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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGGAAGAAGGTTAAAGTTCCCACTTTTCTCGTTCCGGCGACACAAAAGgtgataaatgcagcaaacagcaaacacatactgaaatgatcatcctgtggtttcgatttaataataagaatgttaaatctatgtag

Basic information

species Oryza sativa
transcript LOC_Os02g03260.3
intron # 11
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g03260.3 (Oryza sativa), 5'ss of exon 11
lower sequence: GRMZM2G010044_T01 (Zea mays), 5'ss of exon 12
GGGAAGAAGGTTAAAGTTCCCACTTTTCTCGTTCCGGCGACACAAAAGgtgataaatgcagcaaacagcaaacacatactgaaatgatcatcctgtggtttcgatttaataataagaatgtt---aaatctatgtag
|| |||||||||||||||||||| ||||| || || || |||||||||||||||  |       | |  ||| | || |  |  |||||| | ||| |    | |   |   |   ||||||   |||||| || ||
GGAAAGAAGGTTAAAGTTCCCACATTTCTTGTCCCTGCCACACAAAAGgtgatattt-------agaataaaaatattccaatgtgatcaccgtgtagacctgttcataacttggaaatgttgtgaaatctctgcag

upper sequence: LOC_Os02g03260.3 (Oryza sativa), 5'ss of exon 11
lower sequence: GRMZM2G370852_T02 (Zea mays), 5'ss of exon 12
GGGAAGAAGGTTAAAGTTCCCACTTTTCTCGTTCCGGCGACACAAAAGgtgataaatgcagcaaacagcaaacacatactgaaatgatcatcctgtggtttcgatt-taat--aataagaatgttaaatctatgtag
|| |||||||||||||||||||| || || || || || |||||||||||||||  | |||     |  ||| |  | |  |  |||||| | |||||  | | |  ||||     || | ||  ||| || || ||
GGAAAGAAGGTTAAAGTTCCCACATTCCTTGTCCCTGCCACACAAAAGgtgata--ttcag-----aataaaaatgttccaatgtgatcaccgtgtggacttgttcataatttggaaatactgcaaaacctctgcag
















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|33689599|gb|CF317838.1|CF317838
EST:     GGGAAGAAGGTTAAAGTTCCCACTTTTCTCGTTCCGGCGACACAAAAG                         GGTGTGGATGGACATTTATAGCATCCCTGTACCAGGAGCCGGTGGCAAAAC
genomic: GGGAAGAAGGTTAAAGTTCCCACTTTTCTCGTTCCGGCGACACAAAAGgtgataaatg ... atctatgtagG-TGTGGATGGACATTTATAGCATCCCTGTACCAGGAGCCGGTGGCAAAAC
EST: gi|33822977|gb|CF337293.1|CF337293
EST:     CGGGGAAGAAGGTTAAAGTTCCCACTTTTCTCGTTCCGGCGACACAAAAG                         GTGTGGATGGACATTTATAGCATCCCTGTACCAGGAGCCGGTGGCAAAACT
genomic: CGGGGAAGAAGGTTAAAGTTCCCACTTTTCTCGTTCCGGCGACACAAAAGgtgataaatg ... atctatgtagGTGTGGATGGACATTTATAGCATCCCTGTACCAGGAGCCGGTGGCAAAACT
EST: gi|11442959|gb|BF430855.1|BF430855
EST:     GGGAAGAAGGTTAAAGTTCCCACTTTTCTCGTTCCGGCGACACAAAAG                         GTGTGGATGGACATTTATAGCATCCCTGTACCAGGAGCCGGTGGCAAAACT
genomic: GGGAAGAAGGTTAAAGTTCCCACTTTTCTCGTTCCGGCGACACAAAAGgtgataaatg ... atctatgtagGTGTGGATGGACATTTATAGCATCCCTGTACCAGGAGCCGGTGGCAAAACT
EST: gi|29677182|gb|CB673457.1|CB673457
EST:     GGGAAGAAGGTTAAAGTTCCCACTTTTCTCGTTCCGGCGACACAAAAG                         GTGTGGATGGACATTTATAGCATCCCTGTACCAGGAGCCGGTGGCAAAACT
genomic: GGGAAGAAGGTTAAAGTTCCCACTTTTCTCGTTCCGGCGACACAAAAGgtgataaatg ... atctatgtagGTGTGGATGGACATTTATAGCATCCCTGTACCAGGAGCCGGTGGCAAAACT
EST: gi|86493658|gb|CI136291.1|CI136291
EST:     AGAAGGTTAAAGTTCCCACTTTTCTCGTTCCGGCGACACAAAAG                         GTGTGGATGGACATTTATAGCATCCCTGTACCAGGAGCCGGTGGCAAAACT
genomic: AGAAGGTTAAAGTTCCCACTTTTCTCGTTCCGGCGACACAAAAGgtgataaatg ... atctatgtagGTGTGGATGGACATTTATAGCATCCCTGTACCAGGAGCCGGTGGCAAAACT
EST: gi|29632468|gb|CB637477.1|CB637477
EST:     GGGAAGAAGGTTAAAGTTCCCACTTTTCTCGTTCCGGCGACACAAAAG                         GTGTGGATGGACATTTATAGCATCCCTGTACCAGGAGCCGGTGGCAAAACT
genomic: GGGAAGAAGGTTAAAGTTCCCACTTTTCTCGTTCCGGCGACACAAAAGgtgataaatg ... atctatgtagGTGTGGATGGACATTTATAGCATCCCTGTACCAGGAGCCGGTGGCAAAACT
EST: gi|38477001|gb|CF961134.1|CF961134
EST:     GGGAAGAAGGTTAAAGTTCCCACTTTTCTCGTTCCGGCGACGGAAAAG                         GTGTGGATGGACATTTATAGCATCCCTGTACCAGGAGCCGGTGGCAAAACT
genomic: GGGAAGAAGGTTAAAGTTCCCACTTTTCTCGTTCCGGCGACACAAAAGgtgataaatg ... atctatgtagGTGTGGATGGACATTTATAGCATCCCTGTACCAGGAGCCGGTGGCAAAACT
EST: gi|58666580|gb|CK055266.1|CK055266
EST:     GGGAAGAAGGTTAAAGTTCCCACTTTTCTCGTTCCGGCGACACAAAAG                         GTGTGGATGGACATTTATAGCATCCCTGTACCAGGAGCCGGTGGCAAAACT
genomic: GGGAAGAAGGTTAAAGTTCCCACTTTTCTCGTTCCGGCGACACAAAAGgtgataaatg ... atctatgtagGTGTGGATGGACATTTATAGCATCCCTGTACCAGGAGCCGGTGGCAAAACT
EST: gi|86503655|gb|CI146288.1|CI146288
EST:     GGGAAGAAGGTTAAAGTTCCCACTTTTCTCGTTCCGGCGACACAAAAG                         GTGTGGATGGACATTTATAGCATCCCTGTACCAGGAGCCGGTGGCAAAACT
genomic: GGGAAGAAGGTTAAAGTTCCCACTTTTCTCGTTCCGGCGACACAAAAGgtgataaatg ... atctatgtagGTGTGGATGGACATTTATAGCATCCCTGTACCAGGAGCCGGTGGCAAAACT
EST: gi|88221360|gb|CI221316.1|CI221316
EST:     TTCCGGCGACACATAAG                         GTGTGGATGGACATTTATAGCATCCCTGTACCAGGAGCCGGTGGCAAAACT
genomic: TTCCGGCGACACAAAAGgtgataaatg ... atctatgtagGTGTGGATGGACATTTATAGCATCCCTGTACCAGGAGCCGGTGGCAAAACT
EST: gi|38478547|gb|CF962680.1|CF962680
EST:     GGGAAGAAGGTTAAAGTTCCCACTTTTCTCGTTCCGGCGACACAAAAG                         GTGTGGATGGACATTTATAGCATCCCTGTACCAGGAGCCGGTGGCAAGGCT
genomic: GGGAAGAAGGTTAAAGTTCCCACTTTTCTCGTTCCGGCGACACAAAAGgtgataaatg ... atctatgtagGTGTGGATGGACATTTATAGCATCCCTGTACCAGGAGCCGGTGGCAAAACT
EST: gi|29658442|gb|CB654717.1|CB654717
EST:     GGGAAGAAGGTTAAAGTTCCCACTTTTCTCGTTCCGGCGACACAAAAG                         GTGTGGATGGACATTTATAGCATCCCTGTACCAGGAGCCGGTGGCAAAACT
genomic: GGGAAGAAGGTTAAAGTTCCCACTTTTCTCGTTCCGGCGACACAAAAGgtgataaatg ... atctatgtagGTGTGGATGGACATTTATAGCATCCCTGTACCAGGAGCCGGTGGCAAAACT
EST: gi|29628819|gb|CB633830.1|CB633830
EST:     GGGAAGAAGGTTAAAGTTCCCACTTTTCTCGTTCCGGCGACACAAAAG                         GTGTGGATGGACATTTATAGCATCCCTGTACCAGGAGCCGGTGGCAAAACT
genomic: GGGAAGAAGGTTAAAGTTCCCACTTTTCTCGTTCCGGCGACACAAAAGgtgataaatg ... atctatgtagGTGTGGATGGACATTTATAGCATCCCTGTACCAGGAGCCGGTGGCAAAACT
EST: gi|29636583|gb|CB641592.1|CB641592
EST:     GGGAAGAAGGTTAAAGTTCCCACTTTTCTCGTTCCGGCGACACAAAAG                         GTGTGGATGGACATTTATAGCATCCCTGTACCAGGAGCCGGTGGCAAAACT
genomic: GGGAAGAAGGTTAAAGTTCCCACTTTTCTCGTTCCGGCGACACAAAAGgtgataaatg ... atctatgtagGTGTGGATGGACATTTATAGCATCCCTGTACCAGGAGCCGGTGGCAAAACT
EST: gi|88223234|gb|CI223083.1|CI223083
EST:     GAAGAAGGTTAAAGTTCCCACTTTTCTCGTTCCGGCGACACAAAAG                         GTGTGGATGGACATTTATAGCATCCCTGTACCAGGAGCCGGTGGCAAAACT
genomic: GAAGAAGGTTAAAGTTCCCACTTTTCTCGTTCCGGCGACACAAAAGgtgataaatg ... atctatgtagGTGTGGATGGACATTTATAGCATCCCTGTACCAGGAGCCGGTGGCAAAACT
EST: gi|29616438|gb|CB621450.1|CB621450
EST:     GGGAAGAAGGTTAAAGTTCCCACTTTTCTCGTTCCGGCGACACAAAAG                         GTGTGGATGGACATTTATAGCATCCCTGTACCAGGAGCCGGTGGCAAAACT
genomic: GGGAAGAAGGTTAAAGTTCCCACTTTTCTCGTTCCGGCGACACAAAAGgtgataaatg ... atctatgtagGTGTGGATGGACATTTATAGCATCCCTGTACCAGGAGCCGGTGGCAAAACT
EST: gi|218490400|gb|FG966882.1|FG966882
EST:     GGGAAGAAGGTTAAAGTTCCCACTTTTCTCGTTCCGGCGACACAAAAG                         GTGTGGATGGACATTTATAGCATCCCTGTACCAGGAGCCGGTGGCAAAACT
genomic: GGGAAGAAGGTTAAAGTTCCCACTTTTCTCGTTCCGGCGACACAAAAGgtgataaatg ... atctatgtagGTGTGGATGGACATTTATAGCATCCCTGTACCAGGAGCCGGTGGCAAAACT
EST: gi|313084027|gb|HO213810.1|HO213810
EST:     GGGAAGAAGGTTAAAGTTCCCACTTTTCTCGTTCCGGCGACACAAAAG                         GTGTGGATGGACATTTATAGCATCCCTGT
genomic: GGGAAGAAGGTTAAAGTTCCCACTTTTCTCGTTCCGGCGACACAAAAGgtgataaatg ... atctatgtagGTGTGGATGGACATTTATAGCATCCCTGT

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: 69 (upstream exon), 75 (downstream exon)
Score: 83

GGGAAGAAGGTTAAAGTTCCCACTTTTCTCGTTCCGGCGACACAAAAGgtgataaatg ... atctatgtagGTGTGGATGGACATTTATAGCATCCCTGTACCAGGAGCCGGTGGCAAAACTTGCTCACAGATATTTGAGGAGGCTGGTTGTGATACACCAGCTAGCCCTA




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGGAAGAAGGTTAAAGTTCCCACTTTTCTCGTTCCGGCGACACAAAAGgtgataaatgcagcaaacagcaaacacatactgaaatgatcatcctgtggtttcgatttaataataagaatgttaaatctatgtag

 GGAAGA
-  AAGAAG