Sequence
atgc intronic sequence ATGC exonic sequence...acgctattatttggtttttaatcaattttagttttatagtttttaagtttaaattaaattgatcgttgatttaattactttgtttacaaattaaatgcagGACTATTGCGGTGTGGTAAAAGCTGCAGATTAAGATGGATAAATTATTTAAGACCTGATTTAAAAAGAGGTCTTTTATCAGAATATGAAGAACAAAAGGT
Basic information
species | Arabidopsis thaliana |
transcript | AT5G16600.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G16600.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA14G39530.1 (Glycine max), 3'ss of exon 1
acgctattatttggtttttaatcaattttagttttatagtttttaagtttaa--attaaattgatcgttgatttaattactttgtttacaaattaaatgcagGACTATTGCGGTGTGGTAAAAGCTGCAGATTAAGATGGATAAATTATTTAAGACCTGATTTAAAAAGAGGTCTTTTATCAGAATATGAAGAACAAAAGGT
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-taatcttcaaaaacataaggttacaacaaaagttagagcttgcagaaacaatgactttactaaaattaaaactaaacaattggagtgtgacttca-tgcagGACTATTAAGGTGTGGGAAGAGTTGCAGGCTGAGGTGGACAAATTACTTGAGGCCAGACTTAAAGAGAGGCCTTTTATCTGAATATGAAGAAAAAATGGT
upper sequence: AT5G16600.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA02G41180.1 (Glycine max), 3'ss of exon 1
acgctattatttggtttttaatcaattttagttttatagtttttaagtttaaat--taaattgatc---gttgatttaattactttgtttacaaattaaatgcagGACTATTGCGGTGTGGTAAAAGCTGCAGATTAAGATGGATAAATTATTTAAGACCTGATTTAAAAAGAGGTCTTTTATCAGAATATGAAGAACAAAAGGT
| | |||| | || |||||| | | | | || | ||| | | || | || | || | | || | | | || | |||||| || || ||||||| || || ||||| | || |||| |||||| || || || || ||||| |||||||||||||||||||| |||||| ||| |||
--cttcatgtttgttcgttttgtaattttgaat--aaaaatgctaggcagaaacaattacttcactaaaattaaatttaacaattggagtgtgacttca-tgcagGGCTTTTAAGGTGTGGGAAGAGTTGCAGGCTCAGGTGGACAAATTACTTGAGGCCAGACTTAAAGAGAGGTCTTTTATCAGAATACGAAGAAAAAATGGT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.agtttaaattaaattgatcgttgatttaattactttgtttacaaattaaatgcagGACTATTGCGGTGTGGTAAAAGCTGCAGATTAAGATGGATAAATTATTTAAGACCTGATTTAAAAAGAGGTCTTTTATCAGAATATGAAGAACAAAAGGT
atttaat putative branch site (score: 4)
ttgatttaattacttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
acgctattatttggtttttaatcaattttagttttatagtttttaagtttaaattaaattgatcgttgatttaattactttgtttacaaattaaatgcagGACTATTGCGGTGTGGTAAAAGCTGCAGATTAAGATGGATAAATTATTTAAGACCTGATTTAAAAAGAGGTCTTTTATCAGAATATGAAGAACAAAAGGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC
- - - -tatttgg
- - - - - - - - - taatcaa
- - - - - - - - - - - - - - - - - - - - - - - - - -aattaaa