Sequence
atgc intronic sequence ATGC exonic sequence...atatttatatatgaaagaatagatccaacttttctcttatgttgttgagatgctagtgttaggtgctttgtaccactaaaggtcaatgttcttttggcagTCTATGCAAAAAGGTGATCCATCTTGGAGCGGTTACATCTATGCTTTCTCAATCTTCGCTGGAGTG
Basic information
species | Oryza sativa |
transcript | LOC_Os04g52900.1 |
intron # | 8 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os04g52900.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G084181_T01 (Zea mays), 3'ss of exon 8
------------------------------------------atatttatatatga-aagaatagatccaacttttctcttatg---ttgttgagatgctagtgttaggtgctttgtaccactaaaggtcaatgttct---tttggcagTCTATGCAAAAAGGTGATCCATCTTGGAGCGGTTACATCTATGCTTTCTCAATCTTCGCTGGAGTG
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gtacacttctcattccatgacccctacccatcattaacagtgctactgaagtgcattgattctagaacagactgtgcgattatgcatttcttagcgcacctttattatgctctttgcaccaataaactttgtttcccccccttttccagTCTATGCAAAAAGGTGATCCATCTTGGAGCGGGTACATCTATGCTTTCTCAATCTTTGCAGGAGTG
upper sequence: LOC_Os04g52900.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GLYMA06G46940.1 (Glycine max), 3'ss of exon 9
-atatttatatatgaaagaatagatccaacttttctcttatgttgttgagatgctagtgttaggtgctttgt-accactaaaggtcaatgttcttttggcagTCTATGCAAAAAGGTGATCCATCTTGGAGCGGTTACATCTATGCTTTCTCAATCTTCGCTGGAGTG
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taattttgttattacgttgatgatttcatttctacaagtatgtttgtggcttgttc-tgctagctacattatcatttattgtgatttatgctgaat-gacagTCAATGCAAAGAGGAGACCCATCTTGGATTGGTTACATCTATGCCTTCTCAATATTTGTTGGAGTG
upper sequence: LOC_Os04g52900.1 (Oryza sativa), 3'ss of exon 8
lower sequence: Vv10s0003g04390.t01 (Vitis vinifera), 3'ss of exon 8
atatttatatatgaaagaa---tagatccaacttttctcttatgttgttgagatgctagtgttaggtgctttgtaccactaaaggtcaatgttcttttggcagTCTATGCAAAAAGGTGATCCATCTTGGAGCGGTTACATCTATGCTTTCTCAATCTTCGCTGGAGTG
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--gtttaggcacagtagatgtccaaatcacagatctgattatcttagttattttttttcttctaactgttat-cgcttatattatttgatgaatcatgtgcagTCTATGCAACAAGGAGATCCAGCTTGGATTGGTTATATCTATGCTTTCTCAATTTTTGTTGGAGTG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgagatgctagtgttaggtgctttgtaccactaaaggtcaatgttcttttggcagTCTATGCAAAAAGGTGATCCATCTTGGAGCGGTTACATCTATGCTTTCTCAATCTTCGCTGGAGTG
cactaaa putative branch site (score: 2)
tgttctttt putative PPT
ttctttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
atatttatatatgaaagaatagatccaacttttctcttatgttgttgagatgctagtgttaggtgctttgtaccactaaaggtcaatgttcttttggcagTCTATGCAAAAAGGTGATCCATCTTGGAGCGGTTACATCTATGCTTTCTCAATCTTCGCTGGAGTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA