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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgttcaaaccttttaagagaggatatgtagccgacagactatatgttatgacaaatggtgtcaaatcatataaatatctgacattctgactgcttgatgtcctacaaatgtagGTGTGCATATGATCAGCAAGGCCAGCTTTTGGCCTCACCAGCTAAGACCGATGGGATCCTTGGTCTTAGTAGTGCAGGAATAAGCCTTCCCAGTCAGCTG

Basic information

species Oryza sativa
transcript LOC_Os02g49800.1
intron # 3
splice site 3'
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|29658892|gb|CB655167.1|CB655167
EST:     CATATTATCACTACTAATGGTGGAAGGGAAAAACTAGATTTTGTGTTTGG                         GTGTGCATATGATCAGCAAGGCCAGCTTTTGGCCTC
genomic: CATATTATCACTACTAATGGTGGAAGGGAAAAACTAGATTTTGTGTTTGGgtatgttcaa ... acaaatgtagGTGTGCATATGATCAGCAAGGCCAGCTTTTGGCCTC
EST: gi|29666293|gb|CB662568.1|CB662568
EST:     CATATTATCACTACTAATGGTGGAAGGGAAAAACTAGATTTTGTGTTTGG                         GTGTGCATATGATCAG
genomic: CATATTATCACTACTAATGGTGGAAGGGAAAAACTAGATTTTGTGTTTGGgtatgttcaa ... acaaatgtagGTGTGCATATGATCAG
EST: gi|427111|gb|D23192.1|D23192
EST:     CATATTATCACTACTAATGGTGGAAGGGAAAAACTAGATTTTGTGTTTGG                         GTGTGCATATGATCAGCAAGGCCAGCTTTTGGCCTCACCAGCTAAGACCGA
genomic: CATATTATCACTACTAATGGTGGAAGGGAAAAACTAGATTTTGTGTTTGGgtatgttcaa ... acaaatgtagGTGTGCATATGATCAGCAAGGCCAGCTTTTGGCCTCACCAGCTAAGACCGA
EST: gi|86843806|gb|CI336615.1|CI336615
EST:     CATATTATCACTACTAATGGTGGAAGGGAAAAACTAGATTTTGTGTTTGG                         GTGTGCATATGATCAGCAAGGCCAGCTTTTGGCCTCACCAGCTAAGACCGA
genomic: CATATTATCACTACTAATGGTGGAAGGGAAAAACTAGATTTTGTGTTTGGgtatgttcaa ... acaaatgtagGTGTGCATATGATCAGCAAGGCCAGCTTTTGGCCTCACCAGCTAAGACCGA
EST: gi|27576738|gb|CA999432.1|CA999432
EST:     CATATTATCACTACTAATGGTGGAAGGGAAAAACTAGATTTTGTGTTTGG                         GTGTGCATATGATCAGCAAGGCCAGCTTTTGGCCTCACCAGCTAAGACCGA
genomic: CATATTATCACTACTAATGGTGGAAGGGAAAAACTAGATTTTGTGTTTGGgtatgttcaa ... acaaatgtagGTGTGCATATGATCAGCAAGGCCAGCTTTTGGCCTCACCAGCTAAGACCGA
EST: gi|2310453|gb|C26608.1|C26608
EST:     CATATTATCACTACTAATGGTGGAAGGGAAAAACTAGATTTTGTGTTTGG                         GTGTGCATATGATCAGCAAGGCCAGCTTTTGGCCTCACCAGCTAAGACCGA
genomic: CATATTATCACTACTAATGGTGGAAGGGAAAAACTAGATTTTGTGTTTGGgtatgttcaa ... acaaatgtagGTGTGCATATGATCAGCAAGGCCAGCTTTTGGCCTCACCAGCTAAGACCGA
EST: gi|88276836|gb|CI395999.1|CI395999
EST:     CATATTATCACTACTAATGGTGGAAGGGAAAAACTAGATTTTGTGTTTGG                         GTGTGCATATGATCAGCAAGGCCAGCTTTTGGCCTCACCAGCTAAGACCGA
genomic: CATATTATCACTACTAATGGTGGAAGGGAAAAACTAGATTTTGTGTTTGGgtatgttcaa ... acaaatgtagGTGTGCATATGATCAGCAAGGCCAGCTTTTGGCCTCACCAGCTAAGACCGA
EST: gi|86835611|gb|CI348068.1|CI348068
EST:     CATATTATCACTACTAATGGTGGAAGGGAAAAACTAGATTTTGTGTTTGG                         GTGTGCATATGATCAGCAAGGCCAGCTTTTGGCCTCACCAGCTAAGACCGA
genomic: CATATTATCACTACTAATGGTGGAAGGGAAAAACTAGATTTTGTGTTTGGgtatgttcaa ... acaaatgtagGTGTGCATATGATCAGCAAGGCCAGCTTTTGGCCTCACCAGCTAAGACCGA
EST: gi|29642625|gb|CB647632.1|CB647632
EST:     CATATTATCACTACTAATGGTGGAAGGGAAAAACTAGATTTTGTGTTTGG                         GTGTGCATATGATCAGCAAGGCCAGCTTTTGGCCTCACCAGCTAAGACCGA
genomic: CATATTATCACTACTAATGGTGGAAGGGAAAAACTAGATTTTGTGTTTGGgtatgttcaa ... acaaatgtagGTGTGCATATGATCAGCAAGGCCAGCTTTTGGCCTCACCAGCTAAGACCGA
EST: gi|29669337|gb|CB665612.1|CB665612
EST:     CATATTATCACTACTAATGGTGGAAGGGAAAAACTAGATTTTGTGTTTGG                         GTGTGCATATGATCAGCAAGGCCAGCTTTTGGCCTCACCAGCTAAGACCGA
genomic: CATATTATCACTACTAATGGTGGAAGGGAAAAACTAGATTTTGTGTTTGGgtatgttcaa ... acaaatgtagGTGTGCATATGATCAGCAAGGCCAGCTTTTGGCCTCACCAGCTAAGACCGA
EST: gi|88969944|gb|CI383446.1|CI383446
EST:     CATATTATCACTACTAATGTTGGAAGGGAAAAACTAGATTTTGTGTTTGG                         GTGTGCATATGATCAGCAAGGCCAGCTTTTGGCCTCACCAGCTAAGACCGA
genomic: CATATTATCACTACTAATGGTGGAAGGGAAAAACTAGATTTTGTGTTTGGgtatgttcaa ... acaaatgtagGTGTGCATATGATCAGCAAGGCCAGCTTTTGGCCTCACCAGCTAAGACCGA
EST: gi|157650384|gb|EX450018.1|EX450018
EST:     CATATTATCACTACTAATGGTGGAAGGGAAAAACTAGATTTTGTGTTTGG                         GTGTGCATATGATCAGCAAGGCCAGCTTTTGGCCTCACCAGCTAAGACCGA
genomic: CATATTATCACTACTAATGGTGGAAGGGAAAAACTAGATTTTGTGTTTGGgtatgttcaa ... acaaatgtagGTGTGCATATGATCAGCAAGGCCAGCTTTTGGCCTCACCAGCTAAGACCGA
EST: gi|29664921|gb|CB661196.1|CB661196
EST:     CATATTATCACTACTAATGGTGGAAGGGAAAAACTAGATTTTGTGTTTGG                         GTGTGCATATGATCAGCAAGGCCAGCTTTTGGCCTCACCAGCTAAGACCGA
genomic: CATATTATCACTACTAATGGTGGAAGGGAAAAACTAGATTTTGTGTTTGGgtatgttcaa ... acaaatgtagGTGTGCATATGATCAGCAAGGCCAGCTTTTGGCCTCACCAGCTAAGACCGA
EST: gi|427119|gb|D23201.1|D23201
EST:     CATATTATCACTACTAATGGTGGAAGGGAAAAACTAGATTTTGTGTTTGG                         GTGTGCATATGATCAGCAAGGCCAGCTTTTGGCCTCACCAGCTAAGACCGA
genomic: CATATTATCACTACTAATGGTGGAAGGGAAAAACTAGATTTTGTGTTTGGgtatgttcaa ... acaaatgtagGTGTGCATATGATCAGCAAGGCCAGCTTTTGGCCTCACCAGCTAAGACCGA

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), 74 (downstream exon)
Score: 116

AATATGCTGATCGAAGCTCCTCCATGGGTGTCCTTGCTAGGGATGATATGCATATTATCACTACTAATGGTGGAAGGGAAAAACTAGATTTTGTGTTTGGgtatgttcaa ... acaaatgtagGTGTGCATATGATCAGCAAGGCCAGCTTTTGGCCTCACCAGCTAAGACCGATGGGATCCTTGGTCTTAGTAGTGCAGGAATAAGCCTTCCCAGTCAGCTG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtcaaatcatataaatatctgacattctgactgcttgatgtcctacaaatgtagGTGTGCATATGATCAGCAAGGCCAGCTTTTGGCCTCACCAGCTAAGACCGATGGGATCCTTGGTCTTAGTAGTGCAGGAATAAGCCTTCCCAGTCAGCTG
     aatcatataaatatct  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgttcaaaccttttaagagaggatatgtagccgacagactatatgttatgacaaatggtgtcaaatcatataaatatctgacattctgactgcttgatgtcctacaaatgtagGTGTGCATATGATCAGCAAGGCCAGCTTTTGGCCTCACCAGCTAAGACCGATGGGATCCTTGGTCTTAGTAGTGCAGGAATAAGCCTTCCCAGTCAGCTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG