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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTGGTACTGATGTTGCATTTGATACTGCAACTGGGGACTTCACCAAGTACAATGCGGGACTGAGCCACACTACTCCAGATCTCACTGCAGCACTGCTTCTgtaagcagtttcatccaattctttggtgtattaacacttctctaatattcgtactgttgttttggccctttacctgttgtttaactcctccaagtcccaa...

Basic information

species Oryza sativa
transcript LOC_Os05g45950.1
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g45950.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GRMZM2G088132_T02 (Zea mays), 5'ss of exon 3
TTGGTACTGATGTTGCATTTGATACTGCAACTGGGGACTTCACCAAGTACAATGCGGGACTGAGCCACACTACTCCAGATCTCACTGCAGCACTGCTTCTgtaagcagtttcatccaattctttggtgtattaacacttctctaatattcgtactgttgttttggccctttacctgttgtttaactcctccaagtcccaa
||||| |||||||||||||||||||| || | ||| |||| ||||| |||||||| ||||||||| || | ||  | ||  ||  ||| |||     | ||||||  ||||  ||| ||  ||    || |       |  ||  |||| ||    | |   |     |   |||     |          |  || | |
TTGGTGCTGATGTTGCATTTGATACTTCATCCGGGAACTTAACCAAATACAATGCTGGACTGAGCTACTCCACGTCTGACTTCGTTGCTGCAGCTACTTTgtaagtggtttgttcctatgtttaacagtttctgtttgtgactgttatttgtgtcctagggatccggttcgccctagcactagcacaaatgatatctcta

upper sequence: LOC_Os05g45950.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GRMZM2G115049_T01 (Zea mays), 5'ss of exon 5
TTGGTACTGATGTTGCATTTGATACTGCAACTGGGGACTTCACCAAGTACAATGCGGGACTGAGCCACACTACTCCAGATCTCACTGCAGCACTGCTTCTgtaagcagtttcatccaattctttggtgtattaacacttctctaatattcgtactgttgttttggccctttacctgttgtttaactcctccaagtcccaa
||||  |||||| ||||||||||||| |  |||||||||| ||||| |||||||| ||||||||| |||| || || ||  |   ||| |||  |  | |||||| ||| |    |||| |||    || |       |  ||  |||| ||    | |   |  |  ||  |||       ||  ||  |       ||
TTGGCGCTGATGCTGCATTTGATACTTCTTCTGGGGACTTAACCAAATACAATGCTGGACTGAGCTACACGACGCCTGACTTTGTTGCTGCAGCGACTTTgtaagtagtctgtcacaatgcttaacagtttctgtttgtaactgttattagtgtcctagggatcacatttgcccttagcaccaatgccatctctagggaa
















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|33689640|gb|CF317879.1|CF317879
EST:     AATGCGGGACTGAGCCACACTACTCCAGATCTCACTGCAGCACTGCTTTT                         GAACAACAAGGGAGACAGCCTTGCTGCTTCCTACTACCACAAGGTGAGCAA
genomic: AATGCGGGACTGAGCCACACTACTCCAGATCTCACTGCAGCACTGCTTCTgtaagcagtt ... caaatttcagGAACAACAAGGGAGACAGCCTTGCTGCTTCCTACTACCACAAGGTGAGCAA
EST: gi|29687459|gb|CB683734.1|CB683734
EST:     AATGCGGGACTGAGCCACACTACTCCAGATCTCACTGCAGCACTGCTTCT                         GAACAACAAGGGAGACAGCCTTGCTGCTTCCTACTACCACAAGGTGAGCAA
genomic: AATGCGGGACTGAGCCACACTACTCCAGATCTCACTGCAGCACTGCTTCTgtaagcagtt ... caaatttcagGAACAACAAGGGAGACAGCCTTGCTGCTTCCTACTACCACAAGGTGAGCAA
EST: gi|218498478|gb|FG959836.1|FG959836
EST:     AATGCGGGACTGAGCCACACTACTCCAGATCTCACTGCAGCACTGCTTCT                         GAACAACAAGGGAGACAGCCTTGCTGCTTCCTACTACCACAAGGTGAGCAA
genomic: AATGCGGGACTGAGCCACACTACTCCAGATCTCACTGCAGCACTGCTTCTgtaagcagtt ... caaatttcagGAACAACAAGGGAGACAGCCTTGCTGCTTCCTACTACCACAAGGTGAGCAA
EST: gi|86508493|gb|CI151126.1|CI151126
EST:     AATGCGGGACTGAGCCACACTACTCCAGATCTCACTGCAGCACTGCTTCT                         GAACAACAAGGGAGACAGCCTTGCTGCTTCCTACTACCACAAGGTGAGCAA
genomic: AATGCGGGACTGAGCCACACTACTCCAGATCTCACTGCAGCACTGCTTCTgtaagcagtt ... caaatttcagGAACAACAAGGGAGACAGCCTTGCTGCTTCCTACTACCACAAGGTGAGCAA
EST: gi|86499611|gb|CI142244.1|CI142244
EST:     TGCGGGACTGAGCCACACTACTCCAGATCTCACTGCAGCACTGCTTCT                         GAACAACAAGGGAGACACCCTTGCTGCTTCCTACTACCACAAGGTGAGCAA
genomic: TGCGGGACTGAGCCACACTACTCCAGATCTCACTGCAGCACTGCTTCTgtaagcagtt ... caaatttcagGAACAACAAGGGAGACAGCCTTGCTGCTTCCTACTACCACAAGGTGAGCAA
EST: gi|88844877|gb|CI022231.1|CI022231
EST:     AATGCGGGACTGAGCCACACTACTCCAGATCTCACTGCAGCACTGCTTCT                         GAACAACAAGGGAGACAGCCTTGCTGCTTCCTACTACCACAAGGTGAGCCA
genomic: AATGCGGGACTGAGCCACACTACTCCAGATCTCACTGCAGCACTGCTTCTgtaagcagtt ... caaatttcagGAACAACAAGGGAGACAGCCTTGCTGCTTCCTACTACCACAAGGTGAGCAA
EST: gi|29661979|gb|CB658254.1|CB658254
EST:     AATGCGGGACTGAGCCACACTACTCCAGATCTCACTGCAGCACTGCTTCT                         GAACAACAAGGGAGACAGCCTTGCTGCTTCCTACTACCACAAGGTGAGCAA
genomic: AATGCGGGACTGAGCCACACTACTCCAGATCTCACTGCAGCACTGCTTCTgtaagcagtt ... caaatttcagGAACAACAAGGGAGACAGCCTTGCTGCTTCCTACTACCACAAGGTGAGCAA
EST: gi|29687058|gb|CB683333.1|CB683333
EST:     AATGCGGGACTGAGCCACACTACTCCAGATCTCACTGCAGCACTGCTTCT                         GAACAACAAGGGAGACAGCCTTGCTGCTTCCTACTACCACAAGGTGAGCAA
genomic: AATGCGGGACTGAGCCACACTACTCCAGATCTCACTGCAGCACTGCTTCTgtaagcagtt ... caaatttcagGAACAACAAGGGAGACAGCCTTGCTGCTTCCTACTACCACAAGGTGAGCAA
EST: gi|8956441|gb|BE230244.1|BE230244
EST:     AATGCGGGACTGAGCCACACTACTCCAGATCTCACTGCAGCACTGCTTCT                         GAACAACAAGGGAGACAGCCTTGCTGCTTCCTACTACCACAAGGTGAGCAA
genomic: AATGCGGGACTGAGCCACACTACTCCAGATCTCACTGCAGCACTGCTTCTgtaagcagtt ... caaatttcagGAACAACAAGGGAGACAGCCTTGCTGCTTCCTACTACCACAAGGTGAGCAA
EST: gi|8956076|gb|BE229880.1|BE229880
EST:     AATGCGGGACTGAGCCACACTACTCCAGATCTCACTGCAGCACTGCTTCT                         GAACAACAAGGGAGACAGCCTTGCTGCTTCCTACTACCACAAGG
genomic: AATGCGGGACTGAGCCACACTACTCCAGATCTCACTGCAGCACTGCTTCTgtaagcagtt ... caaatttcagGAACAACAAGGGAGACAGCCTTGCTGCTTCCTACTACCACAAGG
EST: gi|66915098|gb|CX101946.1|CX101946
EST:     AATGCGGGACTGAGCCACACTACTCCAGATCTCACTGCAGCACTGCTTCT                         GAACAACAAGGGAGACAGCCTTGCTGCTTCCTACTACCACAAGGTGAGCAA
genomic: AATGCGGGACTGAGCCACACTACTCCAGATCTCACTGCAGCACTGCTTCTgtaagcagtt ... caaatttcagGAACAACAAGGGAGACAGCCTTGCTGCTTCCTACTACCACAAGGTGAGCAA
EST: gi|33665355|gb|CF296322.1|CF296322
EST:     AATGCGGGACTGAGCCACACTACTCCAGATCTCACTGCAGCACTGCTTCT                         GAACAACAAGGGAGACAGCCTTGCTGCTTCCTACTACCACAAGGTGAGCAA
genomic: AATGCGGGACTGAGCCACACTACTCCAGATCTCACTGCAGCACTGCTTCTgtaagcagtt ... caaatttcagGAACAACAAGGGAGACAGCCTTGCTGCTTCCTACTACCACAAGGTGAGCAA
EST: gi|33692205|gb|CF320444.1|CF320444
EST:     AATGCGGGACTGAGCCACACTACTCCAGATCTCACTGCAGCACTGCTTCT                         GAACAACAAGGGAGACAGCCTTGCTGCTTCCTACTACCACAAGGTGAGCAA
genomic: AATGCGGGACTGAGCCACACTACTCCAGATCTCACTGCAGCACTGCTTCTgtaagcagtt ... caaatttcagGAACAACAAGGGAGACAGCCTTGCTGCTTCCTACTACCACAAGGTGAGCAA
EST: gi|8528059|gb|AU092874.1|AU092874
EST:     AATGCGGGACTGAGCCACACTACTCCAGATCTCACTGCAGCACTGCTTCT                         GAACAACAAGGGAGACAGCCTTGCTGCTTCCTACTACCACAAGGTGAGCAA
genomic: AATGCGGGACTGAGCCACACTACTCCAGATCTCACTGCAGCACTGCTTCTgtaagcagtt ... caaatttcagGAACAACAAGGGAGACAGCCTTGCTGCTTCCTACTACCACAAGGTGAGCAA
EST: gi|86859568|gb|CI278938.1|CI278938
EST:     AATGCGGGACTGAGCCACACTACTCCAGATCTCACTGCAGCACTGCTTCT                         GAACAACAAGGGAGACAGCCTTGCTGCTTCCTACTACCACAAGGTGAGCAA
genomic: AATGCGGGACTGAGCCACACTACTCCAGATCTCACTGCAGCACTGCTTCTgtaagcagtt ... caaatttcagGAACAACAAGGGAGACAGCCTTGCTGCTTCCTACTACCACAAGGTGAGCAA
EST: gi|58608189|gb|CK036222.1|CK036222
EST:     AATGCGGGACTGAGCCACACTACTCCAGATCTCACTGCAGCACTGCTTCT                         GAACAACAAGGGA
genomic: AATGCGGGACTGAGCCACACTACTCCAGATCTCACTGCAGCACTGCTTCTgtaagcagtt ... caaatttcagGAACAACAAGGGA
EST: gi|86511839|gb|CI154472.1|CI154472
EST:     AATGCGGGACTGAGCCACACTACTCCAGATCTCACTGCAGCACTGCTTCT                         GAACAACAAGGGAGACAGCCTTGCTGCTTCCTACTACCACAAGGTGAGCAA
genomic: AATGCGGGACTGAGCCACACTACTCCAGATCTCACTGCAGCACTGCTTCTgtaagcagtt ... caaatttcagGAACAACAAGGGAGACAGCCTTGCTGCTTCCTACTACCACAAGGTGAGCAA
EST: gi|38474605|gb|CF958738.1|CF958738
EST:     AATGCGGGACTGAGCCACACTACTCCAGATCTCACTGCAGCACTGCTTCT                         GAACAACAAGGGAGACAGCCTTGCTGCTTCCTACTACCACAAGGTGAGCAA
genomic: AATGCGGGACTGAGCCACACTACTCCAGATCTCACTGCAGCACTGCTTCTgtaagcagtt ... caaatttcagGAACAACAAGGGAGACAGCCTTGCTGCTTCCTACTACCACAAGGTGAGCAA
EST: gi|5055971|gb|AU075350.1|AU075350
EST:     ACACTACTTCCCAAATCTTCACTGCAGCACTGCTTTCT                         GAACACCAAGGGAGACAGCCTTGCTGCTTCCTANCTACCACAAGGTGAGC
genomic: ACACTAC-T-CCAGATC-TCACTGCAGCACTGC-TTCTgtaagcagtt ... caaatttcagGAACAACAAGGGAGACAGCCTTGCTGCTTCCTA-CTACCACAAGGTGAGC
EST: gi|3760364|gb|C97618.1|C97618
EST:     AATGCGGGACTGAGCCACACTACTCCAGATCTCACTGCAGCACTGCTTCT                         GAACAACAAGGGAGACAGCCTTGCTGCTTCCTACTACCACAAGGTGAGCAA
genomic: AATGCGGGACTGAGCCACACTACTCCAGATCTCACTGCAGCACTGCTTCTgtaagcagtt ... caaatttcagGAACAACAAGGGAGACAGCCTTGCTGCTTCCTACTACCACAAGGTGAGCAA
EST: gi|8528259|gb|AU093074.1|AU093074
EST:     ATGCGGGACTGAGCCACANTACTCCAGATCTCACTGCAGCACTGCTTTCT                         NAACAACAAGGGAGACAGCCTTGCTGCTTCCTACTACCACAAGGTGAGCA
genomic: ATGCGGGACTGAGCCACACTACTCCAGATCTCACTGCAGCACTGC-TTCTgtaagcagtt ... caaatttcagGAACAACAAGGGAGACAGCCTTGCTGCTTCCTACTACCACAAGGTGAGCA
EST: gi|87013141|gb|CI281655.1|CI281655
EST:     AATGCGGGACTGAGCCACACTACTCCAGATCTCACTGCAGCACTGCTTCT                         GAACAACAAGGGAGACAGCCTTGCTGCTTCCTACTACCACAAGGTGAGCAA
genomic: AATGCGGGACTGAGCCACACTACTCCAGATCTCACTGCAGCACTGCTTCTgtaagcagtt ... caaatttcagGAACAACAAGGGAGACAGCCTTGCTGCTTCCTACTACCACAAGGTGAGCAA
EST: gi|33810860|gb|CF331321.1|CF331321
EST:     AATGCGGGACTGAGCCACACTACTCCAGATCTCACTGCAGCACTGCTTCT                         GAACA-CAAGGGAGACAGCCTTGCTGCTTCCTACTACCACAAGGTGAGCAA
genomic: AATGCGGGACTGAGCCACACTACTCCAGATCTCACTGCAGCACTGCTTCTgtaagcagtt ... caaatttcagGAACAACAAGGGAGACAGCCTTGCTGCTTCCTACTACCACAAGGTGAGCAA

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: 83

TTGGTACTGATGTTGCATTTGATACTGCAACTGGGGACTTCACCAAGTACAATGCGGGACTGAGCCACACTACTCCAGATCTCACTGCAGCACTGCTTCTgtaagcagtt ... caaatttcagGAACAACAAGGGAGACAGCCTTGCTGCTTCCTACTACCACAAGGTGAGCAAAACAAGTGCTGTTGGAGCAGAGCTGGCTCACAGCTTCTCGAGCAACGAG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTGGTACTGATGTTGCATTTGATACTGCAACTGGGGACTTCACCAAGTACAATGCGGGACTGAGCCACACTACTCCAGATCTCACTGCAGCACTGCTTCTgtaagcagtttcatccaattctttggtgtattaacacttctctaatattcgtactgttgttttggccctttacctgttgtttaactcctccaagtcccaa

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctcctcc