Sequence
atgc intronic sequence ATGC exonic sequencegttagcctagaacaccgatgttagaacttaggatagaacttaaaagatcactctttgaatcagtggaaactgtttttttctgaagctcaagaagtggattcttgatgatgctttatcacacagGTTATGACACAGGTTGATTTAGGACTTGCTGATGCTTATATCAATGGAGATTTTTCATTTGTCAATAAGGAAACAGGACTTTTGAATCTGATCATG
Basic information
species | Arabidopsis thaliana |
transcript | AT3G23460.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G23460.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA20G34340.1 (Glycine max), 3'ss of exon 14
---------------------gttagcctagaacaccgat--gttagaacttagg-atagaacttaaaagat-cactc-tttgaatcagtggaaactgtttttttctgaagct--caagaagtggattcttgatgatgctt---tatcacacagGTTATGACACAGGTTGATTTAGGACTTGCTGATGCTTATATCAATGGAGATTTTTCATTTGTCAATAAGGAAACAGGACTTTTGAATCTGATCATG
| | | || | ||| | | ||| ||| | | ||||| || | | ||| || || || | || | |||| |||| || | || || || | ||| ||||| |||||||||| |||||||| ||||| ||||| ||||||||||| || ||||||||||| |||| || ||| || |||||||| || ||
gtatatacttttaaatttcacatgaactatgattattgattcatgtcattctagctgcggaagtgacaagatatgcttatctttgtcaatgcaa-ctctaaaattaagtagctagcaaggagctaaaact-aatcatttgtacgtatatttcagGTGATGACACAGGCAGATTTAGGCCTTGCAGATGCATATATCAATGGGGACTTTTCATTTGTTGATAAAGATGAAGGTCTCTTGAATCTTATTTTG
upper sequence: AT3G23460.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv05s0049g01620.t01 (Vitis vinifera), 3'ss of exon 9
gttagcctagaacaccgatgttagaacttaggatagaacttaaaagatcactctttgaatcagtggaaactgtttttttctgaagctcaagaagtggattc---ttgatgatgctt---tatcacacagGTTATGACACAGGTTGATTTAGGACTTGCTGATGCTTATATCAATGGAGATTTTTCATTTGTCAATAAGGAAACAGGACTTTTGAATCTGATCATG
||| | || | | ||| | || || | | || |||| || || | | | | | ||| | |||| || ||||||| ||||||||| ||||| ||||| |||||||||||||||||||| |||| |||| || ||| ||| | ||| |||||
----------------------------aagggtttttttttcttattttttttttctcttggtacaatc-atattgttctatagacaaaattatcaccacaattgaacaacacttgcattctgtacagATTGCTACACAGGCTGATTTAGGCCTTGCAGATGCATATATCAATGGAGATTTTTCTCTTGTTGATAAAGACGAAGGGCTTCAAAGTCTTTTCATG
upper sequence: AT3G23460.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv05s0049g01650.t01 (Vitis vinifera), 3'ss of exon 13
gttagcctagaacaccgatgttagaacttaggatagaacttaaaagatcactctttgaatcagtggaaactgtttttttctgaagctcaagaagtggattc---ttgatgatgctt---tatcacacagGTTATGACACAGGTTGATTTAGGACTTGCTGATGCTTATATCAATGGAGATTTTTCATTTGTCAATAAGGAAACAGGACTTTTGAATCTGATCATG
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---------------------------------------------gtcttttttttttcttggttgaatc-atattgttctatagacaaaattatcaccacaattgaacagCACTTGCATTCTTTACAGATTGCTACACAGGCTGATTTAGGCCTTGCAGATGCATATATCAATGGAGATTTTTCTCTTGTTGATAAAGACGAAGGGCTTC-------------- atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.actgtttttttctgaagctcaagaagtggattcttgatgatgctttatcacacagGTTATGACACAGGTTGATTTAGGACTTGCTGATGCTTATATCAATGGAGATTTTTCATTTGTCAATAAGGAAACAGGACTTTTGAATCTGATCATG
tcttgat putative branch site (score: 4)
ctttatc putative PPT
ttttttct 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttagcctagaacaccgatgttagaacttaggatagaacttaaaagatcactctttgaatcagtggaaactgtttttttctgaagctcaagaagtggattcttgatgatgctttatcacacagGTTATGACACAGGTTGATTTAGGACTTGCTGATGCTTATATCAATGGAGATTTTTCATTTGTCAATAAGGAAACAGGACTTTTGAATCTGATCATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA