||||||||||||||||||||| ||||| |||||
gttagtcactgatttataataaatcatgttactacgcaaacaattgttcatgataataatataaaagtggatttgttttctcaagtttttcgttgacactttctt--ttatcctctg---aagGGTTTTTGGAAAGATCATCTGCGAGGAAGACCGTACCATATCAG
















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|428266|gb|D24414.1|D24414
EST:     CATTCTGCGATAACAACAAGGAGATGGATGGCTATCGATTTTGGAAGCAA                         GGTTTCTGGAAAGATCATCTGCGAGGAAGACCATACCACATCAG
genomic: CATTCTGCGATAACAACAAGGAGATGGATGGCTATCGATTTTGGAAGCAAgtaagttacc ... tctgtgaaagGGTTTCTGGAAAGATCATCTGCGAGGAAGACCATACCACATCAG
EST: gi|58658861|gb|CK047541.1|CK047541
EST:     CATTCTGCGATAACAACAAGGAGATGGATGGCTATCGATTTTGGAAGCAA                         GGTTTCTGGAAAGATCATCTGCGAGGAAGACCATACCACATCAG
genomic: CATTCTGCGATAACAACAAGGAGATGGATGGCTATCGATTTTGGAAGCAAgtaagttacc ... tctgtgaaagGGTTTCTGGAAAGATCATCTGCGAGGAAGACCATACCACATCAG
EST: gi|58609426|gb|CK037459.1|CK037459
EST:     CATTCTGCGATAACAACAAGGAGATGGATGGCTATCGATTTTGGAAGCAA                         GGTTTCTGGAAAGATCATCTGCGAGGAAGACCATACCACATCAG
genomic: CATTCTGCGATAACAACAAGGAGATGGATGGCTATCGATTTTGGAAGCAAgtaagttacc ... tctgtgaaagGGTTTCTGGAAAGATCATCTGCGAGGAAGACCATACCACATCAG
EST: gi|88401279|gb|CI685275.1|CI685275
EST:     CATTCTGCGATAACAACAAGGAGATGGATGGCTATCGATTTTGGAAGCAA                         GGTTTCTGGAAAGATCATCTGCGAGGAAGACCATACCACATCAG
genomic: CATTCTGCGATAACAACAAGGAGATGGATGGCTATCGATTTTGGAAGCAAgtaagttacc ... tctgtgaaagGGTTTCTGGAAAGATCATCTGCGAGGAAGACCATACCACATCAG
EST: gi|58594812|gb|CF993120.1|CF993120
EST:     ATTCTGCGATAGACGACAAGGAGATGGATGGCTATCGATTTTGGAAGCAA                         GGTTTCTGGAAAGATCATCTGCGAGGAAGACCATACCACATCAG
genomic: ATTCTGCGATA-ACAACAAGGAGATGGATGGCTATCGATTTTGGAAGCAAgtaagttacc ... tctgtgaaagGGTTTCTGGAAAGATCATCTGCGAGGAAGACCATACCACATCAG
EST: gi|58678387|gb|CK067074.1|CK067074
EST:     CATTCTGCGATAACAACAAGGAGATGGATGGCTATCGATTTTGGAAGCAA                         GGTTTCTGGAAAGATCATCTGCGAGGAAGACCATACCACATCAG
genomic: CATTCTGCGATAACAACAAGGAGATGGATGGCTATCGATTTTGGAAGCAAgtaagttacc ... tctgtgaaagGGTTTCTGGAAAGATCATCTGCGAGGAAGACCATACCACATCAG
EST: gi|218480649|gb|FG956875.1|FG956875
EST:     CATTCTGCGATAACAACAAGGAGATGGATGGCTATCGATTTTGGAAGCAA                         GGTTTCTGGAAAGATCATCTGCGAGGAAGACCATACCACATCAG
genomic: CATTCTGCGATAACAACAAGGAGATGGATGGCTATCGATTTTGGAAGCAAgtaagttacc ... tctgtgaaagGGTTTCTGGAAAGATCATCTGCGAGGAAGACCATACCACATCAG
EST: gi|58692422|gb|CK081109.1|CK081109
EST:     CATTCTGCGATAACAACAAGGAGATGGATGGCTATCGATTTTGGAAGCAA                         GGTTTCTGGAAAGATCATCTGCGAGGAAGACCATACCACATCAG
genomic: CATTCTGCGATAACAACAAGGAGATGGATGGCTATCGATTTTGGAAGCAAgtaagttacc ... tctgtgaaagGGTTTCTGGAAAGATCATCTGCGAGGAAGACCATACCACATCAG
EST: gi|88321783|gb|CI672927.1|CI672927
EST:     CATTCTGCGATAACAACAAGGAGATGGATGGCTATCGATTTTGGAAGCAA                         GGTTTCTGGAAAGATCATCTGCGAGGAAGACCATACCACATCAG
genomic: CATTCTGCGATAACAACAAGGAGATGGATGGCTATCGATTTTGGAAGCAAgtaagttacc ... tctgtgaaagGGTTTCTGGAAAGATCATCTGCGAGGAAGACCATACCACATCAG
EST: gi|58687397|gb|CK076084.1|CK076084
EST:     CATTCTGCGATAACAACAAGGAGATGGATGGCTATCGATTTTGGAAGCAA                         GGTTTCTGGAAAGATCATCTGCGAGGAAGACCATACCACATCAG
genomic: CATTCTGCGATAACAACAAGGAGATGGATGGCTATCGATTTTGGAAGCAAgtaagttacc ... tctgtgaaagGGTTTCTGGAAAGATCATCTGCGAGGAAGACCATACCACATCAG
EST: gi|428777|gb|D24933.1|D24933
EST:     CATTCTGCGATAACAACAAGGAGATGGATGGCTATCGATTTTGGAAGCAA                         GGTTTCTGGAAAGATCATCTGCGAGGAAGACCATACCACATCAG
genomic: CATTCTGCGATAACAACAAGGAGATGGATGGCTATCGATTTTGGAAGCAAgtaagttacc ... tctgtgaaagGGTTTCTGGAAAGATCATCTGCGAGGAAGACCATACCACATCAG
EST: gi|58658473|gb|CK047153.1|CK047153
EST:     CATTCTGCGATAACAACAAGGAGATGGATGGCTATCGATTTTGGAAGCAA                         GGTTTCTGGAAAGATCATCTGCGAGGAAGACCATACCACATCAG
genomic: CATTCTGCGATAACAACAAGGAGATGGATGGCTATCGATTTTGGAAGCAAgtaagttacc ... tctgtgaaagGGTTTCTGGAAAGATCATCTGCGAGGAAGACCATACCACATCAG
EST: gi|88371879|gb|CI681390.1|CI681390
EST:     CATTCTGCGATAACAACAAGGAGATGGATGGCTATCGATTTTGGAAGCAA                         GGTTTCTGGAAAGATCATCTGCGAGGAAGACCATACCACATCAG
genomic: CATTCTGCGATAACAACAAGGAGATGGATGGCTATCGATTTTGGAAGCAAgtaagttacc ... tctgtgaaagGGTTTCTGGAAAGATCATCTGCGAGGAAGACCATACCACATCAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aatgttttttggtcaagttgtttgctaactcccttttgctttccctctgtgaaagGGTTTCTGGAAAGATCATCTGCGAGGAAGACCATACCACATCAG
                      tgctaac  putative branch site (score: 1)
                    tttgctaactcccttt  CT-rich tract
     ttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagttaccaaattgttgttggttacataataaatgttttttggtcaagttgtttgctaactcccttttgctttccctctgtgaaagGGTTTCTGGAAAGATCATCTGCGAGGAAGACCATACCACATCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGATCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA