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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CATTTGAAGCTGTGAAGGTTCGTGTGCAAACCCAACCTGGATTCGCTCGTGGACTGAGTGATGGGCTCCCCAAGTTCGTCAGATCTGAAGGCGCTCTTGGgtaagtataaataacatgtttttatcttagaatctgatatgtggcaactctttctctagttttatgcgccttgacaaatctcattccttgataatgacag

Basic information

species Oryza sativa
transcript LOC_Os02g52860.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g52860.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G152827_T01 (Zea mays), 5'ss of exon 2
CATTTGAAGCTGTGAAGGTTCGTGTGCAAACCCAACCTGGATTCGCTCGTGGACTGAGTGATGGGCTCCCCAAGTTCGTCAGATCTGAAGGCGCTCTTGGgtaagtataaataacatgtttttatcttagaatctgatatgtggcaactctttctctagttttatgcgccttgacaaatctcattccttgataatgacag
| ||||||||||||||||| |||||||| || ||||||||||| ||||||||| ||||||||||||||||||| || ||| ||||||| || | ||||||||||| |            |||     || ||  |    | |    |||     ||| |   | ||  |    | |  |||   | ||| ||| |   ||
CTTTTGAAGCTGTGAAGGTACGTGTGCAGACACAACCTGGATTTGCTCGTGGATTGAGTGATGGGCTCCCCAAATTTGTCCGATCTGAGGGTGTTCTTGGgtaagcaa-----------tttggctctaaaaaatatcgt-tcaagacttgacttctggccatgtgtcctaatatagctcttgctgcttaatatttttag

upper sequence: LOC_Os02g52860.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G060630_T01 (Zea mays), 5'ss of exon 2
CATTTGAAGCTGTGAAGGTTCGTGTGCAAACCCAACCTGGATTCGCTCGTGGACTGAGTGATGGGCTCCCCAAGTTCGTCAGATCTGAAGGCGCTCTTGGgtaagtataaataacatgtttttatcttag-aatctgatatgtggcaactctttctctagttttatgcgccttgacaaatctcattccttgataatgacag
| ||||||||||||||||| |||||||| || ||||||||||| ||||||||| ||||||| || || ||||| || ||| ||||||| || ||||||||||||| | || |     | |   |  |||   || | ||   | |  |||   | ||| |    ||  ||| | |||  ||||| | ||| |||||   ||
CTTTTGAAGCTGTGAAGGTACGTGTGCAGACACAACCTGGATTTGCTCGTGGATTGAGTGACGGTCTTCCCAAATTTGTCCGATCTGAGGGTGCTCTTGGgtaagca-aattggttagctagaaaattattgatttcatgatttgagacttggtttctggc--catctgccctaacatctctcactgcttaataattttag

upper sequence: LOC_Os02g52860.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G015401_T01 (Zea mays), 5'ss of exon 2
CATTTGAAGCTGTGAAGGTTCGTGTGCAAACCCAACCTGGATTCGCTCGTGGACTGAGTGATGGGCTCCCCAAGTTCGTCAGATCTGAAGGCGCTCTTGGgtaagtataaataacatgtttttatcttagaatctgatatgtggcaactctttctctagttttatgcgccttgacaaatctcattccttgataatgacag
| ||||||||||||||||| |||||||| || ||||||||||| ||||||||| ||||||||||||||||||| || ||| ||||||| || | ||||||||||| | || |  |         ||| | ||  |    | |    |||     ||| |   | ||  |    | |  |||   | ||| ||| |   ||
CTTTTGAAGCTGTGAAGGTACGTGTGCAGACACAACCTGGATTTGCTCGTGGATTGAGTGATGGGCTCCCCAAATTTGTCCGATCTGAGGGTGTTCTTGGgtaagca-aattggc---------tctaaaaaaatatcgt-tcaagacttggcttctggccatgtgtcctaatatagctcttgctgcttaatatttttag

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|116875543|gb|EC366051.1|EC366051
EST:     GGACTGAGTGATGGGCTCCCCAAGTTCGTCAGATCTGAAGGCGCTCTTGG                         GCTTTACAAGGGAATTGTTCCTCTGTGGGGTCGCCAAATCCCTT
genomic: GGACTGAGTGATGGGCTCCCCAAGTTCGTCAGATCTGAAGGCGCTCTTGGgtaagtataa ... ataatgacagGCTTTACAAGGGAATTGTTCCTCTGTGGGGTCGCCAAATCCCTT
EST: gi|218484707|gb|FG949606.1|FG949606
EST:     GGACTGAGTGATGGGCTCCCCAAGTTCGTCAGATCTGAAGGCGCTCTTGG                         GCTTTACAAGGGAATTGTTCCTCTGTGGGGTCGCCAAATCCCTT
genomic: GGACTGAGTGATGGGCTCCCCAAGTTCGTCAGATCTGAAGGCGCTCTTGGgtaagtataa ... ataatgacagGCTTTACAAGGGAATTGTTCCTCTGTGGGGTCGCCAAATCCCTT
EST: gi|29677043|gb|CB673318.1|CB673318
EST:     GGACTGAGTGATGGGCTCCCCAAGTTCGTCAGATCTGAAGGCGCTCTTGG                         GCTTTACAAGGGAATTGTTCCTCTGTGGGGTCGCCAAATCCCTTATACTAT
genomic: GGACTGAGTGATGGGCTCCCCAAGTTCGTCAGATCTGAAGGCGCTCTTGGgtaagtataa ... ataatgacagGCTTTACAAGGGAATTGTTCCTCTGTGGGGTCGCCAAATCCCTTATACTAT
EST: gi|218490441|gb|FG950234.1|FG950234
EST:     GGACTGAGTGATGGGCTCCCCAAGTTCGTCAGATCTGAAGGCGCTCTTGG                         GCTTTACAAGGGAATTGTTCCTCTGTGGGGTCGCCAAATCCCTT
genomic: GGACTGAGTGATGGGCTCCCCAAGTTCGTCAGATCTGAAGGCGCTCTTGGgtaagtataa ... ataatgacagGCTTTACAAGGGAATTGTTCCTCTGTGGGGTCGCCAAATCCCTT
EST: gi|163928501|gb|EG711386.1|EG711386
EST:     CCCAAGTTCGTCAGATCTGAAGGCGCTCTTGG                         GCTTTACAAGGGAATTGTTCCTCTGTGGGGTCGCCAAATCCCTT
genomic: CCCAAGTTCGTCAGATCTGAAGGCGCTCTTGGgtaagtataa ... ataatgacagGCTTTACAAGGGAATTGTTCCTCTGTGGGGTCGCCAAATCCCTT
EST: gi|218505349|gb|FG953708.1|FG953708
EST:     GGACTGAGTGATGGGCTCCCCAAGTTCGTTAGATCTGAAGGCGCTCTTGG                         GCTTTACAAGGGAATTGTTCCTCTGTGGGGTCGCCAAATCCCTT
genomic: GGACTGAGTGATGGGCTCCCCAAGTTCGTCAGATCTGAAGGCGCTCTTGGgtaagtataa ... ataatgacagGCTTTACAAGGGAATTGTTCCTCTGTGGGGTCGCCAAATCCCTT
EST: gi|58680384|gb|CK069071.1|CK069071
EST:     AGGCGCTCTTGG                         GCTTTACAAGGGAATTGTTCCTCTGTGGGGTCGCCAAATCCCTT
genomic: AGGCGCTCTTGGgtaagtataa ... ataatgacagGCTTTACAAGGGAATTGTTCCTCTGTGGGGTCGCCAAATCCCTT
EST: gi|66913316|gb|CX100164.1|CX100164
EST:     GGACTGAGTGATGGGCTCCCCAAGTTCGTCAGATCTGAAGGCGCTCTTGG                         GCTTTACAAGGGAATTGTTCCTCTGTGGGGTCGCCAAATCCCTT
genomic: GGACTGAGTGATGGGCTCCCCAAGTTCGTCAGATCTGAAGGCGCTCTTGGgtaagtataa ... ataatgacagGCTTTACAAGGGAATTGTTCCTCTGTGGGGTCGCCAAATCCCTT
EST: gi|29658502|gb|CB654777.1|CB654777
EST:     GGACTGAGTGATGGGCTCCCCAAGTTCGTCAGATCTGAAGGCGCTCTTGG                         GCTTTACAAGGGAATTGTTCCTCTGTGGGGTCGCCAAATCCCTT
genomic: GGACTGAGTGATGGGCTCCCCAAGTTCGTCAGATCTGAAGGCGCTCTTGGgtaagtataa ... ataatgacagGCTTTACAAGGGAATTGTTCCTCTGTGGGGTCGCCAAATCCCTT
EST: gi|116874996|gb|EC365504.1|EC365504
EST:     GGACTGAGTGATGGGCTCCCCAAGTTCGTCAGATCTGAAGGCGCTCTTGG                         GCTTTACAAGGGAATTGTTCCTCTGTGGGGTCGCCAAATCCCTT
genomic: GGACTGAGTGATGGGCTCCCCAAGTTCGTCAGATCTGAAGGCGCTCTTGGgtaagtataa ... ataatgacagGCTTTACAAGGGAATTGTTCCTCTGTGGGGTCGCCAAATCCCTT
EST: gi|14192020|gb|AU184231.1|AU184231
EST:     GGACTGAGTGATGGGCTCCCCAAGTTCGTCAGATCTGAAGGCGCTCTTGG                         GCTTTACAAGGGAATTGTTCCTCTGTGGGGTCGCCAAATCCCTT
genomic: GGACTGAGTGATGGGCTCCCCAAGTTCGTCAGATCTGAAGGCGCTCTTGGgtaagtataa ... ataatgacagGCTTTACAAGGGAATTGTTCCTCTGTGGGGTCGCCAAATCCCTT
EST: gi|29630079|gb|CB635088.1|CB635088
EST:     GGACTGAGTGATGGGCTCCCCAAGTTCGTTAGATCTGAAGGCGCTCTTGG                         GCTTTACAAGGGAATTGTTCCTCTGAGGGGTCGCCAAATCCCTT
genomic: GGACTGAGTGATGGGCTCCCCAAGTTCGTCAGATCTGAAGGCGCTCTTGGgtaagtataa ... ataatgacagGCTTTACAAGGGAATTGTTCCTCTGTGGGGTCGCCAAATCCCTT
EST: gi|29658501|gb|CB654776.1|CB654776
EST:     GGACTGAGTGATGGGCTCCCCAAGTTCGTCAGATCTGAAGGCGCTCTTGG                         GCTTTACAAGGGAATTGTTCCTCTGTGGGGTCGCCAAATCCCTT
genomic: GGACTGAGTGATGGGCTCCCCAAGTTCGTCAGATCTGAAGGCGCTCTTGGgtaagtataa ... ataatgacagGCTTTACAAGGGAATTGTTCCTCTGTGGGGTCGCCAAATCCCTT
EST: gi|218501146|gb|FG957968.1|FG957968
EST:     GGACTGAGTGATGGGCTCCCCAAGTTCGTTAGATCTGAAGGCGCTCTTGG                         GCTTTACAAGGGAATTGTTCCTCTGTGGGGTCGCCAAATCCCTT
genomic: GGACTGAGTGATGGGCTCCCCAAGTTCGTCAGATCTGAAGGCGCTCTTGGgtaagtataa ... ataatgacagGCTTTACAAGGGAATTGTTCCTCTGTGGGGTCGCCAAATCCCTT
EST: gi|163929256|gb|EG713081.1|EG713081
EST:     GGACTGAGTGATGGGCTCCCCAAGTTCGTCAGATCTGAAGGCGCTCTTGG                         GCTTTACAAGGGAATTGTTCCTCTGTGGGGTCGCCAAATCCCTT
genomic: GGACTGAGTGATGGGCTCCCCAAGTTCGTCAGATCTGAAGGCGCTCTTGGgtaagtataa ... ataatgacagGCTTTACAAGGGAATTGTTCCTCTGTGGGGTCGCCAAATCCCTT
EST: gi|116875503|gb|EC366011.1|EC366011
EST:     GGACTGAGTGATGGGCTCCCCAAGTTCGTCAGATCTGAAGGCGCTCTTGG                         GCTTTACAAGGGAATTGTTCCTCTGTGGGGTCGCCAAATCCCTT
genomic: GGACTGAGTGATGGGCTCCCCAAGTTCGTCAGATCTGAAGGCGCTCTTGGgtaagtataa ... ataatgacagGCTTTACAAGGGAATTGTTCCTCTGTGGGGTCGCCAAATCCCTT
EST: gi|38470606|gb|CF954737.1|CF954737
EST:     GGACTGAGTGATGGGCTCCCCAAGTTCGTTAGATCTGAAGGCGCTCTTGG                         GCTTTACAAGGGAATTGTTCCTCTGTGGGGTCGCCAAATCCCTT
genomic: GGACTGAGTGATGGGCTCCCCAAGTTCGTCAGATCTGAAGGCGCTCTTGGgtaagtataa ... ataatgacagGCTTTACAAGGGAATTGTTCCTCTGTGGGGTCGCCAAATCCCTT

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: 75 (upstream exon), 75 (downstream exon)
Score: 111

CATTTGAAGCTGTGAAGGTTCGTGTGCAAACCCAACCTGGATTCGCTCGTGGACTGAGTGATGGGCTCCCCAAGTTCGTCAGATCTGAAGGCGCTCTTGGgtaagtataa ... ataatgacagGCTTTACAAGGGAATTGTTCCTCTGTGGGGTCGCCAAATCCCTT




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CATTTGAAGCTGTGAAGGTTCGTGTGCAAACCCAACCTGGATTCGCTCGTGGACTGAGTGATGGGCTCCCCAAGTTCGTCAGATCTGAAGGCGCTCTTGGgtaagtataaataacatgtttttatcttagaatctgatatgtggcaactctttctctagttttatgcgccttgacaaatctcattccttgataatgacag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG