Sequence
atgc intronic sequence ATGC exonic sequencegtaagaatgctaaacatttactctcaatatgccgacaccttttcacaatgttttcctttttatttccctggcataatcatggtaatacaattgacatcttgtctagGCAATGCAGCAGTTTCTAAAAATGTGAAGAACAAGGTTTTCTCCATCGATCTTGTTTCAGAGGACCCTTCAGTCATTGCCTGTGATATGGCTCAT
Basic information
species | Oryza sativa |
transcript | LOC_Os02g38060.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os02g38060.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM5G876003_T03 (Zea mays), 3'ss of exon 4
gtaagaatgctaaacatttact--ctcaatatgccgacaccttttcacaatgttttcctttttatttccctggcataatcatggtaatacaattgacatcttgtctagGCAATGCAGCAGTTTCTAAAAATGTGAAGAACAAGGTTTTCTCCATCGATCTTGTTTCAGAGGACCCTTCAGTCATTGCCTGTGATATGGCTCAT
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------attcttacggtcttgtagctggttctttttgcaagtttcttcctgttatatctttttattttcttggctcagttatgagaatactattcatatttt--ccagGCAATGCAGCAGTTGCAAAAAATCTGAAGAACAAGGTTTTCTCCATTGATCTCGTTTCAGATGAACCTTCAGTGATTGCTTGTGATATGGCTCAT
upper sequence: LOC_Os02g38060.2 (Oryza sativa), 3'ss of exon 4
lower sequence: AT5G40530.1 (Arabidopsis thaliana), 3'ss of exon 4
gtaagaatgctaaacatttactctcaatatgccgacaccttttcacaatgttttcctttttatttccctggcata-atcatggtaatacaattgacatcttgtctagGCAATGCAGCAGTTTCTAAAAATGTGAAGAACAAGGTTTTCTCCATCGATCTTGTTTCAGAGGACCCTTCAGTCATTGCCTGTGATATGGCTCAT
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--------------------gtgagaat-ttcttatcctgtattgctatatcttactttttgcctgctgaaattgtatcactctatcgacactaatattgtctc-agGTGATGCAAGGATTGCTAAAAGTGTGAAGAACAAAGTTTTCTCCTTTGATCTTGTCTCAAAGAACCCCTCTGTTATTGCCTGCGATATGTCAAAT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttcctttttatttccctggcataatcatggtaatacaattgacatcttgtctagGCAATGCAGCAGTTTCTAAAAATGTGAAGAACAAGGTTTTCTCCATCGATCTTGTTTCAGAGGACCCTTCAGTCATTGCCTGTGATATGGCTCAT
aattgac putative branch site (score: 3)
tcttgtct CT-rich tract
tttttattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagaatgctaaacatttactctcaatatgccgacaccttttcacaatgttttcctttttatttccctggcataatcatggtaatacaattgacatcttgtctagGCAATGCAGCAGTTTCTAAAAATGTGAAGAACAAGGTTTTCTCCATCGATCTTGTTTCAGAGGACCCTTCAGTCATTGCCTGTGATATGGCTCAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA