Sequence
atgc intronic sequence ATGC exonic sequence...caatgcctttaaattgtcatgcttttagtttgtggcatgtgctgttagtagtacagttgaaattttgagtagtgatgagagaaatgtgttgtacctgcagGAGGGAGTGCAACAGCTTGTTCTTGGGTTGTACATCATAAGGGGCGACAACAT
Basic information
species | Oryza sativa |
transcript | LOC_Os05g51650.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os05g51650.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM5G872417_T01 (Zea mays), 3'ss of exon 4
caatgcctttaaattgtcatgcttttagtttgtggcatgtgctgttagt---agtacagttgaaattttgagtagtgatgagagaaatgtgttgtacctgcagGAGGGAGTGCAACAGCTTGTTCTTGGGTTGTACATCATAAGGGGCGACAACAT
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-tgcgtactgcatgtggcactatcatattctctaatttctgctgttcatgagaatttggcagcacatttggatccttatgataaacatg-attg-acttgcagGAGGGAGTCCAACAACTTGTTCTTGGTCTGTACATTATCAGGGGTGACAACAT
upper sequence: LOC_Os05g51650.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA08G18410.1 (Glycine max), 3'ss of exon 4
----caatgcctttaaattgtcatgcttttagtttgtggcatgtgctgttagtagtacagttgaaattttgagtagtgatgagagaaatgtgttgtacctgcagGAGGGAGTGCAACAGCTTGTTCTTGGGTTGTACATCATAAGGGGCGACAACAT
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tttatattagctgcagattttttttctttaaagtcacagtttaagccttgcacaattttttt----ctgtctgatgtcatcatcattcttgtttctaactacagGAAGGTGTGCAACAACTTGTTCTTGGTTTGTACATCATCAGGGGTGACAATAT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tagtagtacagttgaaattttgagtagtgatgagagaaatgtgttgtacctgcagGAGGGAGTGCAACAGCTTGTTCTTGGGTTGTACATCATAAGGGGCGACAACAT
ttgaaatttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
caatgcctttaaattgtcatgcttttagtttgtggcatgtgctgttagtagtacagttgaaattttgagtagtgatgagagaaatgtgttgtacctgcagGAGGGAGTGCAACAGCTTGTTCTTGGGTTGTACATCATAAGGGGCGACAACAT
caatgcc
- - - - - - - -gtcatgc
- - - - - - - - - - - - - - - - tggcatg
- - - - - - - - - - - - - - - - - - - -tgctgtt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gtgatga