Sequence
atgc intronic sequence ATGC exonic sequence...ctctaggtcactaaatgatcttcatctatatattatacatttttttcttttcatctatgctttctaggttgtcattaattatctgtttaaatatttgcagAGAGTATTTTGGAGAGGTGTTGTTGAAGAGCTTTTGTGGTTTATTAGTGGTTCAACAAATGCAAAG
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv18s0001g12940.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: LOC_Os12g26060.1 (Oryza sativa), 3'ss of exon 3
ctctaggtcactaaatgatcttcat-ctatatattatacatttttttcttttcatctatgctttctaggttgtcattaattatctgtttaaatatttgcagAGAGTATTTTGGAGAGGTGTTGTTGAAGAGCTTTTGTGGTTTATTAGTGGTTCAACAAATGCAAAG
| || | | | | | ||| ||| | ||| || |||||| | | || || || | | ||| ||| ||| | || ||||| ||||||||| | |||||| |||||||||| |||||||| |||||||| |||||||||||||||
cccttgtgtatttactaatcctcaaacagcataacatttatttttatttattatcctggactacttttgaaaagtgaaatgttctctttgcct-ttaccagAGGGTATTTTGGCGTGGTGTTCTTGAAGAGCTATTGTGGTTCATTAGTGGCTCAACAAATGCAAAG
upper sequence: Vv18s0001g12940.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: LOC_Os11g29390.1 (Oryza sativa), 3'ss of exon 4
------ctctaggtcactaaatgatcttcatctatatattatacatttttttcttttcatctatgctttctaggttgtcattaattatctgtttaaatatttgcagAGAGTATTTTGGAGAGGTGTTGTTGAAGAGCTTTTGTGGTTTATTAGTGGTTCAACAAATGCAAAG
| ||| |||| |||| | || |||| | | | || || | | || | | | || | | | | || |||| ||||||||||| |||||||||||||| || ||||||| || ||||| || |||| |||||||
atgtatatgtagaa-actagcccctcttaagctgtataatgtgagtgttgggtttccttttctttattattgaaatataataacatgatgctct-----ttaacagAAGGTATTTTGGAGGGGTGTTGTTGAAGAACTCCTGTGGTTCATCAGTGGCTCGACAAGTGCAAAG
upper sequence: Vv18s0001g12940.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GRMZM2G005990_T01 (Zea mays), 3'ss of exon 4
---ctctaggtcactaaatgatcttcatctatatattatacatttttttcttttcatctatgctttctaggttgtcattaattatctgtttaaatatttgcagAGAGTATTTTGGAGAGGTGTTGTTGAAGAGCTTTTGTGGTTTATTAGTGGTTCAACAAATGCAAAG
|| | | |||| | || | ||||||| || | | || | ||| |||| || | | | | | || ||||| ||||||||| | |||||||| ||||| || | ||||| || ||||| |||||||||||||||
ccaatccaaagtccaaaataaagtttgaagaactattatatgttaccatatatttagctaccaattct---ttattaatggaacaacatgtgctctttaacagAGGGTATTTTGGCGTGGTGTTGTCGAAGAACTCCTTTGGTTCATCAGTGGCTCAACAAATGCAAAG
upper sequence: Vv18s0001g12940.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA06G01280.1 (Glycine max), 3'ss of exon 4
------------------------------------------------------------------------------------ctctaggtcactaaatgatcttcatctatatattatacatttttttc----------ttttcatctatgctttctaggttgtcattaa---ttatctgtttaaatatttgcagAGAGTATTTTGGAGAGGTGTTGTTGAAGAGCTTTTGTGGTTTATTAGTGGTTCAACAAATGCAAAG
|| | | | ||| || | | || || | ||| | | | || | | || | ||| | || | || | | ||| ||| |||||||||| |||| ||||||||||||||| | |||||||| ||||| ||||||||||| |||
gcatgtattagagattatggtttaagatgtgtttgatctgctgtgtaaaataacttgtcttttgtgtgaattcttttctttttcctttggttttgataattattgtgtttactactttggatgtttgctatggaaggggaatatctatttgtaaattttgatagagaatttgacttgatttcttcgattgattgtagAAAGTATTTTGGCGAGGGGTTGTTGAAGAGCTTCTTTGGTTTATCAGTGGCTCAACAAATGCCAAG
upper sequence: Vv18s0001g12940.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA04G01240.1 (Glycine max), 3'ss of exon 4
ctctaggtcactaaatgatcttcatctatatattatacatttttttcttttcatctatgctttctaggttgtcattaattatctgtttaaatatttgcagAGAGTATTTTGGAGAGGTGTTGTTGAAGAGCTTTTGTGGTTTATTAGTGGTTCAACAAATGCAAAG
| || || ||| | | || | || || | ||| |||||||||||||| |||| ||||||||||||||| | |||||||| ||||| ||||| ||||| |||
----------------------------------------------------gtaaat-tttggtagagaatttcacttgatttcttcaattgattgtagAGAGTATTTTGGCGAGGGGTTGTTGAAGAGCTTCTTTGGTTTATCAGTGGGTCAACGAATGCCAAG
upper sequence: Vv18s0001g12940.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA12G04480.1 (Glycine max), 3'ss of exon 4
-----------------------------------------------------------------------------------------ctctaggtcactaaatgatcttcatctatatattatacatttttttcttttcatctatgctttctaggttgtcattaattatctgtttaaatatttgcagAGAGTATTTTGGAGAGGTGTTGTTGAAGAGCTTTTGTGGTTTATTAGTGGTTCAACAAATGCAAAG
| | | || | | | | | | | | | | | | | ||||| || | | | |||| ||| | |||| ||| || ||| |||||||||| |||| || |||||||||||| | |||||||| ||||| ||||||| ||| |||
gtatgtatgaattttggttttgggttcatatatactactgcatagtaatttcttatttgtgtgctacttatctgatgcaattgttgtttgtgtttattgcttgaaagtttattggagaagactgaagaatatctgttgtacatct-tgatataaaagttgacatgatttattcatttgg---ttcctagAAAGTATTTTGGCGAGGGGTAGTTGAAGAGCTTCTTTGGTTTATCAGTGGCTCAACAAGTGCCAAG
upper sequence: Vv18s0001g12940.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: AT4G34570.1 (Arabidopsis thaliana), 3'ss of exon 6
-------ctctaggtcactaaatgatcttcatctatatattatacatttttttcttttcatctatgc-tttctaggttgtcattaattatctgtttaaatatttgcagAGAGTATTTTGGAGAGGTGTTGTTGAAGAGCTTTTGTGGTTTATTAGTGGTTCAACAAATGCAAAG
| || || | | | || | | || | ||| | || || ||| | || | | || | | | || | || ||||||| || ||||||||||||||||| || ||| | ||||| || || |||||||| |||||||||
gtatgttcacttttacattgacttttcatgttttaagcccaaagagagtttgcttcgtcttccctgcatatccggactaacaagatctgtttgcatttcacttgaaagAGAGTTTTCTGGAGAGGTGTTGTTGAGGAACTTCTATGGTTCATAAGCGGTTCAACCAATGCAAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tcttttcatctatgctttctaggttgtcattaattatctgtttaaatatttgcagAGAGTATTTTGGAGAGGTGTTGTTGAAGAGCTTTTGTGGTTTATTAGTGGTTCAACAAATGCAAAG
cattaat putative branch site (score: 3)
ttgtcattaattatct 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ctctaggtcactaaatgatcttcatctatatattatacatttttttcttttcatctatgctttctaggttgtcattaattatctgtttaaatatttgcagAGAGTATTTTGGAGAGGTGTTGTTGAAGAGCTTTTGTGGTTTATTAGTGGTTCAACAAATGCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - cactaaa