Sequence
atgc intronic sequence ATGC exonic sequencegttattattattttatctttaataatgtgttttataattgcacttgcctttcctgaagattatgttgttgatgcttttggatttgtttgattaatatattgctgtagTGCACTTGAAGGGGCTGAATCAACTTTGGTTATGGCATCTGGGATGTGTGCAAGCACTGTTATGCTTTTGGCATTGGTTCCTGCTGGTGGACACATTGTC
Basic information
species | Arabidopsis thaliana |
transcript | AT3G01120.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G01120.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA18G49660.1 (Glycine max), 3'ss of exon 3
gttattattattttatctttaataatgtgttttataattgcacttgcctttcctgaagattatgttgttgatgcttttggatttgtttgattaatatattgctgtagTGCACTTGAAGGGGCTGAATCAACTTTGGTTATGGCATCTGGGATGTGTGCAAGCACTGTTATGCTTTTGGCATTGGTTCCTGCTGGTGGACACATTGTC
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------gtttgtgtgt-tttgattttgttatttactatta-acttgtaatgtgttttaagtgtggtggtcatttgatgaggtttgtt--gtcattat-taaccccagTATATTGGAGGGGGCTGAATCAACTGTGATAATGGCATCTGGAATGTGTGCTAGCGTAGTCCTATTTATGGCACTGGTTCCAGCTGGTGGACATCTTGTG
upper sequence: AT3G01120.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv14s0108g01110.t01 (Vitis vinifera), 3'ss of exon 3
gttattattattttatctttaataatgtgttttataattgcacttgcctttcctgaagattatgttgttgatgcttttggatttgtttgattaatatattgctgtagTGCACTTGAAGGGGCTGAATCAACTTTGGTTATGGCATCTGGGATGTGTGCAAGCACTGTTATGCTTTTGGCATTGGTTCCTGCTGGTGGACACATTGTC
| | || | |||| | | | | ||| | |||| || | || ||||||||||| ||||||||||||||| || | ||||||||||| |||||||| || || |||||| | ||||||||||||| ||||||| || || ||
----------------------gtttacactccattctaatacttttttgttggtagaacccatttgatccaatttttaatgaggtccttctctctctctggaacagTGCACTTGAGGGGGCTGAATCAACTGTGATAATGGCATCTGGAATGTGTGCTAGTACAGTTATGTTGCTGGCATTGGTTCCACCTGGTGGGCATATGGTG
upper sequence: AT3G01120.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: EFJ33292 (Selaginella moellendorffii), 3'ss of exon 3
gttattattattttatctttaataatgtgttttataattgcacttgcctttcctgaagattatgttgttgatgcttttggatttgtttgattaatatattgctgtagTGCACTTGAAGGGGCTGAATCAACTTTGGTTATGGCATCTGGGATGTGTGCAAGCACTGTTATGCTTTTGGCATTGGTTCCTGCTGGTGGACACATTGTC
||| | || | | | || | | | | || | || | || || ||||| || || || |||||| ||||| || ||| || || |||||||| ||| ||||| ||||| |||||||| |||||||||||||||||
-----------------------------------------------gtttgcgattga--aagatagaaatccatctcatacttttcatctcatct-tttctacagTGCTCTAGAGGGTGCTGAAGAGACTTTAGTCTCGGCTTCCGGTATGTGTGCTGCAACTACAATGCTCTTGGCTTTGGTTCCGGCTGGTGGACACATTGTA
upper sequence: AT3G01120.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: EFJ15929 (Selaginella moellendorffii), 3'ss of exon 3
gttattattattttatctttaataatgtgttttataattgcacttgcctttcctgaagattatgttgttgatgcttttggatttgtttgattaatatat---tgctgtagTGCACTTGAAGGGGCTGAATCAACTTTGGTTATGGCATCTGGGATGTGTGCAAGCACTGTTATGCTTTTGGCATTGGTTCCTGCTGGTGGACACATTGTC
| || |||| | || | | || | || | || ||||| || || || |||||| ||||| || ||| || || |||||||| ||| ||||| ||||| ||||||||||||||||||||||||||
-----------------------------------------------------------gtttgcgattgaaagatagaaatccatctcatcatctcatcttttctacagTGCTCTAGAGGGTGCTGAAGAGACTTTAGTCTCGGCTTCCGGTATGTGTGCTGCAACTACAATGCTCTTGGCTTTGGTTCCTGCTGGTGGACACATTGTA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ctgaagattatgttgttgatgcttttggatttgtttgattaatatattgctgtagTGCACTTGAAGGGGCTGAATCAACTTTGGTTATGGCATCTGGGATGTGTGCAAGCACTGTTATGCTTTTGGCATTGGTTCCTGCTGGTGGACACATTGTC
gattaat putative branch site (score: 3)
atttgtttgattaata 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttattattattttatctttaataatgtgttttataattgcacttgcctttcctgaagattatgttgttgatgcttttggatttgtttgattaatatattgctgtagTGCACTTGAAGGGGCTGAATCAACTTTGGTTATGGCATCTGGGATGTGTGCAAGCACTGTTATGCTTTTGGCATTGGTTCCTGCTGGTGGACACATTGTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA