Sequence
atgc intronic sequence ATGC exonic sequencegtatgttatgttcaatatctgaaattttgtctagagattccaacacctgaaattaatgtaattttccttatttacgacaaatttaggctatacaattctacatattaagttgttctgattattctattcagGTATGTGCATAGTTACCAGAGTTACTTATGGAACCATGCTGCAAGTATGAGAGTTCAAAAGTATG
Basic information
species | Oryza sativa |
transcript | LOC_Os01g56620.1 |
intron # | 11 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os01g56620.1 (Oryza sativa), 3'ss of exon 11
lower sequence: GRMZM2G459702_T01 (Zea mays), 3'ss of exon 11
gtatgttatgttcaatatctgaaattttgtctagagattccaacacctgaaattaatgtaa---ttttccttatttacgacaaatttaggctatacaattctacatattaagttgttctgattattctattcagGTATGTGCATAGTTACCAGAGTTACTTATGGAACCATGCTGCAAGTATGAGAGTTCAAAAGTATG
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---------------tgtaagaaacta-gtattcaaaatctattgtcagaatatattgttagggcttttcgtatttac------tttgtgctctggtactcca--------atggatcc----atgctgtgcagGTATGTACATAGCTACCAGAGTTACTTATGGAATCATGCTGCAAGTATGAGAGTGGAAAAGTATG
upper sequence: LOC_Os01g56620.1 (Oryza sativa), 3'ss of exon 11
lower sequence: GLYMA03G40600.1 (Glycine max), 3'ss of exon 12
gtatgttatgttcaatatctgaaattttgtctagagattccaacacctgaaattaatgtaattttccttatttacgacaaatttaggctatacaattctacatattaagttgttctgattattctattcagGTATGTGCATAGTTACCAGAGTTACTTATGGAACCATGCTGCAAGTATGAGAGTTCAAAAGTATG
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-------------------------tctgctcagaac-----acaaataaagttg-taatatattattcaagatcatttatttgaaggattatattggtattcattatatagttccactgcttttttttagGTATGTTCATAGTTACCAAAGCTATTTGTGGAACCATGCTGCAAGTAAGAGGGTGCAAAAATATG
upper sequence: LOC_Os01g56620.1 (Oryza sativa), 3'ss of exon 11
lower sequence: GLYMA19G43270.1 (Glycine max), 3'ss of exon 12
gtatgttatgttcaatatctgaaattttgtctagagattccaacacctgaaattaatgtaattttccttatttacgacaaatttaggctatacaattctacatattaagttgttctgattattctattcagGTATGTGCATAGTTACCAGAGTTACTTATGGAACCATGCTGCAAGTATGAGAGTTCAAAAGTATG
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-----------------------agtctggtcagagc-----acaaataaaagt--tgttatattattcaagatcatttatttgaaggattatattggtatttattttat-acttcaactactttttttagGTATGTTCATAGTTACCAAAGCTATTTATGGAACCATGCTGCAAGTAAGAGGGTGCAAAAATATG
upper sequence: LOC_Os01g56620.1 (Oryza sativa), 3'ss of exon 11
lower sequence: AT3G04820.1 (Arabidopsis thaliana), 3'ss of exon 12
------gtatgttatgttca-atatctgaaattttgtctagag-attccaacacctgaaattaatgtaattttccttatttacgacaaatttaggctatacaa-ttctacatattaagttgt-tctgattattct-attcagGTATGTGCATAGTTACCAGAGTTACTTATGGAACCATGCTGCAAGTATGAGAGTTCAAAAGTATG
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gtaagcgctcgattctttaatatatctttagtaccttccggaacagtgttccttttgcgactggttatgacatgccaagccacagggcacaggcgcagatcaagttttttagcttactgtatatctgatccttatcatgcagGTATGTACATAGTTATCAAAGCTACTTATGGAACAATGCAGCAAGTCTGCGCGTCAAAAATTATG
upper sequence: LOC_Os01g56620.1 (Oryza sativa), 3'ss of exon 11
lower sequence: Vv14s0030g01850.t01 (Vitis vinifera), 3'ss of exon 7
gtatgttatgttcaatatctgaaattttgtctagagattccaacacctgaaattaatgtaattttccttatttacgacaaatttaggctatacaattctacatattaagttgttctgattattctattcagGTATGTGCATAGTTACCAGAGTTACTTATGGAACCATGCTGCAAGTATGAGAGTTCAAAAGTATG
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-------------------agaaatgagaggtgaatacttc----ttttcgactcctgtggacatgaaactttgtgat---tttagact-tccaatttgac-catt---ttattctggttctacttttcagGTATGTACATAGTTACCAAAGCTATCTGTGGAACCATGCAGCTAGTATGAGAGTGCAAAACTATGMapped 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|58670071|gb|CK058757.1|CK058757EST: GGCAACTATCTACAAGCACTAATGGCTATACCTAGAACACTGAGACTGAT GTATGTGCATAGTTACCAGAGTTACCTATGGAACCATG
genomic: GGCAACTATCTACAAGCACTAATGGCTATACCTAGAACACTGAGACTGATgtatgttatg ... ttctattcagGTATGTGCATAGTTACCAGAGTTACTTATGGAACCATG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.acaaatttaggctatacaattctacatattaagttgttctgattattctattcagGTATGTGCATAGTTACCAGAGTTACTTATGGAACCATGCTGCAAGTATGAGAGTTCAAAAGTATG
ttctgat putative branch site (score: 3)
ttctattc putative PPT
aattctacatattaa TA-rich tract
Putative cis-regulatory sequences
atgc | intron | ATGC | exonic elements by Pertea et al. |
ATGC | exon | atgc | putative intronic elements |
| | ATGC | putative exonic elements identified for retained introns |
10 20 30 40 50 60 70 80 90 100 110 120 130 140 150 160 170 180 190 200 210 220
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatgttatgttcaatatctgaaattttgtctagagattccaacacctgaaattaatgtaattttccttatttacgacaaatttaggctatacaattctacatattaagttgttctgattattctattcagGTATGTGCATAGTTACCAGAGTTACTTATGGAACCATGCTGCAAGTATGAGAGTTCAAAAGTATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC