Sequence
atgc intronic sequence ATGC exonic sequencegtgctcgtcgcgggaggtttcctagGTGCTGGAGCGCCCCAACGCCGGCCTCGTCCTCATCACCACCGCTCGCTTCTACGCCGTCGTCCTCCCGCCCCGCGACCAGCTCACCCACGACGAATCCT
Basic information
species | Oryza sativa |
transcript | LOC_Os03g48160.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os03g48160.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G030839_T02 (Zea mays), 3'ss of exon 2
---------------------------------------------------------------------------------------------------------------------gtgctcgtcgcgggaggtttcctagGTGCTGGAGCGCCCCAACGCCGGCCTCGTCCTCATCACCACCGCTCGCTTCTACGCCGTCGTCCTCCCGCCCCGCGACCAGCTCACCCACGACGAATCCT
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gtcagtactcgctagcagcctagcaccgtcctttcactgtctcgctcccccgctaaggttccgcactgggccccgatctgaccgcgttgtcgcagGGTGGCGTCGGCGCCGGGGAAGGTGCTCATCGCGGGAGGATACCTCG-TGCTGGAGCGCCCCAACGCCGGCCTAGTTCTCAGCACCACCGCCCGCTTCTAC----------------------------------------------
upper sequence: LOC_Os03g48160.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G019260_T01 (Zea mays), 3'ss of exon 1
-------------------------------------------------------------------------------------------------------------------------------gtgctcgtcgcgggaggtttcctagGTGCTGGAGCGCCCCAACGCCGGCCTCGTCCTCATCACCACCGCTCGCTTCTACGCCGTCGTCCTCCCGCCCCGCGACCAGCTCACCCACGACGAATCCT
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gtgaggagcactcgctagcaccgtcatttcactgtcccgctcgcacgctaaggttccgcatctacctacctatctctgggctccgatctgacggcgttgtcgcagGGTGGCGTCGGCGCCGGGGAAGGTGCTCATCGCGGGAGGATACCTCG-TGCTGGAGCGCCCCAACGCCGGCCTAGTCCTCAGCACCACCGCCCGCTTCTAC---------------------------------------------- atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gtgctcgtcgcgggaggtttcctagGTGCTGGAGCGCCCCAACGCCGGCCTCGTCCTCATCACCACCGCTCGCTTCTACGCCGTCGTCCTCCCGCCCCGCGACCAGCTCACCCACGACGAATCCT
tttcct CT-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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgctcgtcgcgggaggtttcctagGTGCTGGAGCGCCCCAACGCCGGCCTCGTCCTCATCACCACCGCTCGCTTCTACGCCGTCGTCCTCCCGCCCCGCGACCAGCTCACCCACGACGAATCCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA