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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gatacaacgtaaattatgttagatgtttaaactagacctcagatagtgggttatacctgtttctacttgttctgaagtatgttgtccattgctaatttagGATGGCAAGGAGGAGGTCATCGAAGCTTGGTACATGGATGACAGTGAAGAGGACCAGAGGCTTCCTCATCATCGTGAGCCCAAAGAATTCATTCCTCTTA

Basic information

species Oryza sativa
transcript LOC_Os03g06620.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g06620.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G165998_T03 (Zea mays), 3'ss of exon 1
gatacaacgtaaattatgttagatgtttaaactagacctcagatagtgggttatacc-tgtttctacttgttctgaagtatgttgtccattgctaatttagGATGGCAAGGAGGAGGTCATCGAAGCTTGGTACATGGATGACAGTGAAGAGGACCAGAGGCTTCCTCATCATCGTGAGCCCAAAGAATTCATTCCTCTTA
 || | |  |   |  |  | | |  ||   ||  || |      |   |  |||   ||  |       || |   ||    ||   ||| | |   |||| ||||||||||||||||||| |||| ||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||  
catgctat-tgggtggtcatggttcctttgtctgaacatgcttgtgcttgccatattatgcattccgacattatatcgttgaatggttatttccatcatagGTTGGCAAGGAGGAGGTCATCCAAGCATGGTACATGGACGACAGTGAAGAGGACCAGAGGCTTCCTCATCATCGTGAGCCCAAAGAATTCATTCCTCTCG

upper sequence: LOC_Os03g06620.1 (Oryza sativa), 3'ss of exon 1
lower sequence: AT4G14716.1 (Arabidopsis thaliana), 3'ss of exon 1
gatacaacgtaaattatgttag-atgtttaaactagacctcagatagtgggttatacctgtttctacttgttctgaagtatgttgtccattgctaatttagGATGGCAAGGAGGAGGTCATCGAAGCTTGGTACATGGATGACAGTGAAGAGGACCAGAGGCTTCCTCATCATCGTGAGCCCAAAGAATTCATTCCTCTTA
||     |  || || ||     |   | | | || |  | | |||   |   ||  |  |  | |    |        || |||        |   ||||||||| |  || || || ||  |||||||||| |||||||| ||||||||||| ||||| |||||||| ||    || || ||||| ||  |  |  |  
gaattgtctgaagttttgaagctaaaatcagattaaatataaaatatctgaacattgcc-tcccaaggaatctaatcccatcttgatgtgcttttgcttagGATGGGAGAGAAGAAGTGATTCAAGCTTGGTATATGGATGATAGTGAAGAGGATCAGAGACTTCCTCACCACAAGGATCCTAAAGAGTTTGTATCGTTGG
















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|33664076|gb|CF295043.1|CF295043
EST:     GACTCAGGAGCGGCGTCTGAGAGGTTTCANAGATGGAGAACCAGTTCCAG                         GATGGCAAGGAGGAGGTCATCGAAGCTTGGTACATGGATGACAGTGAAGAG
genomic: GACTCAGGAGCGGCGTCTGAGAGGTTTCAGAGATGGAGAACCAGTTCCAGgtgagatctc ... gctaatttagGATGGCAAGGAGGAGGTCATCGAAGCTTGGTACATGGATGACAGTGAAGAG
EST: gi|88410806|gb|CI578612.1|CI578612
EST:     GACTCAGGAGCGGCGTCTGAGAGGTTTCAGAGATGGAGAACCAGTTCCAG                         GATGGCAAGGAGGAGGTCATCGAAGCTTGGTACATGGATGACAGTGAAGAG
genomic: GACTCAGGAGCGGCGTCTGAGAGGTTTCAGAGATGGAGAACCAGTTCCAGgtgagatctc ... gctaatttagGATGGCAAGGAGGAGGTCATCGAAGCTTGGTACATGGATGACAGTGAAGAG
EST: gi|88432267|gb|CI565300.1|CI565300
EST:     GACTCAGGAGCGGCGTCTGAGAAGTTTCAGAGATGGAGAACCAGTTCCAG                         GATGGCAAGGAGGAGGTCATCGAAGCTTGGTACATGGATGACAGTGAAGAG
genomic: GACTCAGGAGCGGCGTCTGAGAGGTTTCAGAGATGGAGAACCAGTTCCAGgtgagatctc ... gctaatttagGATGGCAAGGAGGAGGTCATCGAAGCTTGGTACATGGATGACAGTGAAGAG
EST: gi|88392897|gb|CI614779.1|CI614779
EST:     GACTCAGGAGCGGCGTCTGAGAGGTTTCAGAGATGGAGAACCAGTTCCAG                         GATGGCAAGGAGGAGGTCATCGAAGCTTGGTACATGGATGACAGTGAAGAG
genomic: GACTCAGGAGCGGCGTCTGAGAGGTTTCAGAGATGGAGAACCAGTTCCAGgtgagatctc ... gctaatttagGATGGCAAGGAGGAGGTCATCGAAGCTTGGTACATGGATGACAGTGAAGAG
EST: gi|700773|gb|D47064.1|D47064
EST:     GACTCAGGAGCGGCGTCTGAGAGGTTTCAGAGATGGAGAACCAGTTCCAG                         GATGGCAAGGAGGAGGTCATCGAAGCTTGGTACATGGATGACAGTNAAGAG
genomic: GACTCAGGAGCGGCGTCTGAGAGGTTTCAGAGATGGAGAACCAGTTCCAGgtgagatctc ... gctaatttagGATGGCAAGGAGGAGGTCATCGAAGCTTGGTACATGGATGACAGTGAAGAG
EST: gi|58591300|gb|CF989608.1|CF989608
EST:     GAGAGGTTTCAGAGATGGAGAACCAGTTCCAG                         GATGGCAAGGAGGAGGTCATCGAAGCTTGGTACATGGATGACAGTGAAGAG
genomic: GAGAGGTTTCAGAGATGGAGAACCAGTTCCAGgtgagatctc ... gctaatttagGATGGCAAGGAGGAGGTCATCGAAGCTTGGTACATGGATGACAGTGAAGAG
EST: gi|88300984|gb|CI592164.1|CI592164
EST:     GACTCAGGAGCGGCGTCTGAGAGGTTTCAGAGATGGAGAACCAGTTCCAG                         GATGGCAAGGAGGAGGTCATCGAAGCTTGGTACATGGATGACAGTGAAGAG
genomic: GACTCAGGAGCGGCGTCTGAGAGGTTTCAGAGATGGAGAACCAGTTCCAGgtgagatctc ... gctaatttagGATGGCAAGGAGGAGGTCATCGAAGCTTGGTACATGGATGACAGTGAAGAG
EST: gi|218497580|gb|FG955135.1|FG955135
EST:     GACTCAGGAGCGGCGTCTGAGAGGTTTCAGAGATGGAGAACCAGTTCCAG                         GATGGCAAGGAGGAGGTCATCGAAGCTTGGTACATGGATGACAGTGAAGAG
genomic: GACTCAGGAGCGGCGTCTGAGAGGTTTCAGAGATGGAGAACCAGTTCCAGgtgagatctc ... gctaatttagGATGGCAAGGAGGAGGTCATCGAAGCTTGGTACATGGATGACAGTGAAGAG
EST: gi|88573345|gb|CI664916.1|CI664916
EST:     GACTCAGGAGCGGCGTCTGAGAGGTTTCAGAGATGGAGAACCAGTTCCAG                         GATGGCAAGGAGGAGGTCATCGAAGCTTGGTACATGGATGACAGTGAAGAG
genomic: GACTCAGGAGCGGCGTCTGAGAGGTTTCAGAGATGGAGAACCAGTTCCAGgtgagatctc ... gctaatttagGATGGCAAGGAGGAGGTCATCGAAGCTTGGTACATGGATGACAGTGAAGAG
EST: gi|33662546|gb|CF293513.1|CF293513
EST:     GACTCAGGAGCGGCGTCTGAGAGGTTTCAGAGATGGAGAACCAGTTCCAG                         GATGGCAAGGAGGAGGTCATCGAAGCTTGGTACATGGATGACAGTGAAGAG
genomic: GACTCAGGAGCGGCGTCTGAGAGGTTTCAGAGATGGAGAACCAGTTCCAGgtgagatctc ... gctaatttagGATGGCAAGGAGGAGGTCATCGAAGCTTGGTACATGGATGACAGTGAAGAG
EST: gi|117246064|gb|CT862529.1|CT862529
EST:     GACTCAGGAGCGGCGTCTGAGAGGTTTCAGAGATGGAGAACCAGTTCCAG                         GATGGCAAGGAGGAGGTCATCGAAGCTTGGTACATGGATGACAGTGAAGAG
genomic: GACTCAGGAGCGGCGTCTGAGAGGTTTCAGAGATGGAGAACCAGTTCCAGgtgagatctc ... gctaatttagGATGGCAAGGAGGAGGTCATCGAAGCTTGGTACATGGATGACAGTGAAGAG
EST: gi|66916156|gb|CX103004.1|CX103004
EST:     GACTCAGGAGCGGCGTCTGAGAGGTTTCAGAGATGGAGAACCAGTTCCAG                         GATGGCAAGGAGGAGGTCATCGAAGCTTGGTACATGGATGACAGTGAAGAG
genomic: GACTCAGGAGCGGCGTCTGAGAGGTTTCAGAGATGGAGAACCAGTTCCAGgtgagatctc ... gctaatttagGATGGCAAGGAGGAGGTCATCGAAGCTTGGTACATGGATGACAGTGAAGAG
EST: gi|88738682|gb|CI762190.1|CI762190
EST:     GACTCAGGAGCGGCGTCTGAGAGGTTTCAGAGATGGAGAACCAGTTCCAG                         GATGGCAAGGAGGAGGTCATCGAAGCTTGGTACATGGATGACAGTGAAGAG
genomic: GACTCAGGAGCGGCGTCTGAGAGGTTTCAGAGATGGAGAACCAGTTCCAGgtgagatctc ... gctaatttagGATGGCAAGGAGGAGGTCATCGAAGCTTGGTACATGGATGACAGTGAAGAG
EST: gi|88423723|gb|CI617075.1|CI617075
EST:     GACTCAGGAGCGGCGTCTGAGAGGTTTCAGAGATGGAGAACCAGTTCCAG                         GATGGCAAGGAGGAGGTCATCGAAGCTTGGTACATGGATGACAGTGAAGAG
genomic: GACTCAGGAGCGGCGTCTGAGAGGTTTCAGAGATGGAGAACCAGTTCCAGgtgagatctc ... gctaatttagGATGGCAAGGAGGAGGTCATCGAAGCTTGGTACATGGATGACAGTGAAGAG
EST: gi|88341716|gb|CI641468.1|CI641468
EST:     GACTCAGGAGCGGCGTCTGAGAGGTTTCAGAGATGGAGAACCAGTTCCAG                         GATGGCAAGGAGGAGGTCATCGAAGCTTGGTACATGGATGACAGTGAAGAG
genomic: GACTCAGGAGCGGCGTCTGAGAGGTTTCAGAGATGGAGAACCAGTTCCAGgtgagatctc ... gctaatttagGATGGCAAGGAGGAGGTCATCGAAGCTTGGTACATGGATGACAGTGAAGAG
EST: gi|88311755|gb|CI574972.1|CI574972
EST:     GACTCAGGAGCGGCGTCTGAGAGGTTTCAGAGATGGAGAACCAGTTCCAG                         GATGGCAAGGAGGAGGTCATCGAAGCTTGGTACATGGATGACAGTGAAGAG
genomic: GACTCAGGAGCGGCGTCTGAGAGGTTTCAGAGATGGAGAACCAGTTCCAGgtgagatctc ... gctaatttagGATGGCAAGGAGGAGGTCATCGAAGCTTGGTACATGGATGACAGTGAAGAG
EST: gi|88728915|gb|CI752425.1|CI752425
EST:     GACTCAGGAGCGGCGTCTGAGAGGTTTCAGAGATGGAGAACCAGTTCCAG                         GATGGCAAGGAGGAGGTCATCGAAGCTTGGTACATGGATGACAGTGAAGAG
genomic: GACTCAGGAGCGGCGTCTGAGAGGTTTCAGAGATGGAGAACCAGTTCCAGgtgagatctc ... gctaatttagGATGGCAAGGAGGAGGTCATCGAAGCTTGGTACATGGATGACAGTGAAGAG
EST: gi|88354257|gb|CI637823.1|CI637823
EST:     GACTCAGGAGCGGCGTCTGAGAGGTTTCAGAGATGGAGAACCAGTTCCAG                         GATGGCAAGGAGGAGGTCATCGAAGCTTGGTACATGGATGACAGTGAAGAG
genomic: GACTCAGGAGCGGCGTCTGAGAGGTTTCAGAGATGGAGAACCAGTTCCAGgtgagatctc ... gctaatttagGATGGCAAGGAGGAGGTCATCGAAGCTTGGTACATGGATGACAGTGAAGAG
EST: gi|88398782|gb|CI601118.1|CI601118
EST:     GACTCAGGAGCGGCGTCTGAGAGGTTTCAGAGATGGAGAACCAGTTCCAG                         GATGGCAAGGAGGAGGTCATCGAAGCTTGGTACATGGATGACAGTGAAGAG
genomic: GACTCAGGAGCGGCGTCTGAGAGGTTTCAGAGATGGAGAACCAGTTCCAGgtgagatctc ... gctaatttagGATGGCAAGGAGGAGGTCATCGAAGCTTGGTACATGGATGACAGTGAAGAG
EST: gi|88354747|gb|CI614025.1|CI614025
EST:     GACTCAGGAGCGGCGTCTGAGAGGTTTCAGAGATGGAGAACCAGTTCCAG                         GATGGCAAGGAGGAGGTCATCGAAGCTTGGTACATGGATGACAGTGAAGAG
genomic: GACTCAGGAGCGGCGTCTGAGAGGTTTCAGAGATGGAGAACCAGTTCCAGgtgagatctc ... gctaatttagGATGGCAAGGAGGAGGTCATCGAAGCTTGGTACATGGATGACAGTGAAGAG
EST: gi|88337236|gb|CI629526.1|CI629526
EST:     GACTCAGGAGCGGCGTCTGAGAGGTTTCAGAGATGGAGAANCAGTTCCAG                         GATGGCAAGGAGGAGGTCATCGAAGCTTGGTACATGGATGACAGTGAAGAG
genomic: GACTCAGGAGCGGCGTCTGAGAGGTTTCAGAGATGGAGAACCAGTTCCAGgtgagatctc ... gctaatttagGATGGCAAGGAGGAGGTCATCGAAGCTTGGTACATGGATGACAGTGAAGAG
EST: gi|88719684|gb|CI743194.1|CI743194
EST:     GACTCAGGAGCGGCGTCTGAGAGGTTTCAGAGATGGAGAACCAGTTCCAG                         GATGGCAAGGAGGAGGTCATCGAAGCTTGGTACATGGATGACAGTGAAGAG
genomic: GACTCAGGAGCGGCGTCTGAGAGGTTTCAGAGATGGAGAACCAGTTCCAGgtgagatctc ... gctaatttagGATGGCAAGGAGGAGGTCATCGAAGCTTGGTACATGGATGACAGTGAAGAG
EST: gi|88447697|gb|CI579773.1|CI579773
EST:     GACTCAGGAGCGGCGTCTGAGAGGTTTCAGAGATGGAGAACCAGTTCCAG                         GATGGCAAGGAGGAGGTCATCGAAGCTTGGTACATGGATGACAGTGAAGAG
genomic: GACTCAGGAGCGGCGTCTGAGAGGTTTCAGAGATGGAGAACCAGTTCCAGgtgagatctc ... gctaatttagGATGGCAAGGAGGAGGTCATCGAAGCTTGGTACATGGATGACAGTGAAGAG
EST: gi|33659100|gb|CF281713.1|CF281713
EST:     GACTCAGGAGCGGCGTCTGAGAGGTTTCAGAGATGGAGAACCAGTTCCAG                         GATAGCAAGGAGGAGGTCATCGAAGCTTGGTACATGGATGACAGTGAAGAG
genomic: GACTCAGGAGCGGCGTCTGAGAGGTTTCAGAGATGGAGAACCAGTTCCAGgtgagatctc ... gctaatttagGATGGCAAGGAGGAGGTCATCGAAGCTTGGTACATGGATGACAGTGAAGAG
EST: gi|88570475|gb|CI661848.1|CI661848
EST:     GACTCAGGAGCGGCGTCTGAGAGGTTTCAGAGATGGAGAACCAGTTCCAG                         GATGGCAAGGAGGAGGTCATCGAAGCTTGGTACATGGATGACAGTGAAGAG
genomic: GACTCAGGAGCGGCGTCTGAGAGGTTTCAGAGATGGAGAACCAGTTCCAGgtgagatctc ... gctaatttagGATGGCAAGGAGGAGGTCATCGAAGCTTGGTACATGGATGACAGTGAAGAG
EST: gi|88371298|gb|CI600146.1|CI600146
EST:     GACTCAGGAGCGGCGTCTGAGAGGTTTCAGAGATGGAGAACCAGTTCCAG                         GATGGCAAGGAGGAGGTCATCGAAGCTTGGTACATGGATGACAGTGAAGAG
genomic: GACTCAGGAGCGGCGTCTGAGAGGTTTCAGAGATGGAGAACCAGTTCCAGgtgagatctc ... gctaatttagGATGGCAAGGAGGAGGTCATCGAAGCTTGGTACATGGATGACAGTGAAGAG
EST: gi|88693640|gb|CI737215.1|CI737215
EST:     GACTCAGGAGCGGCGTCTGAGAGGTTTCAGAGATGGAGAACCAGTTCCAG                         GATGGCAAGGAGGAGGTCATCGAAGCTTGGTACATGGATGACAGTGAAGAG
genomic: GACTCAGGAGCGGCGTCTGAGAGGTTTCAGAGATGGAGAACCAGTTCCAGgtgagatctc ... gctaatttagGATGGCAAGGAGGAGGTCATCGAAGCTTGGTACATGGATGACAGTGAAGAG
EST: gi|88445319|gb|CI587213.1|CI587213
EST:     GACTCAGGAGCGGCGTCTGAGAGGTTTCAGAGATGGAGAACCAGTTCCAG                         GATGGCAAGGAGGAGGTCATCGAAGCTTGGTACATGGATGACAGTGAAGAG
genomic: GACTCAGGAGCGGCGTCTGAGAGGTTTCAGAGATGGAGAACCAGTTCCAGgtgagatctc ... gctaatttagGATGGCAAGGAGGAGGTCATCGAAGCTTGGTACATGGATGACAGTGAAGAG
EST: gi|88575234|gb|CI669379.1|CI669379
EST:     GACTCAGGAGCGGCGTCTGAGAGGTTTCAGAGATGGAGAACCAGTTCCAG                         GATGGCAAGGAGGAGGTCATCGAAGCTTGGTACATGGATGACAGTGAAGAG
genomic: GACTCAGGAGCGGCGTCTGAGAGGTTTCAGAGATGGAGAACCAGTTCCAGgtgagatctc ... gctaatttagGATGGCAAGGAGGAGGTCATCGAAGCTTGGTACATGGATGACAGTGAAGAG
EST: gi|88669169|gb|CI720126.1|CI720126
EST:     GACTCAGGAGCGGCGTCTGAGAGGTTTCAGAGATGGAGAACCAGTTCCAG                         GATGGCAAGGAGGAGGTCATCGAAGCTTGGTACATGGATGACAGTGAAGAG
genomic: GACTCAGGAGCGGCGTCTGAGAGGTTTCAGAGATGGAGAACCAGTTCCAGgtgagatctc ... gctaatttagGATGGCAAGGAGGAGGTCATCGAAGCTTGGTACATGGATGACAGTGAAGAG
EST: gi|569576|gb|D40425.1|D40425
EST:     GACTCAGGAGCGGCGTCTGAGAGGTTTCAGAGATGGAGAACCAGTTCCAG                         GATGGCAAGGAGGAGGTCATCGAAGCTTGGTACATGGATGACAGTNAAGAG
genomic: GACTCAGGAGCGGCGTCTGAGAGGTTTCAGAGATGGAGAACCAGTTCCAGgtgagatctc ... gctaatttagGATGGCAAGGAGGAGGTCATCGAAGCTTGGTACATGGATGACAGTGAAGAG
EST: gi|88730508|gb|CI754121.1|CI754121
EST:     GACTCAGGAGCGGCGTCTGAGAGGTTTCAGAGATGGAGAACCAGTTCCAG                         GATGGCAAGGAGGAGGTCATCGAAGCTTGGTACATGGATGACAGTGAAGAG
genomic: GACTCAGGAGCGGCGTCTGAGAGGTTTCAGAGATGGAGAACCAGTTCCAGgtgagatctc ... gctaatttagGATGGCAAGGAGGAGGTCATCGAAGCTTGGTACATGGATGACAGTGAAGAG

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: 190

TTCCAGGCTATCCGGAATCGGGAGGGTTTCCCAATAGGAAAGCAACTCAGGACTCAGGAGCGGCGTCTGAGAGGTTTCAGAGATGGAGAACCAGTTCCAGgtgagatctc ... gctaatttagGATGGCAAGGAGGAGGTCATCGAAGCTTGGTACATGGATGACAGTGAAGAGGACCAGAGGCTTCCTCATCATCGTGAGCCCAAAGAATTCATTCCTCTTA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtgggttatacctgtttctacttgttctgaagtatgttgtccattgctaatttagGATGGCAAGGAGGAGGTCATCGAAGCTTGGTACATGGATGACAGTGAAGAGGACCAGAGGCTTCCTCATCATCGTGAGCCCAAAGAATTCATTCCTCTTA
                                            tgctaat  putative branch site (score: 190)
                                               taattta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gatacaacgtaaattatgttagatgtttaaactagacctcagatagtgggttatacctgtttctacttgttctgaagtatgttgtccattgctaatttagGATGGCAAGGAGGAGGTCATCGAAGCTTGGTACATGGATGACAGTGAAGAGGACCAGAGGCTTCCTCATCATCGTGAGCCCAAAGAATTCATTCCTCTTA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
gatacaa
- - - - - - -ttatgtt
- - - - - - - - - - - - - - - - - - - - - - - - - - atacctg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - atgttgt