Sequence
atgc intronic sequence ATGC exonic sequencegtaaataacaccccttctctctcagatgttgtgtgtgtgtgtatgtgtgtgtaagggctctctcagatgttcaagagcttgtacctgctgagtgctaacttctttcctgcatcatgcttcagGTATAAGATTATTAAGGAAGTTGGTGACGGAACATTTGGGAGTGTTTGGCGCGCGATCAACAAAGAGAGTGGTGAAGTG
Basic information
species | Oryza sativa |
transcript | LOC_Os06g02555.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os06g02555.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM5G864414_T02 (Zea mays), 3'ss of exon 4
gtaaataacaccccttctctctcagatgttgtgtgtgtgtgtatgtgtgtgtaagggctctctcagatgttcaagagcttgtacctgctgagtgctaacttctttcctgcatcatgcttcagGTATAAGATTATTAAGGAAGTTGGTGACGGAACATTTGGGAGTGTTTGGCGCGCGATCAACAAAGAGAGTGGTGAAGTG
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----------------------gtgagaatg-gtctataaccagacgattataacaaattagaatactgtctaag---ctgt-ttggatgtcttcttaccttgtttttgcattgcgctccagATATACAATTATCAACGAAGTTGGTGATGGAACATTTGGGAGTGTTTGGCGTGCAACCAATAAGGAAAGCGGTGAAGTG
upper sequence: LOC_Os06g02555.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GLYMA16G17580.1 (Glycine max), 3'ss of exon 1
gtaaataacaccccttctctctcagatgttgtgtgtgtgtgtatgtgtgtgtaagggctctctcagatgttcaagagcttgtacctgctgagtgctaacttctttcctgcatcatgcttcagGTATAAGATTATTAAGGAAGTTGGTGACGGAACATTTGGGAGTGTTTGGCGCGCGATCAACAAAGAGAGTGGTGAAGTG
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---------------------gtgagtatttgttgcagaagcctgaagttactatacccctct----tttttactgtcaaatatct-ttaaggtttttcttccttccgtgaaca-----cagGTACAAGTTAATTAAGGAAGTTGGTGATGGAACATTTGGGAGTGTTTGGAGAGCCATTAATAAGCAAAGTGGTGAAGTT
upper sequence: LOC_Os06g02555.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GLYMA16G08080.1 (Glycine max), 3'ss of exon 1
gtaaataacaccccttctctctcagatgttgtgtgtgtgtgtatgtgtgtgtaagggctctctcagatgttcaagagcttgtacctgctgagtgct-----aacttctttcctgcatcatgcttcagGTATAAGATTATTAAGGAAGTTGGTGACGGAACATTTGGGAGTGTTTGGCGCGCGATCAACAAAGAGAGTGGTGAAGTG
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------------------------------------gtgagtatttgtttcagaagcctgaaattgctatacccctctttttac-tgttgaatatccttaaggtttttctcccttccctgaacacagGTACAAGTTAATTAAGGAAGTAGGTGATGGAACATTTGGGAGTGTTTGGAGAGCCATTAATAAGCAAAGTGGTGAAGTT
upper sequence: LOC_Os06g02555.1 (Oryza sativa), 3'ss of exon 1
lower sequence: AT5G45430.1 (Arabidopsis thaliana), 3'ss of exon 3
gtaaataacaccccttctctctcagatgttgtgtgtgtgtgtatgtgtgtgtaagggctctctcagatgttcaagagcttgtacctgctgagtgctaacttctttcctgcatcatgcttcagGTATAAGATTATTAAGGAAGTTGGTGACGGAACATTTGGGAGTGTTTGGCGCGCGATCAACAAAGAGAGTGGTGAAGTG
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----------------gtaggtttgatttctctcatctttttctctattcttt--ggcttccgagccgggtttatagtttgt----gcttaattctcaatgcctta-tgca----attgtagGTATACATTACTCAAAGAAGTTGGTGACGGAACATTTGGGAATGTTTGGCGAGCTGTCAATAAACAGACGAATGAAGTT
upper sequence: LOC_Os06g02555.1 (Oryza sativa), 3'ss of exon 1
lower sequence: Vv02s0033g01110.t01 (Vitis vinifera), 3'ss of exon 1
gtaaataacaccccttctctctcagatgttgtgtgtgtgtgtatgtgtgtgtaagggctctctcagatgttcaagagcttgtacctgctgagtgctaacttctttcctgcatcatgcttc---agGTATAAGATTATTAAGGAAGTTGGTGACGGAACATTTGGGAGTGTTTGGCGCGCGATCAACAAAGAGAGTGGTGAAGTG
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--------------------------------------gtgagtgggcttgtatggaa---cttgcttgtt--aatatttgtattt-taatgtgttgatatgtctgagagttttggcctctacagGTATACGATAATCAAGGAAGTTGGTGATGGGACTTTTGGAAGTGTTTGGCGAGCAATAAATAAGCAGACTGGTGAAGTT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgttcaagagcttgtacctgctgagtgctaacttctttcctgcatcatgcttcagGTATAAGATTATTAAGGAAGTTGGTGACGGAACATTTGGGAGTGTTTGGCGCGCGATCAACAAAGAGAGTGGTGAAGTG
tgctaac putative branch site (score: 1)
cttctttcctgcatc CT-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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaaataacaccccttctctctcagatgttgtgtgtgtgtgtatgtgtgtgtaagggctctctcagatgttcaagagcttgtacctgctgagtgctaacttctttcctgcatcatgcttcagGTATAAGATTATTAAGGAAGTTGGTGACGGAACATTTGGGAGTGTTTGGCGCGCGATCAACAAAGAGAGTGGTGAAGTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA