Sequence
atgc intronic sequence ATGC exonic sequence...ctcactctctgttaacgttcacctaaatatttacatggaatatgtaaaattagtgtgattacaaatatttgaagcattctgtttttgcctgtgctaacagGTTCAGCTGATAGAACTGTAAAATTCTGGGATCTGGAAACATTCGAGCTGATTGGTTCTGGTGGACCTGAG
Basic information
species | Arabidopsis thaliana |
transcript | AT5G23430.2 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G23430.2 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GRMZM2G160702_T01 (Zea mays), 3'ss of exon 5
ctcactctctgttaacg-ttcacctaaatatttacatggaatatgtaaaattagtgtgattacaaatatttgaagcattctgttt-----ttgcctgtgctaacagGTTCAGCTGATAGAACTGTAAAATTCTGGGATCTGGAAACATTCGAGCTGATTGGTTCTGGTGGACCTGAG
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------ggcagtgaagaatgtattcatatgtttgtgtgggagctcagaagactgtattccttttgaaactatatctctcttatgtaaaacttgttgcttcattcagGTTCAGCTGATAAAACTGTCAAATTCTGGGATTTGGAGACATTTGAATTGATTGGATCTACAGGACCTGAG
upper sequence: AT5G23430.2 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GRMZM2G406553_T04 (Zea mays), 3'ss of exon 5
ctcactctctgttaacgttcacctaaatatttacatggaatatgtaaaattagtgtgattacaaatatttgaagcattctgt---ttttgcctgtgctaacagGTTCAGCTGATAGAACTGTAAAATTCTGGGATCTGGAAACATTCGAGCTGATTGGTTCTGGTGGACCTGAG
| | || | || | | ||||||| ||| | | || | | | | | | | || ||| |||| | | ||||||||||||||| |||||| || ||||||||| |||| ||||| ||| ||||||| ||| |||||||||
--taggcagtgaaga-gtgtattcatatatttatgtgggagctcagaagagtatattccttttgaaactaaatctcttatgtaaaatttgttgcttccttcagGTTCAGCTGATAAAACTGTCAAGTTCTGGGATTTGGAGACATTTGAGTTGATTGGATCTACAGGACCTGAG
upper sequence: AT5G23430.2 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA19G00890.1 (Glycine max), 3'ss of exon 6
--ctcactctctgttaacgttcacctaaatatttacatggaatatgtaaaattagtgtgattaca---aatatttgaagcattctgtttttgcctgtgctaacagGTTCAGCTGATAGAACTGTAAAATTCTGGGATCTGGAAACATTCGAGCTGATTGGTTCTGGTGGACCTGAG
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tgctggattcttg--ggttttcttttggatgcatccatttttttt-taatttgaatgaagtcaagtgtaatttttatttcatttatctctttcccacgtt--tagGCTCGGCAGATAGAACAGTTAAATTCTGGGATCTTGAAACCTTTGAGCTTATTGGTTCAGCTGGTCCTGAG
upper sequence: AT5G23430.2 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA05G09360.1 (Glycine max), 3'ss of exon 6
ctcactctctgttaacgttcacctaaatatttacatggaatatgtaaaattagtgtgattaca---aatatttgaagcattctgtttttgcctgtgctaacagGTTCAGCTGATAGAACTGTAAAATTCTGGGATCTGGAAACATTCGAGCTGATTGGTTCTGGTGGACCTGAG
| | ||| | || ||| || | | | ||| | | || | | ||| ||| |||| | || |||| | | ||| ||||| |||||||| || ||||||||||| || ||||| || ||||| |||||||| | ||| ||||||
ccgggttcttgtgttttcttttggaagtatctatttttttttt-taatttgaatgaagtcaagtgtaatttttatttcatttatctctttcctgggtt--tagGCTCAGCAGATAGAACAGTTAAATTCTGGGACCTCGAAACCTTTGAGCTTATTGGTTCAGCTGGTCCTGAG
upper sequence: AT5G23430.2 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: Vv10s0071g01150.t01 (Vitis vinifera), 3'ss of exon 5
------ctcactctctgttaacgttcacctaaatatttacatggaatatgtaaaattagtgtgattacaaatatttgaagcattctgtttttgcctgtgctaacagGTTCAGCTGATAGAACTGTAAAATTCTGGGATCTGGAAACATTCGAGCTGATTGGTTCTGGTGGACCTGAG
| | ||||| ||| | | | ||| || || | || | || || || || || | || | ||| | | | ||||||||||||||||||||||| ||||||||||| || ||||| || ||| |||||||||| | ||||||||||
ttatgttttatgctctgacttatcacacttttgttctgtcatctaaaat-tgtgttttatatggtttattttactttaa---ctttggtcttgtcctt--tcacagGTTCAGCTGATAGAACTGTTAAATTCTGGGACCTTGAAACTTTTGAGTTGATTGGTTCAGCTGGACCTGAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aaaattagtgtgattacaaatatttgaagcattctgtttttgcctgtgctaacagGTTCAGCTGATAGAACTGTAAAATTCTGGGATCTGGAAACATTCGAGCTGATTGGTTCTGGTGGACCTGAG
attacaaatatttgaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ctcactctctgttaacgttcacctaaatatttacatggaatatgtaaaattagtgtgattacaaatatttgaagcattctgtttttgcctgtgctaacagGTTCAGCTGATAGAACTGTAAAATTCTGGGATCTGGAAACATTCGAGCTGATTGGTTCTGGTGGACCTGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA