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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTGGCTCGCCGAGTACCCGCACCAGGGCGCCGACAAGCGGCCGCGGAAGCGGCCCCGCCTCGCCTGGGATGTCGCGCCCCCGCTGTTCCAGCCCCCCAAGgtataatccatgcgctatgtgctgcgtcgatccggtctctctcgggcgtgtgggttgcggtggtagtttttggctagatctagtcgtggtttcgctagat...

Basic information

species Oryza sativa
transcript LOC_Os01g62080.2
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g62080.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G386991_T01 (Zea mays), 5'ss of exon 1
GTGGCTCGCCGAGTACCCGCACCAGGGCGCCGACAAGCGGCCGCGGAAGCGGCCCCGCCTCGCCTGGGATGTCGCGCCCCCGCTGTTCCAGCCCCCCAAGgtataatccatgcgctatgtgctgcgtcgatccggtctctctcg-ggcgtgtgggttgcggtggtagt--ttttggctagatctagtcgtggtttcgctagat
||||||||| ||||| ||||||||||| ||||||||||||||||| || ||| |||| ||||||||||||||||||||| ||||||||||||||||||||||||  | |  || |     || || |||||  | |  |  ||| || || ||| | |   |||  |   |||| ||||||| | |  || | || | | |  
GTGGCTCGCGGAGTATCCGCACCAGGGGGCCGACAAGCGGCCGCGCAAACGGGCCCGGCTCGCCTGGGATGTCGCGCCCACGCTGTTCCAGCCCCCCAAGgtatggttctggccccgctcgccgcatcgattggctaccagtcgtggggtttggctagatctgggcgcggttttcgctagatttgga-gtcggttggttcg--
















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|58593612|gb|CF991920.1|CF991920
EST:     GGCCCCGCCTCGCCTGGGATGTCGCGCCCCCGCTGTTCCAGCCCCCCAAG                         GCAATTGGTATGCTATATTGCGGGCAGGAACTAATCAATGGAAATTTTGCG
genomic: GGCCCCGCCTCGCCTGGGATGTCGCGCCCCCGCTGTTCCAGCCCCCCAAGgtataatcca ... atttttgtagGCAATTCCTATGCTATATTGCGGGCAGGAACTAATCAATGGAAATTTTGCG
EST: gi|58680098|gb|CK068785.1|CK068785
EST:     GGCCCCGCCTCGCCTGGGATGTCGCGCCCCCGCTGTTCCAGCCCCCCAAG                         GCAATTCCTATGCTATATTGCGGGCAGGAACTAATCAATGGAAATTTTGCG
genomic: GGCCCCGCCTCGCCTGGGATGTCGCGCCCCCGCTGTTCCAGCCCCCCAAGgtataatcca ... atttttgtagGCAATTCCTATGCTATATTGCGGGCAGGAACTAATCAATGGAAATTTTGCG
EST: gi|117243444|gb|CT848361.1|CT848361
EST:     GGCCCCGCCTCGCCTGGGATGTCGCGCCCCCGCTGTTCCAGCCCCCCAAG                         GCAATTCCTATGCTATATTGCGGGCAGGAACTAATCAATGGAAATTTTGCG
genomic: GGCCCCGCCTCGCCTGGGATGTCGCGCCCCCGCTGTTCCAGCCCCCCAAGgtataatcca ... atttttgtagGCAATTCCTATGCTATATTGCGGGCAGGAACTAATCAATGGAAATTTTGCG
EST: gi|88576664|gb|CI670809.1|CI670809
EST:     GGCCCCGCCTCGCCTGGGATGTCGCGCCCCCGNTGTTCCAGCCCCCCAAG                         GCAATTCCTATGCTATATTGCGGGCAGGAACTAATCAATGGAAATTTTGCG
genomic: GGCCCCGCCTCGCCTGGGATGTCGCGCCCCCGCTGTTCCAGCCCCCCAAGgtataatcca ... atttttgtagGCAATTCCTATGCTATATTGCGGGCAGGAACTAATCAATGGAAATTTTGCG
EST: gi|88307805|gb|CI644845.1|CI644845
EST:     GGCCCCGCCTCGCCTGGGATGTCGCGCCCCCGCTGTTCCAGCCCCCCAAG                         GCAATTCCTATGCTATATTGCGGGCAGGAACTAATCAATGGAAATTTTGCG
genomic: GGCCCCGCCTCGCCTGGGATGTCGCGCCCCCGCTGTTCCAGCCCCCCAAGgtataatcca ... atttttgtagGCAATTCCTATGCTATATTGCGGGCAGGAACTAATCAATGGAAATTTTGCG
EST: gi|58694718|gb|CK083405.1|CK083405
EST:     GGCCCCGCCTCGCCTGGGATGTCGCGCCCCCGCTGTTCCAGCCCCCCAAG                         GCAATTCCTATGCTATATTGCGGGCAGGAACTAATCAATGGAAATTTTGCG
genomic: GGCCCCGCCTCGCCTGGGATGTCGCGCCCCCGCTGTTCCAGCCCCCCAAGgtataatcca ... atttttgtagGCAATTCCTATGCTATATTGCGGGCAGGAACTAATCAATGGAAATTTTGCG
EST: gi|88337067|gb|CI628153.1|CI628153
EST:     GGCCCCGCCTCGCCTGGGATGTCGCGCCCCCGCTGTTCCAGCCCCCCAAG                         GCAATTCCTATGCTATATTGCGGGCAGGAACTAATCAATGGAAATTTTGCG
genomic: GGCCCCGCCTCGCCTGGGATGTCGCGCCCCCGCTGTTCCAGCCCCCCAAGgtataatcca ... atttttgtagGCAATTCCTATGCTATATTGCGGGCAGGAACTAATCAATGGAAATTTTGCG
EST: gi|88420986|gb|CI620304.1|CI620304
EST:     GGCCCCGCCTCGCCTGGGATGTCGCGCCCCCGCTGTTCCAGCCCCCCAAG                         GCAATTCCTATGCTATATTGCGGGCAGGAACTAATCAATGGAAATTTTGCG
genomic: GGCCCCGCCTCGCCTGGGATGTCGCGCCCCCGCTGTTCCAGCCCCCCAAGgtataatcca ... atttttgtagGCAATTCCTATGCTATATTGCGGGCAGGAACTAATCAATGGAAATTTTGCG
EST: gi|88390894|gb|CI611120.1|CI611120
EST:     GGCCCCGCCTCGCCTGGGATGTCGCGCCCCCGCTGTTCCAGCCCCCCAAG                         GCAATTCCTATGCTATATTGCGGGCAGGAACTAATCAATGGAAATTTTGCG
genomic: GGCCCCGCCTCGCCTGGGATGTCGCGCCCCCGCTGTTCCAGCCCCCCAAGgtataatcca ... atttttgtagGCAATTCCTATGCTATATTGCGGGCAGGAACTAATCAATGGAAATTTTGCG
EST: gi|58695186|gb|CK083873.1|CK083873
EST:     GGCCCCGCCTCGCCTGGGATGTCGCGCCCCCGCTGTTCCAGCCCCCCAAG                         GCAATTCCTATGCTATATTGCGGGCAGGAACTAATCAATGGAAATTTTGCG
genomic: GGCCCCGCCTCGCCTGGGATGTCGCGCCCCCGCTGTTCCAGCCCCCCAAGgtataatcca ... atttttgtagGCAATTCCTATGCTATATTGCGGGCAGGAACTAATCAATGGAAATTTTGCG
EST: gi|58654607|gb|CK043287.1|CK043287
EST:     GG--CCGCCTCGCCTGGGATGTCGCGCCCCCGCTGTTCCAGCCCCCCAAG                         GCAATTCCTATGGTATATTGCGGGCAGGAACTAATCAATGGAAATTTTGCG
genomic: GGCCCCGCCTCGCCTGGGATGTCGCGCCCCCGCTGTTCCAGCCCCCCAAGgtataatcca ... atttttgtagGCAATTCCTATGCTATATTGCGGGCAGGAACTAATCAATGGAAATTTTGCG
EST: gi|29665089|gb|CB661364.1|CB661364
EST:     GGCCCCGCCTCGCCTGGGATGTCGCGCCCCCGCTGTTCCAGCCCCCCAAG                         GCAATTCCTATGCTATATTGCGGGCAGGAACTAATCAATGGAAATTTTGCG
genomic: GGCCCCGCCTCGCCTGGGATGTCGCGCCCCCGCTGTTCCAGCCCCCCAAGgtataatcca ... atttttgtagGCAATTCCTATGCTATATTGCGGGCAGGAACTAATCAATGGAAATTTTGCG
EST: gi|88412995|gb|CI578846.1|CI578846
EST:     GGCCCCGCCTCGCCTGGGATGTCGCGCGCCCGCTGTTCCAGCCCCCCAAG                         GCAATTCCTATGCTATATTGCGGGCAGGAACTAATCAATGGAAATTTTGCG
genomic: GGCCCCGCCTCGCCTGGGATGTCGCGCCCCCGCTGTTCCAGCCCCCCAAGgtataatcca ... atttttgtagGCAATTCCTATGCTATATTGCGGGCAGGAACTAATCAATGGAAATTTTGCG
EST: gi|58691283|gb|CK079970.1|CK079970
EST:     GGCCCCGCCTCGCCTGGGATGTCGCGCCCCCGCTGTTCCAGCCCCCCAAG                         GCAATTCCTATGCTATATTGCGGGCAGGAACTAATCAATGGAAATTTTGCG
genomic: GGCCCCGCCTCGCCTGGGATGTCGCGCCCCCGCTGTTCCAGCCCCCCAAGgtataatcca ... atttttgtagGCAATTCCTATGCTATATTGCGGGCAGGAACTAATCAATGGAAATTTTGCG
EST: gi|88362877|gb|CI614233.1|CI614233
EST:     GGCCCCGCCTCGCCTGGGATGTCGCGCCCCCGCTGTTCCAGCCCCCCAAG                         GCAATTCCTATGCTATATTGCGGGCAGGAACTAATCAATGGAAATTTTGGG
genomic: GGCCCCGCCTCGCCTGGGATGTCGCGCCCCCGCTGTTCCAGCCCCCCAAGgtataatcca ... atttttgtagGCAATTCCTATGCTATATTGCGGGCAGGAACTAATCAATGGAAATTTTGCG
EST: gi|58593129|gb|CF991437.1|CF991437
EST:     GGCCCCGCCTCGCCTGGGATGTCGCGCCCCCGCTGTTCCAGCCCCCCAAG                         GCGGGTCCTATGCTATATTGCGGGCAGGAACTAATCAATGGAAATTTTGCG
genomic: GGCCCCGCCTCGCCTGGGATGTCGCGCCCCCGCTGTTCCAGCCCCCCAAGgtataatcca ... atttttgtagGCAATTCCTATGCTATATTGCGGGCAGGAACTAATCAATGGAAATTTTGCG
EST: gi|88431020|gb|CI572010.1|CI572010
EST:     GGCCCCGCCTCGCCTGGGATGTCGCGCCCCCGCTGTTCCAGCCCCCCAAG                         GCAATTCCTATGCTATATTGCGGGCAGGAACTAATCAATGGAAATTTTGCG
genomic: GGCCCCGCCTCGCCTGGGATGTCGCGCCCCCGCTGTTCCAGCCCCCCAAGgtataatcca ... atttttgtagGCAATTCCTATGCTATATTGCGGGCAGGAACTAATCAATGGAAATTTTGCG
EST: gi|29679261|gb|CB675536.1|CB675536
EST:     GGCCCCGCCTCGCCTGGGATGTCGCGCCCCCGCTGTTCCAGCCCCCCAAG                         GCAATTCCTATGCTATATTGCGGGCAGGAACTAATCAATGGAAATTTTGCG
genomic: GGCCCCGCCTCGCCTGGGATGTCGCGCCCCCGCTGTTCCAGCCCCCCAAGgtataatcca ... atttttgtagGCAATTCCTATGCTATATTGCGGGCAGGAACTAATCAATGGAAATTTTGCG
EST: gi|86891175|gb|CI305952.1|CI305952
EST:     GGCCCCGCCTCGCCTGGGATGTCGCGCCCCCGCTGTTCCAGCCCCCCAAG                         GCAATTCCTATGCTATATTGCGGGCAGGAACTAATCAATGGAAA
genomic: GGCCCCGCCTCGCCTGGGATGTCGCGCCCCCGCTGTTCCAGCCCCCCAAGgtataatcca ... atttttgtagGCAATTCCTATGCTATATTGCGGGCAGGAACTAATCAATGGAAA

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: 61 (upstream exon), 75 (downstream exon)
Score: 14

GTGGCTCGCCGAGTACCCGCACCAGGGCGCCGACAAGCGGCCGCGGAAGCGGCCCCGCCTCGCCTGGGATGTCGCGCCCCCGCTGTTCCAGCCCCCCAAGgtataatcca ... atttttgtagGCAATTCCTATGCTATATTGCGGGCAGGAACTAATCAATGGAAATTTTGCGACCGCTTTTCTGCCACCGCCACCAATCTATTATACAGGACCACCACGCA




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTGGCTCGCCGAGTACCCGCACCAGGGCGCCGACAAGCGGCCGCGGAAGCGGCCCCGCCTCGCCTGGGATGTCGCGCCCCCGCTGTTCCAGCCCCCCAAGgtataatccatgcgctatgtgctgcgtcgatccggtctctctcgggcgtgtgggttgcggtggtagtttttggctagatctagtcgtggtttcgctagat

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGTT