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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatcccctcctccgaaccccccctcctcttccttgccgtgccctcttgggttatccaggtcctaacgaagaatctctctctgtgcgtgcttgtttggttgcagCATATGCAGGACGAGGACGCCGGCCGGCCGTACAGGAAGTTTCTGTGAGTGCTGCCTCCGGTGGATGCCTCGAGACTGCGACCGGGAGAAGGACTCTCCG

Basic information

species Oryza sativa
transcript LOC_Os01g54730.1
intron # 1
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|88466667|gb|CI542244.1|CI542244
EST:     TCGGACTCGCCGTCCCCATCCTCGTCTACAAGGGCATCGTCCGCGAATTC                         CATATGCAGGACGAGGACGCCGGCCGGCCGTACAGGAAGTTTCTGTGAGTG
genomic: TCGGACTCGCCGTCCCCATCCTCGTCTACAAGGGCATCGTCCGCGAATTCgtaatcccct ... ttggttgcagCATATGCAGGACGAGGACGCCGGCCGGCCGTACAGGAAGTTTCTGTGAGTG
EST: gi|88975483|gb|CI023734.1|CI023734
EST:     TCGGACTCGCCGTCCCCATCCTCGTCTACAAGGGCATCGTCCGCGAATTC                         CATATGCAGGACGAGGACGCCGGCCGGCCGTACAGGAAGTTTCTGTGAGTG
genomic: TCGGACTCGCCGTCCCCATCCTCGTCTACAAGGGCATCGTCCGCGAATTCgtaatcccct ... ttggttgcagCATATGCAGGACGAGGACGCCGGCCGGCCGTACAGGAAGTTTCTGTGAGTG
EST: gi|88529609|gb|CI457944.1|CI457944
EST:     TCGGACTCGCCGTCCCCATCCTCGTGTACAAGGGCATCGTCCGCGAATTC                         CATATGCAGGACGAGGACGCCGGCCGGCCGTACAGGAAGTTTCTGTGAGTG
genomic: TCGGACTCGCCGTCCCCATCCTCGTCTACAAGGGCATCGTCCGCGAATTCgtaatcccct ... ttggttgcagCATATGCAGGACGAGGACGCCGGCCGGCCGTACAGGAAGTTTCTGTGAGTG
EST: gi|33657190|gb|CF279804.1|CF279804
EST:     GACTCGCCGTCCCCATCCTCGTTTACAAGGGCATCGTCCGCGAATTC                         CATATGCAGGACGAGGACGCCGGCCGGCCGTACAGGAAGTTTCTGTGAGTG
genomic: GACTCGCCGTCCCCATCCTCGTCTACAAGGGCATCGTCCGCGAATTCgtaatcccct ... ttggttgcagCATATGCAGGACGAGGACGCCGGCCGGCCGTACAGGAAGTTTCTGTGAGTG
EST: gi|88513285|gb|CI440791.1|CI440791
EST:     TCGGACTCGCCGTCCCCATCCTCGTCTACAAGGGCATCGTCCGCGAATTC                         CATATGCAGGACGAGGACGCCGGCCGGCCGTACAGGAAGTTTCTGTGAGTG
genomic: TCGGACTCGCCGTCCCCATCCTCGTCTACAAGGGCATCGTCCGCGAATTCgtaatcccct ... ttggttgcagCATATGCAGGACGAGGACGCCGGCCGGCCGTACAGGAAGTTTCTGTGAGTG
EST: gi|88511372|gb|CI438878.1|CI438878
EST:     TCGGACTCGCCGTCCCCATCCTCGTCTACAAGGGCATCGTCCGCGAATTC                         CATATGCAGGACGAGGACGCCGGCCGGCCGTACAGGAAGTTTCTGTGAGTG
genomic: TCGGACTCGCCGTCCCCATCCTCGTCTACAAGGGCATCGTCCGCGAATTCgtaatcccct ... ttggttgcagCATATGCAGGACGAGGACGCCGGCCGGCCGTACAGGAAGTTTCTGTGAGTG
EST: gi|11233370|gb|AU164782.1|AU164782
EST:     TCGGACTCGCCGTCCCCATCCTCGTCTACAAGGGCATCGTCCGCGAATTC                         CATATGCAGGACGAGGACGCCGGCCGGCCGTACAGGAAGTTTCTGTGAGTN
genomic: TCGGACTCGCCGTCCCCATCCTCGTCTACAAGGGCATCGTCCGCGAATTCgtaatcccct ... ttggttgcagCATATGCAGGACGAGGACGCCGGCCGGCCGTACAGGAAGTTTCTGTGAGTG
EST: gi|89171288|gb|CI040565.1|CI040565
EST:     TCGGACTCGCCGTCCCCATCCTCGTCTACAAGGGCATCGTCCGCGAATTC                         CATATGCAGGACGAGGACGCCGGCCGGCCGTACAGGAAGTTTCTGTGAGTG
genomic: TCGGACTCGCCGTCCCCATCCTCGTCTACAAGGGCATCGTCCGCGAATTCgtaatcccct ... ttggttgcagCATATGCAGGACGAGGACGCCGGCCGGCCGTACAGGAAGTTTCTGTGAGTG
EST: gi|88323083|gb|CI550762.1|CI550762
EST:     TCGGACTCGCCGTCCCCATCCTCGTCTACAAGGGCATCGTCCGCGAATTC                         CATATGCAGGACGAGGACGCCGGCCGGCCGTACAGGAAGTTTCTGTGAGTG
genomic: TCGGACTCGCCGTCCCCATCCTCGTCTACAAGGGCATCGTCCGCGAATTCgtaatcccct ... ttggttgcagCATATGCAGGACGAGGACGCCGGCCGGCCGTACAGGAAGTTTCTGTGAGTG
EST: gi|88385130|gb|CI561786.1|CI561786
EST:     TCGGACTCGCCGTCCCCATCCTCGTCTACAAGGGCATCGTCCGCGAATTC                         CATATGCAGGACGAGGACGCCGGCCGGCCGTACAGGAAGTTTCTGTGAGTG
genomic: TCGGACTCGCCGTCCCCATCCTCGTCTACAAGGGCATCGTCCGCGAATTCgtaatcccct ... ttggttgcagCATATGCAGGACGAGGACGCCGGCCGGCCGTACAGGAAGTTTCTGTGAGTG
EST: gi|86530443|gb|CI170649.1|CI170649
EST:     TCGGACTCGCCGTCCCCATCCTCGTCTACAAGGGCATCGTCCGCGAATTC                         CATATGCAGGACGAGGACGCCGGCCGGCCGTACAGGAAGTTTCTGTGAGTG
genomic: TCGGACTCGCCGTCCCCATCCTCGTCTACAAGGGCATCGTCCGCGAATTCgtaatcccct ... ttggttgcagCATATGCAGGACGAGGACGCCGGCCGGCCGTACAGGAAGTTTCTGTGAGTG
EST: gi|88284752|gb|CI406198.1|CI406198
EST:     TCGGACTCGCCGTCCCCATCCTCGTCTACAAGGGCATCGTCCGCGAATTC                         CATATGCAGGACGAGGACGCCGGCCGGCCGTACAGGAAGTTTCTGTGAGTG
genomic: TCGGACTCGCCGTCCCCATCCTCGTCTACAAGGGCATCGTCCGCGAATTCgtaatcccct ... ttggttgcagCATATGCAGGACGAGGACGCCGGCCGGCCGTACAGGAAGTTTCTGTGAGTG
EST: gi|88266857|gb|CI368633.1|CI368633
EST:     TCGGACTCGCCGTCCCCATCCTCGTCTACAAGGGCATCGTCCGCGAATTC                         CATACGCAGGACGA-GACGCCGGCCGGCCGTACAGGAAGTTTCTGTGAGTG
genomic: TCGGACTCGCCGTCCCCATCCTCGTCTACAAGGGCATCGTCCGCGAATTCgtaatcccct ... ttggttgcagCATATGCAGGACGAGGACGCCGGCCGGCCGTACAGGAAGTTTCTGTGAGTG
EST: gi|88276720|gb|CI397522.1|CI397522
EST:     TCGGACTCGCCGTCCCCATCCTCGTCTACAAGGGCATCGTCCGCGAATTC                         CATATGCAGGACGAGGACGCCGGCCGGCCGTACAGGAAGTTTCTGTGAGTG
genomic: TCGGACTCGCCGTCCCCATCCTCGTCTACAAGGGCATCGTCCGCGAATTCgtaatcccct ... ttggttgcagCATATGCAGGACGAGGACGCCGGCCGGCCGTACAGGAAGTTTCTGTGAGTG
EST: gi|3762033|gb|C99281.1|C99281
EST:     TCGGACTCGCCGTCCCCATCCTCGTCTACAAGGGCATCGTCCGCGAATTC                         CATATGCAGGACGAGGACGCCGGCCGGCCGTACAGGAAGTTTCTGTGAGTG
genomic: TCGGACTCGCCGTCCCCATCCTCGTCTACAAGGGCATCGTCCGCGAATTCgtaatcccct ... ttggttgcagCATATGCAGGACGAGGACGCCGGCCGGCCGTACAGGAAGTTTCTGTGAGTG
EST: gi|88986272|gb|CI033552.1|CI033552
EST:     GGCATCGTCCGCGAATTC                         CATATGCAGGACGAGGACGCCGGCCGGCCGTACAGGAAGTTTCTGTGAGTG
genomic: GGCATCGTCCGCGAATTCgtaatcccct ... ttggttgcagCATATGCAGGACGAGGACGCCGGCCGGCCGTACAGGAAGTTTCTGTGAGTG
EST: gi|88560920|gb|CI491624.1|CI491624
EST:     TCGGACTCGCCGTCCCCATCCTCGTCTACAAGGGCATCGTCCGCGAATTC                         CATATGCAGGACGAGGACGCCGGCCGGCCGTACAGGAAGTTTCTGTGAGTG
genomic: TCGGACTCGCCGTCCCCATCCTCGTCTACAAGGGCATCGTCCGCGAATTCgtaatcccct ... ttggttgcagCATATGCAGGACGAGGACGCCGGCCGGCCGTACAGGAAGTTTCTGTGAGTG
EST: gi|27578041|gb|CB000736.1|CB000736
EST:     TCGGACTCGCCGTCCCCATCCTCGTCTACAAGGGCATCGTCCGCGAATTC                         CATATGCAGGACGAGGACGCCGGCCGGCCGTACAGGAAGTTTCTGTGAGTG
genomic: TCGGACTCGCCGTCCCCATCCTCGTCTACAAGGGCATCGTCCGCGAATTCgtaatcccct ... ttggttgcagCATATGCAGGACGAGGACGCCGGCCGGCCGTACAGGAAGTTTCTGTGAGTG
EST: gi|88297276|gb|CI545366.1|CI545366
EST:     TCGGACTCGCCGTCCCCATCCTCGTCTACAAGGGCATCGTCCGCGAATTC                         CATATGCAGGACGAGGACGCCGGCCGGCCGTACAGGAAGTTTCTGTGAGTG
genomic: TCGGACTCGCCGTCCCCATCCTCGTCTACAAGGGCATCGTCCGCGAATTCgtaatcccct ... ttggttgcagCATATGCAGGACGAGGACGCCGGCCGGCCGTACAGGAAGTTTCTGTGAGTG
EST: gi|88558686|gb|CI489197.1|CI489197
EST:     TCGGACTCGCCGTCCCCATCCTCGTCTACAAGGGCATCGTCCGCGAATTC                         CATATGCAGGACGAGGACGCCGGCCGGCCGTACAGGAAGTTTCTGTGAGTG
genomic: TCGGACTCGCCGTCCCCATCCTCGTCTACAAGGGCATCGTCCGCGAATTCgtaatcccct ... ttggttgcagCATATGCAGGACGAGGACGCCGGCCGGCCGTACAGGAAGTTTCTGTGAGTG
EST: gi|88523105|gb|CI450907.1|CI450907
EST:     TCGGACTCGCCGTCCCCATCCTCGTCTACAAGGGCATCGTCCGCGAATTC                         CATATGCAGGACGAGGACGCCGGCCGGCCGTACAGGAAGTTTCTGTGAGTG
genomic: TCGGACTCGCCGTCCCCATCCTCGTCTACAAGGGCATCGTCCGCGAATTCgtaatcccct ... ttggttgcagCATATGCAGGACGAGGACGCCGGCCGGCCGTACAGGAAGTTTCTGTGAGTG
EST: gi|88210728|gb|CI210577.1|CI210577
EST:     TCGGACTCGCCGTCCCCATCCTCGTCTACAAGGGCATCGTCCGCGAATTC                         CATATGCAGGACGAGGACGCCGGCCGGCCGTACAGGAAGTTTCTGTGAGTG
genomic: TCGGACTCGCCGTCCCCATCCTCGTCTACAAGGGCATCGTCCGCGAATTCgtaatcccct ... ttggttgcagCATATGCAGGACGAGGACGCCGGCCGGCCGTACAGGAAGTTTCTGTGAGTG
EST: gi|88323650|gb|CI556281.1|CI556281
EST:     TCGGACTCGCCGTCCCCATCCTCGTCTACAAGGGCATCGTCCGCGAATTC                         CATATGCAGGACGAGGACGCCGGCCGGCCGTACAGGAAGTTTCTGTGAGTG
genomic: TCGGACTCGCCGTCCCCATCCTCGTCTACAAGGGCATCGTCCGCGAATTCgtaatcccct ... ttggttgcagCATATGCAGGACGAGGACGCCGGCCGGCCGTACAGGAAGTTTCTGTGAGTG
EST: gi|89170616|gb|CI039893.1|CI039893
EST:     TCGGACTCGCCGTCCCCATCCTCGTCTACAAGGGCATCGTCCGCGAATTC                         CATATGCAGGACGAGGACGCCGGCCGGCCGTACAGGAAGTTTCTGTGAGTG
genomic: TCGGACTCGCCGTCCCCATCCTCGTCTACAAGGGCATCGTCCGCGAATTCgtaatcccct ... ttggttgcagCATATGCAGGACGAGGACGCCGGCCGGCCGTACAGGAAGTTTCTGTGAGTG
EST: gi|88282299|gb|CI403695.1|CI403695
EST:     TCGGACTCGCCGTCCCCATCCTCGTCTACAAGGGCATCGTCCGCGAATTC                         CATATGCAGGACGAGGACGCCGGCCGGCCGTACAGGAAGTTTCTGTGAGTG
genomic: TCGGACTCGCCGTCCCCATCCTCGTCTACAAGGGCATCGTCCGCGAATTCgtaatcccct ... ttggttgcagCATATGCAGGACGAGGACGCCGGCCGGCCGTACAGGAAGTTTCTGTGAGTG
EST: gi|88448995|gb|CI558067.1|CI558067
EST:     TCGGACTCGCCGTCCCCATCCTCGTCTACAAGGGCATCGTCCGCGAATTC                         CATATGCAGGACGAGGACGCCGGCCGGCCGTACAGGAAGTTTCTGTGAGTG
genomic: TCGGACTCGCCGTCCCCATCCTCGTCTACAAGGGCATCGTCCGCGAATTCgtaatcccct ... ttggttgcagCATATGCAGGACGAGGACGCCGGCCGGCCGTACAGGAAGTTTCTGTGAGTG
EST: gi|86597273|gb|CI280410.1|CI280410
EST:     TCGGACTCGCCGTCCCCATCCTCGTCTACAAGGGCATCGTCCGCGAATTC                         CATATGCAGGACGAGGACGCCGGCCGGCCGTACAGGAAGTTTCTGTGAGTG
genomic: TCGGACTCGCCGTCCCCATCCTCGTCTACAAGGGCATCGTCCGCGAATTCgtaatcccct ... ttggttgcagCATATGCAGGACGAGGACGCCGGCCGGCCGTACAGGAAGTTTCTGTGAGTG

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: 74 (upstream exon), 75 (downstream exon)
Score: 41

CGAGTTCAACTTCCGCTGGACCCGCCGCAGCCTCGCCGTCGTCGGCCTCTTCGGACTCGCCGTCCCCATCCTCGTCTACAAGGGCATCGTCCGCGAATTCgtaatcccct ... ttggttgcagCATATGCAGGACGAGGACGCCGGCCGGCCGTACAGGAAGTTTCTGTGAGTGCTGCCTCCGGTGGATGCCTCGAGACTGCGACCGGGAGAAGGACTCTCCG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggttatccaggtcctaacgaagaatctctctctgtgcgtgcttgtttggttgcagCATATGCAGGACGAGGACGCCGGCCGGCCGTACAGGAAGTTTCTGTGAGTGCTGCCTCCGGTGGATGCCTCGAGACTGCGACCGGGAGAAGGACTCTCCG
           tcctaac  putative branch site (score: 41)
                                        cttgttt  putative PPT
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaatcccctcctccgaaccccccctcctcttccttgccgtgccctcttgggttatccaggtcctaacgaagaatctctctctgtgcgtgcttgtttggttgcagCATATGCAGGACGAGGACGCCGGCCGGCCGTACAGGAAGTTTCTGTGAGTGCTGCCTCCGGTGGATGCCTCGAGACTGCGACCGGGAGAAGGACTCTCCG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA