Sequence
atgc intronic sequence ATGC exonic sequencegtatactttcatgattttgttagtgtttctggtggggtcaaaatatccttcgtatgtattagaaagtgaaattcatgcatttatgtgtgttctttaactctttgcagAAACACAACCTCAAAAGTGTATCCTGCTATGTATATTGAGAATGTTACTGAGCTTGCTTTTGATGATATTACTCCCGAAGACCCTGATTTTTCTTCCATT
Basic information
species | Arabidopsis thaliana |
transcript | AT5G23890.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G23890.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: LOC_Os03g64400.4 (Oryza sativa), 3'ss of exon 4
gtatactttcatgattttgttagtgtttctggtggggtcaaaatatccttcgtatgtattagaaagtgaaattcatgcatttatgtgtgttctttaactctttgcagAAACACAACCTCAAAAGTGTATCCTGCTATGTATATTGAGAATGTTACTGAGCTTGCTTTTGATGATATTACTCCCGAAGACCCTGATTTTTCTTCCATT
| | | |||| | | | || | | || | | | ||| | | | | | || | || || | |||| | || ||||| |||| ||||||||||| || ||||||||||||||||| ||||| ||||| ||||||||||| || || ||||| ||||||| | | ||
-caaaggatgg-aatttcatatttttgccttataattttgaatttggttcacttagtaattcattccatagactaagttcttgtttggatt-tccaactat----agGAACACTTCCTCCAAAGTGTATCCAGCAATGTATATTGAGAATGTGACTGAACTTGCCTTTGATGATATCACACCTGAAGATTTTGATTTTCCATTTATA
upper sequence: AT5G23890.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM2G077222_T01 (Zea mays), 3'ss of exon 4
-----------------------------------------------------------------------------------------gtatact-ttcatgatttt---gttagtgtttctggtggggtcaaaatatccttcgtatgtattagaaagtgaaattcatgcatttatgtgtgttctttaactctttgcagAAACACAACCTCAAAAGTGTATCCTGCTATGTATATTGAGAATGTTACTGAGCTTGCTTTTGATGATATTACTCCCGAAGACCCTGATTTTTCTTCCATT
||| | ||||| ||| || | || ||| || || ||| | || | | | | | | | | | | | || | || | ||| ||||| ||||||||||||||| || ||||||||||| ||||| ||||| ||||| ||||| ||| | || || ||||| ||||||||| | | |||
gtgcatatctattattcctttgtatcagtagacctcccaagtgtttgttgcaaatatgcagtatggtcccatttctcttttgtcctatttcatattcttcatacgtttaaggtcattgcctct--tgctgttaaattttcagttttgctctcttaggtgattattctgttaaccaacttattctcgtggtttccatacagGAACACTTTCTCAAAAGTGTATCCAGCAATGTATATTGATAATGTCACTGAACTTGCATTTGACGATGTCACACCTGAAGATCCTGATTTTCCATTCATA
upper sequence: AT5G23890.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM2G140874_T01 (Zea mays), 3'ss of exon 1
-----------------------------------------------------------------------------------------gtatact-ttcatgatttt---gttagtgtttctggtggggtcaaaatatccttcgtatgtattagaaagtgaaattcatgcatttatgtgtgttctttaactctttgcagAAACACAACCTCAAAAGTGTATCCTGCTATGTATATTGAGAATGTTACTGAGCTTGCTTTTGATGATATTACTCCCGAAGACCCTGATTTTTCTTCCATT
||| | ||||| ||| || | || ||| || |||||| | || | | | | | | | | | | || | || | ||| ||||| |||||||||||||| || ||||||||||| ||||| ||||| ||||| ||||| ||| | || || ||||| ||||||||| | | |||
gtgcatatctattattcctttgtatcagtagacctcccaagtgtttgttgcaaatatgcagtatggtcccatttctcttttgtcatatttcatattcttcatacgtttaaggtcattgcctct--tgctgtcaaattttcagttttgctctcttaggtgattattctgttaaccaccttattctcgtggtttccatacagGAACACTTTCTCAAAAGTGTATCTAGCAATGTATATTGATAATGTCACTGAACTTGCATTTGACGATGTCACACCTGAAGATCCTGATTTTCCATTCATA
upper sequence: AT5G23890.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA16G30160.1 (Glycine max), 3'ss of exon 4
gtatactttcatgattttgt-tagtgtttctggtggggtcaaaatatccttcgtatgtattagaaagtgaaattcatgcatttatgtgtgttctttaactctttgcagAAACACAACCTCAAAAGTGTATCCTGCTATGTATATTGAGAATGTTACTGAGCTTGCTTTTGATGATATTACTCCCGAAGACCCTGATTTTTCTTCCATT
|| | || || | | || | || |||||| | | | | |||| || | | ||| ||| || ||||| || || | |||| ||||||||||||||||| |||||||| || |||| |||||||||||| ||||||||| | |||||||| |||||||||||||||||||||
--gtagtaatttgtttctaccttctgcatatgtgaataacaaaatgtgttacatgtgtaatatttggcattacgtgtgcctttctgg--------taacttgtt--agGAGCACAGTTTCAAAAGTGTATCCTGCCATGTATATAGACAATGCTACTGAGCTTGCATTTGATGATGTCACTCCCGAGGACCCTGATTTTTCTTCCATT
upper sequence: AT5G23890.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA09G25200.1 (Glycine max), 3'ss of exon 8
gtatactttcatgattttgttagtgtttctggtggggtcaaaatatccttcgtatgtattagaaagtgaaattcatgcatttatgtgtgttctttaactctttgcagAAACACAACCTCAAAAGTGTATCCTGCTATGTATATTGAGAATGTTACTGAGCTTGCTTTTGATGATATTACTCCCGAAGACCCTGATTTTTCTTCCATT
| | ||| || | | || |||||| | | | |||||| || | | || ||| || ||||| || || | |||| ||||||||||||||||| ||||| || || ||||||||||||||||| ||||||||| | | ||||| |||||||||||||||||||||
--------gtagtaatttatttctacatatgtgaataacaaaatgtgttacatatgtaatatttggcattacatgtgactttctgg--------taacttgtt--agGAGCACAGTTTCAAAAGTGTATCCTGCCATGTACATAGACAATGTTACTGAGCTTGCATTTGATGATGTCATCCCCGAGGACCCTGATTTTTCTTCCATT
upper sequence: AT5G23890.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA10G37850.1 (Glycine max), 3'ss of exon 7
------gtatactttcatgattttgttagtgtttctggtggggtcaaaatatcc------ttcgtatgtattagaaagtgaaattcatgcatttatgtgtgt-tctttaact--ctttgcagAAACACAACCTCAAAAGTGTATCCTGCTATGTATATTGAGAATGTTACTGAGCTTGCTTTTGATGATATTACTCCCGAAGACCCTGATTTTTCTTCCATT
|| || |||| | || | | | | || | ||| |||| || | | | | || ||| || |||||||| | | | | | |||| || || || | |||||| || |||||||| |||| | || | ||||||||||||||| ||||||||||| || || || |||||||||||||||| ||||
gtagttgttta-tttcttctttctatcactattatgtgaaataacaatatataaaaaaggttggctattttctattattgtaatatgtggtgatatgtgtgcctttctgattacctttttagGAAAACTATCTCAAAGGTATATCCTGCCATGTTCGTAGACAGTGTTACTGAGCTTGCATTTGATGATATCACCCCTGAGGACCCTGATTTTTCTTTCATT
upper sequence: AT5G23890.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA20G29970.1 (Glycine max), 3'ss of exon 3
--------gtatactttcatgattttgttagtgtttc---tggtggggt-caaaatatccttcgtatgtattagaaagtgaaattcatgcatttatgtgtgt-tctttaact--ctttgcagAAACACAACCTCAAAAGTGTATCCTGCTATGTATATTGAGAATGTTACTGAGCTTGCTTTTGATGATATTACTCCCGAAGACCCTGATTTTTCTTCCATT
||| ||| | | | ||| | | | | | | |||| | | ||| | || | || ||| || ||| |||| | | | | | |||| || || |||| |||||| || |||||||| | ||| || || |||||||||| || ||| ||||||||||| || || || |||||||||||||||| || |
gtagttggttatttcttcttcctctgattactatgtgaaataacaagatataaaaaagtttagctatttgctattat-tgtaatatgtggcgatatctgtgcctttctgattacctttttagGAAAACAATCTCAAAGGTATATCCTGCCACGTACATAGACAATGTTACTGGGCATGCATTTGATGATATCACCCCTGAGGACCCTGATTTTTCTTGCACT
upper sequence: AT5G23890.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv16s0050g00600.t01 (Vitis vinifera), 3'ss of exon 5
gtatactttcatgattttgttagtgtttctggtggggtcaaaatatccttcgtatgtattagaaagtgaaattcatgcatttatgtgtgttctttaactctttgcagAAACACAACCTCAAAAGTGTATCCTGCTATGTATATTGAGAATGTTACTGAGCTTGCTTTTGATGATATTACTCCCGAAGACCCTGATTTTTCTTCCATT
| || || || | | || | | | | ||| ||| | ||| || ||| | |||| ||| | | | | || ||| || || ||| ||||| || ||||| |||||||| || | ||| ||||||| ||||| |||||||||||||| || ||||||||||||||||| ||||||
ctgtagcttgtagagtgcatcagcatctgaag-gctaccaacataa-----attcacattggatgttgataa-catgtgattaataatttctatccattccttgtagGAATACAGTTTCAAAGGTATATCCAGCTATGTACATAGGAAATATTACTGAACTTGCATTTGATGATATTACACCTGAAGACCCTGATTTTTCATCCATT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tatgtattagaaagtgaaattcatgcatttatgtgtgttctttaactctttgcagAAACACAACCTCAAAAGTGTATCCTGCTATGTATATTGAGAATGTTACTGAGCTTGCTTTTGATGATATTACTCCCGAAGACCCTGATTTTTCTTCCATT
ctttaac putative branch site (score: 3)
ttctttaactcttt CT-rich tract
attagaaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatactttcatgattttgttagtgtttctggtggggtcaaaatatccttcgtatgtattagaaagtgaaattcatgcatttatgtgtgttctttaactctttgcagAAACACAACCTCAAAAGTGTATCCTGCTATGTATATTGAGAATGTTACTGAGCTTGCTTTTGATGATATTACTCCCGAAGACCCTGATTTTTCTTCCATT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CGAAGA