Sequence
atgc intronic sequence ATGC exonic sequence...tgagaattggatcggaacttttcaatttcagtgtctggaaatcttcgattctgtgatttttttacagtgaaattgattcgttattggtttctgggtacagTATATTGTATAATCGTGCAGTTTATCCAGAGGAAAGTTTTGTGAAAGTGAAGAAATATGGACTTCCGATGTTGCTTATTGAAGATGAATCCGTCAAATCT
Basic information
species | Arabidopsis thaliana |
transcript | AT3G25980.2 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G25980.2 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA11G37380.1 (Glycine max), 3'ss of exon 2
---tgagaattg-gatcggaacttttcaa--tttcagtgtctggaa----atcttcgattctgtgattttttt-----acagtgaaattg----attcgt---tattggtttctgggta------cagTATATTGTATAATCGTGCAGTTTATCCAGAGGAAAGTTTTGTGAAAGTGAAGAAATATGGACTTCCGATGTTGCTTATTGAAGATGAATCCGTCAAATCT
||| ||| | | | | |||| || ||| | | | | || || || ||| | | | | |||||| ||| | |||| | | |||| | ||| || | || || |||| |||||||||||| ||||| |||||||| || ||||||||||| || || |||||||||| ||||||||| |||||| ||
gtttgatccttgtgtcctgcattttttaaattttttttattttgggccttatttttcgcattgcaattatgtatgtggccggaaaaattgtgatatttataagtatttgaatttgggaatttgatcagCATTCTTTACAACCGTGGAGTTTATCCAGAAGAAAGCTTTGTGAAGGTTAAGAAATATGGCCTCCCCATGTTGCTTACTGAAGATGAGGGTGTCAAAACT
upper sequence: AT3G25980.2 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA11G37380.3 (Glycine max), 3'ss of exon 2
---tgagaattggatcg-gaacttttcaa--tttcagtgtctggaa----atcttcgattctgtgattttttta-----cagtgaaattg----attcgt---tattggtttctgggta------cagTATATTGTATAATCGTGCAGTTTATCCAGAGGAAAGTTTTGTGAAAGTGAAGAAATATGGACTTCCGATGTTGCTTATTGAAGATGAATCCGTCAAATCT-----------------------------
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gtttgatccttgtgtcctgcattttttaaattttttttattttgggccttatttttcgcattgcaattatgtatgtggccggaaaaattgtgatatttataagtatttgaatttgggaatttgatcagcattctttacaaccgtggagtttatccagAAGAAAGCTTTGTGAAGGTTAAGAAATATGGCCTCCCCATGTTGCTTACTGAAGATGAGGGTGTCAAAACTTTTTTAGCCAATCTAACTGCTCAGCTCTC
upper sequence: AT3G25980.2 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA15G34480.1 (Glycine max), 3'ss of exon 1
tgagaattggatcggaacttttcaatttcagtgtctggaaatcttcgattctgtgatttttttacagtgaaattgattcgttattggtttctgggtacagTATATTGTATAATCGTGCAGTTTATCCAGAGGAAAGTTTTGTGAAAGTGAAGAAATATGGACTTCCGATGTTGCTTATTGAAGATGAATCCGTCAAATCT--------------------
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------------------tatttttttgcattgcaattatgcatgtggctggaaaatttgtgatatttataagtattttaatat-gataatttgat-caacattctctacaaccgtggagTTTATCCAGAAGAAAGCTTTGTGAAAGTTAAGAAATATGGCCTCCCCATGTTGCTAACGGAAGATGAGGGTGTCAAATCTTTTCTAGCAAATCTAACCGC
upper sequence: AT3G25980.2 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA18G01350.1 (Glycine max), 3'ss of exon 2
--------------------------------tgagaattggatcggaacttttcaatttcagtgtctggaaatcttcgattctgtgatttttttacagtgaaattgattcgttattggtttctgggtacagTATATTGTATAATCGTGCAGTTTATCCAGAGGAAAGTTTTGTGAAAGTGAAGAAATATGGACTTCCGATGTTGCTTATTGAAGATGAATCCGTCAAATCT
| | || || ||| | || || || | | | | | || | | || | || ||| || | || ||| || | || || |||| |||||||||||| ||||| |||||||| || ||||||||||| || || |||||||| | |||||||| |||||||||
gtttgatcctcgtgtcctgcattttttatttttttaatttattatgggtcttattttttgcattgcaattatgcatgtggctggaaaagttgtgatatttataagtattttaatatgggaatttgat--cagCATTCTCTACAACCGTGGAGTTTATCCAGAAGAAAGCTTTGTGAAGGTTAAGAAATATGGCCTCCCCATGTTGCTAACGGAAGATGAGGGTGTCAAATCT
upper sequence: AT3G25980.2 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: Vv01s0010g02430.t01 (Vitis vinifera), 3'ss of exon 2
---tgagaattggatcggaacttttcaatttcagtgtctggaaatcttcg----attctgtgatttttttacagt----gaaattgattc-gttattggtttctgggtacagTATATTGTATAATCGTGCAGTTTATCCAGAGGAAAGTTTTGTGAAAGTGAAGAAATATGGACTTCCGATGTTGCTTATTGAAGATGAATCCGTCAAATCT
||| ||| | | || |||| ||| | | || | | | ||| | ||||| | | | |||| ||||| | | || |||||| | || ||||| | ||||||||| || ||| ||||| ||||||||||||||||| ||||| ||| |||||| | ||||||| || |||||
gtatgaacattaaaataaacggattgaattgtagtttatttaattttctgttgaatttttagatttatgtttgggttgggaaagtgattttgatgggaaagaaaatgttcagTATTCTATACAATCGCGGAGTTTATCCGGAAGAATCTTTTGGAAAAGTGAAGAAATATGGCCTTCCAATGCTGCTTACTCAAGATGAGGGTGTTAAATCG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cgattctgtgatttttttacagtgaaattgattcgttattggtttctgggtacagTATATTGTATAATCGTGCAGTTTATCCAGAGGAAAGTTTTGTGAAAGTGAAGAAATATGGACTTCCGATGTTGCTTATTGAAGATGAATCCGTCAAATCT
aattgat putative branch site (score: 4)
tttct putative PPT
tgattttttta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tgagaattggatcggaacttttcaatttcagtgtctggaaatcttcgattctgtgatttttttacagtgaaattgattcgttattggtttctgggtacagTATATTGTATAATCGTGCAGTTTATCCAGAGGAAAGTTTTGTGAAAGTGAAGAAATATGGACTTCCGATGTTGCTTATTGAAGATGAATCCGTCAAATCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG