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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATACCGAGACTTAAAACCAGAGAATATCTTACTTCATAGAGATGGGCACATCTCCCTTACAGACTTCGATTTGTCTTGTCTAACATCTTGCAGACCGCAGgtaataatttgataaatctcttctcataaaagtaatattaattcatgaacctctttctcttccaaaaagaatcataaaacgtcacaattataatgcgcta...

Basic information

species Oryza sativa
transcript LOC_Os12g01140.1
intron # 18
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os12g01140.5 (Oryza sativa), 5'ss of exon 14
lower sequence: GRMZM2G001457_T02 (Zea mays), 5'ss of exon 17
ATACCGAGACTTAAAACCAGAGAATATCTTACTTCATAGAGATGGGCACATCTCCCTTACAGACTTCGATTTGTCTTGTCTAACATCTTGCAGACCGCAGgtaata--atttgataaatctcttctcataaa--agtaatattaattcatgaacctctttc-----tcttccaaaaagaatcataaaacgtcacaattataatgcgcta-
 ||| |||||||||| |||||||| || ||||||||||||||||||||||| ||  | |||||||| |||||||||||  | ||||| ||| |||| || |||||   | || || ||| |    | ||  |  | | ||    |||  |  | ||| ||      | || |  |      | |||  |   |  ||| |  |  | || 
CTACAGAGACTTAAAGCCAGAGAACATTTTACTTCATAGAGATGGGCACATTTCATTGACAGACTTTGATTTGTCTTGCTTGACATCCTGCCGACCACAAgtaatgtcacttcattaatataccttaatggacaattcatggctattagtttaactccttggtctatttttcttagttgcacttaagtcactattattgttgtttgatag
















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|66913937|gb|CX100785.1|CX100785
EST:     TCTCCCTTACAGACTTCGATTTGTCTTGTCTAACATCTTGCAGACCGCAG                         GTCTTTCTTCCCGAAGATGCTGATGAGAAAAAAGGGAGAAAAAACGGGAGT
genomic: TCTCCCTTACAGACTTCGATTTGTCTTGTCTAACATCTTGCAGACCGCAGgtaataattt ... tatttggtagGTCTTTCTTCCCGAAGATGCTGATGAGAAAAAAGGGAGAAAAAACGGGAGT
EST: gi|29623925|gb|CB628936.1|CB628936
EST:     TCTCCCTTACAGACTTCGATTTGTCTTGTCTAACATCTTGCAGACCGCAG                         GTCTTTCTTCCCGAAGATGCTGATGAGAAAAAAGGGAGAAAAAACGGGAGT
genomic: TCTCCCTTACAGACTTCGATTTGTCTTGTCTAACATCTTGCAGACCGCAGgtaataattt ... tatttggtagGTCTTTCTTCCCGAAGATGCTGATGAGAAAAAAGGGAGAAAAAACGGGAGT
EST: gi|86908120|gb|CI300633.1|CI300633
EST:     TCTCCCTTACAGACTTCGATTTGTCTTGTCTAACATCTTGCAGACCGCAG                         GTCTTTCTTCCCGAAGATGCTGATGAGAAAAAAGGGAGAAAAAACGGGAGT
genomic: TCTCCCTTACAGACTTCGATTTGTCTTGTCTAACATCTTGCAGACCGCAGgtaataattt ... tatttggtagGTCTTTCTTCCCGAAGATGCTGATGAGAAAAAAGGGAGAAAAAACGGGAGT
EST: gi|29630467|gb|CB635476.1|CB635476
EST:     CTTGCAGACCGCAG                         TTCTTTCTTCCCGAAAATGCTGATGAGAAAAAAGGGAGAAAAAACGGGAGT
genomic: CTTGCAGACCGCAGgtaataattt ... tatttggtagGTCTTTCTTCCCGAAGATGCTGATGAGAAAAAAGGGAGAAAAAACGGGAGT
EST: gi|29622723|gb|CB627734.1|CB627734
EST:     TCTCCCTTACAGACTTCGATTTGTCTTGTCTAACATCTTGCAGACCGCAG                         GTCTTTCTTCCCGAAAATGCTGATGAGAAAAAAGGGAGAAAAAACGGGAGT
genomic: TCTCCCTTACAGACTTCGATTTGTCTTGTCTAACATCTTGCAGACCGCAGgtaataattt ... tatttggtagGTCTTTCTTCCCGAAGATGCTGATGAGAAAAAAGGGAGAAAAAACGGGAGT
EST: gi|88299110|gb|CI570080.1|CI570080
EST:     GTCTTGTCTAACATCTTGCAGACCGGAG                         GTCTTTCTTCCCGAAGATGCTGATGAGAAAAAAGGGAGAAAAAACGGGAGT
genomic: GTCTTGTCTAACATCTTGCAGACCGCAGgtaataattt ... tatttggtagGTCTTTCTTCCCGAAGATGCTGATGAGAAAAAAGGGAGAAAAAACGGGAGT
EST: gi|27334351|gb|CA882802.1|CA882802
EST:     TCTCCCTTACAGACTTCGATTTGTCTTGTCTAACATCTTGCAGACCGCAG                         GTCTTTCTTCCCGAAGATGCTGATGAGAAAAAAGGGAGAAAAAACGGGAGT
genomic: TCTCCCTTACAGACTTCGATTTGTCTTGTCTAACATCTTGCAGACCGCAGgtaataattt ... tatttggtagGTCTTTCTTCCCGAAGATGCTGATGAGAAAAAAGGGAGAAAAAACGGGAGT
EST: gi|29630120|gb|CB635129.1|CB635129
EST:     TCTCCCTTACAGATTTCGATTTGTCTTGTCTAACATCTTGCAGACCGCAG                         GTCTTTCTTCCCGAAAATGCTGATGAGAAAAAAGGGAGAAAAAACGGGAGT
genomic: TCTCCCTTACAGACTTCGATTTGTCTTGTCTAACATCTTGCAGACCGCAGgtaataattt ... tatttggtagGTCTTTCTTCCCGAAGATGCTGATGAGAAAAAAGGGAGAAAAAACGGGAGT
EST: gi|58695041|gb|CK083728.1|CK083728
EST:     TCTCCCTTACAGACTTCGATTTGTCTTGTCTAACATCTTGCAGACCGCAG                         GTCTTTCTTCCCGAAGATGCTGATGAGAAAAAAGGGAGAAAAAACGGGAGT
genomic: TCTCCCTTACAGACTTCGATTTGTCTTGTCTAACATCTTGCAGACCGCAGgtaataattt ... tatttggtagGTCTTTCTTCCCGAAGATGCTGATGAGAAAAAAGGGAGAAAAAACGGGAGT
EST: gi|29623926|gb|CB628937.1|CB628937
EST:     TCTCCCTTACAGACTTCGATTTGTCTTGTCTAACATCTTGCAGACCGCAG                         GTCTTTCTTCCCGAAGATGCTGATGAGAAAAAAGGGAGAAAAAACGGGAGT
genomic: TCTCCCTTACAGACTTCGATTTGTCTTGTCTAACATCTTGCAGACCGCAGgtaataattt ... tatttggtagGTCTTTCTTCCCGAAGATGCTGATGAGAAAAAAGGGAGAAAAAACGGGAGT
EST: gi|29641400|gb|CB646407.1|CB646407
EST:     TCTCCCTTACAGACTTCGATTTGTCTTGTCTAACATCTTGCAGACCGCAG                         GTCTTTCTTCCCGAAGATGCTGATGAGAAAAAAGGGAGAAAAAACGGGAGT
genomic: TCTCCCTTACAGACTTCGATTTGTCTTGTCTAACATCTTGCAGACCGCAGgtaataattt ... tatttggtagGTCTTTCTTCCCGAAGATGCTGATGAGAAAAAAGGGAGAAAAAACGGGAGT
EST: gi|33680724|gb|CF308963.1|CF308963
EST:     TCTCCCTTACAGACTTCGATTTGTCTTGTCTAACATCTTGCAGACCGCAG                         GTCTTTCTTCCCGAAGATGCTGATGAGAAAAAAGGGAGAAAAAACGGGAGT
genomic: TCTCCCTTACAGACTTCGATTTGTCTTGTCTAACATCTTGCAGACCGCAGgtaataattt ... tatttggtagGTCTTTCTTCCCGAAGATGCTGATGAGAAAAAAGGGAGAAAAAACGGGAGT
EST: gi|29622724|gb|CB627735.1|CB627735
EST:     TCTCCCTTACAGACTTCGATTTGTCTTGTCTAACATCTTGCAGACCGCAG                         GTCTTTCTTCCCGAAAATGCTGATGAGAAAAAAGGGAGAAAAAACGGGAGT
genomic: TCTCCCTTACAGACTTCGATTTGTCTTGTCTAACATCTTGCAGACCGCAGgtaataattt ... tatttggtagGTCTTTCTTCCCGAAGATGCTGATGAGAAAAAAGGGAGAAAAAACGGGAGT
EST: gi|29677072|gb|CB673347.1|CB673347
EST:     TTGCAGACCGCAG                         GTCTTTCTTCCCGAAGATGCTGATGAGAAAAAAGGGAGAAAAAACGGGAGT
genomic: TTGCAGACCGCAGgtaataattt ... tatttggtagGTCTTTCTTCCCGAAGATGCTGATGAGAAAAAAGGGAGAAAAAACGGGAGT

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: 60 (upstream exon), 71 (downstream exon)
Score: 40

ATACCGAGACTTAAAACCAGAGAATATCTTACTTCATAGAGATGGGCACATCTCCCTTACAGACTTCGATTTGTCTTGTCTAACATCTTGCAGACCGCAGgtaataattt ... tatttggtagGTCTTTCTTCCCGAAGATGCTGATGAGAAAAAAGGGAGAAAAAACGGGAGTTACCCCATATTTTTTGCTGAACCTATGCGAGCATCCAATTCATTTGTTG




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