Sequence
atgc intronic sequence ATGC exonic sequencegtaatgccttggatgcacaatatattggttgtaattctgcagaaaattttgtgctggatttattaaagttctcgccgcatgtaattgtttttgcagACATTGTGTCGAATGTTCATCATTAATGCTGGGCCAGGATTCCGACTTCTTTGGAGCACAGTGAAGAGTTTCCTTGACCCAAAGACCACAGCAAAGATTC
Basic information
species | Oryza sativa |
transcript | LOC_Os02g24430.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os02g24430.2 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G162461_T01 (Zea mays), 3'ss of exon 6
gtaatgccttggatgcacaatatattggttgtaattctgcagaaaattt-tgtgctggatt--tattaaagttctcgccgcatgtaattgtttttgc-agACATTGTGTCGAATGTTCATCATTAATGCTGGGCCAGGATTCCGACTTCTTTGGAGCACAGTGAAGAGTTTCCTTGACCCAAAGACCACAGCAAAGATTC
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gtaatccctttgatatgtgttttgccttcagacattttatctgaattttgtaagcaatattgttcttaccatgccagtttttcttctcttttggtgctagACCCTGTGCCGCATGTTCATCATCAATGCAGGCCAGGGATTCCGGCTTCTATGGGGCACCGTCAAGAGCTTTCTTGACCCAAAGACCACTGCAAAGATTC
upper sequence: LOC_Os02g24430.2 (Oryza sativa), 3'ss of exon 6
lower sequence: AT2G21540.3 (Arabidopsis thaliana), 3'ss of exon 5
--------gtaatgccttggatgcacaatatattggttgtaattctgcagaaaattttgtgctggatttattaaagttctcgccgcatgtaattgtttttgcagACATTGTGTCGAATGTTCATCATTAATGCTGGGCCAGGATTCCGACTTCTTTGGAGCACAGTGAAGAGTTTCCTTGACCCAAAGACCACAGCAAAGATTC
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gttactatgttgttttcttaatggttttgaaatagtttgtaattatctctatcaagttaaaatggcacta--agaattgtttttgtgttta-tggatcatatagACATTGAACCGTATGTTCATTATCAACGCTGGTAGTGGATTCAGGCTTCTGTGGAGCACTGTGAAATCTTTCCTTGACCCAAAGACCACCGCAAAGATTC
upper sequence: LOC_Os02g24430.2 (Oryza sativa), 3'ss of exon 6
lower sequence: AT2G18180.1 (Arabidopsis thaliana), 3'ss of exon 5
gtaatgccttggatgcacaatat-attggttgtaattctgcagaaaattttgtgctggatttattaaagttctcgccgcatgtaattgtttttg---cagACATTGTGTCGAATGTTCATCATTAATGCTGGGCCAGGATTCCGACTTCTTTGGAGCACAGTGAAGAGTTTCCTTGACCCAAAGACCACAGCAAAGATTC
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gtg-cactttatattattatcatcattggtttatcttttatgaatgatt-----cttgctctctcaacttttttttttcatttatctgtcattggctcagACCTTGAACAGGATGTTTATCATCAATGCTGGCTCAGGATTCAGGATGTTGTGGAACACGGTTAAGTCTTTCCTTGACCCAAAGACTACAGCAAAGATCC
upper sequence: LOC_Os02g24430.2 (Oryza sativa), 3'ss of exon 6
lower sequence: AT4G39180.1 (Arabidopsis thaliana), 3'ss of exon 6
gtaatgccttggatgcacaatatattggttgtaattctgcagaaaattttgtgctggatttattaaagttctcgccgcatgtaattgtttttgcagACATTGTGTCGAATGTTCATCATTAATGCTGGGCCAGGATTCCGACTTCTTTGGAGCACAGTGAAGAGTTTCCTTGACCCAAAGACCACAGCAAAGATTC
|| | || | | | || ||| |||| | | | || | || | | | | | | | | ||| |||| || || ||||||||||| |||||||| || || | ||| | |||| ||||||||| |||||||||||||||||| |||||||||||||
gtttagttatgtttttggacgttcttctttgagtttctataatggttctgacgc-------agcaacatgacctctgtgtttgtgtttcgttgtagACGCTGAACCGTATGTTCATCATCAATGCTGGTTGTGGGTTTAGGCTTTTATGGAACACAGTGAAATCTTTCCTTGACCCAAAGACTACAGCAAAGATTC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gaaaattttgtgctggatttattaaagttctcgccgcatgtaattgtttttgcagACATTGTGTCGAATGTTCATCATTAATGCTGGGCCAGGATTCCGACTTCTTTGGAGCACAGTGAAGAGTTTCCTTGACCCAAAGACCACAGCAAAGATTC
ttgttttt CT-rich tract
atttattaaagttct 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaatgccttggatgcacaatatattggttgtaattctgcagaaaattttgtgctggatttattaaagttctcgccgcatgtaattgtttttgcagACATTGTGTCGAATGTTCATCATTAATGCTGGGCCAGGATTCCGACTTCTTTGGAGCACAGTGAAGAGTTTCCTTGACCCAAAGACCACAGCAAAGATTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG