Sequence
atgc intronic sequence ATGC exonic sequence...actagctgagatcacttggtttgatagtggagttgcagctttgacctttttgttcgataattaccttatttgatgatgggtttgatcacattgagtgtagGTACGTGGGATGTTTTATCATGCCTTTGATGGATATATGAACAATGCGTTTCCACTCGATGAATTGAGACCGTTATCTTGCCAAGGAGAAGATACTCTTG
Basic information
species | Arabidopsis thaliana |
transcript | AT5G43710.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G43710.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: LOC_Os01g56670.3 (Oryza sativa), 3'ss of exon 1
------actagctgagatcacttggtttgatagtggagttgcagctttgacctttttgttcgataattaccttatttgatgatgg-gtttgatcacattgagtgtagGTACGTGGGATGTTTTATCATGCCTTTGATGGATATATGAACAATGCGTTTCCACTCGATGAATTGAGACCGTTATCTTGCCAAGGAGAAGATACTCTTG
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aacctcattaagagatatcttccacttcaaca----agacgccatcttg---tttacaattaacatgtgcagaatctagtattcatatggaaatgtcttttatgtagGTCAAAGATATGTTCTATCATGCATTTGATGGGTACATGCAACATGCTTTTCCACTTGATGAATTGCGGCCTTTAAGTTGCCAAGGAGAAGATTCACTTG
upper sequence: AT5G43710.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GRMZM2G173868_T02 (Zea mays), 3'ss of exon 1
----actagctgagatcacttggtttgatagtggagttgcagctttgacctttttgttcgataattaccttatttgatgatgggtttgatcacattgagtgtagGTACGTGGGATGTTTTATCATGCCTTTGATGGATATATGAACAATGCGTTTCCACTCGATGAATTGAGACCGTTATCTTGCCAAGGAGAAGATACTCTTG
|| | || | | | | | || || ||| | || | | | | | | | | | || || ||||||| | ||||| |||||||| ||||||||||| ||||| |||| || ||||||||||| || | || ||| ||||||||
tcatacctacaaggacaagctagccttgttgttgaccccttatttt-atggcaagatttatttgcttaaacactggctaaaaaat---agcatctttcatgtagGTGAAAGATATGTTCTATCATGCGTTTGATGGATACATGAAGTATGCTTTCCCACTCGATGAGCTGCGGCCCTTAAGTTGCCAAG---------------
upper sequence: AT5G43710.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GRMZM2G020359_T02 (Zea mays), 3'ss of exon 1
----actagctgagatcacttggtttgatagtggagttgcagctttgacctttttgttcgataattaccttatttgatgatgggtttgatcacattgagtgtagGTACGTGGGATGTTTTATCATGCCTTTGATGGATATATGAACAATGCGTTTCCACTCGATGAATTGAGACCGTTATCTTGCCAAGGAGAAGATACTCTTG
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tcatacctacaaggacaagctagccttgttgttgaccccttatttt-atggcaagatttatttgcttaaacactggctaaaaaat---agcatctttcatgtagGTGAAAGATATGTTCTATCATGCGTTTGATGGATACATGAAGTATGCTTTCCCACTCGATGAGCTGCGGCCCTTAAGTTGCCAAGGTGAAGACTCCCTTG
upper sequence: AT5G43710.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: Vv05s0020g04650.t01 (Vitis vinifera), 3'ss of exon 1
actagctgagatcacttggtttgatagtggagttgcagctttgacctttttgttcgataattaccttat--ttgatgatgggtttgatcacattgagt-gtagGTACGTGGGATGTTTTATCATGCCTTTGATGGATATATGAACAATGCGTTTCCACTCGATGAATTGAGACCGTTATCTTGCCAAGGAGAAGATACTCTTG
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--taatgattcgaacttaagggaataggaaaattccaa-tatgagttgggatttagctaaatggtttatggttggtaattgatgcatttaccgtatgccatagGTACGTGGCATGTTCTATCATGCGTTTGATGGATATATGGAGAATGCTTTTCCTTTAGATGAATTAAGACCTCTGACATGCGAGGGAGAAGACACACTAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ctttttgttcgataattaccttatttgatgatgggtttgatcacattgagtgtagGTACGTGGGATGTTTTATCATGCCTTTGATGGATATATGAACAATGCGTTTCCACTCGATGAATTGAGACCGTTATCTTGCCAAGGAGAAGATACTCTTG
gtttgat putative branch site (score: 5)
ataattaccttattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
actagctgagatcacttggtttgatagtggagttgcagctttgacctttttgttcgataattaccttatttgatgatgggtttgatcacattgagtgtagGTACGTGGGATGTTTTATCATGCCTTTGATGGATATATGAACAATGCGTTTCCACTCGATGAATTGAGACCGTTATCTTGCCAAGGAGAAGATACTCTTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - -ggtttga