Sequence
atgc intronic sequence ATGC exonic sequencegtatagtatactcatcttagcatgcttttgtgcctcttcgtggagaccatgtcttgtgtcatgtgatctgttcatcattcctcacttcctcgtcattaaatgactgacacaaatatctttaaatttgatagGTCAATCCTATTGCTGTGAACAGCAAATATTGTAATGTTTTCACCGAGAACAAACGAGTTGTTTCAATAATCTCAACTTCAGAGTTTGGAAAG
Basic information
species | Oryza sativa |
transcript | LOC_Os01g72940.1 |
intron # | 15 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os01g72940.1 (Oryza sativa), 3'ss of exon 15
lower sequence: GRMZM2G133885_T02 (Zea mays), 3'ss of exon 2
gtatagtatactcatcttagcatgcttttgtgcctct-tcgtggagaccatgtcttgtgtcatgtgatctgttcatcattcctcacttcctcgtcattaaatgactgacacaaatatctttaaatttgatagGTCAATCCTATTGCTGTGAACAGCAAATATTGTAATGTTTTCACCGAGAACAAACGAGTTGTTTCAATAATCTCAACTTCAGAGTTTGGAAAG
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gtatataatacttatatcggcacgctttgatgtcactgtggtaactggaaagggatatgtt-tgtgttctgctc--tatttcttgtcatttc-tcagcatctg-ctgatgctggtctacctgcatttgacagGTGAATCCCATCGCTGTGAATAGCAAGTATTGCAATGTATTCACTGAGAATAAAAGAGTTGTATCAATGATATCAACTTCAGAGTTTGGAAAG
upper sequence: LOC_Os01g72940.1 (Oryza sativa), 3'ss of exon 15
lower sequence: GLYMA08G19310.2 (Glycine max), 3'ss of exon 16
gtatagtatactcatcttagcatgcttttgtgcctcttcgtggagaccatgtcttgtgtcatgtg-atctgttcatcattcctcacttcctcgtcattaaatgactgacacaaatatctttaaatttgatagGTCAATCCTATTGCTGTGAACAGCAAATATTGTAATGTTTTCACCGAGAACAAACGAGTTGTTTCAATAATCTCAACTTCAGAGTTTGGAAAG
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-------gtatgtgtaataataa---cttgagaaaaatgataagtcatatatatatatatatatatatttgtctattttctttctgttaattctcatttg-tgttttccccctattgtgttctactcctcagGTCAATCCCATTGCTGTAAATAGCAAGTACTGCAATGTCTTCACGGAGAACAAGAGAGTTGTTTCAATAGTTTCAACTGTAGATTTTGGAAAG
upper sequence: LOC_Os01g72940.1 (Oryza sativa), 3'ss of exon 15
lower sequence: Vv12s0055g00710.t01 (Vitis vinifera), 3'ss of exon 14
gtatagtatactcatcttagcatgcttttgtgcctcttcgtggagaccatgtcttgtgtcatgtgatctgttcatcattcctcacttcctcgtcattaaatgactgacacaaatatctttaaatttgatagGTCAATCCTATTGCTGTGAACAGCAAATATTGTAATGTTTTCACCGAGAACAAACGAGTTGTTTCAATAATCTCAACTTCAGAGTTTGGAAAG
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-------------------gtatgtgcaattattatctgttgaaattcatgt-ttgttttgcaaactgtttttttgtttcttcagaacttc-ccat--gatcttttac-----tttatttctttctgctagGTTAATCCCATTGCTGTGAATAGCAAGTATTGCAATGTATTCACAGAGAACAAGCGAGTAGTATCTGTTATTTCAACATCAGATTTTGGGAAGMapped 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|33655366|gb|CF277980.1|CF277980EST: TCTCAGGAACTTTGGAGAAATTTGTGGAAATTCCTGGATGCTTGTACACG GTCAATCCTATTGCTGTGAACAGCAAATATTGTAATGTTTTCACCGAGAAC
genomic: TCTCAGGAACTTTGGAGAAATTTGTGGAAATTCCTGGATGCTTGTACACGgtatagtata ... aatttgatagGTCAATCCTATTGCTGTGAACAGCAAATATTGTAATGTTTTCACCGAGAAC
EST:
gi|58606058|gb|CK034091.1|CK034091EST: TCTCAGGAACTTTGGAGAAATTTGTGGAAATTCCTGGATGCTTGTACACG GTCAATCCTATTGCTGTGAACAGCAA
genomic: TCTCAGGAACTTTGGAGAAATTTGTGGAAATTCCTGGATGCTTGTACACGgtatagtata ... aatttgatagGTCAATCCTATTGCTGTGAACAGCAA
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:
73 (upstream exon),
51 (downstream exon)
Score:
3GATTACCATAGGTTTCATGTTCCCGTCTCAGGAACTTTGGAGAAATTTGTGGAAATTCCTGGATGCTTGTACACGgtatagtata ... aatttgatagGTCAATCCTATTGCTGTGAACAGCAAATATTGTAATGTTTTCACCGAGAACAAACGAGTTGTTTCAATAATCTCAACTTCAGAGTTTGGAAAG
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atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.attcctcacttcctcgtcattaaatgactgacacaaatatctttaaatttgatagGTCAATCCTATTGCTGTGAACAGCAAATATTGTAATGTTTTCACCGAGAACAAACGAGTTGTTTCAATAATCTCAACTTCAGAGTTTGGAAAG
gactgac putative branch site (score: 3)
acaaatatctttaaat TA-rich tract