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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaggttttgttgcccatgctcttgaagtagtcaaagctacattagcacagttcggtgaatttgacacccaaaacccttcaatttgcagCTCGATTATGTCCTAGGTAAGAACCCACTGAAGATGAGCTACGTTGTGGGTTTTGGAAACAAGTACCCCAAGCGCGCTCATCACAGAGGTGCATCAATCC

Basic information

species Oryza sativa
transcript LOC_Os03g52630.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g52630.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G147849_T01 (Zea mays), 3'ss of exon 5
gtaaggttttgttgcccatgctcttgaagtagtcaaagctacattagcacagttcggtgaatttgacacccaaaacccttcaatttgcagCTCGATTATGTCCTAGGTAAGAACCCACTGAAGATGAGCTACGTTGTGGGTTTTGGAAACAAGTACCCCAAGCGCGCTCATCACAGAGGTGCATCAATCC
||||    || ||    |  ||| | | ||   |||   |||||||||| ||    |||  |  |      ||| |   || |||||||||| || ||  |||| || ||||||||| ||||||||||||||||||||||||| |||||||||||||| |||||| |||| ||||||||||| || || |
gtaaatcgttcttcttaactctccttaggtgcccaaccttacattagcagagaa-agtgggtcggtagttaaaatctgctcgatttgcagCTTGACTACATCCTTGGAAAGAACCCATTGAAGATGAGCTACGTTGTGGGTTTCGGAAACAAGTACCCGAAGCGCCCTCACCACAGAGGTGCGTCGATAC

upper sequence: LOC_Os03g52630.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G110735_T01 (Zea mays), 3'ss of exon 5
gtaag-gttttgttgcccatgctcttgaagtagtcaaagctacattagcacagttcggtgaatttgacacccaaaacccttcaatttgcagCTCGATTATGTCCTAGGTAAGAACCCACTGAAGATGAGCTACGTTGTGGGTTTTGGAAACAAGTACCCCAAGCGCGCTCATCACAGAGGTGCATCAATCC
||||  |  |||||    |||||||  ||||   ||| | |||    |   |||    |  ||     |   ||| |  || |||||||||||||| ||  |||| || ||||||||| ||||||||||||||||||||||||| |||||||||||||| |||||| ||||||||||||| || || || |
gtaaaagcattgttcttaatgctctcaaagtgcccaacg-tacg---gggaagtgaaattgatagttaaattaaatctgttaaatttgcagCTCGACTACATCCTTGGCAAGAACCCATTGAAGATGAGCTACGTTGTGGGTTTCGGAAACAAGTACCCGAAGCGCCCTCATCACAGAGGCGCGTCGATAC

upper sequence: LOC_Os03g52630.2 (Oryza sativa), 3'ss of exon 4
lower sequence: EFJ31524 (Selaginella moellendorffii), 3'ss of exon 5
gtaaggttttgttgcccatgctcttgaagtagtcaaagctacattagcacagttcggtgaatttgacacccaaaacccttcaatttgcagCTCGATTATGTCCTAGGTAAGAACCCACTGAAGATGAGCTACGTTGTGGGTTTTGGAAACAAGTACCCCAAGCGCGCTCATCACAGAGGTGCATCAATCC
                                                       | |    ||        ||    ||   | | ||| | || ||  | || || |||||||||| | | ||||||||||||||||| || || |||||||| ||||||  ||  || ||| |||  |||||  | |
-------------------------------------------------------gttttccttcgagttataactagtttcctatccagATGGACTACATTCTCGGGAAGAACCCACGGCATATGAGCTACGTTGTGGGATTCGGCAACAAGTATCCCAAGTACGTCCACCACCGAGCAGCATCGGTTC

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|58670607|gb|CK059293.1|CK059293
EST:     GACCTACTTTCTACACTACAGAAGTCCTCCGCAAATTTGCAAGGTCACAG                         CTCGATTATGTCCTAGGTAAGAACCCACTGAAGATG
genomic: GACCTACTTTCTACACTACAGAAGTCCTCCGCAAATTTGCAAGGTCACAGgtaaggtttt ... caatttgcagCTCGATTATGTCCTAGGTAAGAACCCACTGAAGATG
EST: gi|2280737|gb|C25232.1|C25232
EST:     ACAGAAGTCCTCCGCAAATTTGCAAGGTCACAG                         CTCGATTATGTCCTAGGTAAGAACCCACTGAAGATGAGCTACGTTGTGGGT
genomic: ACAGAAGTCCTCCGCAAATTTGCAAGGTCACAGgtaaggtttt ... caatttgcagCTCGATTATGTCCTAGGTAAGAACCCACTGAAGATGAGCTACGTTGTGGGT
EST: gi|27576324|gb|CA999018.1|CA999018
EST:     GACCTACTTTCTACACTACAGAAGTCCTCCGCAAATTTGCAAGGTCACAG                         CTCGATTATGT
genomic: GACCTACTTTCTACACTACAGAAGTCCTCCGCAAATTTGCAAGGTCACAGgtaaggtttt ... caatttgcagCTCGATTATGT
EST: gi|29639819|gb|CB644828.1|CB644828
EST:     ACAGAAGTCCTCCGCAAATTTGCAAGGTCACAG                         CTCGATTATGTCCTAGGTAAGAACCCACTGAAGATGAGCTACGTTGTGGGT
genomic: ACAGAAGTCCTCCGCAAATTTGCAAGGTCACAGgtaaggtttt ... caatttgcagCTCGATTATGTCCTAGGTAAGAACCCACTGAAGATGAGCTACGTTGTGGGT
EST: gi|29674436|gb|CB670711.1|CB670711
EST:     CACTACAGAAGTCCTCCGCAAATTTGCAAGGTCACAG                         CTCGATTATGTCCTAGGTAAGAACCCACTGAAGATGAGCTACGTTGTGGGT
genomic: CACTACAGAAGTCCTCCGCAAATTTGCAAGGTCACAGgtaaggtttt ... caatttgcagCTCGATTATGTCCTAGGTAAGAACCCACTGAAGATGAGCTACGTTGTGGGT
EST: gi|29624498|gb|CB629509.1|CB629509
EST:     GACCTACTTTCTACACTACAGAAGTCCTCCGCAAATTTGCAAGGTCACAG                         CTCGATTATGTCCTAGGTAAGAACCCACTGAAGATGAGCTACGTTGTGGGT
genomic: GACCTACTTTCTACACTACAGAAGTCCTCCGCAAATTTGCAAGGTCACAGgtaaggtttt ... caatttgcagCTCGATTATGTCCTAGGTAAGAACCCACTGAAGATGAGCTACGTTGTGGGT
EST: gi|29639818|gb|CB644827.1|CB644827
EST:     GACCTACTTTCTACACTACAGAAGTCCTCCGCAAATTTGCAAGGTCACAG                         CTCGATTATGTCCTAGGTAAGAACCCACTGAAGATGAGCTACGTTGTGGGT
genomic: GACCTACTTTCTACACTACAGAAGTCCTCCGCAAATTTGCAAGGTCACAGgtaaggtttt ... caatttgcagCTCGATTATGTCCTAGGTAAGAACCCACTGAAGATGAGCTACGTTGTGGGT
EST: gi|58663082|gb|CK051768.1|CK051768
EST:     GACCTACTTTCTACACTACAGAAGTCCTCCGCAAATTTGCAAGGTCACAG                         CTCGATTATGTCCTAGGTAAGAACCCACTGAAGATGAGCTACGTTGTGGGT
genomic: GACCTACTTTCTACACTACAGAAGTCCTCCGCAAATTTGCAAGGTCACAGgtaaggtttt ... caatttgcagCTCGATTATGTCCTAGGTAAGAACCCACTGAAGATGAGCTACGTTGTGGGT
EST: gi|29629441|gb|CB634450.1|CB634450
EST:     ACACTACAGAAGTCCTCCGCAAATTTGCAAGGTCACAG                         CTCGATTATGTCCTAGGTAAGAACCCACTGAAGATGAGCTACGTTGTGGGT
genomic: ACACTACAGAAGTCCTCCGCAAATTTGCAAGGTCACAGgtaaggtttt ... caatttgcagCTCGATTATGTCCTAGGTAAGAACCCACTGAAGATGAGCTACGTTGTGGGT
EST: gi|27578175|gb|CB000870.1|CB000870
EST:     CTACTTTCTACACTACAGAAGTCCTCCGCAAATTTGCAAGGTCACAG                         CTCGATTATGTCCTAGGTAAGAACCCACTGAAGATGAGCTACGTTGTGGGT
genomic: CTACTTTCTACACTACAGAAGTCCTCCGCAAATTTGCAAGGTCACAGgtaaggtttt ... caatttgcagCTCGATTATGTCCTAGGTAAGAACCCACTGAAGATGAGCTACGTTGTGGGT
EST: gi|38469334|gb|CF953465.1|CF953465
EST:     GACCTACTTTCTACACTACAGAAGTCCTCCGCAAATTTGCAAGGTCACAG                         CTCGATTATGTCCTAGGTAAGAACCCACTGAAGATGAGCTACGTTGTGGGT
genomic: GACCTACTTTCTACACTACAGAAGTCCTCCGCAAATTTGCAAGGTCACAGgtaaggtttt ... caatttgcagCTCGATTATGTCCTAGGTAAGAACCCACTGAAGATGAGCTACGTTGTGGGT
EST: gi|29629254|gb|CB634265.1|CB634265
EST:     GTCCTCCGCAAATTTGCAAGGTCACAG                         CTCGATTATGTCTTAGGTAAGAACCCACTGAAGATGAGCTACGTTGTGGGT
genomic: GTCCTCCGCAAATTTGCAAGGTCACAGgtaaggtttt ... caatttgcagCTCGATTATGTCCTAGGTAAGAACCCACTGAAGATGAGCTACGTTGTGGGT
EST: gi|396941140|gb|HO188349.1|HO188349
EST:     GACCTACTTTCTACACTACAGAAGTCCTCCGCAAATTTGCAAGGTCACAG                         CTCGATTATGTCCTAGGTAAGAACCCACTGAAGATGAGCTACGTTGTGGGT
genomic: GACCTACTTTCTACACTACAGAAGTCCTCCGCAAATTTGCAAGGTCACAGgtaaggtttt ... caatttgcagCTCGATTATGTCCTAGGTAAGAACCCACTGAAGATGAGCTACGTTGTGGGT
EST: gi|29623193|gb|CB628204.1|CB628204
EST:     GACCTACTTTCTACACTACAGAAGTCCTCCGCAAATTTGCAAGGTCACAG                         CTCGATTATGTCCTAGGTAAGAACCCACTGAAGATGAGCTACGTTGTGGGT
genomic: GACCTACTTTCTACACTACAGAAGTCCTCCGCAAATTTGCAAGGTCACAGgtaaggtttt ... caatttgcagCTCGATTATGTCCTAGGTAAGAACCCACTGAAGATGAGCTACGTTGTGGGT
EST: gi|29643849|gb|CB648856.1|CB648856
EST:     ACTACAGAAGTCCTCCGCAAATTTGCAAGGTCACAG                         CTCGATTATGTCCTAGGTAAGAACCCACTGAAGATGAGCTACGTTGTGGGT
genomic: ACTACAGAAGTCCTCCGCAAATTTGCAAGGTCACAGgtaaggtttt ... caatttgcagCTCGATTATGTCCTAGGTAAGAACCCACTGAAGATGAGCTACGTTGTGGGT
EST: gi|29630277|gb|CB635286.1|CB635286
EST:     GACCTACTTTCTACACTACAGAAGTCCTCCGCAAATTTGCAAGGTCACAG                         CTCGATTATGTCCTAGGTAAGAACCCACTGAAGATGAGCTACGTTGTGGGT
genomic: GACCTACTTTCTACACTACAGAAGTCCTCCGCAAATTTGCAAGGTCACAGgtaaggtttt ... caatttgcagCTCGATTATGTCCTAGGTAAGAACCCACTGAAGATGAGCTACGTTGTGGGT
EST: gi|29673808|gb|CB670083.1|CB670083
EST:     GCAAATTTGCAAGGTCACAG                         CTCGATTATGTCTTAGGTAAGAACCCACTGAAGATGAGCTACGTTGTGGGT
genomic: GCAAATTTGCAAGGTCACAGgtaaggtttt ... caatttgcagCTCGATTATGTCCTAGGTAAGAACCCACTGAAGATGAGCTACGTTGTGGGT
EST: gi|163926677|gb|EG713693.1|EG713693
EST:     GACCTACTTTCTACACTACAGAAGTCCTCCGCAAATTTGCAAGGTCACAG                         CTCGATTATGTCCTAGGTAAGAACCCACTGAAGATGAGCTACGTTGTGGGT
genomic: GACCTACTTTCTACACTACAGAAGTCCTCCGCAAATTTGCAAGGTCACAGgtaaggtttt ... caatttgcagCTCGATTATGTCCTAGGTAAGAACCCACTGAAGATGAGCTACGTTGTGGGT
EST: gi|29668386|gb|CB664661.1|CB664661
EST:     GACCTACTTTCTACACTACAGAAGTCCTCCGCAAATTTGCAAGGTCACAG                         CTCGATTATGTCCTAGGTAAGAACCCACTGAAGATGAGCTACGTTGTGGGT
genomic: GACCTACTTTCTACACTACAGAAGTCCTCCGCAAATTTGCAAGGTCACAGgtaaggtttt ... caatttgcagCTCGATTATGTCCTAGGTAAGAACCCACTGAAGATGAGCTACGTTGTGGGT

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: 62 (upstream exon), 72 (downstream exon)
Score: 47

TCTATACAGCGATTACCTGGATGCTGCAGATACACCTGGGTGGTATTGTGGACCTACTTTCTACACTACAGAAGTCCTCCGCAAATTTGCAAGGTCACAGgtaaggtttt ... caatttgcagCTCGATTATGTCCTAGGTAAGAACCCACTGAAGATGAGCTACGTTGTGGGTTTTGGAAACAAGTACCCCAAGCGCGCTCATCACAGAGGTGCATCAATCC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aagctacattagcacagttcggtgaatttgacacccaaaacccttcaatttgcagCTCGATTATGTCCTAGGTAAGAACCCACTGAAGATGAGCTACGTTGTGGGTTTTGGAAACAAGTACCCCAAGCGCGCTCATCACAGAGGTGCATCAATCC
                         atttgac  putative branch site (score: 47)
                                        cccttc  putative PPT
                                           ttcaattt  TA-rich tract