Sequence
atgc intronic sequence ATGC exonic sequencegtaagatatttttacactcttagtcctgcttgtaattgtctcaatgaattcattattttgctattcagctatatgcttttgttcttctagttttatttcttgctccttatctttctctttggcagGCCCAGAAACTTATAAGCCTGTGTGGATGGGAGCCAAGATGGCTTCCAAATGTTCAAGACTGCGAAGAGCATTCTGCTCAATCAGCTAGAAATGGATGTT
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv10s0003g04030.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: LOC_Os03g57160.1 (Oryza sativa), 3'ss of exon 4
gtaagatatttttacactcttagtcctgcttgtaattgtctcaatgaattcattattttgctattcagctatatgcttttgttcttctagttttatttcttgctccttatctttctctttggcagGCCCAGAAACTTATAAGCCTGTGTGGATGGGAGCCAAGATGGCTTCCAAATGTTCAAGACTGCGAAGAGCATTCTGCTCAATCAGCTAGAAATGGATGTT
||| | | ||| | | | || || | | || | |||| ||| | || | | |||| | | | | | | || | || | || ||| || |||| ||| ||||||||||| |||||||||||||| || ||||||||||||||||||||||| ||||| |||| | || ||||||| ||||| | ||
gtatgtttacttttcttccatgttctcatgtgatgtcttggttttggcattattagtttacaatgactttggagactttagctttcgttgatataacttctgat--ttgcttttgctttc--tagGCTAGGAAGCTTATAAGCCTTTGTGGATGGGAGCCTAGGTGGCTTCCAAATGTTCAAGACTGTGAAGAAAATTCAACCCACTCAGCTAAAAATGCAGATT
upper sequence: Vv10s0003g04030.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: LOC_Os07g05610.2 (Oryza sativa), 3'ss of exon 4
gtaagatatttttacactcttagtcctgcttgtaattgtctcaatgaattcattattttgctattcagctatatgcttttgttcttctagttttatt---tcttgctccttatctttctctttggc-agGCCCAGAAACTTATAAGCCTGTGTGGATGGGAGCCAAGATGGCTTCCAAATGTTCAAGACTGCGAAGAGCATTCTGCTCAATCAGCTAGAAATGGATGTT
|| || ||||| ||| | | | || ||||| || | | |||||| | | | || | | |||||| ||| | || | | | ||| | |||| ||||||||||||||||| ||||||||||| || ||||||||||||||||| || ||||| ||||| |||| | | || || | | || | |
-------------------gtaaatct-cttgttatttatgctctcatatctttatt---ctttgctgctatagtcctcagaatttgtggctttatttaatctaggtcacttccatctaatttatctagGCACAGAAACTTATAAGCCTTTGTGGATGGGAACCTAGATGGCTTCCAAATGTACAGGACTGGGAAGAAAATTCAACCCGTTCTGCCAAACATACAGCCT
upper sequence: Vv10s0003g04030.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM2G040145_T01 (Zea mays), 3'ss of exon 4
gtaagatatttttacactcttagtcctgcttgtaat-tgtctcaatgaattcattattttgctattcagctatatgcttttgttcttctagttttatttcttgctccttatctttctctttggcagGCCCAGAAACTTATAAGCCTGTGTGGATGGGAGCCAAGATGGCTTCCAAATGTTCAAGACTGCGAAGAGCATTCTGCTCAATCAGCTAGAAATGGATGTT
|| | | | | | | | || || | | | | || | || | ||| || | || | | | || ||| | ||| ||||| | |||| |||| || || || ||||||||||||||||||||||| || ||||||||||||||||||||||| ||||| |||| | || ||||||| |||| | |
---gtatgctggtcccttttcatgtacacatgctatgttttttattggcgctaacatgctattatcttgcgttgc-ctccagcttctttaatttaggtgctt-----ttatcaatgagtttg-tagGCACAAAAGCTCATAAGCCTGTGTGGATGGGAGCCTAGGTGGCTTCCAAATGTTCAAGACTGTGAAGAAAATTCAACGCATTCAGCTAAAAATTTACCCT
upper sequence: Vv10s0003g04030.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM2G013114_T01 (Zea mays), 3'ss of exon 4
gtaagatatttttacactcttagtcctgcttgtaattgtctcaatgaattcattattttgctattcagctatatgcttttgttcttctagttttatttcttgctccttatctttctctttggcagGCCCAGAAACTTATAAGCCTGTGTGGATGGGAGCCAAGATGGCTTCCAAATGTTCAAGACTGCGAAGAGCATTCTGCTCAATCAGCTAGAAATGGATGTT
|||| | | || | | | | | | | | |||||| | | |||| | | | | | | | | | || || |||| |||| | | |||| ||||| ||||| ||| | |||||||||||||| ||||||||||| ||||||||||| || |||||| |||| | | || || ||||||| | | |
---gtatatctcttcatctcttgccattgattccttcttgttgcctttttcattgatgtattattt--tcagaacatggagctttatttgatctaggtc--actccc-atctgattgat--atagGCACAGAAGCTTATTAGCGTTTGTGGATGGGAGCCTAGATGGCTTCCTAATGTTCAAGATTGGGAAGAGAATTCGACACGCTCTGCCAGAAATGCAGGCT
upper sequence: Vv10s0003g04030.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA05G27480.1 (Glycine max), 3'ss of exon 4
gtaagatatttttacactcttagtcctgcttgtaattgtctcaatgaattcattattttgctattcagctatatgcttttgttcttctagttttatttcttgctccttatctttctctttggcagGCCCAGAAACTTATAAGCCTGTGTGGATGGGAGCCAAGATGGCTTCCAAATGTTCAAGACTGCGAAGAGCATTCTGCTCAATCAGCTAGAAATGGATGTT
|| || || | | ||| | ||||| | ||| | || || |||| || | | |||||| | |||| || | | ||| |||||||||| ||||| ||||||||||| ||||| ||||| |||| |||||| |||| ||||||| || ||||| || ||||| ||||| | |||||||||| ||
-----------gtaagcttttt-ttttacttttttatgtcttg-tcaatactttggtt-gctactctgtcacatgcttattttctattaat-----------------gtacttccttttggcagGCACAGAAGCTTATAAGCCTTTGTGGGTGGGAATCAAGCTGGCTTTTAAATATTCAAGATTGTGAAGAACACTCTGCCCAATCTGAAAGAAATGGATATT
upper sequence: Vv10s0003g04030.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA08G24890.1 (Glycine max), 3'ss of exon 4
--------------------gtaagatatttttacactcttagtcctgcttgtaattgtctcaatgaattcattattttgctattcagctatatgcttttgttcttctagtt--ttatttcttgctccttatctttctctttggcagGCCCAGAAACTTATAAGCCTGTGTGGATGGGAGCCAAGATGGCTTCCAAATGTTCAAGACTGCGAAGAGCATTCTGCTCAATCAGCTAGAAATGGATGTT
||||| | ||| || | || || | | || | | | ||| | | | || | | || | | ||| || | |||||| | | | ||| |||||||||| ||||| ||||||||||| ||||| ||||| |||| |||| | |||||||||||| || ||||| || ||||| ||||| | |||||||||| ||
gtatctgaccttgaaaatgctcaagatgaggc-atactgtttatact-ctcgcataagttttttttttctttttaatgtcttgttaatacttttgttgctactctgttacatgattattttctattaatgtatcttcattttggcagGCACAGAAGCTTATAAGCCTTTGTGGGTGGGAATCAAGCTGGCGTTTAAATGTTCAAGATTGTGAAGAACACTCTGCCCAATCTGAAAGAAATGGATATT
upper sequence: Vv10s0003g04030.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA08G10480.1 (Glycine max), 3'ss of exon 6
gtaagatatttttacactcttagtcctgcttgtaattgtctcaatgaattcattattttgctattcagctatatgcttttgttcttctagttttatttcttgctccttatctttctctttggcagGCCCAGAAACTTATAAGCCTGTGTGGATGGGAGCCAAGATGGCTTCCAAATGTTCAAGACTGCGAAGAGCATTCTGCTCAATCAGCTAGAAATGGATGTT
||||| | ||||| | || | | ||| | | ||||| | | | || | |||||| || | || |||||| | |||| || | | ||||| || |||||||||| ||||| ||||||||||| ||||| ||||| |||| |||| | |||||||||||| || ||||| || ||||| ||||| | |||||||||| ||
gtaag-tgttttt---tttttttttttactttttaatgtcttgctaa--tacttttgttgctactctgttacatgcttattttctattaatgt---------------atcttcct-tttggcagGCACAGAAGCTTATAAGCCTTTGTGGGTGGGAATCAAGCTGGCGTTTAAATGTTCAAGATTGTGAAGAACACTCTGCCCAATCTGAAAGAAATGGATATT
upper sequence: Vv10s0003g04030.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: AT1G17210.1 (Arabidopsis thaliana), 3'ss of exon 4
gtaagatatttttacactcttagtcctgcttgtaattgtctcaatgaattcattattttgctat-tcagctatatgcttttgttcttctagttttatttcttgctccttatctttctctttggcagGCCCAGAAACTTATAAGCCTGTGTGGATGGGAGCCAAGATGGCTTCCAAATGTTCAAGACTGCGAAGAGCATTCTGCTCAATCAGCTAGAAATGGATGTT
| ||| ||| ||| | || ||| | | || | ||| | || |||||| | | | ||| |||| | |||| || || || |||||||| |||||||||||||| ||||||||||||||| | ||||| || ||||| |||||||| ||||||||||||||||| ||
-----------------------------------------gtaagaactcaggattcaggaatatcaa--acttactagccataaactactattgtttcttaatttatgt-tttatctt--gtagGCTCAAAAGCTGATAAGCCTATGTGGATGGGAGCCTAGATGGCTTCCAAATATCCAAGATTGTGAAGAACATTCTGCCCAATCAGCTAGAAATGGGTGCC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atatgcttttgttcttctagttttatttcttgctccttatctttctctttggcagGCCCAGAAACTTATAAGCCTGTGTGGATGGGAGCCAAGATGGCTTCCAAATGTTCAAGACTGCGAAGAGCATTCTGCTCAATCAGCTAGAAATGGATGTT
ttcttctagttttatt CT-rich tract
ttctagttttattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagatatttttacactcttagtcctgcttgtaattgtctcaatgaattcattattttgctattcagctatatgcttttgttcttctagttttatttcttgctccttatctttctctttggcagGCCCAGAAACTTATAAGCCTGTGTGGATGGGAGCCAAGATGGCTTCCAAATGTTCAAGACTGCGAAGAGCATTCTGCTCAATCAGCTAGAAATGGATGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TCAGCT