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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgtttggttcacctatgattaaattttaagtttttctactgtttatctgtatgattaaatattgttcacttgaacaaattgcagGATGCAGAAGAATGCTGGACCCAATTGGTGTATACACTTTCTCAAACTCTTACATCAGAAACAAG

Basic information

species Oryza sativa
transcript LOC_Os01g36930.1
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g36930.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G017086_T03 (Zea mays), 3'ss of exon 7
gtttgtttggttcacctatgattaaattttaagtttttctactgtttatctgta---tgattaaatattgttcacttgaacaaattgcagGATGCAGAAGAATGCTGGACCCAATTGGTGTATACACTTTCTCAAACTCTTACATCAGAAACAAG
|||  ||    |||||||  |||||   ||    | | ||  ||  | ||||||   |  || |   || |||  ||  | ||| | ||||||||||||||||||||||| || ||||||||||| ||||||||||||||||| |||||  ||||
gttccttctaatcacctacaattaagagtttgtatctactcttgaatttctgtaatgttgttcatcttttttcttttttaaaaaatacagGATGCAGAAGAATGCTGGACACAGTTGGTGTATACGCTTTCTCAAACTCTTACCTCAGATTCAAG

upper sequence: LOC_Os01g36930.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G028733_T02 (Zea mays), 3'ss of exon 9
gtttgtttggttcacctatgattaaattttaagtttttctactgtttatctgtatgattaaatattgttcacttgaacaaattgcagGATGCAGAAGAATGCTGGACCCAATTGGTGTATACACTTTCTCAAACTCTTACATCAGAAACAAG
||   ||    |||||||  | |   ||||  ||| |    |||  | ||||||    |    ||  ||   || || ||| |  |||||||||||||||||||||| || ||||||||||||||||||||||||||||| |||||  ||||
gtcccttctaatcacctacaaatgtgtttt--gttat----ctgaatttctgtaatgctgttcatcttttttttaaaaaaaatatagGATGCAGAAGAATGCTGGACACAGTTGGTGTATACACTTTCTCAAACTCTTACCTCAGATTCAAG

upper sequence: LOC_Os01g36930.1 (Oryza sativa), 3'ss of exon 7
lower sequence: EFJ12930 (Selaginella moellendorffii), 3'ss of exon 6
------------------gtt--tgtttggttcacctatgattaaatttta-agtttttctactgtttatctgtatgatt-----aaatattgttcacttga----acaaattgcagGATGCAGAAGAATGCTGGACCCAATTGGTGTATACACTTTCTCAAACTCTTACATCAGAAACAAG
                  |||  |  ||| |  ||  |||  |   | ||  || | ||     |    | |  |   ||     ||  |     || | ||    |||    ||||||||| |||||||||||||| ||| | ||||||||||                            
gtactctagcattgctacgttgctccttgatatactcatggctccctattgtagCTGTTGCGAAGCAAGTTTCCACAGTTCGCTCAACAAGCCAACAATGGAGCTTACATGCAGCAGGATGCGGAAGAATGCTGGACGCAACTCGTGTATACAC----------------------------

upper sequence: LOC_Os01g36930.1 (Oryza sativa), 3'ss of exon 7
lower sequence: EFJ09332 (Selaginella moellendorffii), 3'ss of exon 6
------------------gtt--tgtttggttcacctatgattaaattttaagtttttctactgtttatctgtatgatt-----aaatattgttcacttga----acaaattgcagGATGCAGAAGAATGCTGGACCCAATTGGTGTATACACTTTCTCAAACTCTTACATCAGAAACAAG
                  |||  |  ||| |  ||  |||  |    ||  || | ||     |    | |  |   ||     ||  |     || | ||    |||    ||||||||| |||||||||||||| ||| | ||||||||||                            
gtactctagcattgctacgttgctccttgatatactcatggctcctattgtagCTGTTGCGAAGCAAGTTTCCACAGTTCGCTCAACAAGCCAACAATGGAGCTTACATGCAGCAGGATGCGGAAGAATGCTGGACGCAACTCGTGTATACAC----------------------------

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|163920010|gb|EG709816.1|EG709816
EST:     ATATGCAACAG                         GATGCAGAAGAATGCTGGA-CCAATTGGTGTATACACTTTCTCAAACTCTT
genomic: ATATGCAACAGgtttgtttgg ... caaattgcagGATGCAGAAGAATGCTGGACCCAATTGGTGTATACACTTTCTCAAACTCTT
EST: gi|29646291|gb|CB651298.1|CB651298
EST:     AAAAGTATCCCCAGTTTGCGCAACAACAAAATAATGTTTATATGCAACAG                         GATGCAGAAGAATGCTGGACCCAATTGGTGTATACACTTTCTCAAACTCTT
genomic: AAAAGTATCCCCAGTTTGCGCAACAACAAAATAATGTTTATATGCAACAGgtttgtttgg ... caaattgcagGATGCAGAAGAATGCTGGACCCAATTGGTGTATACACTTTCTCAAACTCTT
EST: gi|29689095|gb|CB685370.1|CB685370
EST:     AAAAGTATCCCCAGTTTGCGCAACAACAAAATAATGTTTATATGCAACAG                         GATGCAGAAGAATGCTGGACCCAATTGGTGTATACACTTTCTCAAACTCTT
genomic: AAAAGTATCCCCAGTTTGCGCAACAACAAAATAATGTTTATATGCAACAGgtttgtttgg ... caaattgcagGATGCAGAAGAATGCTGGACCCAATTGGTGTATACACTTTCTCAAACTCTT
EST: gi|29679500|gb|CB675775.1|CB675775
EST:     AAAAGTATCCCCAGTTTGCGCAACAACAAAATAATGTTTATATGCAACAG                         GATGCAGAAGAATGCTGGACCCAATTGGTGTATACACTTTCTCAAACTCTT
genomic: AAAAGTATCCCCAGTTTGCGCAACAACAAAATAATGTTTATATGCAACAGgtttgtttgg ... caaattgcagGATGCAGAAGAATGCTGGACCCAATTGGTGTATACACTTTCTCAAACTCTT
EST: gi|29615418|gb|CB620430.1|CB620430
EST:     AAAAGTATCCCCAGTTTGCGCAACAACAAAATAATGTTTATATGCAACAG                         GATGCAGAAGAATGCTGGACCCAATTGGTGTATACACTTTCTCAAACTCTT
genomic: AAAAGTATCCCCAGTTTGCGCAACAACAAAATAATGTTTATATGCAACAGgtttgtttgg ... caaattgcagGATGCAGAAGAATGCTGGACCCAATTGGTGTATACACTTTCTCAAACTCTT
EST: gi|29674105|gb|CB670380.1|CB670380
EST:     AAAAGTATCCCCAGTTTGCGCAACAACAAAATAATGTTTATATGCAACAG                         GATGCAGAAGAATGCTGGACCCAATTGGTGTATACACTTTCTCAAACTCTT
genomic: AAAAGTATCCCCAGTTTGCGCAACAACAAAATAATGTTTATATGCAACAGgtttgtttgg ... caaattgcagGATGCAGAAGAATGCTGGACCCAATTGGTGTATACACTTTCTCAAACTCTT
EST: gi|58601182|gb|CK011710.1|CK011710
EST:     AAAAGTATCCCCAGTTTGCGCAACAACAAAATAATGTTTATATGCAACAG                         GATGCAGAAGAATGCTGGACCCAATTGGTGTATACACTTTCTCAAACTCTT
genomic: AAAAGTATCCCCAGTTTGCGCAACAACAAAATAATGTTTATATGCAACAGgtttgtttgg ... caaattgcagGATGCAGAAGAATGCTGGACCCAATTGGTGTATACACTTTCTCAAACTCTT
EST: gi|218489926|gb|FG960730.1|FG960730
EST:     AAAAGTATCCCCAGTTTGCGCAACAACAAAATAATGTTTATATGCAACAG                         GATGCAGAAGAATGCTGGACCCAATTGGTGTATACACTTTCTCAAACTCTT
genomic: AAAAGTATCCCCAGTTTGCGCAACAACAAAATAATGTTTATATGCAACAGgtttgtttgg ... caaattgcagGATGCAGAAGAATGCTGGACCCAATTGGTGTATACACTTTCTCAAACTCTT
EST: gi|3766733|gb|AU030843.1|AU030843
EST:     AAAAGTATCCCCAGTTTGCGCAACAACAAAATAATGTTTATATGCAACAG                         GATGCAGAAGAATGCTGGACCCAATTGGTGTATACACTTTCTCAAACTCTT
genomic: AAAAGTATCCCCAGTTTGCGCAACAACAAAATAATGTTTATATGCAACAGgtttgtttgg ... caaattgcagGATGCAGAAGAATGCTGGACCCAATTGGTGTATACACTTTCTCAAACTCTT
EST: gi|29615343|gb|CB620355.1|CB620355
EST:     AAAAGTATCCCCAGTTTGCGCAACAACAAAATAATGTTTATATGCAACAG                         GATGCAGAAGAATGCTGGACCCAATTGGTGTATACACTTTCTCAAACTCTT
genomic: AAAAGTATCCCCAGTTTGCGCAACAACAAAATAATGTTTATATGCAACAGgtttgtttgg ... caaattgcagGATGCAGAAGAATGCTGGACCCAATTGGTGTATACACTTTCTCAAACTCTT

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: 70 (upstream exon), 69 (downstream exon)
Score: 45

ACGCTGCGTAAAAAGTATCCCCAGTTTGCGCAACAACAAAATAATGTTTATATGCAACAGgtttgtttgg ... caaattgcagGATGCAGAAGAATGCTGGACCCAATTGGTGTATACACTTTCTCAAACTCTTACATCAGAAACAAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtttttctactgtttatctgtatgattaaatattgttcacttgaacaaattgcagGATGCAGAAGAATGCTGGACCCAATTGGTGTATACACTTTCTCAAACTCTTACATCAGAAACAAG
            tttatctgtatgatta  TA-rich tract