Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttgctaagtaatcggtggtggcgatgttctgatgtattgttatttcgctgggtcattgttggctttgtttaaaatcggcttgcaacctgtttgtttgcagTACAAGGTGTGCTCGTGGATCGCTATCATCTTCTGCGCGCAGTCTCTGGTGAACATGAAGAATTTCGAGAATGATCTCAAGCAGTTATCCATGGCTTTCA

Basic information

species Oryza sativa
transcript LOC_Os03g54980.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g54980.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G023833_T01 (Zea mays), 3'ss of exon 1
ttgctaagtaatcggtggtggcgatgttctgatgtattgttatt-tcgctg-ggtcattgttggctttgtttaaaatcggcttgcaacctgttt--gtttgcagTACAAGGTGTGCTCGTGGATCGCTATCATCTTCTGCGCGCAGTCTCTGGTGAACATGAAGAATTTCGAGAATGATCTCAAGCAGTTATCCATGGCTTTCA
    |   | || |||| ||    ||   |  ||   || |    ||| |    |    ||| |   |   || |   |  ||  || |  |||  ||||||||||||||||||||||||||||||| |||||||||||||| |||||  |||  ||||||||||| || ||||| ||||| |||||| | || ||||| ||||
---attgatgat-ggtgttgtgcttgccttactgggctgctggcgtcgatataatttcggtttgtgctagctacatgtgaattctaatcgatttcggtttgcagTACAAGGTGTGCTCGTGGATCGCAATCATCTTCTGCGCTCAGTCGTTGGCAAACATGAAGAACTTTGAGAACGATCTGAAGCAGCTTTCTATGGCCTTCA

upper sequence: LOC_Os03g54980.1 (Oryza sativa), 3'ss of exon 1
lower sequence: EFJ10500 (Selaginella moellendorffii), 3'ss of exon 1
ttgctaagtaatcggtggtggcgatgttctgatgtattgttatttcgctgggtcattgttggctttg--tttaaaatcggcttgcaacctgtttgtttgcagTACAAGGTGTGCTCGTGGATCGCTATCATCTTCTGCGCGCAGTCTCTGGTGAACATGAAGAATTTCGAGAATGATCTCAAGCAGTTATCCATGGCTTTCA
                                              |   | | ||| |  |||| |  |||  |   ||    ||    | |    || || ||||| |  | |||||| | ||  |||| || |||||||| || || | ||||||||||||||| ||||| |||||||||||  |   ||||||  |  
----------------------------------------------gtgagttgattttgagcttggattttggagctggagctca--tagatctggtgtagAACAAGATCGGATCGTGGCTTGCCCTCATTTTTTGCGCGCAATCGCTCGCGAACATGAAGAATTTGGAGAACGATCTCAAGCAAGTGGTCATGGCACTGG

upper sequence: LOC_Os03g54980.1 (Oryza sativa), 3'ss of exon 1
lower sequence: EFJ19241 (Selaginella moellendorffii), 3'ss of exon 1
ttgctaagtaatcggtggtggcgatgttctgatgtattgttatttcgctgggtcattgttggctttg--tttaaaatcggcttgcaacctgtttgtttgcagTACAAGGTGTGCTCGTGGATCGCTATCATCTTCTGCGCGCAGTCTCTGGTGAACATGAAGAATTTCGAGAATGATCTCAAGCAGTTATCCATGGCTTTCA
                                                || || ||| |  |||| |  |||  |   ||    ||    | |    || || ||||| |  | |||||| ||||  |||| || |||||||| || || | ||||||||||||||| ||||| |||||||||||  |   ||||||  |  
-----------------------------------------------gtgagtgattttgagcttggattttggagctggagctca--tggatctggtgtagAACAAGATCGGATCGTGGCTCGCCCTCATTTTTTGCGCGCAATCGCTCGCGAACATGAAGAATTTGGAGAACGATCTCAAGCAAGTGGTCATGGCACTGG

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|88323611|gb|CI556242.1|CI556242
EST:     ACGCGGGGTTCCTCGCCGTCGTCTTCGGCGTCCTTGGCGTCATGCTCCGG                         TACAAGGTGTGCTCGTGGATCGCTATCATCTTCTGCGCGCAGTCTCTGGTG
genomic: ACGCGGGGTTCCTCGCCGTCGTCTTCGGCGTCCTCGGCGTCATGCTCCGGgtacggtatc ... ttgtttgcagTACAAGGTGTGCTCGTGGATCGCTATCATCTTCTGCGCGCAGTCTCTGGTG
EST: gi|87023978|gb|CI254542.1|CI254542
EST:     ACGCGGGGTTCCTCGCCGTCGTCTTCGGCGTCCTCGGCGTCATGCTCCGG                         TACAAGGTGTGCTCGTGGATCGCTATCATCTTCTGCGCGCAGTCTCTGGTG
genomic: ACGCGGGGTTCCTCGCCGTCGTCTTCGGCGTCCTCGGCGTCATGCTCCGGgtacggtatc ... ttgtttgcagTACAAGGTGTGCTCGTGGATCGCTATCATCTTCTGCGCGCAGTCTCTGGTG
EST: gi|88518450|gb|CI446104.1|CI446104
EST:     ACGCGGGGTTCCTCCCCGTCGTCTTCGGCGTCCTCGGCGTCATGCTCCGG                         TACAAGGTGTGCTCGTGGATCGCTATCATCTTCTGCGCGCAGTCTCTGGTG
genomic: ACGCGGGGTTCCTCGCCGTCGTCTTCGGCGTCCTCGGCGTCATGCTCCGGgtacggtatc ... ttgtttgcagTACAAGGTGTGCTCGTGGATCGCTATCATCTTCTGCGCGCAGTCTCTGGTG
EST: gi|88432140|gb|CI562971.1|CI562971
EST:     ACGCGGGGTTCCTCGCCGTCGTCTTCGGCGTCCTCGGCGTCATGCTCCGG                         TACAAGGTGTGCTCGTGGATCGCTATCATCTTCTGCGCGCAGTCTCTGGTG
genomic: ACGCGGGGTTCCTCGCCGTCGTCTTCGGCGTCCTCGGCGTCATGCTCCGGgtacggtatc ... ttgtttgcagTACAAGGTGTGCTCGTGGATCGCTATCATCTTCTGCGCGCAGTCTCTGGTG
EST: gi|88212823|gb|CI210674.1|CI210674
EST:     ACGCGGGGTTCCTCGCCGTCGTCTTCGGCGTCCTCGGCGTCATGCTCCGG                         TACAAGGTGTGCTCGTGGATCGCTATCATCTTCTGCGCGCAGTCTCTGGTG
genomic: ACGCGGGGTTCCTCGCCGTCGTCTTCGGCGTCCTCGGCGTCATGCTCCGGgtacggtatc ... ttgtttgcagTACAAGGTGTGCTCGTGGATCGCTATCATCTTCTGCGCGCAGTCTCTGGTG
EST: gi|86846588|gb|CI280885.1|CI280885
EST:     ACGCGGGGTTCCTCGCCGTCGTCTTCGGCGTCCTCGGCGTCATGCTCCGG                         TACAAGGTGTGCTCGTGGATCGCTATCATCTTCTGCGCGCAGTCTCTGGTG
genomic: ACGCGGGGTTCCTCGCCGTCGTCTTCGGCGTCCTCGGCGTCATGCTCCGGgtacggtatc ... ttgtttgcagTACAAGGTGTGCTCGTGGATCGCTATCATCTTCTGCGCGCAGTCTCTGGTG
EST: gi|87025902|gb|CI282479.1|CI282479
EST:     ACGCGGGGTTCCTCGCCGTCGTCTTCGGCGTCCTCGGCGTCATGCTCCGG                         TACAAGGTGTGCTCGTGGATCGCTATCATCTTCTGCGCGCAGTCTCTGGTG
genomic: ACGCGGGGTTCCTCGCCGTCGTCTTCGGCGTCCTCGGCGTCATGCTCCGGgtacggtatc ... ttgtttgcagTACAAGGTGTGCTCGTGGATCGCTATCATCTTCTGCGCGCAGTCTCTGGTG
EST: gi|86531447|gb|CI171653.1|CI171653
EST:     ACGCGGGGTTCCTCGCCGTCGTCTTCGGCGTCCTCGGCGTCATGCTCCGG                         TACAAGGTGTGCTCGTGGATCGCTATCATCTTCTGCGCGCAGTCTCTGGTG
genomic: ACGCGGGGTTCCTCGCCGTCGTCTTCGGCGTCCTCGGCGTCATGCTCCGGgtacggtatc ... ttgtttgcagTACAAGGTGTGCTCGTGGATCGCTATCATCTTCTGCGCGCAGTCTCTGGTG
EST: gi|86599143|gb|CI355760.1|CI355760
EST:     ACGCGGGGTTCCTCGCCGTCGTCTTCGGCGTCCTCGGCGTCATGGTCCGG                         TACAAGGTGTGCTCGTGGATCGCTATCATCTTCTGCGGGCAGTCTCTGGTG
genomic: ACGCGGGGTTCCTCGCCGTCGTCTTCGGCGTCCTCGGCGTCATGCTCCGGgtacggtatc ... ttgtttgcagTACAAGGTGTGCTCGTGGATCGCTATCATCTTCTGCGCGCAGTCTCTGGTG
EST: gi|88209099|gb|CI208948.1|CI208948
EST:     ACGCGGGGTTCCTCGCCGTCGTCTTCGGCGTCCTCGGCGTCATGCTCCGG                         TACAAGGTGTGCTCGTGGATCGCTATCATCTTCTGCGCGCAGTCTCTGGTG
genomic: ACGCGGGGTTCCTCGCCGTCGTCTTCGGCGTCCTCGGCGTCATGCTCCGGgtacggtatc ... ttgtttgcagTACAAGGTGTGCTCGTGGATCGCTATCATCTTCTGCGCGCAGTCTCTGGTG
EST: gi|88983305|gb|CI028542.1|CI028542
EST:     ACGCGGGGTTCCTCGCCGTCGTCTTCGGCGTCCTCGGCGTCATGCTCCGG                         TACAAGGTGTGCTCGTGGATCGCTATCATCTTCTGCGCGCAGTCTCTGGTG
genomic: ACGCGGGGTTCCTCGCCGTCGTCTTCGGCGTCCTCGGCGTCATGCTCCGGgtacggtatc ... ttgtttgcagTACAAGGTGTGCTCGTGGATCGCTATCATCTTCTGCGCGCAGTCTCTGGTG
EST: gi|44666211|gb|CR279645.1|CR279645
EST:     ACGCGGGGTTCCTCGCCGTCGTCTTCGGCGTCCTCGGCGTCATGCTCCGG                         TACAAGGTGTGCTCGTGGATCGCTATCATCTTCTGCGCGCAGTCTCTGGTG
genomic: ACGCGGGGTTCCTCGCCGTCGTCTTCGGCGTCCTCGGCGTCATGCTCCGGgtacggtatc ... ttgtttgcagTACAAGGTGTGCTCGTGGATCGCTATCATCTTCTGCGCGCAGTCTCTGGTG
EST: gi|86533465|gb|CI173671.1|CI173671
EST:     ACGCGGGGTTCCTCGCCGTCGTCTTCGGCGTCCTCGGCGTCATGCTCCGG                         TACAAGGTGTGCTCGTGGATCGCTATCATCTTCTGCGCGCAGTCTCTGGTG
genomic: ACGCGGGGTTCCTCGCCGTCGTCTTCGGCGTCCTCGGCGTCATGCTCCGGgtacggtatc ... ttgtttgcagTACAAGGTGTGCTCGTGGATCGCTATCATCTTCTGCGCGCAGTCTCTGGTG
EST: gi|87028616|gb|CI266015.1|CI266015
EST:     ACGCGGGGTTCCTCGCCGTCGTCTTCGGCGTCCTCGGCGTCATGCTCCGG                         TACAAGGTGTGCTCGTGGATCGCTATCATCTTCTGCGCGCAGTCTCTGGTG
genomic: ACGCGGGGTTCCTCGCCGTCGTCTTCGGCGTCCTCGGCGTCATGCTCCGGgtacggtatc ... ttgtttgcagTACAAGGTGTGCTCGTGGATCGCTATCATCTTCTGCGCGCAGTCTCTGGTG
EST: gi|86882394|gb|CI325802.1|CI325802
EST:     ACGCGGGGTTCCTCGCCGTCGTCTTCGGCGTCCTCGGCGTCATGCTCCGG                         TACAAGGTGTGCTCGTGGATCGCTATCATCTTCTGCGCGCAGTCTCTGGTG
genomic: ACGCGGGGTTCCTCGCCGTCGTCTTCGGCGTCCTCGGCGTCATGCTCCGGgtacggtatc ... ttgtttgcagTACAAGGTGTGCTCGTGGATCGCTATCATCTTCTGCGCGCAGTCTCTGGTG
EST: gi|88988868|gb|CI040600.1|CI040600
EST:     ACGCGGGGTTCCTCGCCGTCGTCTTCGGCGTCCTCGGCGTCATGCTCCGG                         TACAAGGTGTGCTCGTGGATCGCTATCATCTTCTGCGCGCAGTCTCTGGTG
genomic: ACGCGGGGTTCCTCGCCGTCGTCTTCGGCGTCCTCGGCGTCATGCTCCGGgtacggtatc ... ttgtttgcagTACAAGGTGTGCTCGTGGATCGCTATCATCTTCTGCGCGCAGTCTCTGGTG
EST: gi|88237206|gb|CI237055.1|CI237055
EST:     ACGCGGGGTTCCTCGCCGTCGTCTTCGGCGTCCTCGGCGTCATGCTCCGG                         TACAAGGTGTGCTCGTGGATCGCTATCATCTTCTGCGCGCAGTCTCTGGTG
genomic: ACGCGGGGTTCCTCGCCGTCGTCTTCGGCGTCCTCGGCGTCATGCTCCGGgtacggtatc ... ttgtttgcagTACAAGGTGTGCTCGTGGATCGCTATCATCTTCTGCGCGCAGTCTCTGGTG
EST: gi|88281726|gb|CI403122.1|CI403122
EST:     ACGCGGGGTTCCTCCCCGTCGTCTTCGGCGTCCTCGGCGTCATGCTCCGG                         TACAAGGTGTGCTCGTGGATCGCTATCATCTTCTGCGCGCAGTCTCTGGTG
genomic: ACGCGGGGTTCCTCGCCGTCGTCTTCGGCGTCCTCGGCGTCATGCTCCGGgtacggtatc ... ttgtttgcagTACAAGGTGTGCTCGTGGATCGCTATCATCTTCTGCGCGCAGTCTCTGGTG
EST: gi|88238517|gb|CI238366.1|CI238366
EST:     TCGGCGTCCTCGGCGTCATGCTCCGG                         TACAAGGTGTGCTCGTGGATCGCTATCATCTTCTGCGCGCAGTCTCTGGTG
genomic: TCGGCGTCCTCGGCGTCATGCTCCGGgtacggtatc ... ttgtttgcagTACAAGGTGTGCTCGTGGATCGCTATCATCTTCTGCGCGCAGTCTCTGGTG
EST: gi|86251592|gb|CI016881.1|CI016881
EST:     ACGCGGGGTTCCTCGCCGTCGTCTTCGGCGTCCTCGGCGTCATGCTCCGG                         TACAAGGTGTGCTCGTGGATCGCTATCATCTTCTGCGCGCAGTCTCTGGTG
genomic: ACGCGGGGTTCCTCGCCGTCGTCTTCGGCGTCCTCGGCGTCATGCTCCGGgtacggtatc ... ttgtttgcagTACAAGGTGTGCTCGTGGATCGCTATCATCTTCTGCGCGCAGTCTCTGGTG
EST: gi|86846634|gb|CI280912.1|CI280912
EST:     ACGCGGGGTTCCTCGCCGTCGTCTTCGGCGTCCTCGGCGTCATGCTCCGG                         TACAAGGTGTGCTCGTGGATCGCTATCATCTTCTGCGCGCAGTCTCTGGTG
genomic: ACGCGGGGTTCCTCGCCGTCGTCTTCGGCGTCCTCGGCGTCATGCTCCGGgtacggtatc ... ttgtttgcagTACAAGGTGTGCTCGTGGATCGCTATCATCTTCTGCGCGCAGTCTCTGGTG
EST: gi|87032212|gb|CI261994.1|CI261994
EST:     ACGCGGGGTTCCTCGCCGTCGTCTTCGGCGTCCTCGGCGTCATGCTCCGG                         TACAAGGTGTGCTCGTGGATCGCTATCATCTTCTGCGCGCAGTCTCTGGTG
genomic: ACGCGGGGTTCCTCGCCGTCGTCTTCGGCGTCCTCGGCGTCATGCTCCGGgtacggtatc ... ttgtttgcagTACAAGGTGTGCTCGTGGATCGCTATCATCTTCTGCGCGCAGTCTCTGGTG
EST: gi|88988152|gb|CI036122.1|CI036122
EST:     ACGCGGGGTTCCTCGCCGTCGTCTTCGGCGTCCTCGGCGTCATGCTCCGG                         TACAAGGTGTGCTCGTGGATCGCTATCATCTTCTGCGCGCAGTCTCTGGTG
genomic: ACGCGGGGTTCCTCGCCGTCGTCTTCGGCGTCCTCGGCGTCATGCTCCGGgtacggtatc ... ttgtttgcagTACAAGGTGTGCTCGTGGATCGCTATCATCTTCTGCGCGCAGTCTCTGGTG

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), 72 (downstream exon)
Score: 42

GAGGCAGTACACGCCGCCGAAGCTGTCGCCGCAGGACCTGCCCATCGACTACGCGGGGTTCCTCGCCGTCGTCTTCGGCGTCCTCGGCGTCATGCTCCGGgtacggtatc ... ttgtttgcagTACAAGGTGTGCTCGTGGATCGCTATCATCTTCTGCGCGCAGTCTCTGGTGAACATGAAGAATTTCGAGAATGATCTCAAGCAGTTATCCATGGCTTTCA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cgctgggtcattgttggctttgtttaaaatcggcttgcaacctgtttgtttgcagTACAAGGTGTGCTCGTGGATCGCTATCATCTTCTGCGCGCAGTCTCTGGTGAACATGAAGAATTTCGAGAATGATCTCAAGCAGTTATCCATGGCTTTCA
                                        cctgttt  CT-rich tract
                  tttgtttaaaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttgctaagtaatcggtggtggcgatgttctgatgtattgttatttcgctgggtcattgttggctttgtttaaaatcggcttgcaacctgtttgtttgcagTACAAGGTGTGCTCGTGGATCGCTATCATCTTCTGCGCGCAGTCTCTGGTGAACATGAAGAATTTCGAGAATGATCTCAAGCAGTTATCCATGGCTTTCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
ttgctaa
- - - - - - -ggtggtg
- - - - - - - - - - - - - - ctgatgt
- - - - - - - - - - - - - - - - - - - - - - - - - - - attgttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gcttgca