Sequence
atgc intronic sequence ATGC exonic sequencegttagtatgcttttcatcttgaatctactggttgaaacaactctgtaacaatctgctgaagatattattaacgatctattttactgagatgtttcagGTGCCCTGCAGTAAGGACAACTATGCTTATCTGTTGCACGATGAAGACACCGGAACAGTTGGAGTCGTTGATCCTTCTGAGGCTGCACCTGTTATAGAAG
Basic information
species | Arabidopsis thaliana |
transcript | AT2G43430.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT2G43430.2 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GRMZM2G120300_T01 (Zea mays), 3'ss of exon 2
gttagtatgcttttcatcttgaatctactgg--ttgaaacaactctgtaacaatctgctgaag----atattatt-aacgatctattttactgagatgttt-cagGTGCCCTGCAGTAAGGACAACTATGCTTATCTGTTGCACGATGAAGACACCGGAACAGTTGGAGTCGTTGATCCTTCTGAGGCTGCACCTGTTATAGAAG
| ||| || | | ||||| | || || | | || | | || || || | | ||| || | | | | ||| | | ||||| || ||| | || |||||||| ||| | |||| |||| || || |||||||||||||| || ||||||||||||||| ||| ||||| | |
----atcagctgtt-accatgaatttgttgctctttacataattaccctcctatatgtagatatttcttgtcattcaatcaacatctgtcctggttcatatgcagGTACCATGCCTTCGAGATAACTATGCGTATATCCTGCATGATGTTGATACTGGAACAGTTGGAGTAGTGGATCCTTCTGAGGCTATGCCTATTATAAATG
upper sequence: AT2G43430.2 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA13G42070.2 (Glycine max), 3'ss of exon 2
---------------------------------gttagtatgcttttcatcttgaat----ctactggttgaaacaa---ctctgtaacaatctgctgaagat---attattaacgatctattttactgagatgtttc----agGTGCCCTGCAGTAAGGACAACTATGCTTATCTGTTGCACGATGAAGACACCGGAACAGTTGGAGTCGTTGATCCTTCTGAGGCTGCACCTGTTATAGAAG
| | |||| || | ||| || || | || |||| | ||| || |||| | | | ||| | | | | | | | ||| |||| || ||| |||||||| |||||||||||||| || |||| ||||| || |||||||| || |||||||||||||| |||| ||| | ||||| |
gtgagagcaggtctcttatcagtcttttctgttttcatagtgctattggattacaattaggtcacccgtgctgataagttttctgaagaaatatgatgaaagcttaagttctgacgttattgtgttttaaattttttttgttagGTACCTTGCCTGAAGGACAATTATGCTTATCTGTTACATGATGTGGACACGGGTACAGTTGGTGTTGTTGATCCTTCTGAAGCTGTGCCTATCATAGATG
upper sequence: AT2G43430.2 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA15G03320.1 (Glycine max), 3'ss of exon 2
----------------------------gttagtatgct----tttcatcttgaat---ctactggttgaaacaa---ctctgtaacaatctgctgaagatattattaacgatctattttact------gagatgtt-tcagGTGCCCTGCAGTAAGGACAACTATGCTTATCTGTTGCACGATGAAGACACCGGAACAGTTGGAGTCGTTGATCCTTCTGAGGCTGCACCTGTTATAGAAG
||| | || | || || | ||| || || | || |||| | ||| ||||||| | | | || |||| | | | || || | |||| || ||| |||||||| ||||| |||||||| || |||| ||| || || |||||||| || |||||||||||||| |||| ||||| ||||| |
gtgagagcgggtctcttattagttttcagttgctgtggtcctgttggattataaataggtcacccgtgctgataagttttctgaagaaatatgctgaaagcctaaattgtgacttattgtctttaaaaaaaaatattgttagGTACCTTGCCTGAAGGACAATTATGCATATCTGTTACATGATGTAGATACGGGTACAGTTGGTGTTGTTGATCCTTCTGAAGCTGTGCCTGTCATAGATG
upper sequence: AT2G43430.2 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA11G13470.1 (Glycine max), 3'ss of exon 2
---------------------------------------------------gttagtatgcttttcatcttgaatctactggttgaaacaactctgtaacaatctgctgaagatat-----------tattaacgatct-attttactga--gatgtttcagGTGCCCTGCAGTAAGGACAACTATGCTTATCTGTTGCACGATGAAGACACCGGAACAGTTGGAGTCGTTGATCCTTCTGAGGCTGCACCTGTTATAGAAG
||||||| | ||| | | | | | | | ||||| | |||| ||||||| | | | ||| |||| ||||| || || | | |||| || ||| || |||||| ||||| ||||| || ||||||| || || || |||||||| || |||||||||||||| ||||||||| | ||||| |
gtgagcagatctcttcttccttttttaaaggtttttttgtgatgcaattagattagtat-ttagtcactcaagttgctcaagctaata-agctctggagcaatatgctgaaattctagtgtgtgctgtgttacttatctcatttttctttttgaattgttagGTTCCATGCCTTAGGGACAATTATGCATATCTTTTACACGATGTGGATACGGGGACAGTTGGTGTTGTTGATCCTTCTGAAGCTGCACCTATCATAGATG
upper sequence: AT2G43430.2 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: Vv05s0102g01180.t01 (Vitis vinifera), 3'ss of exon 4
----gttagtatgcttttcatcttgaatctactggttga-aacaactctgta-acaatctgctgaagatattattaacgatctattttactgagatgtttcagGTGCCCTGCAGTAAGGACAACTATGCTTATCTGTTGCACGATGAAGACACCGGAACAGTTGGAGTCGTTGATCCTTCTGAGGCTGCACCTGTTATAGAAG
|| ||| | ||| | | | ||| |||| ||| | | | | | || | | || | ||| ||||||| || || |||||||||||||| ||||| || || || | || || || ||||||||||| |||||||||||||| || | |||||||||||| |
cttaattgactcacttggtaacttaattgactcgcttggtaacagttctttttgtgcttcctttcacacataaatctttgtcaactttttccgt---cttcagGTACCATGTCTGAAGGACAACTATGCATATCTTTTACATGACGTCGATACAGGCACAGTTGGAGTTGTTGATCCTTCTGAAGCCGTACCTGTTATAGATG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ctgtaacaatctgctgaagatattattaacgatctattttactgagatgtttcagGTGCCCTGCAGTAAGGACAACTATGCTTATCTGTTGCACGATGAAGACACCGGAACAGTTGGAGTCGTTGATCCTTCTGAGGCTGCACCTGTTATAGAAG
tattaac putative branch site (score: 1)
atattattaacgatct 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttagtatgcttttcatcttgaatctactggttgaaacaactctgtaacaatctgctgaagatattattaacgatctattttactgagatgtttcagGTGCCCTGCAGTAAGGACAACTATGCTTATCTGTTGCACGATGAAGACACCGGAACAGTTGGAGTCGTTGATCCTTCTGAGGCTGCACCTGTTATAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG