Sequence
atgc intronic sequence ATGC exonic sequencegttggtttctggatttcctcttcaaatgtataattgttcccttcaaatggatttcaaatgctgatgaaattgtttattatagGTGATGCGGTTTTTGACCAATCCCCACAAGCCAATGATTCTGGCTCTGTCAAGACCTGATCCAAAGAAGAACATCACCACCCTTGTCAAAGCATTTGGAG
Basic information
species | Oryza sativa |
transcript | LOC_Os01g69030.4 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os01g69030.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM5G875238_T01 (Zea mays), 3'ss of exon 5
gttggtttctgg-----atttcctcttcaaatgtataattgttcccttcaaatggatttcaaatgctgatgaaattg---------tttattatagGTGATGCGGTTTTTGACCAATCCCCACAAGCCAATGATTCTGGCTCTGTCAAGACCTGATCCAAAGAAGAACATCACCACCCTTGTCAAAGCATTTGGAG
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gttggtgcttgatcccaaattcctttgcagacctacaacaactgtcttcacaagtgtcgtaaatcttaaggtcgctgcatgacaactttgtcgcagGTGATGCGGTTCCTGACCAACCCTCACAAGCCGATGATCCTGGCGTTATCAAGACCAGACCCGAAGAAGAACATCACTACCCTCGTCAAAGCGTTTGGAG
upper sequence: LOC_Os01g69030.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G140107_T01 (Zea mays), 3'ss of exon 6
gttggtttctggat-----ttcctcttcaaatgtataattgttcccttcaaatg-----gatttcaaa--tgctg-atgaaattgtttattatagGTGATGCGGTTTTTGACCAATCCCCACAAGCCAATGATTCTGGCTCTGTCAAGACCTGATCCAAAGAAGAACATCACCACCCTTGTCAAAGCATTTGGAG
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gttggtgtttgatcccaggttcttctgcataccgacaataactgccttcacatatcgtaagtcttaaggtcactgcatgataac-ttcgtcacagGTGATGCGGTTCCTAACCAATCCTCACAAGCCGATGATCCTGGCGCTGTCGAGGCCAGACCCGAAGAAGAACATCACTACCCTCGTCAAAGCCTTTGGAG
upper sequence: LOC_Os01g69030.1 (Oryza sativa), 3'ss of exon 6
lower sequence: Vv05s0029g01140.t01 (Vitis vinifera), 3'ss of exon 6
gttggtttctggatttcctcttcaaatgtataattgttcccttcaaatggatttca--aatgctgatgaaattgtttattatagGTGATGCGGTTTTTGACCAATCCCCACAAGCCAATGATTCTGGCTCTGTCAAGACCTGATCCAAAGAAGAACATCACCACCCTTGTCAAAGCATTTGGAG
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gtgagtatctgg-ttttgtctgtaactatttgtttctgctcatcttcttcatgtcattatctcacatttaacttggttctgcagTTGATGCGCTTCCTCACAAATCCACATAAGCCAATGATCTTGGCCCTATCAAGACCAGATCCAAAAAAGAACATTACCACTCTTCTGAAAGCTTTTGGGG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gtataattgttcccttcaaatggatttcaaatgctgatgaaattgtttattatagGTGATGCGGTTTTTGACCAATCCCCACAAGCCAATGATTCTGGCTCTGTCAAGACCTGATCCAAAGAAGAACATCACCACCCTTGTCAAAGCATTTGGAG
tgctgat putative branch site (score: 3)
atgaaattgtttatta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttggtttctggatttcctcttcaaatgtataattgttcccttcaaatggatttcaaatgctgatgaaattgtttattatagGTGATGCGGTTTTTGACCAATCCCCACAAGCCAATGATTCTGGCTCTGTCAAGACCTGATCCAAAGAAGAACATCACCACCCTTGTCAAAGCATTTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG