Sequence
atgc intronic sequence ATGC exonic sequencegtagtacaacacaaaagcaccatctgttagcatgcagcatgcttgcatttctcgtctgaatagcgaggcgcatgcctgaacattattacattgcgttgtgctgaaaaaacacttgtgttttttgtatgaatatcagGTCGATGGAGTGAAGCACTCGGGCCCTACAAAGATGGTCCTCTACTTCACCGGGGCCACAAACATTCTCTACACCTTCGGTGGGCACGCTGTTACTGT
Basic information
species | Oryza sativa |
transcript | LOC_Os03g14080.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os03g14080.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G149481_T02 (Zea mays), 3'ss of exon 4
gtagtacaacacaaaagcaccatctgttagcatgcagcatgcttgcatttctcgtctgaatagcgaggcgcatgcctgaacattattacattgcgttgtgctgaaaaaacacttgtgttttttgtatgaatatcagGTCGATGGAGTGAAGCACTCGGGCCCTACAAAGATGGTCCTCTACTTCACCGGGGCCACAAACATTCTCTACACCTTCGGTGGGCACGCTGTTACTGT
|| |||| ||| | |||| | | | | ||| | ||| || ||| | | || |||| ||| || | | || | ||||| ||||| ||||||||||| || || || |||||||| ||||||||||||||||||||||||||||||||||| ||||| |||||||||||||| ||
--------gtacgcaagcgtagc--gttgaagcataatatgcattc--tgtgggcctgtggcctgtggcctgtgggtgaccggc----cgagacgatgtgt-------gtgcttctgctgctc-tacttgttgcagGTTGATGGCGTGAAGCACTCCGGGCCGACCAAGATGGTGCTCTACTTCACCGGGGCCACAAACATTCTCTACACTTTCGGAGGGCACGCTGTTACCGT
upper sequence: LOC_Os03g14080.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G149481_T03 (Zea mays), 3'ss of exon 5
gtagtacaacacaaaagcaccatctgttagcatgcagcatgcttgcatttctcgtctgaatagcgaggcgcatgcctgaacattattacattgcgttgtgctgaaaaaacacttgtgttttttgtatgaatatcagGTCGATGGAGTGAAGCACTCGGGCCCTACAAAGATGGTCCTCTACTTCACCGGGGCCACAAACATTCTCTACACCTTCGGTGGGCACGCTGTTACTGT--
|| |||| ||| | |||| | | | | ||| | ||| || ||| | | || |||| ||| || | | || | ||||| ||||| ||||||||||| || || || |||||||| ||||||||||||||||||||||||||||||||||| ||||| |||||||||||||| ||
--------gtacgcaagcgtagc--gttgaagcataatatgcattc--tgtgggcctgtggcctgtggcctgtgggtgaccggc----cgagacgatgtgt-------gtgcttctgctgctc-tacttgttgcagGTTGATGGCGTGAAGCACTCCGGGCCGACCAAGATGGTGCTCTACTTCACCGGGGCCACAAACATTCTCTACACTTTCGGAGGGCACGCTGTTACCGTGT
upper sequence: LOC_Os03g14080.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA11G11310.1 (Glycine max), 3'ss of exon 4
gtagtacaacacaaaagcaccatctgttagcatgcagcatgcttgcatttctcgtctgaatagcgaggcgcatgcctgaacattattacattgcgtt--gtgctgaaaaaacacttgtgttttttgtatgaatatcagGTCGATGGAGTGAAGCACTCGGGCCCTACAAAGATGGTCCTCTACTTCACCGGGGCCACAAACATTCTCTACACCTTCGGTGGGCACGCTGTTACTGT
||| | | | ||| || | | | || | | | ||| | | ||| | | | | ||| | | || || | | | ||| | || ||| | | || | || ||||| ||||| ||||| || || || |||| || || || || ||||||||||||||||||||||| ||||| || || |||||||||||
gtaaca-ataataaatttacaaacagatacgtactactacattattattattattactgatattcaattat-taattatatgcaattgtaattaatttagtagtaatgctatgcttttccgattgttattatgcttagATGGAAGGAGTTAAGCATTCGGGTCCGACCAAATTGGTTCTATATTTTACGGGGGCCACAAACATTCTCTACACATTCGGGGGACATGCTGTTACTGT
upper sequence: LOC_Os03g14080.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA06G11540.1 (Glycine max), 3'ss of exon 5
gtagtacaacacaaaagcaccatctgttagcatgcagcatgcttgcatttctcgtctgaatagcgaggcgcatgcctgaacat-tattacattgcgttgtgctgaaa--aaacacttgtgttttt------------tgtatgaatatc---agGTCGATGGAGTGAAGCACTCGGGCCCTACAAAGATGGTCCTCTACTTCACCGGGGCCACAAACATTCTCTACACCTTCGGTGGGCACGCTGTTACTGT
||| | || | | | | | ||| |||||| | | || |||| | | | ||| |||| | || | | || | || || | ||||||| || ||| || | || |||| || || |||| |||| | || || | || |||| ||||||||||| ||||| || ||||||||||| || || |||||||| |||||||| ||
gtaaaaagactcgatatttaggagcctcaacat-cagcataaaattaaagcaaatc-aaataacaa--tgattgctaacacatgtgatataataagtattattgttgctaattatttgtgttcttcaattaatattctgtgtgtttctctaaagGTTGAGGGGGTGACGCACACAGGGCCAGCCAAATTGGTTCTCTACTTCACTGGGGCGACCAACATTCTCTATACTTTTGGTGGGCATGCTGTTACAGT
upper sequence: LOC_Os03g14080.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA12G03490.1 (Glycine max), 3'ss of exon 4
gtagtacaacacaaaagcaccatctgttagcatgcagcatgcttgcatttctcgtctgaatagcgaggcgc--atgcctgaacattattacattgcgttgtgctgaaaaaacacttgtgttttttgtatgaatatcagGTCGATGGAGTGAAGCACTCGGGCCCTACAAAGATGGTCCTCTACTTCACCGGGGCCACAAACATTCTCTACACCTTCGGTGGGCACGCTGTTACTGT
|||||| | || | || | | | ||| | | | | | ||| | | | | | | | || | | | || | || ||| | | || | || ||||| ||||| ||||| || || || |||| || || || || ||||||||||||||||||||||| ||||| || || |||||||||||
--gtgacaacaatattcataaattaagttacaaataatttattattattattatttcatacattaaattattaatgatatgaaactgtcat-taatatagtagtaatgctatgtttttccaattgttattatgcttagATGGAAGGAGTTAAGCATTCGGGTCCGACCAAATTGGTTCTATATTTTACGGGGGCCACAAACATTCTCTACACATTCGGGGGACATGCTGTTACTGT
upper sequence: LOC_Os03g14080.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA04G43150.2 (Glycine max), 3'ss of exon 5
gtagtacaacacaaaagcaccatctgttagcat----gcagcatgcttgcatttctcgtc-tgaatagcgaggcgcatgcc-tgaacattattacattgcgttgtgctgaaaaaacacttgtgttttttgtatgaatatca-gGTCGATGGAGTGAAGCACTCGGGCCCTACAAAGATGGTCCTCTACTTCACCGGGGCCACAAACATTCTCTACACCTTCGGTGGGCACGCTGTTACTGT
||| | || | | | | ||||| | || ||| || | ||| | | | || | | |||||| || || || | | | || | ||| | | | | || || || |||| |||| | || || | || |||| ||||||||||| ||||| || ||||||||||| || || ||||| || |||||||| ||
gtaaaaagactcgatatttaggagcctcagcatcatcataaaattaaagcaaatcatataatgattgctaacacatgtgatataagtattattgttgccaattttg-tgttcttcaattaatattctgtgtgtttctctgaagGCTGAGGGGGTGACGCACACAGGGCCAGCCAAATTGGTTCTCTACTTCACTGGGGCTACCAACATTCTCTATACTTTTGGTGGACATGCTGTTACAGT
upper sequence: LOC_Os03g14080.1 (Oryza sativa), 3'ss of exon 4
lower sequence: AT2G21050.1 (Arabidopsis thaliana), 3'ss of exon 4
gtagtacaacacaaaagcaccatctgttagcatgcagcatgcttgcatttctcgtctgaatagcgaggcgcatgcctgaacattattacattgcgttgtgctgaaaaaacacttgtgttttttgtatgaatatcagGTCGATGGAGTGAAGCACTCGGGCCCTACAAAGATGGTCCTCTACTTCACCGGGGCCACAAACATTCTCTACACCTTCGGTGGGCACGCTGTTACTGT
|||| | || | | ||| | | || |||| || ||| | | || || |||| || || || |||| || ||||||||||| || || || | ||| |||| | |||||||| ||||||||||||||||| ||||| |||||||| || |||||||||||
-----------------------------------ttaatgcataaatgttatatacttgtagagttgtagataattgaattttcttatagaaggagaataatgtaatgtaccaatgttggaataataaaaat-agGTAGAAGGAGTGAAGCATTCAGGACCAAGCAAGCTGGTTTTATACTTCACAGGGGCCACAAACATTCTTTACACATTCGGTGGACATGCTGTTACTGT
upper sequence: LOC_Os03g14080.1 (Oryza sativa), 3'ss of exon 4
lower sequence: AT1G77690.1 (Arabidopsis thaliana), 3'ss of exon 4
gtagtacaacacaaaagcaccatctgttagcatgcagcatgcttgcatttctcgtctgaatagcgaggcgcatgcctgaacattattacattgcgttgtgctgaaaaaacacttgtgttttttgtatgaatatcagGTCGATGGAGTGAAGCACTCGGGCCCTACAAAGATGGTCCTCTACTTCACCGGGGCCACAAACATTCTCTACACCTTCGGTGGGCACGCTGTTACTGT
|| || ||| || | | || || ||| | ||| || | |||| ||| || | || | | | ||||| ||| || | ||| || | ||||| ||||| || || || | ||||| || ||||||||||| ||||| ||||||||||||||||| ||||| ||||| || || ||
---------------gtcattata-attaacacaaatcttgttttgattatt--ataagatatagacatatagtcctggttattgttgttt----------------aatatatttatttttcatataaaaa--agGCTGAGGATGTGAAACACTCTGGTCCAACCACAATGGTGCTTTACTTCACCGGAGCCACCAACATTCTCTACACCTTTGGTGGCCACGCCGTCACAGT
upper sequence: LOC_Os03g14080.1 (Oryza sativa), 3'ss of exon 4
lower sequence: Vv03s0038g02140.t01 (Vitis vinifera), 3'ss of exon 4
gtagtacaacacaaaagcaccatctgttagcatgcagcatgcttgcatttc--tcgtctgaatagc-gaggcgcatgcc-tgaacattattacattgcgttgtgctgaaaaaacacttgtgttttttgtatgaatatcagGTCGATGGAGTGAAGCACTCGGGCCCTACAAAGATGGTCCTCTACTTCACCGGGGCCACAAACATTCTCTACACCTTCGGTGGGCACGCTGTTACTGT
| | || | | || || || | |||| | | | ||| | || |||| || || || | | | | || | || ||||| | | ||| | || |||||||| ||||| || || | ||| |||| || |||||||| ||||| ||||||||||||||||| ||||| || || ||||| |||||
---------------------------------gtactatacatatatctcattcaaccaaatatccaaaacatatgatattaaaattagtaaatgattttat-ttatttatttatttat-ttatttgt-taatgggcagATGGAAGGAGTGAAACACTCAGGTCCATCCAAGCTGGTGCTATACTTCACAGGGGCTACAAACATTCTCTACACATTCGGGGGACATGCTGTGACTGT
upper sequence: LOC_Os03g14080.1 (Oryza sativa), 3'ss of exon 4
lower sequence: Vv18s0001g03540.t01 (Vitis vinifera), 3'ss of exon 4
gtagtaca-acacaaaagcaccatctgttagcatgcagcatgcttgcatttctcgtctgaatagcgaggcgcatgcctgaacattattacattgcgttgtgctgaaaaaacacttgtgttttttgtatgaatatcagGTCGATGGAGTGAAGCACTCGGGCCCTACAAAGATGGTCCTCTACTTCACCGGGGCCACAAACATTCTCTACACCTTCGGTGGGCACGCTGTTACTGT
||| | | | | |||| ||| || | || ||||| | ||| | | | | | || ||||||| || | || | | || | || | | |||| || || ||||||||||| ||||| || || ||||| ||||||||||| ||||| || ||||||||||||||||| ||||| || ||||| || ||
---gtatgtatttaccttaattagctgtattcat-cacttagttttaatttcaaat---aattcccataatcccatcccccctttgatacattgatttatttattaagtaatcccatgctgatttgcttgtttgaagGTTGAGGGGGTGAAGCACTCTGGCCCAACCAAAATGGTTCTCTACTTCACTGGGGCTACCAACATTCTCTACACCTTTGGTGGTCATGCTGTCACAGT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.attattacattgcgttgtgctgaaaaaacacttgtgttttttgtatgaatatcagGTCGATGGAGTGAAGCACTCGGGCCCTACAAAGATGGTCCTCTACTTCACCGGGGCCACAAACATTCTCTACACCTTCGGTGGGCACGCTGTTACTGT
ttttttgtatgaatat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtagtacaacacaaaagcaccatctgttagcatgcagcatgcttgcatttctcgtctgaatagcgaggcgcatgcctgaacattattacattgcgttgtgctgaaaaaacacttgtgttttttgtatgaatatcagGTCGATGGAGTGAAGCACTCGGGCCCTACAAAGATGGTCCTCTACTTCACCGGGGCCACAAACATTCTCTACACCTTCGGTGGGCACGCTGTTACTGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT