Sequence
atgc intronic sequence ATGC exonic sequence...tacctgcatctatctcacacatacatatagctatacctcatcaccaacaattttgcttcttgtgctgctcctaattttgcttcttgtgttgcaccaccagGAGCAGCAAGGAGGCATCTGCAGGAGCTTATGATCATCTGGGGGAGCTGGACCAGGCCTTGTTCATGTACCTGGATCATGGCAGCCATGCGGCGTCGCAC
Basic information
species | Oryza sativa |
transcript | LOC_Os09g31390.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os09g31390.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G125934_T01 (Zea mays), 3'ss of exon 1
-tacctgcatctatctcacacatacatatagctatacctcatcaccaacaattttgctt-cttgtgctgctcctaattttgcttcttgtgttgcaccaccagGAGCAGCAAGGAGGCATCTGCAGGAGCTTATG------ATCATCTGGGGGAGCTGGACCAGGCCTTGTTCATGTACCTGGATCATGGCAGCCATGCGGCGTCGCAC
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aaatcccgtgccaaaaagcgtctatatatatcaataatgtcacatcagtgttgtcacatacgtatg-tatacacacatgtg-tatttctgtctcacgagcagGAGCGGCAAGGAGGCGTCGTCAGGAGCGTATGCGTATGACCATCTGGGCGAGCTGGACCAGGCGTTGTTCATGTACCTGGATCACGGCAG--AAGCCATGGC----
upper sequence: LOC_Os09g31390.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G006578_T03 (Zea mays), 3'ss of exon 1
tacctgcatctatctcaca-catacatat-agctatacctcatcaccaacaattttgcttcttgtgctgctcctaattttgcttcttgtgttgcaccaccagGAGCAGCAAGGAGGCATCTGCAGGAGCTTATGATCATCTGGGGGAGCTGGACCAGGCCTTGTTCATGTACCTGGATCATGGCAGC---CATG-CGGCGTCGCAC
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gcctttcagagttttcagagcgtctatatcagtagtgtcaca-cagtcacatcagtgttgttacagatgtatccatgtgtg-tatttctgtttcacaagcagGAGCGGCAAGGAGGCGTC---AGGGGCGTATGACCATCTGGGCGAGCTGGACCAGGCGCTGTTCATGTACCTGGATCACGGCAGCAGCCATGGCGGCGGCGCC- atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aacaattttgcttcttgtgctgctcctaattttgcttcttgtgttgcaccaccagGAGCAGCAAGGAGGCATCTGCAGGAGCTTATGATCATCTGGGGGAGCTGGACCAGGCCTTGTTCATGTACCTGGATCATGGCAGCCATGCGGCGTCGCAC
tcctaat putative branch site (score: 2)
taatttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tacctgcatctatctcacacatacatatagctatacctcatcaccaacaattttgcttcttgtgctgctcctaattttgcttcttgtgttgcaccaccagGAGCAGCAAGGAGGCATCTGCAGGAGCTTATGATCATCTGGGGGAGCTGGACCAGGCCTTGTTCATGTACCTGGATCATGGCAGCCATGCGGCGTCGCAC
-acctgca
- - - - - - - - - -catacat
- - - - - - - - - - - - - - - - - - - - -caccaac
- - - - - - - - - - - - - - - - - - - - - - - - - - -tgcttct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgctgct