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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ggattgaaatattgaatggcccctaaatctatatatcggcatatatggttgtcatttggtacatctctgtctgaagttgtttatatttttatatccttagATCAACAGTCTTATTGGAACCAAGGTGGAGTGGGTCTATCATATGTTACAAGCATTCAACACCGGCAACCTAGCTCTCTACCAAGAACTATGTAGGGTCC

Basic information

species Oryza sativa
transcript LOC_Os03g11570.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g11570.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G083076_T03 (Zea mays), 3'ss of exon 4
ggattgaaatattgaatggcccctaaatctatatatcggcatatatggttgtcatttggtacatctctgtctgaagt-tgtttatatttt-tatatccttagATCAACAGTCTTATTGGAACCAAGGTGGAGTGGGTCTATCATATGTTACAAGCATTCAACACCGGCAACCTAGCTCTCTACCAAGAACTATGTAGGGTCC
  |   |  | || | |    | | | |  ||  |   | | || |  |||| ||||| ||| |  |  |   |  |   |||||||| | | || ||||||||||| ||||||||||||||||||||||||||||| |||||||||||||||||||||||||| |||||||| ||| ||||||||||||| || ||||| |
atacaaaccttttaattaaatcatgactagat-cactagaacatttt-ttgtgatttgatactttgccctaaaacttacttttatattatatgtacccttagATCAATAGTCTTATTGGAACCAAGGTGGAGTGGGTTTATCATATGTTACAAGCATTCAACACGGGCAACCTTGCTTTCTACCAAGAACTTTGCAGGGTTC

upper sequence: LOC_Os03g11570.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM5G868757_T04 (Zea mays), 3'ss of exon 4
ggattgaaatattgaatggcccctaaatc-tat-atatcggca-tatatggttgtcatttggtacatctctgtctgaagttgtttatatttttatatccttagATCAACAGTCTTATTGGAACCAAGGTGGAGTGGGTCTATCATATGTTACAAGCATTCAACACCGGCAACCTAGCTCTCTACCAAGAACTATGTAGGGTCC
 | ||||    | ||   |||  | ||||  || ||| |   | ||| |  |||| ||||| ||| ||| ||    ||    ||||  ||| | || ||||||||||| |||||||||||||| |||||||||||||| ||||||||||||||||||||||||| ||||||||| || |||||||||||||| || ||||| |
-gtttgagtgttcgacatgccttttaatcacatcataactatagtatttttttgtgatttgatacttctttggtctaaa--atttagttttatgtacccttagATCAATAGTCTTATTGGAACTAAGGTGGAGTGGGTTTATCATATGTTACAAGCATTCAACAGCGGCAACCTTGCCCTCTACCAAGAACTTTGCAGGGTTC
















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|29673013|gb|CB669288.1|CB669288
EST:     TGCTTGGTGATAACATCTACAACTTTGGGGAATTGTTAGCTCACCCGATT                         ATCAACAGTCTTATTGGAACCAACGTGGAGTGGGTCTATCATATGTTACAA
genomic: TGCTTGGTGATAACATCTACAACTTTGGGGAATTGTTAGCTCACCCGATTgtaagttgga ... atatccttagATCAACAGTCTTATTGGAACCAAGGTGGAGTGGGTCTATCATATGTTACAA
EST: gi|396941592|gb|HO188249.1|HO188249
EST:     GTTAGCTCACCCGATT                         ATCAACAGTCTTATTGGAACCAAGGTAGAGTGGGTCTATCATATG-TANCA
genomic: GTTAGCTCACCCGATTgtaagttgga ... atatccttagATCAACAGTCTTATTGGAACCAAGGTGGAGTGGGTCTATCATATGTTA-CA
EST: gi|40492914|gb|BX900508.1|BX900508
EST:     TGCTTGGTGATAACATCTACAACTTTGGGGAATTGTTAGCTCACCCGATT                         ATCAACAGTCTTATTGGAACCAAGGTAGAGTGGGTCTATCATATGTTACAA
genomic: TGCTTGGTGATAACATCTACAACTTTGGGGAATTGTTAGCTCACCCGATTgtaagttgga ... atatccttagATCAACAGTCTTATTGGAACCAAGGTGGAGTGGGTCTATCATATGTTACAA
EST: gi|428304|gb|D24452.1|D24452
EST:     GCTTGGTGATAACATCTACAACTTTGGGGAATTGTTAGCTCACCCCGATT                         ATCAACAGTCTTATTGGGAACCAAGGTGGAGTTGGGTCTATCATATGGTT
genomic: GCTTGGTGATAACATCTACAACTTTGGGGAATTGTTAGCTCACCC-GATTgtaagttgga ... atatccttagATCAACAGTCTTATTGG-AACCAAGGTGGAGT-GGGTCTATCATATG-TT
EST: gi|19425283|gb|D41570.2|D41570
EST:     TGCTTGGTGATAACATCTACAACTTTGGGGAATTGTTAGCTCACCCGATT                         ATCAACAGTCTTATTGGAACCAAGGTGGAGTNGGGTCTATCATATGTTACA
genomic: TGCTTGGTGATAACATCTACAACTTTGGGGAATTGTTAGCTCACCCGATTgtaagttgga ... atatccttagATCAACAGTCTTATTGGAACCAAGGTGGAGT-GGGTCTATCATATGTTACA
EST: gi|11443013|gb|BF430900.1|BF430900
EST:     TGCTTGGTGATAACATCTACAACTTTGGGGAATTGTTAGCTCACCCGATT                         ATCAACAGTCTTATTGGGACCAAGGT
genomic: TGCTTGGTGATAACATCTACAACTTTGGGGAATTGTTAGCTCACCCGATTgtaagttgga ... atatccttagATCAACAGTCTTATTGGAACCAAGGT
EST: gi|117217002|gb|CT845303.1|CT845303
EST:     TGCTTGGTGATAACATCTACAACTTTGGGGAATTGTTAGCTCACCCGATT                         ATCAACAGTCTTATTGGAACCAAGGTAGAGTGGGTCTATCATATGTTACAA
genomic: TGCTTGGTGATAACATCTACAACTTTGGGGAATTGTTAGCTCACCCGATTgtaagttgga ... atatccttagATCAACAGTCTTATTGGAACCAAGGTGGAGTGGGTCTATCATATGTTACAA
EST: gi|428076|gb|D24224.1|D24224
EST:     TGCTTGGTGATAACATCTACAACTTTGGGGAATTGTTAGCTCACCCGATT                         ATCAACAGTCTTATTGGNACCAAGGTGGAGTGGGTCTATCATATGTTACAA
genomic: TGCTTGGTGATAACATCTACAACTTTGGGGAATTGTTAGCTCACCCGATTgtaagttgga ... atatccttagATCAACAGTCTTATTGGAACCAAGGTGGAGTGGGTCTATCATATGTTACAA

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: 73 (upstream exon), 74 (downstream exon)
Score: 33

GATTTGGCATTTGATCTCTCCCTTGCAGCCTTGCTTGGTGATAACATCTACAACTTTGGGGAATTGTTAGCTCACCCGATTgtaagttgga ... atatccttagATCAACAGTCTTATTGGAACCAAGGTGGAGTGGGTCTATCATATGTTACAAGCATTCAACACCGGCAACCTAGCTCTCTACCAAGAACTATGTAGGGTCC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tggttgtcatttggtacatctctgtctgaagttgtttatatttttatatccttagATCAACAGTCTTATTGGAACCAAGGTGGAGTGGGTCTATCATATGTTACAAGCATTCAACACCGGCAACCTAGCTCTCTACCAAGAACTATGTAGGGTCC
                                        tttttat  CT-rich tract
                          tgaagttgtttatatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ggattgaaatattgaatggcccctaaatctatatatcggcatatatggttgtcatttggtacatctctgtctgaagttgtttatatttttatatccttagATCAACAGTCTTATTGGAACCAAGGTGGAGTGGGTCTATCATATGTTACAAGCATTCAACACCGGCAACCTAGCTCTCTACCAAGAACTATGTAGGGTCC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC
- - - - - - tgaatgg
- - - - - - - - - - - - - - - - - - - - - - atggttg
- - - - - - - - - - - - - - - - - - - - - - - - - -tcatttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gttgttt