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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatggaacatgatcttgttatgctatactgactagccgtcatttccccaagatgctgatatactattttctgcagCTATGGAGAATCATTCCCTATTTCTGCTGAAGTGCTTGATTCTAGTTTCGCTCTGCCAATTGGCAAAGCAAAG

Basic information

species Oryza sativa
transcript LOC_Os09g33500.1
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os09g33500.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G128121_T01 (Zea mays), 3'ss of exon 2
gtatgg-aacatgatcttgttatgctat---actgactagccgtcatttccccaagatgctgatatactattttctgcagCTATGGAGAATCATTCCCTATTTCTGCTGAAGTGCTTGATTCTAGTTTCGCTCTGCCAATTGGCAAAGCAAAG
|||||  |   ||||||||||     ||    ||  ||  |  ||||||  |  |||||||  | ||| ||||   |||| ||||||||||| |||||  ||||||||||||||||||||||||||||    || || ||||||||||| |||
gtatgtcagtctgatcttgttgaatcattttgctagctgcctatcattttgctgagatgctattgtaccattt---gcagTTATGGAGAATCTTTCCCAGTTTCTGCTGAAGTGCTTGATTCTAGTTTTTGCCTACCGATTGGCAAAGCTAAG

upper sequence: LOC_Os09g33500.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G097226_T02 (Zea mays), 3'ss of exon 8
gtatgg-aacatgatcttgttatgctat---actgactagccgtcatttccccaagatgctgatatactattttctgcagCTATGGAGAATCATTCCCTATTTCTGCTGAAGTGCTTGATTCTAGTTTCGCTCTGCCAATTGGCAAAGCAAAG
|||||  |   |||||||||||  | ||    ||  ||| |  ||||||  |  | |||||  |||  ||   | ||||| ||||||||||| |||||  ||||||||||||||||||||||||||||    || || ||||||||||| |||
gtatgtcagtctgatcttgttaaaccattttgctagctacctatcatttagctgaaatgctc-tatcataccatttgcagTTATGGAGAATCTTTCCCAGTTTCTGCTGAAGTGCTTGATTCTAGTTTTTGCCTACCGATTGGCAAAGCTAAG
















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|86600093|gb|CI258433.1|CI258433
EST:     GCTGCGATTAGGGATCCGGACCCTGTTGTTTTCTTGGAAAATGAACTGCT                         CTATGGAGAATCATTCCCTATTTCTGCTGAAGTGCTTGATTCTAGTTTCGC
genomic: GCTGCGATTAGGGATCCGGACCCTGTTGTTTTCTTGGAAAATGAACTGCTgtatggaaca ... ttttctgcagCTATGGAGAATCATTCCCTATTTCTGCTGAAGTGCTTGATTCTAGTTTCGC
EST: gi|87032949|gb|CI187573.1|CI187573
EST:     GCTGCGATTAGGGATCCGGACCCTGTTGTTTTCTTGGAAAATGAACTGCT                         CTATGGAGAATCATTCCCTATTTCTGCTGAAGTGCTTGATTCTAGTTTCGC
genomic: GCTGCGATTAGGGATCCGGACCCTGTTGTTTTCTTGGAAAATGAACTGCTgtatggaaca ... ttttctgcagCTATGGAGAATCATTCCCTATTTCTGCTGAAGTGCTTGATTCTAGTTTCGC
EST: gi|58687862|gb|CK076549.1|CK076549
EST:     GCTGCGATTAGGGATCCGGACCCTGTTGTTTTCTTGGAAAATGAACTGCT                         CTATGGAGAATCATTCCCTATTTCTGCTGAAGTGCTTGATTCTAGTTTCGC
genomic: GCTGCGATTAGGGATCCGGACCCTGTTGTTTTCTTGGAAAATGAACTGCTgtatggaaca ... ttttctgcagCTATGGAGAATCATTCCCTATTTCTGCTGAAGTGCTTGATTCTAGTTTCGC
EST: gi|29637529|gb|CB642538.1|CB642538
EST:     GCTGCGATTAGGGATCCGGACCCTGTTGTTTTCTTGGAAAATGAACTGCT                         CTATGGAGAATCATTCCCTATTTCTGCTGAAGTGCTTGATTCTAGTTTCGC
genomic: GCTGCGATTAGGGATCCGGACCCTGTTGTTTTCTTGGAAAATGAACTGCTgtatggaaca ... ttttctgcagCTATGGAGAATCATTCCCTATTTCTGCTGAAGTGCTTGATTCTAGTTTCGC
EST: gi|33380822|gb|CF196165.1|CF196165
EST:     GCTGCGATTAGGGATCCGGACCCTGTTGTTTTCTTGGAAAATGAACTGCT                         CTATGGAGAATCATTCCCTATTTCTGCTGAAGTGCTTGATTCTAGTTTCGC
genomic: GCTGCGATTAGGGATCCGGACCCTGTTGTTTTCTTGGAAAATGAACTGCTgtatggaaca ... ttttctgcagCTATGGAGAATCATTCCCTATTTCTGCTGAAGTGCTTGATTCTAGTTTCGC
EST: gi|157649975|gb|EX449609.1|EX449609
EST:     GCTGCGATTAGGGATCCGGACCCTGTTGTTTTCTTGGAAAATGAACTGCT                         CTATGGAGAATCATTCCCTATTTCTGCTGAAGTGCTTGATTCTAGTTTCGC
genomic: GCTGCGATTAGGGATCCGGACCCTGTTGTTTTCTTGGAAAATGAACTGCTgtatggaaca ... ttttctgcagCTATGGAGAATCATTCCCTATTTCTGCTGAAGTGCTTGATTCTAGTTTCGC
EST: gi|2312022|gb|C28177.1|C28177
EST:     GCTGCGATTAGGGATCCGGACCCTGTTGTTTTCTTGGAAAATNAACTGCT                         CTATGGAGAATCATTCCCTATTTCTGCTGAAGTGCTTGATTCTAGTTTCGC
genomic: GCTGCGATTAGGGATCCGGACCCTGTTGTTTTCTTGGAAAATGAACTGCTgtatggaaca ... ttttctgcagCTATGGAGAATCATTCCCTATTTCTGCTGAAGTGCTTGATTCTAGTTTCGC
EST: gi|29645720|gb|CB650727.1|CB650727
EST:     GCTGCGATTAGGGATCCGGACCCTGTTGTTTTCTTGGAAAATGAACTGCT                         CTATGGAGAATCATTCCCTATTTCTGCTGAAGTGCTTGATTCTAGTTTCGC
genomic: GCTGCGATTAGGGATCCGGACCCTGTTGTTTTCTTGGAAAATGAACTGCTgtatggaaca ... ttttctgcagCTATGGAGAATCATTCCCTATTTCTGCTGAAGTGCTTGATTCTAGTTTCGC
EST: gi|58586864|gb|CF985172.1|CF985172
EST:     GCTGCGATTAGGGATCCGGACCCTGTTGTTTTCTTGGAAAATGAACTGCT                         CTATGGAGAATCATTCCCTATTTCTGCTGAAGTGCTTGATTCTAGT
genomic: GCTGCGATTAGGGATCCGGACCCTGTTGTTTTCTTGGAAAATGAACTGCTgtatggaaca ... ttttctgcagCTATGGAGAATCATTCCCTATTTCTGCTGAAGTGCTTGATTCTAGT
EST: gi|33666828|gb|CF297795.1|CF297795
EST:     TTTTCTTGGAAAATGAACTGCT                         CTATGGAGAATCATTCCCTATTTCTGCTGAAGTGCTTGATTCTAGTTTCGC
genomic: TTTTCTTGGAAAATGAACTGCTgtatggaaca ... ttttctgcagCTATGGAGAATCATTCCCTATTTCTGCTGAAGTGCTTGATTCTAGTTTCGC
EST: gi|29657623|gb|CB653898.1|CB653898
EST:     GCTGCGATTAGGGATCCGGACCCTGTTGTTTTCTTGGAAAATGAACTGCT                         CTATGGAGAATCATTCCCTATTTCTGCTGAAGTGCTTGATTCTAGTTTCGC
genomic: GCTGCGATTAGGGATCCGGACCCTGTTGTTTTCTTGGAAAATGAACTGCTgtatggaaca ... ttttctgcagCTATGGAGAATCATTCCCTATTTCTGCTGAAGTGCTTGATTCTAGTTTCGC
EST: gi|27576086|gb|CA998780.1|CA998780
EST:     GCTGCGATTAGGGATCCGGACCCTGTTGTTTTCTTGGAAAATGAACTGCT                         CTATGGAGAATCATTCCCTATTTCTGCTGAAGTGCTTGATTCTAGTTTCGC
genomic: GCTGCGATTAGGGATCCGGACCCTGTTGTTTTCTTGGAAAATGAACTGCTgtatggaaca ... ttttctgcagCTATGGAGAATCATTCCCTATTTCTGCTGAAGTGCTTGATTCTAGTTTCGC
EST: gi|86497317|gb|CI139950.1|CI139950
EST:     GCTGCGATTAGGGATCCGGACCCTGTTGTTTTCTTGGAAAATGAACTGCT                         CTATGGAGAATCATTCCCTATTTCTGCTGAAGTGCTTGATTCTAGTTTCGC
genomic: GCTGCGATTAGGGATCCGGACCCTGTTGTTTTCTTGGAAAATGAACTGCTgtatggaaca ... ttttctgcagCTATGGAGAATCATTCCCTATTTCTGCTGAAGTGCTTGATTCTAGTTTCGC

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), 73 (downstream exon)
Score: 82

TTAAGGTTCTGGTTCCATATTCTGCAGAAGATGCTCGTGGCTTGCTCAAAGCTGCGATTAGGGATCCGGACCCTGTTGTTTTCTTGGAAAATGAACTGCTgtatggaaca ... ttttctgcagCTATGGAGAATCATTCCCTATTTCTGCTGAAGTGCTTGATTCTAGTTTCGCTCTGCCAATTGGCAAAGCAAAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgctatactgactagccgtcatttccccaagatgctgatatactattttctgcagCTATGGAGAATCATTCCCTATTTCTGCTGAAGTGCTTGATTCTAGTTTCGCTCTGCCAATTGGCAAAGCAAAG
                                          ctattttct  CT-rich tract
                                   tgatatactatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatggaacatgatcttgttatgctatactgactagccgtcatttccccaagatgctgatatactattttctgcagCTATGGAGAATCATTCCCTATTTCTGCTGAAGTGCTTGATTCTAGTTTCGCTCTGCCAATTGGCAAAGCAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAAG