Sequence
atgc intronic sequence ATGC exonic sequencegtaaacccatctgttcattgtttccattgtattacgtgaaaattcttcatcgcctggcatttccaatctcattatttctcatatatattaagATGGATGAATTGGCATGCTTTGCTCCTGGAATGTTGGCTTTAGGAGCATCTGGGTATAGTGATCCTGCTGAAGGAAAGAAGTTTCTCACACTCGCTGAAG
Basic information
species | Arabidopsis thaliana |
transcript | AT3G21160.1 |
intron # | 10 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G21160.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GRMZM2G130889_T01 (Zea mays), 3'ss of exon 11
-------------gtaaacccatctgttcattgtttccattgtattacg---tgaaaattcttcatcgcctggcatttccaatctcattatttct---catatatatta-agATGGATGAATTGGCATGCTTTGCTCCTGGAATGTTGGCTTTAGGAGCATCTGGGTATAGTGATCCTGCTGAAGGAAAGAAGTTTCTCACACTCGCTGAAG--
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gtaatgtatcctaattcagttggttgttcattgttcttggcaggctgcttgttgaagctaatccctcattcttctctaaaattctgacaagttctgcctgtgactaacacagATGGATGAACTTGCTTGCTTTGCTCCTGGTATGCTGGCCTTAGGAGCCTCTGGTTACGGG---CCAGAAAAATCAGAGCAAATTATGAATCTTGCAAAAGAG
upper sequence: AT3G21160.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GLYMA17G06600.1 (Glycine max), 3'ss of exon 10
gtaaacccatctgttcattgtttccattgtattacgtgaaaattcttcatcgcctggcatttcc----aatctcattatttctcatata-tattaagATGGATGAATTGGCATGCTTTGCTCCTGGAATGTTGGCTTTAGGAGCATCTGGGTATAGTGATCCTGCTGAAGGAAAGAAGTTTCTCACACTCGCTGAAG--
| ||| | | | || | || | | ||| | || || || || | |||| | | | | ||||||||||||| ||||| |||| |||||||||||||||||| ||| | ||| ||| | |||| |||| | || ||||| |||| | || |
--------------gtgctattttga--aaaggaagtctatttttgccttagccgagtatgtcattaaaagaatcttttatctcgtttccttcttagATGGATGAATTAGCATGTTTTGTTCCTGGAATGTTGGCTTTGGGATCTTCTAACTATGGC---CCTGGAGAAGCTGAAAAATTTCTAGCACTTGGAGAGGAG
upper sequence: AT3G21160.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GLYMA13G00470.1 (Glycine max), 3'ss of exon 12
gtaaacccatctgttcattgtttccattgtattacgtgaaaattcttcatcgcctggcatttccaatctcattatttctcatatatattaagATGGATGAATTGGCATGCTTTGCTCCTGGAATGTTGGCTTTAGGAGCATCTGGGTATAGTGATCCTGCTGAAGGAAAGAAGTTTCTCACACTCGCTGAAG--
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--------------------------------------------------------gtatgtaagaatcttttattttgtttccttttta-gATGGATGAATTAGCATGTTTTGTTCCTGGAATGCTGGCTCTGGGATCTTCTAACTATGGC---CTTGGAGAAGCTGAAAAATTTATGGCACTTGCAGAGGAG
upper sequence: AT3G21160.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: Vv09s0054g00370.t01 (Vitis vinifera), 3'ss of exon 10
gtaaacccatctgttcattgtttccattgtattacgtgaaaattcttcatcgcctggcatttccaatctcattatttctc--atatatattaagATGGATGAATTGGCATGCTTTGCTCCTGGAATGTTGGCTTTAGGAGCATCTGGGTATAGTGATCCTGCTGAAGGAAAGAAGTTTCTCACACTCGCTGAAG--
|||| | | || |||| ||| | | | || | | |||||| || || ||| | |||||| | ||||||||||||| ||||||||||| || |||||| | ||||||||| || ||| ||| || |||| ||| |||| || || | || || ||||
gtaatatttgattccaaaatactcatttgttctactgcactaatatttgaccattagcattttggtgctatttgttttttctatatatgtgcagATGGATGAATTAGCATGCTTTGCCCCAGGAATGATTGCTTTAGGATCACTTGGTTATGGT---CCTGAAGAATCTCAGAAATTCCTATCCCTTGCCGAAGAG
upper sequence: AT3G21160.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: Vv11s0052g00140.t01 (Vitis vinifera), 3'ss of exon 10
------gtaaacccatctgttcattgtttccattgtattacgtgaaaattcttcatcgcctggcatttccaatctcattatttctcatatatattaagATGGATGAATTGGCATGCTTTGCTCCTGGAATGTTGGCTTTAGGAGCATCTGGGTATAGTGATCCTGCTGAAGGAAAGAAGTTTCTCACACTCGCTGAAG--
| ||| |||| | || | |||| || || | | ||| ||| | ||||| | |||| ||||||||||||| |||||||||||||| || ||||||||||||| ||| || || || ||||| |||| |||| | ||| |||| || ||||
gtattgttttgatgatcaaaaggagatttctctagtgctggctgaatatgct--gttatggagtcttttaaatgcttctttttctta---atatgcagATGGATGAATTAGCATGCTTTGCTCCAGGGATGTTGGCTTTAGCTTCATATG---ATTATGGTCCTGGAGAAGCTGAGAAATATCTATCACTTGCGGAAGAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gaaaattcttcatcgcctggcatttccaatctcattatttctcatatatattaagATGGATGAATTGGCATGCTTTGCTCCTGGAATGTTGGCTTTAGGAGCATCTGGGTATAGTGATCCTGCTGAAGGAAAGAAGTTTCTCACACTCGCTGAAG
aatctcattatttctc 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaaacccatctgttcattgtttccattgtattacgtgaaaattcttcatcgcctggcatttccaatctcattatttctcatatatattaagATGGATGAATTGGCATGCTTTGCTCCTGGAATGTTGGCTTTAGGAGCATCTGGGTATAGTGATCCTGCTGAAGGAAAGAAGTTTCTCACACTCGCTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG