Sequence
atgc intronic sequence ATGC exonic sequence...ttatacgcccttggtagttttcaagttgtcttactgtgatttatttcatgcccttgatattttggctgcatcgttaataaaactgttttaaaacttgcagTTATTCAGCGGATTACACTGGGCCTGTAAATAACATTGCATGGACGCCTGATAATTCTGCTTTTGCAGTTGGGTGGAAGTCGAGAGGACTTGCAGTTTGG
Basic information
species | Arabidopsis thaliana |
transcript | AT5G28350.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G28350.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: LOC_Os02g54500.1 (Oryza sativa), 3'ss of exon 4
---ttatacgcccttggtagttttcaagttgtcttac-tgtgatttatttcat-gcccttgatattttggctgcatcgttaataaaactgttttaaaacttgcagTTATTCAGCGGATTACACTGGGCCTGTAAATAACATTGCATGGACGCCTGATAATTCTGCTTTTGCAGTTGGGTGGAAGTCGAGAGGACTTGCAGTTTGG
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ttactatgtgtgattttgtgtatttactgtgcaatgcatttcagttattccgttaaagctgatatat-aactgtccctttttc----ctttgggaaaaattgtagGTATTCAGTGGAAGATACTGGTCCTGTTACTTGTATATCTTGGACGCCTGACAATTGTGCTTTTGCAGTTGGATGGAAATTTAGGGGACTTACTGTGTGG
upper sequence: AT5G28350.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G475867_T01 (Zea mays), 3'ss of exon 4
ttatacgcccttggtagttttcaagttgtcttactgtgatttatttca--tgcccttgatattttggctgcatcgttaataaaactgtttta--aaacttgcagTTATTCAGCGGATTACACTGGGCCTGTAAATAACATTGCATGGACGCCTGATAATTCTGCTTTTGCAGTTGGGTGGAAGTCGAGAGGACTTGCAGTTTGG
| || || | || || |||| | ||||| | || ||| ||| || | || | | | ||| ||| || || ||||||| ||| | || || ||||| || | ||||||||||| |||| |||| |||||||||||||||| | || |||||| | || |||
aggtgtaaccgtgccaattcgca--ccactctacttttggttattctatttgaagctga-gctttaactac-tcacttttcttcttttttgggtaaaactgtagGTATTCAGTGGAAGATACCGGTCCTGTTGCCTGTATATCTTGGACGCCTGACAATTGTGCTCTTGCAGTTGGGTGGAAATTTAGGGGACTTACTGTATGG
upper sequence: AT5G28350.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G052750_T01 (Zea mays), 3'ss of exon 4
ttatacgcccttggtagttttcaagttgtcttactgtgatttatttca--tgcccttgatattttggctgcatcgttaataaaactgtt---ttaaaacttgcagTTATTCAGCGGATTACACTGGGCCTGTAAATAACATTGCATGGACGCCTGATAATTCTGCTTTTGCAGTTGGGTGGAAGTCGAGAGGACTTGCAGTTTGG
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--gtgcaaccatgccaattcaca--ccactctacttttggttgttatatttgaagttga-gctttgaccactccttttccttcttttttggataaaaaattgtagGTATTCAGTGGAAGATACCGGGCCTGTTGCTTGTATATCTTGGACGCCTGACAATTGTGCTTTCGCAGTTGGGTGGAAATTTAGGGGACTTACTGTATGG
upper sequence: AT5G28350.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA18G47050.1 (Glycine max), 3'ss of exon 5
--ttatacgcccttggtagttttcaagttgtct--tactgtgatttatttcatgcccttgatattttggctgcatcgttaataaaactgttttaaaacttgcagTTATTCAGCGGATTACACTGGGCCTGTAAATAACATTGCATGGACGCCTGATAATTCTGCTTTTGCAGTTGGGTGGAAGTCGAGAGGACTTGCAGTTTGG
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cactat-tgaatttaaatgtgtttaaatcattatgtactttaataaataataaaatcaagggtggtttgatgtcttga-aatatattgggattat--tttgcagATATTCAATGGATGACACTGGCCCTGTTAGTTTCATTGCTTGGACACCTGATAATTCCGCTTTTGCAGTTGGGTGGAAGTTAAGGGGGCTTACAGTTTGG
upper sequence: AT5G28350.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA09G39270.2 (Glycine max), 3'ss of exon 5
-ttatacgcccttggtagttttcaagttgtcttactgtgatttatttcatgcccttgatattttggctg-catcgttaataaaactgttttaaaacttgcagTTATTCAGCGGATTACACTGGGCCTGTAAATAACATTGCATGGACGCCTGATAATTCTGCTTTTGCAGTTGGGTGGAAGTCGAGAGGACTTGCAGTTTGG
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actattgaatttaagt-gtgtttagatcattatgtacttcaataaataataaaaatcaagggtggtttgatgtcatgaaatatattgtgattat-tttgcagATATTCGATGGATGACACTGGCCCTGTTAGTTGCATTGCTTGGACACCTGATAATTCCGCTTTTGCAGTTGGGTGGAAGTTAAGGGGGCTTACAGTTTGG
upper sequence: AT5G28350.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: Vv15s0046g01890.t01 (Vitis vinifera), 3'ss of exon 5
ttatacgcccttggtagtt--ttcaagttgtcttactgtgatttatttc-atgcccttgatattttggctgcatcgttaataaaactgttttaaaacttgcagTTATTCAGCGGATTACACTGGGCCTGTAAATAACATTGCATGGACGCCTGATAATTCTGCTTTTGCAGTTGGGTGGAAGTCGAGAGGACTTGCAGTTTGG
| || | | || | | || || || || | | | ||| | | ||| ||| | | | |||| || |||||||||||| ||| | ||||| || |||| | ||||||||||||||||||||||| |||||||| ||||| ||||||| ||||| ||| ||||||||
tggaacaatttccattgtacatcagaaatggctagatgcatattgtcactaaatgctttttgtcttgactgtctttgtcttgctcctgtcttc---tgtgcagTTATTCAATGGACGATACTGGTCCGGTAAGTTGTATTGCATGGACGCCTGATAATTCCGCTTTTGCTGTTGGATGGAAGTTAAGAGGGCTTACAGTTTGG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tcatgcccttgatattttggctgcatcgttaataaaactgttttaaaacttgcagTTATTCAGCGGATTACACTGGGCCTGTAAATAACATTGCATGGACGCCTGATAATTCTGCTTTTGCAGTTGGGTGGAAGTCGAGAGGACTTGCAGTTTGG
cgttaat putative branch site (score: 4)
ttaataaaactgtttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttatacgcccttggtagttttcaagttgtcttactgtgatttatttcatgcccttgatattttggctgcatcgttaataaaactgttttaaaacttgcagTTATTCAGCGGATTACACTGGGCCTGTAAATAACATTGCATGGACGCCTGATAATTCTGCTTTTGCAGTTGGGTGGAAGTCGAGAGGACTTGCAGTTTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - attttgg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aataaaa