Sequence
atgc intronic sequence ATGC exonic sequence...tttaatgcattcaacgttctttatgcatccattaagaccattgttaattaatcctcgatatctcaacttgtgtgtattaattagaaacgcatgcatgcagGTGATTGTGAACCAGATAGAACCATTGACGGAGCAACAGATAGTTGGGATATGTGGGCTGCAACAGTCCACACAAGAGGCCGAGGAGGCTCTCTCGCAAG
Basic information
species | Arabidopsis thaliana |
transcript | AT5G06839.1 |
intron # | 8 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G06839.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA10G12000.1 (Glycine max), 3'ss of exon 5
tttaatgcattcaacgttctttatgcatccattaagaccattgttaattaatcctcgatatctcaacttgtgtgtattaattagaa-acgcatgc-atgcagGTGATTGTGAACCAGATAGAACCATTGACGGAGCAACAGATAGTTGGGATATGTGGGCTGCAACAGTCCACACAAGAGGCCGAGGAGGCTCTCTCGCAAG
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gacaatgacattatcttattatataaatcttttattttaatttgggggtaattgat-atatgtttcattgatta-attaattaatgcgtgtttattatttagATTATTCTGGGTCAAATTGAGCCTCTTACGGAGCAACAAATACTTGGGATATGTGGGTTGCAACAATCTACACAAGAGGCAGAAGAGGCTCTTTCCCAAG
upper sequence: AT5G06839.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA02G30090.1 (Glycine max), 3'ss of exon 3
-tttaatgcattcaacgttctttatgcatccattaagacc-attgttaattaatcctcgatatctcaacttgtgtgtattaattagaaacgcatgcatgcagGTGATTGTGAACCAGATAGAACCATTGACGGAGCAACAGATAGTTGGGATATGTGGGCTGCAACAGTCCACACAAGAGGCCGAGGAGGCTCTCTCGCAAG
||| |||| | | ||| ||| || | | | | ||| |||| | ||| | |||||||| | | || | ||| || || || || || | ||||||||||| ||| |||||||||||||| ||||||| || ||||||||||| || |||||||| || ||||
acacaat-cattatataattaatatatatctttttattttgaggggttgataacatgatatatgtttcattgaata-attaattaatgtgtgttaattatagATAATTCTGGGTCAAATTGAGCCTCTTACGGAGCAACAAATACTTGGGATATGTGGGTTGCAACAATCTACACAAGAGGCAGAAGAGGCTCTTTCCCAAG
upper sequence: AT5G06839.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA19G32710.1 (Glycine max), 3'ss of exon 6
tttaatgcattcaacgttctttatgcatccattaagaccattgttaatt---aatcctcgatatctcaacttgtgtgtatt-aattagaaacgcatgcatgcagGTGATTGTGAACCAGATAGAACCATTGACGGAGCAACAGATAGTTGGGATATGTGGGCTGCAACAGTCCACACAAGAGGCCGAGGAGGCTCTCTCGCAAG
|| | || |||| ||| | | | || || | ||| | || | | | || | |||| |||| | || | || | |||||| || || || || | ||||||||||| ||| | || |||||||| ||||||| || |||||||| || || ||||||||||| ||||
---aagaaacaattttttttttaataatctactctctttaatgacaagttgcaatattatatgtttaattttattgatattgaatttaattaatgtgttt-tagATTATTGTGCGTCAAATTGAGCCTCTCACGGAGCAACAAATATTGGGCATATGTGGATTGCAACAATCTACACAAGAAGCAGAAGAGGCTCTCTCCCAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aattaatcctcgatatctcaacttgtgtgtattaattagaaacgcatgcatgcagGTGATTGTGAACCAGATAGAACCATTGACGGAGCAACAGATAGTTGGGATATGTGGGCTGCAACAGTCCACACAAGAGGCCGAGGAGGCTCTCTCGCAAG
tattaat putative branch site (score: 2)
tgtattaattagaaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tttaatgcattcaacgttctttatgcatccattaagaccattgttaattaatcctcgatatctcaacttgtgtgtattaattagaaacgcatgcatgcagGTGATTGTGAACCAGATAGAACCATTGACGGAGCAACAGATAGTTGGGATATGTGGGCTGCAACAGTCCACACAAGAGGCCGAGGAGGCTCTCTCGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - attcaac
- - - - - - - - - - - - - - - - -aagacca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctcaact
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tagaaac