Sequence
atgc intronic sequence ATGC exonic sequence...atatattacttattttgtagtatatggtttccaccaattaatttgatattttaatttctcttgttgaccttcatagtttctcttcttctattgaattcagTTGCTTGGCTATGGATGGGCTGGCCTGTTCAGAAAATACCTAGTGGACTCCCCCTATATGTGGTGGCCATCAAATCTAGTCCAAGTCTCTCTCTTCAG
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv19s0015g00870.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: LOC_Os08g23130.3 (Oryza sativa), 3'ss of exon 3
atatattacttattttgtagtatatggttt-ccaccaattaatttgatattttaatttctcttg-ttgaccttcatagtttctcttcttctattgaattcagTTGCTTGGCTATGGATGGGCTGGCCTGTTCAGAAAATACCTAGTGGACTCCCCCTATATGTGGTGGCCATCAAATCTAGTCCAAGTCTCTCTCTTCAG
|| | | || | | || || || ||| | | | || ||| || | | | | || || || ||| || ||||||||||| ||||||||||| || ||||||| || ||||| || ||||| |||| ||||||||||| ||||| || ||||||||| | ||||||||
----gttgccactcatgcattggttgattagtaacaaatcgaagacctgatcaaacacacattgattaatccaaaaatggccttttatttgatttcatacagTTGCTTGGGTATGGATGGGCCGGATTGTTCAGGAAGTACCTGGTTGACTCAGCCTACATGTGGTGGCCGTCAAACCTCGTCCAAGTCACCCTCTTCAG
upper sequence: Vv19s0015g00870.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: LOC_Os08g38400.1 (Oryza sativa), 3'ss of exon 2
-------------------------------------------------------------------atatattacttattttgtagtatatggtttccaccaatta---atttgatattttaatttctcttgttgaccttcatagtttctcttcttctattgaattcagTTGCTTGGCTATGGATGGGCTGGCCTGTTCAGAAAATACCTAGTGGACTCCCCCTATATGTGGTGGCCATCAAATCTAGTCCAAGTCTCTCTCTTCAG
| |||| ||||| || || | | || |||| | | ||||| ||| || | || | |||| ||| ||| || | || ||||| ||||||||||| |||||||| | || |||||||| || || ||||||||||| ||||| | || || || || ||||||||
gtacatacatgtgacttcgactgacacctgacaaattgtgtcctgaaaattgtttccatgttctagttggaagtactgattttcaggttcataatctttctgtgttgctggtttgctgtcttaatctcttttttc--ttttggctctaatctttctgtgtttgtgggcagCTGATGGGATATGGTTGGGCTGGCCTCTTCAGAAAGTTTCTTGTGGACTCACCTTACATGTGGTGGCCTTCAAACTTGGTACAGGTTTCACTCTTCAG
upper sequence: Vv19s0015g00870.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA02G47140.1 (Glycine max), 3'ss of exon 1
atatattacttattttgtagtatatggtttcca--ccaattaatttgatattttaatttctcttgttgaccttcatagtttctc---ttcttctattgaatt--cagTTGCTTGGCTATGGATGGGCTGGCCTGTTCAGAAAATACCTAGTGGACTCCCCCTATATGTGGTGGCCATCAAATCTAGTCCAAGTCTCTCTCTTCAG
|||| | | | ||| | | | || |||||| | | || | || | | |||||| | ||||||| || ||||||| |||||||||||||| | ||||| | || ||| ||||| ||||| || ||||||||||| ||||| || |||||||| ||||| |||||
-------acttctcccatcacagatgcctcctaatcctattaatcatcaaaagaacttgcattttcaaatatggttagtttactaaaccgtgtcgttgaatttttagATGCTTGGTTATGGATGGGCTGGGATTTTCAGGAGATTCCTTGTGGATTCCCCGTACATGTGGTGGCCTTCAAACCTTGTCCAAGTGTCTCTATTCAG
upper sequence: Vv19s0015g00870.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA14G01610.1 (Glycine max), 3'ss of exon 4
-atatattacttattttgtagtatatggtttccaccaat-taatttgatattttaatttctcttgttgaccttcatagtttctcttcttctattgaattcagTTGCTTGGCTATGGATGGGCTGGCCTGTTCAGAAAATACCTAGTGGACTCCCCCTATATGTGGTGGCCATCAAATCTAGTCCAAGTCTCTCTCTTCAG
|| || |||||| | || | | | |||| | | || | | ||| | | || | | || || || ||||||| |||||||||||||| | ||||| |||| || || || ||||| || ||||||||||| ||||| || |||||||| ||||| |||||
ggaatccacttttctttgtattttacaatcaaaatttctataatagaactctctattatagaaaaatgaaatctgctaaaccgtgtcgttgaatg--tttagATGCTTGGTTATGGATGGGCTGGGATTTTCAGGAAATGTCTTGTAGATTCCCCGTACATGTGGTGGCCTTCAAACCTTGTCCAAGTGTCTCTATTCAG
upper sequence: Vv19s0015g00870.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: AT4G26590.1 (Arabidopsis thaliana), 3'ss of exon 2
atatattacttattttgta-gtatatggtttccaccaattaatttgatattttaatttctcttgttgaccttcatagtttctcttcttctattgaattcagTTGCTTGGCTATGGATGGGCTGGCCTGTTCAGAAAATACCTAGTGGACTCCCCCTATATGTGGTGGCCATCAAATCTAGTCCAAGTCTCTCTCTTCAG
||| ||||| | || | ||||| | | || || | ||||| | | |||| | | || | | || ||||| | || ||||||||||| || ||||||| ||||||||||||||||| || || ||||||||||| ||||||| || |||||||||||||| ||
----------------gtatgtatacacaatatacaatataattcaaaaattacatagtttttgtttg---taacagttacattatttatctgtcatgtagTTGTTGGGATATGGATGGGCGGGTATGTTCAGGAAATACCTAGTGGACTCACCTTACATGTGGTGGCCTGCAAATCTTGTTCAAGTCTCTCTCTTTAG
upper sequence: Vv19s0015g00870.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: AT5G55930.1 (Arabidopsis thaliana), 3'ss of exon 2
---atatattacttattttgtagtatatggtttccaccaattaatttgatattttaatttctcttgttgaccttcatagtttctcttcttctattgaattcagTTGCTTGGCTATGGATGGGCTGGCCTGTTCAGAAAATACCTAGTGGACTCCCCCTATATGTGGTGGCCATCAAATCTAGTCCAAGTCTCTCTCTTCAG
|| || | |||| || | || | || ||||||| | | | ||| ||| | || | | | | |||||| | || |||||||||||||| | ||||| || | ||| ||||| || || |||||||||||||| |||||| | || |||||||| ||||| ||
tgtgggtaatagtcatttaaatac-tagaactatggcctaagaaacaaatatttttaacgatttg--tgatctttaagactttaacaatcatttcttttgcagTTGTTGGGATATGGATGGGCTGGAATCTTCAGGAAGTTCCTTGTGGATTCACCGTATATGTGGTGGCCGTCAAATTTGGTTCAAGTCTCACTCTTTAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atattttaatttctcttgttgaccttcatagtttctcttcttctattgaattcagTTGCTTGGCTATGGATGGGCTGGCCTGTTCAGAAAATACCTAGTGGACTCCCCCTATATGTGGTGGCCATCAAATCTAGTCCAAGTCTCTCTCTTCAG
tgttgac putative branch site (score: 3)
tttctcttcttctatt putative PPT
ttaatttct 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
atatattacttattttgtagtatatggtttccaccaattaatttgatattttaatttctcttgttgaccttcatagtttctcttcttctattgaattcagTTGCTTGGCTATGGATGGGCTGGCCTGTTCAGAAAATACCTAGTGGACTCCCCCTATATGTGGTGGCCATCAAATCTAGTCCAAGTCTCTCTCTTCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - ccaccaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cttgttg