Sequence
atgc intronic sequence ATGC exonic sequencegtatattgtgcatttcaatcatgtctcatgctttgcatctgcgctaatttcagcataaggaatgaatgctcatttgcaaatttcctgttgtctagGACTACAACTGCAGCGTGGAGTTCTTCCGCTCCCCTTTCCTTGTTCAGGAATGGGAGTTCCCCGTCAGGAAGGGTTTAACCAAGGAAACTCTTAGGCTTG
Basic information
species | Oryza sativa |
transcript | LOC_Os02g53380.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os02g53380.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G165961_T01 (Zea mays), 3'ss of exon 2
----gtatattgtgcatttcaatcatgtctc----atgctttgcat-ctgcgctaatttcagcataaggaatgaatgctcatttgcaaatttcctgttgtct---agGACTACAACTGCAGCGTGGAGTTCTTCCGCTCCCCTTTCCTTGTTCAGGAATGGGAGTTCCCCGTCAGGAAGGGTTTAACCA---AGGAAACTCTTAGGCTTG
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gtagatatgccttcttttttatttattttttggctatctctggctttctttgctagtttcatcaactagaacaaactcttacgcacaaacatgctgttgtttcatagGACTACAACTGCAGTGTGGAGTTCTTCCGCTCCCCTTTCCTTGTTCAGGAATGGGAGATGCCAGTCAGCAATGGGAAGGGTACACGGGAAACTCTCAGGC---
upper sequence: LOC_Os02g53380.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM5G843892_T01 (Zea mays), 3'ss of exon 2
gtatat-tgtgcatttcaatcatg-tctcatg--ctttgcatctgcgctaatttcagcataaggaatgaatgctcatt-tgcaaatttcctgttgtct---agGACTACAACTGCAGCGTGGAGTTCTTCCGCTCCCCTTTCCTTGTTCAGGAATGGGAGTTCCCCGTCAGGAAGGGTTTA---ACCAAGGAAACTCTTAGGCTTG
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gtagatacgtacgccttattccagcttttgtcatctctggctctatgctagtttcctcaactagaacagactcttaaagcgcgaacatgctgttgctttatagGACTACAATTGTAGTGTGGAGTTCTTCCGCTCCCCTTTCCTTGTTCAGGAATGGGAGATGCCAATCAGCAACGGAAAGGGTACCCGGGAAACTCTCAGGC--- atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gcgctaatttcagcataaggaatgaatgctcatttgcaaatttcctgttgtctagGACTACAACTGCAGCGTGGAGTTCTTCCGCTCCCCTTTCCTTGTTCAGGAATGGGAGTTCCCCGTCAGGAAGGGTTTAACCAAGGAAACTCTTAGGCTTG
cgctaat putative branch site (score: 3)
tttcctgtt putative PPT
aaattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatattgtgcatttcaatcatgtctcatgctttgcatctgcgctaatttcagcataaggaatgaatgctcatttgcaaatttcctgttgtctagGACTACAACTGCAGCGTGGAGTTCTTCCGCTCCCCTTTCCTTGTTCAGGAATGGGAGTTCCCCGTCAGGAAGGGTTTAACCAAGGAAACTCTTAGGCTTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA