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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTAATCATAGGATCACCTGATCTGAAAGCTAATCATTCCATACAGCAAATTATTGAGGTCATATCTGAACACGAAAAGTATCCCAGgtatctactaataacactattatttacaaagttgtaccatgagctgttcctccaactaaaaatttccatgagttaagttaatgttaacttgtttcttacag

Basic information

species Oryza sativa
transcript LOC_Os01g68320.3
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g68320.1 (Oryza sativa), 5'ss of exon 7
lower sequence: GRMZM2G362850_T03 (Zea mays), 5'ss of exon 8
GTAATCATAGGATCACCTGATCTGAAAGCTAATCATTCCATACAGCAAATTATTGAGGTCATATCTGAACACGAAAAGTATCCCAGgtatctactaataaca--ctattatttacaaagttgtaccatgagctgtt------cctccaactaaaaatttccatgagttaagttaatgttaacttgtttcttacag
||||||||||| |||||||| || |||||||||||||||||||| |||||| |||| || || || || || || |||||||| |||||| ||    | ||   || ||   || ||| || ||   | |  |  |      | | | | || ||||   || |   | |||| || || || | |         
GTAATCATAGGCTCACCTGAACTTAAAGCTAATCATTCCATACAACAAATTGTTGAAGTTATTTCAGATCATGAGAAGTATCCAAGgtatgtatggttgacggtcttttgactaaaaacttttatgctcacttactatgctactttcgattacaaatggacacggtgtgagttgattttcacctct---------

upper sequence: LOC_Os01g68320.1 (Oryza sativa), 5'ss of exon 7
lower sequence: GRMZM2G059020_T01 (Zea mays), 5'ss of exon 9
GTAATCATAGGATCACCTGATCTGAAAGCTAATCATTCCATACAGCAAATTATTGAGGTCATATCTGAACACGAAAAGTATCCCAGgtatctactaataaca--ctattatttacaaagttgtaccatgagctgtt------cctccaactaaaaatttccatgagttaagttaatgttaacttgtttcttacag
||||||||||| |||||||| || |||||||||||||||||||| |||||| |||| || || || || || || |||||||| |||||| ||    | ||   || ||   || ||| || ||   | |  |  |      | | | | || ||||   |||||  | |||| || || || | ||||  | ||
GTAATCATAGGCTCACCTGAACTTAAAGCTAATCATTCCATACAACAAATTGTTGAAGTTATTTCAGACCATGAGAAGTATCCAAGgtatgtatggttgacggtcttttgactaaaaacttttatgctcacttactatgctactttcgattacaaatggacatgatgtgagttgattttcacctctttcccatag

upper sequence: LOC_Os01g68320.1 (Oryza sativa), 5'ss of exon 7
lower sequence: GRMZM2G362850_T01 (Zea mays), 5'ss of exon 8
GTAATCATAGGATCACCTGATCTGAAAGCTAATCATTCCATACAGCAAATTATTGAGGTCATATCTGAACACGAAAAGTATCCCAGgtatctactaataaca--ctattatttacaaagttgtaccatgagctgtt------cctccaactaaaaatttccatgagttaagttaatgttaacttgtttcttacag
||||||||||| |||||||| || |||||||||||||||||||| |||||| |||| || || || || || || |||||||| |||||| ||    | ||   || ||   || ||| || ||   | |  |  |      | | | | || ||||   || |   | |||| || || || | ||||  ||||
GTAATCATAGGCTCACCTGAACTTAAAGCTAATCATTCCATACAACAAATTGTTGAAGTTATTTCAGATCATGAGAAGTATCCAAGgtatgtatggttgacggtcttttgactaaaaacttttatgctcacttactatgctactttcgattacaaatggacacggtgtgagttgattttcacctctttcccacag

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|29627565|gb|CB632576.1|CB632576
EST:     TCCATACAGCAAATTATTGAGGTCATATCTGAACACGAAAAGTATCCCAG                         ACTCAGTAAACTTTTATCTGATCTAATGGATGGAAGCAGAATCTTGATATT
genomic: TCCATACAGCAAATTATTGAGGTCATATCTGAACACGAAAAGTATCCCAGgtatctacta ... tttcttacagACTCAGTAAACTTTTATCTGATCTAATGGATGGAAGCAGAATCTTGATATT
EST: gi|29636635|gb|CB641644.1|CB641644
EST:     TCCATACAGCAAATTATTGAGGTCATATCTGAACACGAAAAGTATCCCAG                         ACTCAGTAAACTTTTATCTGATCTAATGGATGGAAGCAGAATCTTGATATT
genomic: TCCATACAGCAAATTATTGAGGTCATATCTGAACACGAAAAGTATCCCAGgtatctacta ... tttcttacagACTCAGTAAACTTTTATCTGATCTAATGGATGGAAGCAGAATCTTGATATT
EST: gi|29673236|gb|CB669511.1|CB669511
EST:     TCCATACAGCAAATTATTGAGGTCATATCTGAACACGAAAAGTATCCCAG                         ACTCAGTAAACTTTTATCTGATCTAATGGATGGAAGCAGAATCTTGATATT
genomic: TCCATACAGCAAATTATTGAGGTCATATCTGAACACGAAAAGTATCCCAGgtatctacta ... tttcttacagACTCAGTAAACTTTTATCTGATCTAATGGATGGAAGCAGAATCTTGATATT
EST: gi|29640324|gb|CB645333.1|CB645333
EST:     TCCATACAGCAAATTATTGAGGTCATATCTGAACACGAAAAGTATCCCAG                         ACTCAGTAAACTTTTATCTGATCTAATGGATGGAAGCAGAATCTTGATATT
genomic: TCCATACAGCAAATTATTGAGGTCATATCTGAACACGAAAAGTATCCCAGgtatctacta ... tttcttacagACTCAGTAAACTTTTATCTGATCTAATGGATGGAAGCAGAATCTTGATATT
EST: gi|29664446|gb|CB660721.1|CB660721
EST:     TCCATACAGCAAATTATTGAGGTCATATCTGAACACGAAAAGTATCCCAG                         ACTCAGTAAACTTTTATCTGATCTAATGGATGGAAGCAGAATCTTGATATT
genomic: TCCATACAGCAAATTATTGAGGTCATATCTGAACACGAAAAGTATCCCAGgtatctacta ... tttcttacagACTCAGTAAACTTTTATCTGATCTAATGGATGGAAGCAGAATCTTGATATT
EST: gi|29679220|gb|CB675495.1|CB675495
EST:     TCCATACAGCAAATTATTGAGGTCATATCTGAACACGAAAAGTATCCCAG                         ACTCAGTAAACTTTTATCTGATCTAATGGATGGAAGCAGAATCTTGATATT
genomic: TCCATACAGCAAATTATTGAGGTCATATCTGAACACGAAAAGTATCCCAGgtatctacta ... tttcttacagACTCAGTAAACTTTTATCTGATCTAATGGATGGAAGCAGAATCTTGATATT
EST: gi|29644134|gb|CB649141.1|CB649141
EST:     TCCATACAGCAAATTATTGAGGTCATATCTGAACACGAAAAGTATCCCAG                         ACTCAGTAAACTTTTATCTGATCTAATGGATGGAAGCAGAATCTTGATATT
genomic: TCCATACAGCAAATTATTGAGGTCATATCTGAACACGAAAAGTATCCCAGgtatctacta ... tttcttacagACTCAGTAAACTTTTATCTGATCTAATGGATGGAAGCAGAATCTTGATATT
EST: gi|29638139|gb|CB643148.1|CB643148
EST:     TCCATACAGCAAATTATTGAGGTCATATCTGAACACGAAAAGTATCCCAG                         ACTCAGTAAACTTTTATCTGATCTAATGGATGGAAGCAGAATCTTGATATT
genomic: TCCATACAGCAAATTATTGAGGTCATATCTGAACACGAAAAGTATCCCAGgtatctacta ... tttcttacagACTCAGTAAACTTTTATCTGATCTAATGGATGGAAGCAGAATCTTGATATT
EST: gi|88417599|gb|CI581622.1|CI581622
EST:     TCCATACAGCAAATTATTGAGGTCATATCTGAACACGAAAAGTATCC-AG                         ACTCAGTAAACTTTTATCTGATCTAATGGATGGAAGCAGAATCTTGATATT
genomic: TCCATACAGCAAATTATTGAGGTCATATCTGAACACGAAAAGTATCCCAGgtatctacta ... tttcttacagACTCAGTAAACTTTTATCTGATCTAATGGATGGAAGCAGAATCTTGATATT
EST: gi|29633338|gb|CB638347.1|CB638347
EST:     TCCATACAGCAAATTATTGAGGTCATATCTGAACACGAAAAGTATCCCAG                         ACTCAGTAAACTTTTATCTGATCTAATGGATGGAAGCAGAATCTTGATATT
genomic: TCCATACAGCAAATTATTGAGGTCATATCTGAACACGAAAAGTATCCCAGgtatctacta ... tttcttacagACTCAGTAAACTTTTATCTGATCTAATGGATGGAAGCAGAATCTTGATATT
EST: gi|29675369|gb|CB671644.1|CB671644
EST:     TCCATACAGCAAATTATTGAGGTCATATCTGAACACGAAAAGTATCCCAG                         ACTCAGTAAACTTTTATCTGATCTAATGGATGGAAGCAGAATCTTGATATT
genomic: TCCATACAGCAAATTATTGAGGTCATATCTGAACACGAAAAGTATCCCAGgtatctacta ... tttcttacagACTCAGTAAACTTTTATCTGATCTAATGGATGGAAGCAGAATCTTGATATT
EST: gi|218485924|gb|FG959170.1|FG959170
EST:     TCCATACAGCAAATTATTGAGGTCATATCTGAACACGAAAAGTATCCCAG                         ACTCAGTAAACTTT-ATCTGATCTAATGGATG-AAGCAGAATCTTGATATT
genomic: TCCATACAGCAAATTATTGAGGTCATATCTGAACACGAAAAGTATCCCAGgtatctacta ... tttcttacagACTCAGTAAACTTTTATCTGATCTAATGGATGGAAGCAGAATCTTGATATT
EST: gi|29675371|gb|CB671646.1|CB671646
EST:     TCCATACAGCAAATTATTGAGGTCATATCTGAACACGAAAAGTATCCCAG                         ACTCAGTAAACTTTTATCTGATCTAATGGATGGAAGCAGAATCTTGATATT
genomic: TCCATACAGCAAATTATTGAGGTCATATCTGAACACGAAAAGTATCCCAGgtatctacta ... tttcttacagACTCAGTAAACTTTTATCTGATCTAATGGATGGAAGCAGAATCTTGATATT
EST: gi|29645557|gb|CB650564.1|CB650564
EST:     TCCATACAGCAAATTATTGAGGTCATATCTGAACACGAAAAGTATCCCAG                         ACTCAGTAAACTTTTATCTGATCTAATGGATGGAAGCAGAATCTTGATATT
genomic: TCCATACAGCAAATTATTGAGGTCATATCTGAACACGAAAAGTATCCCAGgtatctacta ... tttcttacagACTCAGTAAACTTTTATCTGATCTAATGGATGGAAGCAGAATCTTGATATT
EST: gi|29666768|gb|CB663043.1|CB663043
EST:     TCCATACAGCAAATTATTGAGGTCATATCTGAACACGAAAAGTATCCCAG                         ACTCAGTAAACTTTTATCTGATCTAATGGATGGAAGCAGAATCTTGATATT
genomic: TCCATACAGCAAATTATTGAGGTCATATCTGAACACGAAAAGTATCCCAGgtatctacta ... tttcttacagACTCAGTAAACTTTTATCTGATCTAATGGATGGAAGCAGAATCTTGATATT
EST: gi|29678103|gb|CB674378.1|CB674378
EST:     TCCATACAGCAAATTATTGAGGTCATATCTGAACACGAAAAGTATCCCAG                         ACTCAGTANACTTTTATCTGATCTAATGGATGGAAGCAGAATCTTGATATT
genomic: TCCATACAGCAAATTATTGAGGTCATATCTGAACACGAAAAGTATCCCAGgtatctacta ... tttcttacagACTCAGTAAACTTTTATCTGATCTAATGGATGGAAGCAGAATCTTGATATT
EST: gi|29677571|gb|CB673846.1|CB673846
EST:     TCCATACAGCAAATTATTGAGGTCATATCTGAACACGAAAAGTATCCCAG                         ACTCAGTAAACTTTTATCTGATCTAATGGATGGAAGCAGAATCTTGATATT
genomic: TCCATACAGCAAATTATTGAGGTCATATCTGAACACGAAAAGTATCCCAGgtatctacta ... tttcttacagACTCAGTAAACTTTTATCTGATCTAATGGATGGAAGCAGAATCTTGATATT
EST: gi|29633337|gb|CB638346.1|CB638346
EST:     TCCATACAGCAAATTATTGAGGTCATATCTGAACACGAAAAGTATCCCAG                         ACTCAGTAAACTTTTATCTGATCTAATGGATGGAAGCAGAATCTTGATATT
genomic: TCCATACAGCAAATTATTGAGGTCATATCTGAACACGAAAAGTATCCCAGgtatctacta ... tttcttacagACTCAGTAAACTTTTATCTGATCTAATGGATGGAAGCAGAATCTTGATATT
EST: gi|29667787|gb|CB664062.1|CB664062
EST:     TCCATACAGCAAATTATTGAGGTCATATCTGAACACGAAAAGTATCCCAG                         ACTCAGTAAACTTTTATCTGATCTAATGGATGGAAGCAGAATCTTGATATT
genomic: TCCATACAGCAAATTATTGAGGTCATATCTGAACACGAAAAGTATCCCAGgtatctacta ... tttcttacagACTCAGTAAACTTTTATCTGATCTAATGGATGGAAGCAGAATCTTGATATT
EST: gi|29670396|gb|CB666671.1|CB666671
EST:     TCCATACAGCAAATTATTGAGGTCATATCTGAACACGAAAAGTATCCCAG                         ACTCAGTAAACTTTTATCTGATCTAATGGATGGAAGCAGAATCTTGATATT
genomic: TCCATACAGCAAATTATTGAGGTCATATCTGAACACGAAAAGTATCCCAGgtatctacta ... tttcttacagACTCAGTAAACTTTTATCTGATCTAATGGATGGAAGCAGAATCTTGATATT

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: 75 (upstream exon), 75 (downstream exon)
Score: 85

GTAATCATAGGATCACCTGATCTGAAAGCTAATCATTCCATACAGCAAATTATTGAGGTCATATCTGAACACGAAAAGTATCCCAGgtatctacta ... tttcttacagACTCAGTAAACTTTTATCTGATCTAATGGATGGAAGCAGAATCTTGATATTTTTCCAAACTAAAAAGGACTGTGACAAGGTCACTCGTCAACTTAGAATG




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