Sequence
atgc intronic sequence ATGC exonic sequence...tgggtaactcattatgtgttttaggattttctaatcataaggtttaagcactctgtgaaatgtgatggttattgatctacttgttattttaatttttcagAATGAAGATGGAAGCAAAATTGAATACAGGGTTTGGAACCCCTTCCGTTCAAAGTTGGCTGCTGCCATTCTTGGTGGTGTTGATGAGATCTGGATT
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv16s0050g00880.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: LOC_Os05g08360.2 (Oryza sativa), 3'ss of exon 2
------tgggtaactcattatgtgttttaggatt--ttctaatcataaggtttaagcactctgtgaaatgtgatggttattgatctacttgttattttaatttttcagAATGAAGATGGAAGCAAAATTGAATACAGGGTTTGGAACCCCTTCCGTTCAAAGTTGGCTGCTGCCATTCTTGGTGGTGTTGATGAGATCTGGATT
|| | ||| ||| | | | || |||| ||||| || | | | | | ||| ||| || ||| ||| || | || | | |||||||| ||||||| ||| ||||||||||||| ||||| |||||||||||||||||||||||||| | |||||||||||||| | |||||||||
gtagtgtgatacaaagattgtgtacatgacgcttgtttctgttcata---ttgatctgttttattgtacatgactgttgtt--tctgctt-ttctgcta--tgtacagAATGAGGATGGAACCAAGGTTGAATACAGGGTGTGGAATCCCTTCCGTTCAAAGTTGGCTGCTGCTGTGCTTGGTGGTGTTGACAACATCTGGATT
upper sequence: Vv16s0050g00880.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: LOC_Os02g57590.2 (Oryza sativa), 3'ss of exon 2
-----tgggtaactcattatgtgttttaggattttcta---atcataaggtttaagcactctgtgaaatgtgatggttattgatctacttgttattttaatttttcagAATGAAGATGGAAGCAAAATTGAATACAGGGTTTGGAACCCCTTCCGTTCAAAGTTGGCTGCTGCCATTCTTGGTGGTGTTGATGAGATCTGGATT
| |||| || |||| | ||| | | | || | | || || | || || || ||| |||||| | || | | || |||||||| ||||||| || ||||||||||||| ||||||||||||||||| ||| |||||||||| | ||||||||||| || | |||||||||
aggaatctgtaag--ataatgttctgtagaagtctgtatgttttgttgcattgtagtgtaccctgcaa-gttatgcttattgctgatgtttctgcgtgaa-----cagAATGAGGATGGAACTAAGGTTGAATACAGGGTGTGGAACCCCTTCCGTTCTAAGCTGGCTGCTGCTGTGCTTGGTGGTGTCGACAACATCTGGATT
upper sequence: Vv16s0050g00880.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GRMZM2G105480_T01 (Zea mays), 3'ss of exon 1
tgggtaactcattatgtgttttaggattttctaatcataaggtttaa--gcactctgtgaaa---tgtgatggttattgatctactt--gttattttaatttttcagAATGAAGATGGAAGCAAAATTGAATACAGGGTTTGGAACCCCTTCCGTTCAAAGTTGGCTGCTGCCATTCTTGGTGGTGTTGATGAGATCTGGATT
||| ||| | |||| ||| | | ||| |||| || |||| || || || | | || |||| | || ||||||| ||||||| || | |||| |||||| ||||||||||||||||| |||||||||||||| | |||||||||||||| | |||||||||
-------ctctaaatgcttcagtggatccaagaatgggagagcctaaaagcaccaaatgtgtctttgtgctgtttttttctgttgttagattatctgggcattgtagAATGAGGATGGAACAAAGGTCGAATGCAGGGTGTGGAACCCCTTCCGTTCCAAGTTGGCTGCTGCTGTGCTTGGTGGTGTTGACAACATCTGGATT
upper sequence: Vv16s0050g00880.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GRMZM2G363678_T01 (Zea mays), 3'ss of exon 1
tgggtaactcattatgtgttttag--gattttctaatcataaggttta--agcactctgtgaa---atgtgatggttattgatctacttg-ttattttaatttttcagAATGAAGATGGAAGCAAAATTGAATACAGGGTTTGGAACCCCTTCCGTTCAAAGTTGGCTGCTGCCATTCTTGGTGGTGTTGATGAGATCTGGATT
| || || || || ||| ||| | | || ||||| || |||| || || || | | | |||| | || ||||||| ||||||| || | |||| |||||| ||||||||||||||||| ||| ||| |||||| | |||||||||||||| | |||||||||
--------cctctaaatgcttcagtggatccaagaatgggagagcctaaaagcacaaaatgtgtctttgtgctgttttttctgttgttagattatctgggaattgtagAATGAGGATGGAACAAAGGTCGAATGCAGGGTGTGGAACCCCTTCCGTTCCAAGCTGGTTGCTGCTGTGCTTGGTGGTGTTGACAACATCTGGATT
upper sequence: Vv16s0050g00880.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GRMZM2G110119_T01 (Zea mays), 3'ss of exon 1
tgggtaactcattatgtgttttaggattttctaatcataaggtttaagcactctgtgaaatgtgatggttattgatctacttgttattttaatttttcagAATGAAGATGGAAGCAAAATTGAATACAGGGTTTGGAACCCCTTCCGTTCAAAGTTGGCTGCTGCCATTCTTGGTGGTGTTGATGAGATCTGGATT
|| |||| | | || | | | ||| || ||| || |||| | | | | |||||| || ||||||| ||| ||| || ||||||||||||| |||||||||||||||| ||| ||||| ||| | |||||||||||||| | |||||||||
----------gacataggtttgaaactcatccatt---gggattttggc----tgtagaac-tgatttatttctactgtttgattatttgggcattgtagaatgatgattgaacaaagGTTGAATACAGGGTGTGGAACCCCTTCCGTTTGAAGCTGGCTACTGTTGTGCTTGGTGGTGTTGACAACATCTGGATT
upper sequence: Vv16s0050g00880.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA11G36090.1 (Glycine max), 3'ss of exon 1
tgggtaactcattatgtgttttaggattttctaatcataaggtttaagcactctgtgaaatgtgatggttattgatctacttgttattttaatttttcagAATGAAGATGGAAGCAAAATTGAATACAGGGTTTGGAACCCCTTCCGTTCAAAGTTGGCTGCTGCCATTCTTGGTGGTGTTGATGAGATCTGGATT
|| || | | | | | ||| | | ||| || || | | | || | ||| || ||| ||||| |||||||||||||| | |||| || ||||| |||||||| || ||||| || ||||||||||||||||| |||||||| ||||| | || ||||||
------gttccttttctttctcaccattattt-----ctgtttttctttccttgttggtactgaaccatgtatgcatgaattgatagtttcattttgcagAATGAAGATGGTACCAAAGAGGAGTACAGAGTTTGGAATCCTTTCCGATCCAAGTTGGCTGCTGCCATCCTTGGTGGAGTTGACAACATATGGATT
upper sequence: Vv16s0050g00880.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA06G17310.1 (Glycine max), 3'ss of exon 1
-------------------tgggtaactcattatgtgttttaggattt--tctaatca------taaggtttaagcactctgtgaaatgtgatggttattgatctacttgttattttaatttttcagAATGAAGATGGAAGCAAAATTGAATACAGGGTTTGGAACCCCTTCCGTTCAAAGTTGGCTGCTGCCATTCTTGGTGGTGTTGATGAGATCTGGATT
| | ||||||| |||||| ||| | ||| | ||| || || |||| ||| | | | | ||| | | |||| ||||| ||||| | |||| ||| ||||| |||||||| || |||||||| |||||||| |||||||| |||||||||||||| | || ||||||
gttattttctttctcaccttttaaacatcattatttgtttttttctttcttttaagtagataaataaatgttgtacatctattgaagaagcatg--cgtgaaatgattggttttcatttttttacagAACGAAGACAGTTCCAAAGATGAGTACAGAGTTTGGAATCCTTTCCGTTCGAAGTTGGCCGCTGCCATCCTTGGTGGTGTTGACAACATATGGATT
upper sequence: Vv16s0050g00880.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA04G37770.1 (Glycine max), 3'ss of exon 2
-------------tgggtaactcattat-gtgttttaggattttctaatcataaggtttaagcactctgtgaaatgtgatggttattgatctacttgttattt-taatttttcagAATGAAGATGGAAGCAAAATTGAATACAGGGTTTGGAACCCCTTCCGTTCAAAGTTGGCTGCTGCCATTCTTGGTGGTGTTGATGAGATCTGGATT
| | | | | || ||| |||||| | | || | || | | | || | || || | | | ||| | ||||| ||||| ||||| || |||| ||| ||||| |||||||| || ||||| || ||||||||||||||||| |||||||| ||||| | || ||||||
gttattttctttctcaattttttaacaccatgatttgattttttcttttaagtagat--aaatggtacatctattgaagaagc-atgcatgaaatgatagtttgtcattttgcagAACGAAGACGGTTCCAAAGATGAGTACAGAGTTTGGAATCCTTTCCGCTCGAAGTTGGCTGCTGCCATCCTTGGTGGAGTTGACAACATTTGGATT
upper sequence: Vv16s0050g00880.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA18G02340.1 (Glycine max), 3'ss of exon 2
tgggtaactcattatgtgttttaggattttctaatcataaggtttaagcactctgtgaaatgtgatggttattgatctacttgttattttaatttttcagAATGAAGATGGAAGCAAAATTGAATACAGGGTTTGGAACCCCTTCCGTTCAAAGTTGGCTGCTGCCATTCTTGGTGGTGTTGATGAGATCTGGATT
| || | | | | | ||| | | | | ||||| ||| ||| || || | ||| || ||| ||||| ||||| |||||||| |||| ||| ||||| |||||||| || || || || ||||||||||||||||| |||||||| ||||| | || ||||||
------gtttcttttctttctcaccattatttgttttttcttcttaagtact----gaaccatgga------tgcatgaattgatagtttcattttgcagAACGAAGATGGTTCCAAAGATGAGTACAGAGTTTGGAATCCTTTTCGATCCAAGTTGGCTGCTGCCATCCTTGGTGGAGTTGACAACATATGGATT
upper sequence: Vv16s0050g00880.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: AT4G25630.1 (Arabidopsis thaliana), 3'ss of exon 2
tgggtaactcattatgtgttttaggattttctaatcataaggtttaagcactctgtgaaatgtgatggttattgatc-tacttgttattttaatttttcagAATGAAGATGGAAGCAAAATTGAATACAGGGTTTGGAACCCCTTCCGTTCAAAGTTGGCTGCTGCCATTCTTGGTGGTGTTGATGAGATCTGGATT
||| | || | || ||| | || | | || |||||| | ||| | ||| || || | ||||| ||| | | | ||||| |||||||||| ||| | ||||||||| |||||||| || |||||||| |||||||||||||| |||||||||||||||||| | |||||||||
---gta--ttatagaggattgattaattgattgatggtttgtattt-gcactccttttgatgaatttgtttttaatggttcttgtgatt--gaatctgcagAACGAAGATGGAACCAAGACTGAATACAGAGTTTGGAATCCTTTCCGTTCGAAGTTGGCTGCTGCTATTCTTGGTGGTGTTGATAACATCTGGATT
upper sequence: Vv16s0050g00880.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: AT5G52470.1 (Arabidopsis thaliana), 3'ss of exon 2
tgggtaactcattatgt-gttttaggattttctaatcataaggtttaagcactctgtgaaatgtgatggttattgatctacttgttattttaatttttcagAATGAAGATGGAAGCAAAATTGAATACAGGGTTTGGAACCCCTTCCGTTCAAAGTTGGCTGCTGCCATTCTTGGTGGTGTTGATGAGATCTGGATT
|||| |||| |||||| | | || | | |||| | | || ||| | ||| || || | | || || | |||| |||||||||||||||| || |||||||||| |||||||| || || | || ||||| |||||||| |||||||||||||| || | || |||||
-----------gtatgaagtttgaggattgttt--tctttataattaa--attgagtt---tgtttttgttcttatatta-tagctacttcacttttgcagAATGAAGATGGAACTAAGGTTGAATACAGAGTTTGGAATCCGTTTAGATCTAAGTTAGCTGCTGCAATTCTTGGTGGTGTCGACAACATTTGGATC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aagcactctgtgaaatgtgatggttattgatctacttgttattttaatttttcagAATGAAGATGGAAGCAAAATTGAATACAGGGTTTGGAACCCCTTCCGTTCAAAGTTGGCTGCTGCCATTCTTGGTGGTGTTGATGAGATCTGGATT
ttttaat putative branch site (score: 3)
tttttc CT-rich tract
ttattgatctacttgt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tgggtaactcattatgtgttttaggattttctaatcataaggtttaagcactctgtgaaatgtgatggttattgatctacttgttattttaatttttcagAATGAAGATGGAAGCAAAATTGAATACAGGGTTTGGAACCCCTTCCGTTCAAAGTTGGCTGCTGCCATTCTTGGTGGTGTTGATGAGATCTGGATT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC
- - -aactcat
- - - - - - - - - - - - - - - - - - - - - -ttaagca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gtgatgg
