Sequence
atgc intronic sequence ATGC exonic sequencegtaagtggtttgaaacagtttagcttttgttggatatgttcaatgcttgattattaaaagggtctgcaatttgtacaactttacagGCTTGCTTACTTGCATGAAGCAATAGAACCAAAAGTGGTCCACAGAGACATAAAAGCAAGTAATATATTGATTGATGATGAGTTTAATGCAAAACTCTCT
Basic information
species | Arabidopsis thaliana |
transcript | AT2G42960.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT2G42960.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: LOC_Os01g44110.1 (Oryza sativa), 3'ss of exon 5
gtaagtggtttgaa----acagttta----gcttttgttggatatgtt--caatgcttgattattaaaagggtctgcaatttgtacaactttacagGCTTGCTTACTTGCATGAAGCAATAGAACCAAAAGTGGTCCACAGAGACATAAAAGCAAGTAATATATTGATTGATGATGAGTTTAATGCAAAACTCTCT
|||||| | | |||| || ||||| | |||| | ||| || | | | | || || || | |||| || |||||| | |||||||| |||||||||||||| || ||| |||| |||||| |||| ||||| ||||||||||| || ||||||| || |||||
gtaagtttcatcagcttctcagtctataagatacatgttgtttctgttgtcggaatttgtttgatgatatt-ttggcgggttaatcatgatcacagACTAGCTTACCTTCATGAAGCTATAGAACCAAAAGTTGTGCACCGAGATATAAAATCAAGCAATATCTTGATTGATGAGGAATTTAATGGCAAGGTCTCT
upper sequence: AT2G42960.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: LOC_Os10g35450.1 (Oryza sativa), 3'ss of exon 4
--------------------------------gtaagtggtttgaaacagtttagcttttgttggatatgttcaatgcttgattattaaaagggtctgcaat--ttgtacaactttacagGCTTGCTTACTTGCATGAAGCAATAGAACCAAAAGTGGTCCACAGAGACATAAAAGCAAGTAATATATTGATTGATGATGAGTTTAATGCAAAACTCTCT
||| | | || ||||||| || || || | | ||| || || || | | | || || | | |||||||||||||| || |||||||||||||| |||||||| || ||| | || || ||| |||| || ||| | || ||||| || || |||| ||||| |||
gtaagaaacaaaccatcgtccccgtcaaaaagaaaagaattgttcttcactttagctctt-ttatatgtat---atgtttagttgcataacccattttccataactgaattggtatacagGCTTGCTTATTTACATGAAGCAATAGAGCCAAAAGTTGTACACCGGGATATCAAATCAAGCAACATACTAATCGATGAAGAATTCAATGGCAAACTTTCT
upper sequence: AT2G42960.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GRMZM2G017386_T03 (Zea mays), 3'ss of exon 4
gtaagt---ggtttgaaacagtttagcttttgttggatatgttcaatgcttgattat-taaaagggtctgcaatttgtacaact-------ttacagGCTTGCTTACTTGCATGAAGCAATAGAACCAAAAGTGGTCCACAGAGACATAAAAGCAAGTAATATATTGATTGATGATGAGTTTAATGCAAAACTCTCT
|||||| | | || | || | | | | | || | | ||||| | | |||| | || | || ||||||||||||| | |||||||| || || |||||||| || || |||| |||||| |||| || ||||||||||||||||| ||||||| ||| | |||
gtaagtttcaatcttaatctgtaagttacctacatagtttcctgtgtttttagctgtataaaattggttcttatttttctaattatgatggttgcagGCTTGCTTACCTTCATGAAGCTATTGAGCCAAAAGTTGTACATCGAGATATAAAATCAAGCAACATATTGATTGATGATGAATTTAATGGCAAAGTATCT
upper sequence: AT2G42960.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GRMZM2G026301_T01 (Zea mays), 3'ss of exon 4
-----gtaagtggtttgaaacagtttagcttttgttggatatgttcaatgcttgattattaaaagggtc--tgcaatttgtacaactttacagGCTTGCTTACTTGCATGAAGCAATAGAACCAAAAGTGGTCCACAGAGACATAAAAGCAAGTAATATATTGATTGATGATGAGTTTAATGCAAAACTCTCT
| | | || | ||| || || || ||| | ||| || || || | | | |||| | | |||||||||||||| || |||||||| |||||||||||||| || ||| | || || ||| | || ||||| | ||||||| || || |||| || || |||
gtaagacatggaccattcaatattttgtctcttctttgatgcat---atgttttgccatctaaggcatttttataattgatgatatactacagGCTTGCTTATTTACATGAAGCCATAGAACCAAAAGTTGTGCACCGTGATATCAAATCTAGCAATATCCTAGTTGATGAAGAATTCAATGGCAAGCTTTCT
upper sequence: AT2G42960.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GRMZM2G010953_T01 (Zea mays), 3'ss of exon 2
gtaagtggtttgaa-----acagtttagcttttgttggatatgttcaatgcttgattattaaaagggtctgcaatttgtacaactttacagGCTTGCTTACTTGCATGAAGCAATAGAACCAAAAGTGGTCCACAGAGACATAAAAGCAAGTAATATATTGATTGATGATGAGTTTAATGCAAAACTCTCT
||||| | | ||| ||| || | | || || | || | || | | | |||| ||| | | ||| || |||||||||||||| || |||||||| |||||||||||||| || ||| | || || ||| | || ||||| || |||||||| || || |||| || || |||
gtaagaaatgaaaccattcacaattttgcatcttttatatgcatacatttattaaattaagatgttgtctacaact-gaaca-ctatacagGCTTGCTTATTTACATGAAGCCATAGAACCAAAAGTTGTACACCGTGATATCAAATCGAGCAATATCTTAATTGATGAAGAATTCAATGGCAAGCTTTCT
upper sequence: AT2G42960.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA14G03290.1 (Glycine max), 3'ss of exon 3
gtaagtggtttgaaacagtttag-cttttgttgg----atatgttcaatgcttgat-------tattaaaagggtctgcaatttg-tacaact--ttacagGCTTGCTTACTTGCATGAAGCAATAGAACCAAAAGTGGTCCACAGAGACATAAAAGCAAGTAATATATTGATTGATGATGAGTTTAATGCAAAACTCTCT
||| | || | || |||| | | |||| | | | ||||||| | || | | | | | | | | | | | |||||||||||| || ||||||||||||||||||||||| | ||| | || ||||| | || || ||||||||||||||||| || |||||||| | |||
-ccagtagcttagagtagcttagtcgtctgttcgtgtcaaagattcaatgatggaccttgttctcctgattaaccccttagtgtactgtgattggtggcagGCTTGCTTATTTACATGAAGCAATAGAACCAAAAGTTATTCACCGGGATATAAAGTCTAGCAACATATTGATTGATGATGAATTCAATGCAAAGGTTTCT
upper sequence: AT2G42960.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA18G12830.1 (Glycine max), 3'ss of exon 3
gtaagtggtttg--aaacagtttagcttttgttg-gatatgttcaat-----gcttgatt--attaaa-agggtctgcaatttgtacaact--ttacagGCTTGCTTACTTGCATGAAGCAATAGAACCAAAAGTGGTCCACAGAGACATAAAAGCAAGTAATATATTGATTGATGATGAGTTTAATGCAAAACTCTCT-
|| || || | | | | | |||| | | ||||| || | ||| | | | | || | || || ||| | |||||| |||||||| ||||||||||||||||| ||||| || ||| | || ||||| | || || |||||||||||| |||||| |||||||| | |||
gtgcttgcttcactggatacctaatttactgttatggcagtttcaacattaggcctaattccactgattaaactccttatttactatgactggtggcaggCTAGCTTACTTACATGAAGCAATAGAACCGAAAGTTGTTCACCGGGATATAAAGTCTAGCAACATATTGATTGATACTGAGTTCAATGCAAAGGTTTCTG
upper sequence: AT2G42960.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA08G42170.2 (Glycine max), 3'ss of exon 3
-gtaagtggtttg--aaacagtttagcttttgttg-gatatgttcaat-----gcttgatt--attaaa-agggtctgcaatttgtacaact--ttacagGCTTGCTTACTTGCATGAAGCAATAGAACCAAAAGTGGTCCACAGAGACATAAAAGCAAGTAATATATTGATTGATGATGAGTTTAATGCAAAACTCTCT
|| || || | | | | | |||| | | ||||| || | ||| | | | | || | || || ||| | |||||| |||||||| ||||||||||||||||| ||||| || ||| | || ||||| |||| || |||||||||||| ||| || |||||||| | |||
tgtgcttgcttcattggatacctaatttactgttatggcagtttcaacattaggcctaattccactgattaaactccttatttactatgactggtggcagGCTAGCTTACTTACATGAAGCAATAGAACCGAAAGTCGTTCACCGGGATATAAAGTCAAGCAACATATTGATTGATACTGATTTCAATGCAAAGGTTTCT
upper sequence: AT2G42960.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA02G45540.1 (Glycine max), 3'ss of exon 5
-----gtaagtggtttgaaacagtttagcttttgttggatatgtt-caatg---cttgat-tattaaa-agggtctgcaatttg-tacaact--ttacagGCTTGCTTACTTGCATGAAGCAATAGAACCAAAAGTGGTCCACAGAGACATAAAAGCAAGTAATATATTGATTGATGATGAGTTTAATGCAAAACTCTCT
|| | || | ||| || |||| | | | || | ||| |||| | | ||| | | ||| | | ||| | |||||||||||| || ||||||||||||||||||||||| | ||| | || ||||| | || || ||||||||||| ||||| || |||||||| | |||
atattttacttaattagttacaaatttatttttatggaagattcaacgatggaacttgttctgctaattaacccccctaatgtactgtgactggtggcagGCTTGCTTATTTACATGAAGCAATAGAACCAAAAGTTATTCACCGGGATATAAAGTCTAGCAACATATTGATTGACGATGAATTCAATGCAAAGGTTTCT
upper sequence: AT2G42960.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv12s0028g00310.t01 (Vitis vinifera), 3'ss of exon 5
------gtaagtggtttgaaacagttt---agcttttgttggatatgttcaatgcttgattattaaaagggtctgcaa-----tttgtacaactttacagGCTTGCTTACTTGCATGAAGCAATAGAACCAAAAGTGGTCCACAGAGACATAAAAGCAAGTAATATATTGATTGATGATGAGTTTAATGCAAAACTCTCT
| | || | | | || ||| | || || | || ||| ||| || || || || ||||||||| || |||||||| ||||||||||| ||||| || || ||||||||||| |||| || || ||||||||||||||||| |||||||| | |||
tattccattcagaactgaaatctactccagaactgaaattgaacatcttggtctttcacactttgaaaaagtcaaaaaaatgtttcatattgggttgcagGCTTGCCTATTTGCATGAGGCAATAGAACCGAAAGTTGTTCATCGAGACATAAAATCAAGCAACATCTTGATTGATGATGAGTTCAATGCAAAGGTTTCT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ggatatgttcaatgcttgattattaaaagggtctgcaatttgtacaactttacagGCTTGCTTACTTGCATGAAGCAATAGAACCAAAAGTGGTCCACAGAGACATAAAAGCAAGTAATATATTGATTGATGATGAGTTTAATGCAAAACTCTCT
gcttgat putative branch site (score: 5)
ttgattattaaaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagtggtttgaaacagtttagcttttgttggatatgttcaatgcttgattattaaaagggtctgcaatttgtacaactttacagGCTTGCTTACTTGCATGAAGCAATAGAACCAAAAGTGGTCCACAGAGACATAAAAGCAAGTAATATATTGATTGATGATGAGTTTAATGCAAAACTCTCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG