Sequence
atgc intronic sequence ATGC exonic sequence...gcatctatccattaagattatcagttcttgctatgtggtgatgcaaataggctgtttccagctcactaccaattgcttacctggtttgtttcggttgcagTGTGCCCCACTACCCTGAAAAGGATATGCAGGCAACATGGGATCACCCGTTGGCCTTCCCGGAAGATCAAGAAAGTTGGCCACTCATTAAGGAAACTCCA
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv03s0038g03710.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: LOC_Os09g37710.1 (Oryza sativa), 3'ss of exon 4
gcatctatccattaagattatcagttcttgctatgtggtgatgcaaataggctgtttccagctcactac-caattgcttacctggtttgtttcggttgcagTGTGCCCCACTACCCTGAAAAGGATATGCAGGCAACATGGGATCACCCGTTGGCCTTCCCGGAAGATCAAGAAAGTTGGCCACTCATTAAGGAAACTCCA
|| | | | | | | | | | | | || | || | | || | || | || ||| | | |||| | |||||||||| || ||||||||||| ||||||||||| ||||| || | ||| ||||| || |||||||| |||||||| | ||| || |||||||||| ||
atatgtgtttgatctagtggtaaaaaaat-caaaaaagaggaaaaagcaactgtattaaaattggctgcacatatactcaccacatctttttctctcacagTGTGCCCAACCACCCTGAAAAGAATATGCAGGCAGCATGGCATAAACCGCTGGCCATCACGGAAGATAAAGAAAGTAGACCATTCTCTAAGGAAACTGCA
upper sequence: Vv03s0038g03710.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: LOC_Os03g03900.1 (Oryza sativa), 3'ss of exon 3
gcatctatccattaa-gattatcagttcttgctatgtggtgatgcaaa-taggctgtttccagctcactaccaattgcttacctggtttgtttcggttgcagTGTGCCCCACTACCCTGAAAAGGATATGCAGGCAACATGGGATCACCCGTTGGCCTTCCCGGAAGATCAAGAAAGTTGGCCACTCATTAAGGAAACTCCA
| | ||| | | || | ||| | || ||| ||| | | | | ||| |||| || | | |||| ||| |||||||||| ||||| ||||| || ||||||||||| ||||| || | |||||||| || || ||||||||||||||||| ||||| | | |||| | ||
gaaagtatataggactaatgcttcattcactatttgcatagatataaactgcaatatctgtggctgactattgatcttatgtttctaccgttt--gttccagTGTGCCCGACTACACTGAAGAGAATATGCAGGCAGCATGGAATTAATCGTTGGCCATCACGAAAGATCAAGAAAGTTGGGCACTCCCTGAAGAAATTGCA
upper sequence: Vv03s0038g03710.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GRMZM2G109509_T01 (Zea mays), 3'ss of exon 5
gcatctatccattaagattatcagttcttgctatgtggtgatgcaaataggctgtttccagctcactaccaattgcttacctggtttgtt--tcggttgcagTGTGCCCCACTACCCTGAAAAGGATATGCAGGCAACATGGGATCACCCGTTGGCCTTCCCGGAAGATCAAGAAAGTTGGCCACTCATTAAGGAAACTCCA
|| | | | | || || |||| | || |||| | | | | ||| || ||| || ||| | | ||| |||||||||||||||| ||||| || ||||||||||| ||||| || | |||||||| || |||||||| ||||||||||| ||||| | | |||| | ||
aattccagacggaaggcagattggtcaatgcttgttcactatttgcatagaaacatcaacgttttcatcca--tgtttaactattttaatcatttgtttcagTGTGCCCCACTACACTGAAGAGAATATGCAGGCAGCATGGAATTAATCGTTGGCCATCACGGAAGATTAAGAAAGTTGGGCACTCCCTGAAGAAATTGCA
upper sequence: Vv03s0038g03710.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GRMZM2G048582_T01 (Zea mays), 3'ss of exon 3
gcatctatccattaagattatcagttcttgctatgtggtgatgcaaataggctgtttccagctcactaccaatt-----gcttacctggtttgtt-tcggttgcagTGTGCCCCACTACCCTGAAAAGGATATGCAGGCAACATGGGATCACCCGTTGGCCTTCCCGGAAGATCAAGAAAGTTGGCCACTCATTAAGGAAACTCCA
|| | | | | ||| || || | | |||| ||| |||| | || | | || | ||| | ||| || || | ||||||| ||||| ||||| ||||| ||||||||||||||||| || ||||| ||||| || || ||||||||||| || | |||||| |||| || |||||
---tccagattgtgatagaatct-tttatgacagacagc-atgcttatatatcgtttg-atctggttgcaaacttgcaaatatacttacttttttatctctcccagTGTGTCCCACGACCCTCAAAAGAATATGCAGGCAACATGGTATAACCCGCTGGCCATCACGAAAGATCAAGAAGGTAGACCACTCTCTAAGAAAGCTCCA
upper sequence: Vv03s0038g03710.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GRMZM2G053298_T01 (Zea mays), 3'ss of exon 4
gcatctatccattaagattat--cagttcttgctatgtggtgatgcaaataggctgtttccagctcactaccaattgcttacctggtttgtttcggttgcagTGTGCCCCACTACCCTGAAAAGGATATGCAGGCAACATGGGATCACCCGTTGGCCTTCCCGGAAGATCAAGAAAGTTGGCCACTCATTAAGGAAACTCCA
||| | || ||||| | || | |||| ||||| ||| || | || | | ||| || || ||| | || |||||||||| || ||||| ||||| || |||||||| ||||| || ||||| ||||| || || ||||||||||| || | |||||| |||| || || ||
-cat-tgcatcttcagattgtgatagcatcttttatgacagcatgcatatatatgtgtttgatctggttgcaaatatactaacttttttttatctcccacagTGTGCCCTACGACCCTCAAAAGAATTTGCAGGCAGCATGGTATAACCCGCTGGCCATCGCGAAAGATCAAGAAGGTAGACCACTCTCTAAGAAAGCTTCA
upper sequence: Vv03s0038g03710.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA06G00240.1 (Glycine max), 3'ss of exon 2
gcatctatccattaagattatcagttcttgctatgtggtgatgcaaataggctgtttccagctcactaccaattgcttacctggtttgtttcggttgcagTGTGCCCCACTACCCTGAAAAGGATATGCAGGCAACATGGGATCACCCGTTGGCCTTCCCGGAAGATCAAGAAAGTTGGCCACTCATTAAGGAAACTCCA
| | || | | || ||||| | | | || || | ||||| | ||| | || || ||| || | ||||| || || || || || |||||||||||||| |||||||||||||| | |||||||| |||| || ||||| || |||||||| ||||| ||||| ||
gtacgtaaattattaatttgcttcttcttcttcttctttaatttaatttctttgtttttga-taact--cgatcattt--ctgatt------gcgcgcagTATGTCCTACCACTCTAAAAAGGATATGCAGACAACATGGGATCACAAGGTGGCCTTCAAGGAAAATTAAGAAGGTAGGCCACTCTTTAAGAAAACTTCA
upper sequence: Vv03s0038g03710.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA02G48080.1 (Glycine max), 3'ss of exon 1
gcatctatccattaagattatcagttcttgctatgtggtgatgca--aataggctgtttccagctcac-taccaattgcttacctggtttgtttcggttgcagTGTGCCCCACTACCCTGAAAAGGATATGCAGGCAACATGGGATCACCCGTTGGCCTTCCCGGAAGATCAAGAAAGTTGGCCACTCATTAAGGAAACTCCA
| | || || | || |||| || ||| || | | |||| || | || | | || ||| | | ||||||||| ||||| || ||||||||||||||||| |||||||| || || || |||||||| |||| || ||||| || || ||||| || | |||||| ||
----------------gtgagatattattaatttgatatgatccattaattaattgcattc--ctcatgtagctcttaatgaa-tgaattgcat-gcatgcagTGTGTCCCACAACTCTGAAAAGGATATGCAGACAACATGGCATAACGCGATGGCCTTCAAGGAAAATAAAGAAGGTGGGGCACTCTTTGAAGAAACTACA
upper sequence: Vv03s0038g03710.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA04G00210.1 (Glycine max), 3'ss of exon 5
gcatctatccattaagattatcagttc-ttgctatgtggtgatgcaaataggctgtttccagctcactaccaattgcttacctggtttgtttcggttgcagTGTGCCCCACTACCCTGAAAAGGATATGCAGGCAACATGGGATCACCCGTTGGCCTTCCCGGAAGATCAAGAAAGTTGGCCACTCATTAAGGAAACTCCA
| | | | ||| | || | | | | | ||| | | || | ||| | | || || ||| || | ||||| || || || || || |||||||||||| | |||||||||||||| | |||||||| |||| || ||||| || |||||||| ||||| ||||| ||
--gtacgtacgtaggatgtattaatttgctttttcttatttgttttaatttgtttttgataactcg--atcgatccttt--ctgattgcgccc--ccgcagTATGTCCTACCACTCTTAAAAGGATATGCCGACAACATGGGATCACAAGGTGGCCTTCAAGGAAAATTAAGAAGGTAGGCCACTCCTTAAGAAAACTTCA
upper sequence: Vv03s0038g03710.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA14G00470.1 (Glycine max), 3'ss of exon 2
gcatctatccattaagattatcagttcttgctatgtg-gtgatgcaaataggctgtttccagctcactaccaattgcttacctggtttgtttcggttgcagTGTGCCCCACTACCCTGAAAAGGATATGCAGGCAACATGGGATCACCCGTTGGCCTTCCCGGAAGATCAAGAAAGTTGGCCACTCATTAAGGAAACTCCA
| |||| || | || || || | | | |||||||| ||| | | | | | ||||||||| ||||| || ||||||||||||||||| || || || || || | |||||||| |||| |||||||| || |||||||| || | |||||| ||
-----------gtgagat-atgatccattaataattgcattctttgtctctctctactccagctcttgtttaatgaatgaatgaatgcat---gcatgcagTGTGTCCCACGACTCTGAAAAGGATATGCAGACAGCACGGCATAACGAGGTGGCCTTCAAGGAAAATCAAGAAGGTGGGCCACTCTTTGAAGAAACTTCA
upper sequence: Vv03s0038g03710.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: AT4G35270.1 (Arabidopsis thaliana), 3'ss of exon 3
gcatctatccattaagattatcagttcttgctatgtggtgatgcaaataggctgtttccagctcactaccaattgcttacctggttt--gtttcg-gttgcagTGTGCCCCACTACCCTGAAAAGGATATGCAGGCAACATGGGATCACCCGTTGGCCTTCCCGGAAGATCAAGAAAGTTGGCCACTCATTAAGGAAACTCCA
| |||| | | || ||||| || | | || | ||| | | | | || |||| |||| |||||||| || || |||||| ||||||| |||||||| ||||| ||||| || || |||||||||||||||||||||||||| || || ||||||| |||||||||
-------gtaagaaagaaaacttatagttattatgt--ctatcttatcaatctct---cagaaagtgatgattcattcacgcagtttcattttcatgttgcagTTTGTCCAACTACCTTGAAAAGAATATGCAGACAACACGGGATAACACGATGGCCTTCCCGGAAGATCAAGAAAGTGGGGCATTCATTAAAGAAACTCCA
upper sequence: Vv03s0038g03710.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: AT2G17150.1 (Arabidopsis thaliana), 3'ss of exon 4
gcatctatccattaagattatcagttcttgctatgtggtgatgcaaataggctgttt--ccagctcactaccaattg-cttacctggtttgtttcg---gttgcagTGTGCCCCACTACCCTGAAAAGGATATGCAGGCAACATGGGATCACCCGTTGGCCTTCCCGGAAGATCAAGAAAGTTGGCCACTCATTAAGGAAACTCCA
| | |||| ||| | || |||| ||| | ||| | || | || || ||||| ||| |||||||| || || |||||| ||||||||||||||||||||||||| || | || ||||| ||||| || |||||||| ||||| || || || | |||||||||
------tggtagtggatcaatcatcatgctctacaaacattttcatcatggctatttatctgtctctcagacagtgatctgacaaggtttcgttcttgtgttgcagTTTGTCCAACTACCTTGAAAAGGATATGCAGGCAACATGGAATAATGCGATGGCCCTCCCGAAAAATCAAGAAGGTTGGGCATTCGTTGAAGAAACTCCA
upper sequence: Vv03s0038g03710.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: PP1S109_79V6.1 (Physcomitrella patens), 3'ss of exon 4
-------gcatctatccattaagattatcagttcttgctatgtg-gtgatgcaaataggctgtttccagctcactaccaattgcttacctggtttgtttcggttgcagTGTGCCCCACTACCCTGAAAAGGATATGCAGGCAACATGGGATCACCCGTTGGCCTTCCCGGAAGATCAAGAAAGTTGGCCACTCATTAAGGAAACTCCA
| | ||| ||| || | | ||| | | | | || || | | || || | |||| |||| || |||||||| || || || ||||| |||||||| |||| ||||||||| |||| ||||| || ||||||||||| || || ||| || | | ||| | ||
gcgaagaatgggtgtggatttggatg--tggtatgggttgcgtgcggggtcaagatgggtaggt----gcgtgtagttgatgtggtgtgtggtgggtttggg--gcagTGTGTCCGACGACTCTGAAGCGGATATGCCGGCAGCATGGGATCTCCCGGTGGCCGTCTCGGAAGATCAACAAGGTGAGCCGGTCGCTGAAGAAGTTGCA
upper sequence: Vv03s0038g03710.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: PP1S12_321V6.1 (Physcomitrella patens), 3'ss of exon 3
-gcatctatccat-taagattatcagttcttgctatgtggtgatgcaaataggctgtttccagctcactaccaattgcttacctggtttgtttcggttgcagTGTGCCCCACTACCCTGAAAAGGATATGCAGGCAACATGGGATCACCCGTTGGCCTTCCCGGAAGATCAAGAAAGTTGGCCACTCATTAAGGAAACTCCA
| || | | || | ||| ||| | | | | | | | | || || || | || | | ||||| | ||||| |||||||| || ||||| |||||| |||||||| |||| ||||| ||| |||| |||||||||||||||||||| || || | || ||| ||| || ||
ggtggatagctgtgtagaaagggcaggtctgtatgttctggcgtccgtgtgaaattgtggtaggtccctgctaagtaacatcgtggtt-gattcggc-gcagTGTGTCCGACTACTCTGAAACGGATATGCCGGCAGCATGGCATCTCCCGGTGGCCTTCCCGGAAGATCAACAAGGTGAGTAGGTCGCTAAAGAAGCTGCA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aataggctgtttccagctcactaccaattgcttacctggtttgtttcggttgcagTGTGCCCCACTACCCTGAAAAGGATATGCAGGCAACATGGGATCACCCGTTGGCCTTCCCGGAAGATCAAGAAAGTTGGCCACTCATTAAGGAAACTCCA
tgcttac putative branch site (score: 2)
tttgtttc putative PPT
tttgttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gcatctatccattaagattatcagttcttgctatgtggtgatgcaaataggctgtttccagctcactaccaattgcttacctggtttgtttcggttgcagTGTGCCCCACTACCCTGAAAAGGATATGCAGGCAACATGGGATCACCCGTTGGCCTTCCCGGAAGATCAAGAAAGTTGGCCACTCATTAAGGAAACTCCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - ctatcca
- - - - - - - - - - - - ttcttgc
- - - - - - - - - - - - - - - - - - - -gatgcaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cactacc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tacctgg