Sequence
atgc intronic sequence ATGC exonic sequence...tttctgtaaattatatcttatattcaattctgatcgttttatcttttcttcatacctcatgtttttattctcaagttagattggatctgtttaatgttagGCTATTGCCTCTGCCAGAATGAAAGGAGAATACCCTGAGAGGATGGGGCAACCAGAATGTCAG
Basic information
species | Oryza sativa |
transcript | LOC_Os01g68860.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os01g68860.3 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G107491_T03 (Zea mays), 3'ss of exon 2
----tttctgtaaatt-atatcttatattcaattctgatcgttttatcttttcttcatacctcatgtttttattctcaagttagattggatctgtttaatgttagGCTATTGCCTCTGCCAGAATGAAAGGAGAATACCCTGAGAGGATGGGGCAACCAGAATGTCAG
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tgcttccttgcaaatttacgtctt-tatttaa--ctaatcattgt-tttttacttcatataccat-tttttgttctcaagttaggttgaatctgtttaattttagGCTATTGCCTCTGCCAGAATGAAGGGAGAATATCCTGAGAGAGTGGGACAGCCAGAGTGTCAG
upper sequence: LOC_Os01g68860.3 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G087032_T03 (Zea mays), 3'ss of exon 2
tttctgtaaattatatcttatattcaattctgatcgttttatcttttcttcatacctcatgtttttattctcaagttagattggatctgtttaatgttagGCTATTGCCTCTGCCAGAATGAAAGGAGAATACCCTGAGAGGATGGGGCAACCAGAATGTCAG
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-----------tatgtctt-tatttgag--tactcgtttt--ttttacttcatatcccat-tttttgttctcaagttaggttgaatctgtttaattttaggctattgcctctgccagAATGAAGGGAGAATATCCTGAGAGAGCGGGACAGCCAGAGTGTCAG
upper sequence: LOC_Os01g68860.3 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G087032_T04 (Zea mays), 3'ss of exon 2
-----tttctgtaaatt-atatcttatattcaattctgatcgttttatcttttcttcatacctcatgtttttattctcaagttagattggatctgtttaatgttagGCTATTGCCTCTGCCAGAATGAAAGGAGAATACCCTGAGAGGATGGGGCAACCAGAATGTCAG
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gtgcttctatgcaaatttatgtctt-tatttgag--tactcgtttt--ttttacttcatatcccat-tttttgttctcaagttaggttgaatctgtttaattttagGCTATTGCCTCTGCCAGAATGAAGGGAGAATATCCTGAGAGAGCGGGACAGCCAGAGTGTCAG
upper sequence: LOC_Os01g68860.3 (Oryza sativa), 3'ss of exon 2
lower sequence: Vv04s0023g00370.t01 (Vitis vinifera), 3'ss of exon 2
tttctgtaaattatatcttatattcaattctgatcgttttatcttttcttcatacctcatgtttttattctcaagttagattggatctgtttaatg--ttagGCTATTGCCTCTGCCAGAATGAAAGGAGAATACCCTGAGAGGATGGGGCAACCAGAATGTCAG
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ctaattcaaatagagcagcatgtttctgtatgtacacatgtgcatttacacacata-catgctcatgtt-tcctctaaacttaaccttgattgataatctagGCTATTGCCACTGCAAGGATGAAAGGAGAGTTCCCGGAGAGAATGGGACAGCCAGAATGTCAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttcttcatacctcatgtttttattctcaagttagattggatctgtttaatgttagGCTATTGCCTCTGCCAGAATGAAAGGAGAATACCCTGAGAGGATGGGGCAACCAGAATGTCAG
gtttaat putative branch site (score: 4)
tctgttt CT-rich tract
atgtttttatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tttctgtaaattatatcttatattcaattctgatcgttttatcttttcttcatacctcatgtttttattctcaagttagattggatctgtttaatgttagGCTATTGCCTCTGCCAGAATGAAAGGAGAATACCCTGAGAGGATGGGGCAACCAGAATGTCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG