Sequence
atgc intronic sequence ATGC exonic sequencegttttaaccttgtataagcttcactctgaaatgttaattagaaagccctaacctgccacatcatgtttctaatgaatttgagttcatagGCTTTACTGGAAGCCATGGAGCAGCAATGTGTATCTGTGGCAAAGGCTGGCCTTGTGGCAAGTTTATCAGCCCGTACTTCTGTGCTAGCGGCTGCTAATC
Basic information
species | Oryza sativa |
transcript | LOC_Os05g38850.1 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os05g38850.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM2G163658_T01 (Zea mays), 3'ss of exon 8
------------gttttaaccttgtat-aagcttcactctgaaatgttaattagaaag------ccctaacctgccacatcatgtttctaatgaatttgagttcatagGCTTTACTGGAAGCCATGGAGCAGCAATGTGTATCTGTGGCAAAGGCTGGCCTTGTGGCAAGTTTATCAGCCCGTACTTCTGTGCTAGCGGCTGCTAATC
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gtattacaattatttttcaccttatatgaagctttctcatgaagttttcaccagtgaggaagttcccatgcctatctatttgtgtttctaattgtttctggttctcagGCTTTACTTGAAGCCATGGAGCAGCAATGTGTTTCTATTGCAAAGGCTGGTCTTGTAGCAAGTTTGTCAGCTCGAACTTCAGTGTTGGCAGCTGCAAATC
upper sequence: LOC_Os05g38850.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GLYMA19G36230.1 (Glycine max), 3'ss of exon 8
gttt-taaccttgtataagc---ttcactctgaaatgttaattagaaa-gccctaacctgccacatcatgtttcta-atgaatttgagttcata--gGCTTTACTGGAAGCCATGGAGCAGCAATGTGTATCTGTGGCAAAGGCTGGCCTTGTGGCAAGTTTATCAGCCCGTACTTCTGTGCTAGCGGCTGCTAATC
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gtttgttctctggtgtctggcaatcaatttcttgttactactttaatatattttaaacttttacctgaaaccttaacgtgaaattgtaataatacagGCTTTACTCGAGGCGATGGAGCAACAGTGTGTCTCTATTGCAAAGGCGGGATTAGTAGCAAGTTTATCATCCAGGACTTCTGTCTTAGCGGCTGCAAACC
upper sequence: LOC_Os05g38850.1 (Oryza sativa), 3'ss of exon 9
lower sequence: AT3G09660.1 (Arabidopsis thaliana), 3'ss of exon 9
gttttaaccttgtataagcttcactctgaaatgttaattagaaagccctaacctgccacatcatgtttctaatgaatttgagttcatagGCTTTACTGGAAGCCATGGAGCAGCAATGTGTATCTGTGGCAAAGGCTGGCCTTGTGGCAAGTTTATCAGCCCGTACTTCTGTGCTAGCGGCTGCTAATC
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------gttttttcttatcggcaatgtca----ttacttctgatgttgacatttttctcattac---ttacatcactttgca---acagGCGTTGCTAGAAGCAATGGAACAACAATGTGTCTCTGTTGCAAAGGCTGGGCTTGTAGCTAGTCTATCAGCTCGAACTTCTGTTATAGCAGCAGCAAATC
upper sequence: LOC_Os05g38850.1 (Oryza sativa), 3'ss of exon 9
lower sequence: Vv08s0040g03290.t01 (Vitis vinifera), 3'ss of exon 9
gttttaaccttgtataagcttcactctgaaatgttaattagaaagccctaacctgccacatcatgtttctaatgaatttgagttcat---agGCTTTACTGGAAGCCATGGAGCAGCAATGTGTATCTGTGGCAAAGGCTGGCCTTGTGGCAAGTTTATCAGCCCGTACTTCTGTGCTAGCGGCTGCTAATC
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-------gtttggcctgactaatcattgatgtatcgtttg---acctctaattgtcaagaccacacatttc-taattttgagtttacctcagTCTCTTCTAGAAGCCATGGAGCAACAGTGTGTCTCTGTTGCAAAGGCTGGACTTGTGGCAAGTTTATCAGCACGAACTTCTGTCTTAGCAGCGGCAAATC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.taattagaaagccctaacctgccacatcatgtttctaatgaatttgagttcatagGCTTTACTGGAAGCCATGGAGCAGCAATGTGTATCTGTGGCAAAGGCTGGCCTTGTGGCAAGTTTATCAGCCCGTACTTCTGTGCTAGCGGCTGCTAATC
ttctaat putative branch site (score: 2)
tttctaatgaattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttttaaccttgtataagcttcactctgaaatgttaattagaaagccctaacctgccacatcatgtttctaatgaatttgagttcatagGCTTTACTGGAAGCCATGGAGCAGCAATGTGTATCTGTGGCAAAGGCTGGCCTTGTGGCAAGTTTATCAGCCCGTACTTCTGTGCTAGCGGCTGCTAATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT