Sequence
atgc intronic sequence ATGC exonic sequencegtactaatcacacattttctcatattttgtacttaaaatgctttatgcatcatactgcaaatgttttttttgcagGCTGCGACAAAAGTAATGATGAAGAAGAAAAAG
Basic information
species | Oryza sativa |
transcript | LOC_Os02g30060.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os02g30060.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G043602_T03 (Zea mays), 3'ss of exon 5
------------------gtactaat-cacacattttctcatattttgtacttaaaatgctttatgcatcatactgcaaatgttttttttgcagGCTGCGACAAAAGTAATGATGAAGAAGAAAAAG
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gtatccccccacccccctacacccacacccacacccacacacattttgctcaacagttattgtttccatctta-tatcaacatataccttgcagGCTGCAACAAAAGTAATGATGAAGAAGAAAAAG
upper sequence: LOC_Os02g30060.1 (Oryza sativa), 3'ss of exon 6
lower sequence: EFJ26070 (Selaginella moellendorffii), 3'ss of exon 5
gtactaatcacacattttctcatattttgtacttaaaatgctttatgcatcatactgcaaatgttttttttgcagGCTGCGACAAAAGTAATGATGAAGAAGAAAAAG
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---------------gttcgtccatcagtctttcagactgctcgtctgagaaaagtg--actttatgcactgcagGCTGCTACGAAAGTCATGATGAAGAAGAAAAAG
upper sequence: LOC_Os02g30060.1 (Oryza sativa), 3'ss of exon 6
lower sequence: EFJ14471 (Selaginella moellendorffii), 3'ss of exon 5
gtactaatcacacattttctcatattttgtacttaaaatgctttatgcatcatactgcaaatgttttttttgcagGCTGCGACAAAAGTAATGATGAAGAAGAAAAAG
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-------------gttcgtccat---cagtctttcagactgctcgtccgagaaaa-gtgactttatgcactgcagGCTGCTACGAAAGTCATGATGAAGAAGAAAAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.catattttgtacttaaaatgctttatgcatcatactgcaaatgttttttttgcagGCTGCGACAAAAGTAATGATGAAGAAGAAAAAG
tgtttttttt CT-rich tract
aaatgtttttttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtactaatcacacattttctcatattttgtacttaaaatgctttatgcatcatactgcaaatgttttttttgcagGCTGCGACAAAAGTAATGATGAAGAAGAAAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA