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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTTACCGTTGGGCAGTTTGTCTATGTTGTTCGGAAGCGGATCAAGCTCAGTCCTGAGAAAGCAATCTTCATCTTTGTGAAGAATACTCTTCCACCAACAGgtctgaaaatcccttgaatcattttcctttgaaaacacaaggactttggtcgaatagtatactactgcatggtttatgatcccagtatctcaaagaacctgcatggttcatgttatctcatttcatcactttgttggatttgcag

Basic information

species Oryza sativa
transcript LOC_Os04g53240.2
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g53240.2 (Oryza sativa), 5'ss of exon 6
lower sequence: GRMZM2G419694_T05 (Zea mays), 5'ss of exon 5
CTTACCGTTGGGCAGTTTGTCTATGTTGTTCGGAAGCGGATCAAGCTCAGTCCTGAGAAAGCAATCTTCATCTTTGTGAAGAATACTCTTCCACCAACAGgtctgaaaatcccttgaatcattttcctttgaaaacacaaggactttggtcgaatagtatactactgcatggtttatgatcccagtatctcaaagaacctgcatggttcatgttatctcatttca-tcactttgttggatt--tgcag
||||| || ||||| || || ||||||||| ||||| | |||||||||||| ||||||| || |||||||| |||||||| || || |||||||||||||||||| |||  |  || |            ||||  ||| |  |||  | |      | |  |  ||| |  | || || |  |   | |    | ||  | ||  |   | | |  | |||| | |  |||  ||| |    |||||
CTTACAGTCGGGCAATTCGTGTATGTTGTTAGGAAGAGAATCAAGCTCAGTGCTGAGAAGGCTATCTTCATATTTGTGAAAAACACCCTTCCACCAACAGgtctggaaagtcaatgca------------gaaacaacatgctcttctgac------tctgattttgcttcctataagaactgatggtattcggggacacg-atcctcattctcacttgattttacttgcttgcttgtacccgtgcag

upper sequence: LOC_Os04g53240.2 (Oryza sativa), 5'ss of exon 6
lower sequence: GRMZM2G076826_T01 (Zea mays), 5'ss of exon 6
CTTACCGTTGGGCAGTTTGTCTATGTTGTTCGGAAGCGGATCAAGCTCAGTCCTGAGAAAGCAATCTTCATCTTTGTGAAGAATACTCTTCCACCAACAGgtctgaaaatccctt---gaatcattttcctttgaaaacacaaggactttggtcgaatagt--atactact------gcat---ggtttatgatcccagtatctcaaagaacctgcatggttcatgttatctcatttca-tcactttgttggatttgcag--
||||| ||||| || || || ||||||||| ||||| | |||||||||||| |||||||||| |||||||||||||||||||| || |||||||||||||||||| |||     |   ||  ||   | |||   |  |  |      ||  |  || | |  ||   | |      ||||   ||   ||||||||     ||||    | ||   | |    | | |  | |||| | |  |||   || |  ||     
CTTACGGTTGGACAATTCGTGTATGTTGTTAGGAAGAGAATCAAGCTCAGTGCTGAGAAAGCTATCTTCATCTTTGTGAAGAACACCCTTCCACCAACAGgtctggaaaataaatacagagacaacatacttctgactctgattttgcttcctataagaattgatggcattcgttgagcatttggggacatgatcccccatcctcacttgatcttacttgcat-tctcacttgattttacttgcttccctgaacctgtgcag

upper sequence: LOC_Os04g53240.2 (Oryza sativa), 5'ss of exon 6
lower sequence: Vv19s0090g00580.t01 (Vitis vinifera), 5'ss of exon 5
CTTACCGTTGGGCAGTTTGTCTATGTTGTTCGGAAGCGGATCAAGCTCAGTCCTGAGAAAGCAATCTTCATCTTTGTGAAGAATACTCTTCCACCAACAGgtctgaaaatcccttgaatcattttcctttgaaaacacaaggactttggtcgaatagtata-ctactgca-tggtttatgatcccagtatctcaaagaacctgcatggttcatgttatctcatttcatcactttgttggatttgcag
|| || |||||||||||||| |||||  | |||||| |||||||||| ||| ||||||| || || ||||| ||||| ||||||  ||| ||||| || |||  ||||            | || | ||| || |  |||  ||     |||| |  | ||  | ||| |    ||||| ||     ||| |  |   |  || ||  ||  ||||||| ||                         
CTGACTGTTGGGCAGTTTGTTTATGTGATCCGGAAGAGGATCAAGCTTAGTGCTGAGAAGGCTATTTTCATTTTTGTCAAGAATGTTCTACCACCCACTGgtgagaaag-----------aattcctttttaatattcaaatacacatatcga-tgatgtagtttctgtaactatttattatt----tatattcatttatttgtat--tttgtgttatcacag------------------------

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|33655349|gb|CF277963.1|CF277963
EST:     TCCTGAGAAAGCAATCTTCATCTTTGTGAAGAATACTCTTCCACCAACAG                         CTGCTCTGATGTCCGCAATTTACGAGGAGAACAAGGATGAGGATGGGTTCC
genomic: TCCTGAGAAAGCAATCTTCATCTTTGTGAAGAATACTCTTCCACCAACAGgtctgaaaat ... ggatttgcagCTGCTCTGATGTCCGCAATTTACGAGGAGAACAAGGATGAGGATGGGTTCC
EST: gi|14981112|gb|BI305803.1|BI305803
EST:     TCCTGAGAAAGCAATCTTCATCTTTGTGAAGAATACTCTTCCACCAACAG                         CTGCTCTGATGTCCGCAATTTACGAGGAGAACAAGGATGAGGATGGGTTCC
genomic: TCCTGAGAAAGCAATCTTCATCTTTGTGAAGAATACTCTTCCACCAACAGgtctgaaaat ... ggatttgcagCTGCTCTGATGTCCGCAATTTACGAGGAGAACAAGGATGAGGATGGGTTCC
EST: gi|33670400|gb|CF298639.1|CF298639
EST:     TCCTGAGAAAGCAATTTTCATCTTTGTGAAGAATACTCTTCCACCAACAG                         CTGCTTTGATGTCCGCAATTTACGAGGAGAACAAGGATGAGGATGGGTTCC
genomic: TCCTGAGAAAGCAATCTTCATCTTTGTGAAGAATACTCTTCCACCAACAGgtctgaaaat ... ggatttgcagCTGCTCTGATGTCCGCAATTTACGAGGAGAACAAGGATGAGGATGGGTTCC
EST: gi|33663415|gb|CF294382.1|CF294382
EST:     TCCTGAGAAAGCAATCTTCATCTTTGTGAAGAATACTCTTCCACCAACAG                         CTGCTTTGATGTCCGCAATTTACGAGGAGAACAAGGATGAGGATGGGTTCC
genomic: TCCTGAGAAAGCAATCTTCATCTTTGTGAAGAATACTCTTCCACCAACAGgtctgaaaat ... ggatttgcagCTGCTCTGATGTCCGCAATTTACGAGGAGAACAAGGATGAGGATGGGTTCC
EST: gi|88365198|gb|CI540510.1|CI540510
EST:     TCCTGAGAAAGCAATCTTCATCTTTGTGAAGAATACTCTTCCACCAACAG                         CTGCTCTGATGTCCGCAATTTACGAGGAGAACAAGGATGAGGATGGGTTCC
genomic: TCCTGAGAAAGCAATCTTCATCTTTGTGAAGAATACTCTTCCACCAACAGgtctgaaaat ... ggatttgcagCTGCTCTGATGTCCGCAATTTACGAGGAGAACAAGGATGAGGATGGGTTCC
EST: gi|89179617|gb|CI391950.1|CI391950
EST:     TCCTGAGAAAGCAATCTTCATCTTT-TGAAGAATACTCTTCCACCAACAG                         CTGCTCTGATGTCCGCAATTTACGAGGAGAACAAGGATGAGGATGGGTTCC
genomic: TCCTGAGAAAGCAATCTTCATCTTTGTGAAGAATACTCTTCCACCAACAGgtctgaaaat ... ggatttgcagCTGCTCTGATGTCCGCAATTTACGAGGAGAACAAGGATGAGGATGGGTTCC
EST: gi|86822106|gb|CI357784.1|CI357784
EST:     TCCTGAGAAAGCAATCTTCATCTTTGTGAAGAATACTCTTCCACCAACAG                         CTGCTCTGATGTCCGCAATTTACGAGGAGAACAAGGATGAGGATGGGTTCC
genomic: TCCTGAGAAAGCAATCTTCATCTTTGTGAAGAATACTCTTCCACCAACAGgtctgaaaat ... ggatttgcagCTGCTCTGATGTCCGCAATTTACGAGGAGAACAAGGATGAGGATGGGTTCC
EST: gi|86418393|gb|CI032602.1|CI032602
EST:     TCCTGAGAAAGCAATCTTCATCTTTGTGAAGAATACTCTTCCACCAACAG                         CTGCTCTGATGTCCGCAATTTACGAGGAGAACAAGGATGAGGATGGGTTCC
genomic: TCCTGAGAAAGCAATCTTCATCTTTGTGAAGAATACTCTTCCACCAACAGgtctgaaaat ... ggatttgcagCTGCTCTGATGTCCGCAATTTACGAGGAGAACAAGGATGAGGATGGGTTCC
EST: gi|88477680|gb|CI414951.1|CI414951
EST:     TCCTGAGAAAGCAATCTTCATCTTTGTGAAGAATACTCTTCCACCAACAG                         CTGCTCTGATGTCCGCAATTTACGAGGAGAACAAGGATGAGGATGGGTTCC
genomic: TCCTGAGAAAGCAATCTTCATCTTTGTGAAGAATACTCTTCCACCAACAGgtctgaaaat ... ggatttgcagCTGCTCTGATGTCCGCAATTTACGAGGAGAACAAGGATGAGGATGGGTTCC
EST: gi|16575781|gb|BI803077.1|BI803077
EST:     TCCTGAGAAAGCAATCTTCATCTTTGTGAAGAATACTCTTCCACCAACAG                         CTGCTCTGATGTCCGCAATTTACGAGGAGAACAAGGATGAGGATGGGTTCC
genomic: TCCTGAGAAAGCAATCTTCATCTTTGTGAAGAATACTCTTCCACCAACAGgtctgaaaat ... ggatttgcagCTGCTCTGATGTCCGCAATTTACGAGGAGAACAAGGATGAGGATGGGTTCC
EST: gi|33655295|gb|CF277909.1|CF277909
EST:     TCCTGAGAAAGCAATCTTCATCTTTGTGAAGAATACTCTTCCACCAACAG                         CTGCTTTGATGTCCGCAATTTACGAGGAGAACAAGGATGAGGATGGGTTCC
genomic: TCCTGAGAAAGCAATCTTCATCTTTGTGAAGAATACTCTTCCACCAACAGgtctgaaaat ... ggatttgcagCTGCTCTGATGTCCGCAATTTACGAGGAGAACAAGGATGAGGATGGGTTCC
EST: gi|88996312|gb|CI389023.1|CI389023
EST:     TCCTGAGAAAGCAATCTTCATCTTTGTGAAGAATACTCTTCCACCAACAG                         CTACTCTGATGTCCGCAATTTACGAGGAGAACAAGGATGAGGATGGGTTCC
genomic: TCCTGAGAAAGCAATCTTCATCTTTGTGAAGAATACTCTTCCACCAACAGgtctgaaaat ... ggatttgcagCTGCTCTGATGTCCGCAATTTACGAGGAGAACAAGGATGAGGATGGGTTCC
EST: gi|38481968|gb|CF966032.1|CF966032
EST:     TCCTGAGAAAGCCATCTTCATCTTTGTGAAGAATACTCTTCCACCAACAG                         CTGCTCTGATGTCCGCCATTTACGAGGAGAACAAGGATGAGGATGGGTTCC
genomic: TCCTGAGAAAGCAATCTTCATCTTTGTGAAGAATACTCTTCCACCAACAGgtctgaaaat ... ggatttgcagCTGCTCTGATGTCCGCAATTTACGAGGAGAACAAGGATGAGGATGGGTTCC
EST: gi|33662335|gb|CF293302.1|CF293302
EST:     TCCTGAGAAAGCAATCTTCATCTTTGTGAAGAATACTCTTCCACCAACAG                         CTGCTCTGATGTCCGCAATTTACGAGGAGAACAAGGATGAGGATGGGTTCC
genomic: TCCTGAGAAAGCAATCTTCATCTTTGTGAAGAATACTCTTCCACCAACAGgtctgaaaat ... ggatttgcagCTGCTCTGATGTCCGCAATTTACGAGGAGAACAAGGATGAGGATGGGTTCC
EST: gi|33688345|gb|CF316584.1|CF316584
EST:     TCCTGAGAAAGCAATCTTCATCTTTGTGAAGAATACTCTTCCACCAACAG                         CTGCTCTGATGTCCGCAATTTACGAGGAGAACAAGGATGAGGATGGGTTCC
genomic: TCCTGAGAAAGCAATCTTCATCTTTGTGAAGAATACTCTTCCACCAACAGgtctgaaaat ... ggatttgcagCTGCTCTGATGTCCGCAATTTACGAGGAGAACAAGGATGAGGATGGGTTCC
EST: gi|86836082|gb|CI346147.1|CI346147
EST:     TCCTGAGAAAGCAATCTTCATCTTTGTGAAGAATACTCTTCCACCAACAG                         CTGCTCTGATGTCCGCAATTTACGAGGAGAACAAGGATGAGGATGGGTTCC
genomic: TCCTGAGAAAGCAATCTTCATCTTTGTGAAGAATACTCTTCCACCAACAGgtctgaaaat ... ggatttgcagCTGCTCTGATGTCCGCAATTTACGAGGAGAACAAGGATGAGGATGGGTTCC
EST: gi|88272085|gb|CI388138.1|CI388138
EST:     TCCTGAGAAAGCAATCTTCATCTTTGTGAAGAATACTCTTCCACCAACAG                         CTGCTCTGATGTCCGCAATTTACGAGGAGAACAAGGATGAGGATGGGTTCC
genomic: TCCTGAGAAAGCAATCTTCATCTTTGTGAAGAATACTCTTCCACCAACAGgtctgaaaat ... ggatttgcagCTGCTCTGATGTCCGCAATTTACGAGGAGAACAAGGATGAGGATGGGTTCC

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: 17 (upstream exon), 75 (downstream exon)
Score: 2

CTTACCGTTGGGCAGTTTGTCTATGTTGTTCGGAAGCGGATCAAGCTCAGTCCTGAGAAAGCAATCTTCATCTTTGTGAAGAATACTCTTCCACCAACAGgtctgaaaat ... ggatttgcagCTGCTCTGATGTCCGCAATTTACGAGGAGAACAAGGATGAGGATGGGTTCCTCTACATGACCTACAGTGGCGAGAACACCTTTGGGCTGCTCTAGGCGCG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTTACCGTTGGGCAGTTTGTCTATGTTGTTCGGAAGCGGATCAAGCTCAGTCCTGAGAAAGCAATCTTCATCTTTGTGAAGAATACTCTTCCACCAACAGgtctgaaaatcccttgaatcattttcctttgaaaacacaaggactttggtcgaatagtatactactgcatggtttatgatcccagtatctcaaagaacctgcatggttcatgttatctcatttcatcactttgttggatttgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA