Sequence
atgc intronic sequence ATGC exonic sequencegtatgcacaaatgttcaattccttaaattcttgggttaaattcagtgcaccaaaaaaatgccaaattgtattattcttgatatctaatttctcactttgcagGGCATGTACGGAACATCTATTTTCCTTTTGACATAGAGGCCGATACCGCATTGAGTGTTGCAACTGAGATGGTAGCCGAGCTAGATATAACTGACCATGA
Basic information
species | Oryza sativa |
transcript | LOC_Os07g38530.2 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os07g38530.2 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G089159_T01 (Zea mays), 3'ss of exon 6
gtatgcacaaatgttcaattccttaaattcttgggttaaattcagtgcaccaaaaaaatgccaaattgtattattcttgatatctaatttctcactttgcagGGCATGTACGGAACATCTATTTTCCTTTTGACATAGAGGCCGATACCGCATTGAGTGTTGCAACTGAGATGGTAGCCGAGCTAGATATAACTGACCATGA
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gtatgcacaatt--tctatggcataaacttctg----aagttttg--------aaaaatcgtttttggtatcactgaaagttgttgtttttttcatatgcagGACGGGTACGCAACATCTATTTTCCTTTTGACGTTGAGGCTGATACCGCACTAAGTGTTGCTACTGAAATGGTAGCCGAACTCGATATAACTGACCATGA
upper sequence: LOC_Os07g38530.2 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA20G28410.1 (Glycine max), 3'ss of exon 3
----------gtatgcacaaatgttcaattccttaaattcttgggttaaattcagtgcaccaaaaaaatgccaaattgtattattcttgatatctaatttctcactttgcagGGCATGTACGGAACATCTATTTTCCTTTTGACATAGAGGCCGATACCGCATTGAGTGTTGCAACTGAGATGGTAGCCGAGCTAGATATAACTGACCATGA
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tttctttttagtcttgataatttcatattctgttttttttttttctcatactttctacataagaaaaa----aaaccaaacta------acaatccattcct--ctaaatagGTCGAATTAGAAATATCTACTTCCCATTTGACATTGAGACTGATACCGCATTGAGTGTTGCAAATGAAATGGTAGCTGAGCTCGACATAAATGACCAAGA
upper sequence: LOC_Os07g38530.2 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA10G39390.1 (Glycine max), 3'ss of exon 6
-----------------------------------------gtatgcacaaatgttcaattccttaaattcttgggttaaattcagtgcaccaaaaaaatgccaaattgtattattcttgatatctaatttctcactttgcagGGCATGTACGGAACATCTATTTTCCTTTTGACATAGAGGCCGATACCGCATTGAGTGTTGCAACTGAGATGGTAGCCGAGCTAGATATAACTGACCATGA
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gttagcatttcactttcttattttcttcttgaacttttttagtctttgataat-ttcatattctgttgtttttctgatacttgctacataagcaaaaaaaaccaaacta-acaatgcattcc-tctaaaatctaaat----agGTCGAATTAGAAACATCTACTTCCCATTTGACATTGAGACTGATACCGCACTGAGTGTTGCAAATGAAATGGTAGCTGAGCTTGATATAAATGACCAAGA
upper sequence: LOC_Os07g38530.2 (Oryza sativa), 3'ss of exon 6
lower sequence: AT3G04910.1 (Arabidopsis thaliana), 3'ss of exon 6
gtatgcacaaatgttcaattccttaaattcttgggttaaattcagtgcaccaaaa---aaatgccaaattgtattattcttgatatctaatttctcactttgcagGGCATGTACGGAACATCTATTTTCCTTTTGACATAGAGGCCGATACCGCATTGAGTGTTGCAACTGAGATGGTAGCCGAGCTAGATATAACTGACCATGA
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----gtaacaatattctctttatcttttccttgtttcataacctatgaagaagagtggaaaaaatgcagtttctttcatttgattcatggactggtttgttgcagGACGTGTCCGAAACATTTACTTCCCATTTGACATTGAGACGGACACCGCATTGAGCGTTGCAACAGAGATGGTAGCGGAACTGGATATGGACGATCATGG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.caccaaaaaaatgccaaattgtattattcttgatatctaatttctcactttgcagGGCATGTACGGAACATCTATTTTCCTTTTGACATAGAGGCCGATACCGCATTGAGTGTTGCAACTGAGATGGTAGCCGAGCTAGATATAACTGACCATGA
ttctcac putative branch site (score: 2)
tttctcacttt CT-rich tract
aaattgtattattctt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatgcacaaatgttcaattccttaaattcttgggttaaattcagtgcaccaaaaaaatgccaaattgtattattcttgatatctaatttctcactttgcagGGCATGTACGGAACATCTATTTTCCTTTTGACATAGAGGCCGATACCGCATTGAGTGTTGCAACTGAGATGGTAGCCGAGCTAGATATAACTGACCATGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG