Sequence
atgc intronic sequence ATGC exonic sequencegtaaagaaaaagcatctccaagattacattttatatatatacacacaccactgggactgacactatctacatgtctcttaaacagGAGAAAAATCTGTTCTAGACTGGGCAACACGTGTTAAAATTGCGGCTGGGGCAGCTCGTGGACTAGCTTATCTTCATGAAGATT
Basic information
| species | Arabidopsis thaliana |
| transcript | AT1G68690.1 |
| intron # | 2 |
| splice site | 3' |
| intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G68690.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM5G872442_T02 (Zea mays), 3'ss of exon 3
----------gtaaagaaaaa-gca--tctccaagattaca-----ttttatatatatacacacaccactgggactgacac-tatctacatgtctcttaaacagGAGAAAAATCTGTTCTAGACTGGGCAACACGTGTTAAAATTGCGGCTGGGGCAGCTCGTGGACTAGCTTATCTTCATGAAGATT
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gtcttgttacataggcagaactgcaattatttaggaacagaggtagttctttgtccggac-taaacaattaatgcatacccgcattgatttttcatcatagGACGTGGAGTACCAGTTTTGGAGTGGCCAGCTAGGGTTAAAATTGCGGCTGGTTCGGCTCGTGGAATAGCCTATCTTCACGAAGATT
upper sequence: AT1G68690.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G355636_T01 (Zea mays), 3'ss of exon 3
------------------------------------------------------------------------------------------gtaaagaaa-aagcatctccaagattacattttatatatatacacacaccactgggactgacactatctacatgtc--tcttaa---------acagGA---GAAAAATCTGTTCTAGACTGGGCAACACGTGTTAAAATTGCGGCTGGGGCAGCTCGTGGACTAGCTTATCTTCATGAAGATT
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gtatgttatatgttgtgcaggagcattctttttaccacctctgttccaaaatatttgtacttctagctatggacatggacaagtatttgtgtatgtacataaccagacctgcaattattttggaacgaggtagttctttgtccggactaaacatttaatgcatacccatattgatttttcatcatagGACTTGGAGTACCAGTCTTGGAATGGCCATCTAGGGTTAAAATTGCGGCTGGTTCAGCACGCGGAATAGCCTATCTTCATGAAGATT
upper sequence: AT1G68690.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA02G14310.1 (Glycine max), 3'ss of exon 2
gtaaagaaaaagcatctccaagattacattttatatatatacacacaccactgggactgacactatctacatgtctcttaa---acagGAGAAA---AATCTGTTCTAGACTGGGCAACACGTGTTAAAATTGCGGCTGGGGCAGCTCGTGGACTAGCTTATCTTCATGAAGATT
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---gtaaaactacatctgagtgataatagattgtttcagtttattt-tgattgactttgattgtattaactgatattgtaatttgcagGGGAAGGCCAGCCTGTGCTAGAATGGGCAAACCGTGTTAAAATTGCAGCTGGTGCAGCCCGAGGACTAGCTTATCTCCATGAAGACT
upper sequence: AT1G68690.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA16G19520.1 (Glycine max), 3'ss of exon 3
--------------------------------------------------------gtaa-agaaaaagcatctccaagattacatt--ttatatatatacacacaccactgggactgacactatct--acatgtctcttaaacagGAGAAAAATCTGTTCTAGACTGGGCAACACGTGTTAAAATTGCGGCTGGGGCAGCTCGTGGACTAGCTTATCTTCATGAAGATT
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gtaaagctagttcagagggctagctgaatgattgtttcatgatattttgattaaatgtgtcagtgaatgtgttcaaaagagtgtattgctaacatttctctttgattaaatttaatctgtgctaactgaaagtgaatttgaagGGGAAGGTAGGCCAGTGCTGGACTGGACAAAACGTGTTAAAATTGCGGCTGGGGCAGCCAGAGGAATAGCTTATCTCCATGAAGACT
upper sequence: AT1G68690.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv01s0011g02460.t01 (Vitis vinifera), 3'ss of exon 2
gtaaagaaaaagca-----tctccaagattacattttatatatatacacacaccactgggactgacactatctacatgtctcttaaacagGAGAAAAATCTGTTCTAGACTGGGCAACACGTGTTAAAATTGCGGCTGGGGCAGCTCGTGGACTAGCTTATCTTCATGAAGATT
|||| | || ||||||| | | ||| | || | | | | | || || | | | | | | || | | ||| | |||||||||||||||||||| |||| ||||| |||||||||||| ||||||||||||||||||| |
gtaaggctgtagtgataagcttccaaga--atagtttgtggtaatggataactgattatg--tgttgctccttgtaa---tttgtagGGGAAGGTAGGCCAGTTATGGACTGGGCAACACGTGTTAAGGTTGCTGCTGGTGCAGCTCGTGGAATAGCTTATCTTCATGAAGACT
upper sequence: AT1G68690.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: EFJ20011 (Selaginella moellendorffii), 3'ss of exon 1
gtaaagaaaaagcatctccaagattacattttatatatatacacacaccactgggactgacactatctacatgtctcttaaacagGAGAAAAATCTGTTCTAGACTGGGCAACACGTGTTAAAATTGCGGCTGGGGCAGCTCGTGGACTAGCTTATCTTCATGAAGATT
| |||| || || | | | | | || | || | ||| | | || | || | | | || | || ||| |||| | | ||||| || |||| | |||||||||||||| |||||||||||||| |
---------------gtacaagttt---ttgtccgtgtttttccttgtt-ctcagtctcgttttctctcttgtttttttcagGTAAAGGTAGACCCGTGATGGATTGGCCAACGAGATTGAAAATAGCTTCTGGTTCTGCTCGTGGACTAGCATATCTTCATGAAGACT
upper sequence: AT1G68690.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: EFJ07415 (Selaginella moellendorffii), 3'ss of exon 1
gtaaagaaaaagcatctccaagattacattttatatatatacacacaccactgggactgacactatctacatgtctcttaaacagGAGAAAAATCTGTTCTAGACTGGGCAACACGTGTTAAAATTGCGGCTGGGGCAGCTCGTGGACTAGCTTATCTTCATGAAGATT
| |||| || || | | | | | || | || | ||| | | || | || | | | || | || ||| ||||| | | ||||| || |||| | |||||||||||||| |||||||||||||| |
---------------gtacaagttt---ttgtccgtgtttttccttgtt-ctcagtctcgttttctctcttgtttttttcagGTAAAGGTAGACCCGTGATGGATTGGCCAACAAGATTGAAAATAGCTTCTGGTTCTGCTCGTGGACTAGCATATCTTCATGAAGACT
upper sequence: AT1G68690.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: EFJ19888 (Selaginella moellendorffii), 3'ss of exon 1
gtaaagaaaaagcatctccaagattacattttatatatatacacacaccactgggactgacactatctacatgtctcttaaacagGAGAAAAATCTGTTCTAGACTGGGCAACACGTGTTAAAATTGCGGCTGGGGCAGCTCGTGGACTAGCTTATCTTCATGAAGATT
| |||| || || | | | | | || | || | ||| | ||| | || | | || | | | || | || ||| |||| | | ||||| || |||| | |||||||||||||| |||||||||||||| |
---------------gtacaagttt---ttgtccgtgtttttccttgtt-ctcagtctcgttttctct-cttgttttttcagGTGAAGGTAGAACCGTGATGGATTGGCCAACGAGATTGAAAATAGCTTCTGGTTCTGCTCGTGGACTAGCATATCTTCATGAAGACT
upper sequence: AT1G68690.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: EFJ19890 (Selaginella moellendorffii), 3'ss of exon 1
gtaaagaaaaagcatctccaagattacattttatatatatacacacaccactgggactgacactatctacatgtctct-taaacagGAGAAAAATCTGTTCTAGACTGGGCAACACGTGTTAAAATTGCGGCTGGGGCAGCTCGTGGACTAGCTTATCTTCATGAAGATT
| |||| || || | | | | | || | || | ||| | ||| ||| | | || | | | || | || ||| |||| | | ||||| || |||| | |||||||||||||| |||||||||||||| |
---------------gtacaagttt---ttgtccgtgtttttccttgtt-ctcagtctcgttttctct-cttgtttctatcagGTAAAGGTAGACCCGTGATGGATTGGCCAACGAGATTGAAAATAGCTTCTGGTTCTGCTCGTGGACTAGCATATCTTCATGAAGACT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttatatatatacacacaccactgggactgacactatctacatgtctcttaaacagGAGAAAAATCTGTTCTAGACTGGGCAACACGTGTTAAAATTGCGGCTGGGGCAGCTCGTGGACTAGCTTATCTTCATGAAGATT
gactgac putative branch site (score: 2)
tgtctctt putative PPT
tatataca 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaaagaaaaagcatctccaagattacattttatatatatacacacaccactgggactgacactatctacatgtctcttaaacagGAGAAAAATCTGTTCTAGACTGGGCAACACGTGTTAAAATTGCGGCTGGGGCAGCTCGTGGACTAGCTTATCTTCATGAAGATT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
