Sequence
atgc intronic sequence ATGC exonic sequencegtgagaattggatcggaacttttcaatttcagtgtctggaaatcttcgattctgtgatttttttacagtgaaattgattcgttattggtttctgggtacagTATATTGTATAATCGTGCAGTTTATCCAGAGGAAAGTTTTGTGAAAGTGAAGAAATATGGACTTCCGATGTTGCTTATTGAAGATGAATCCGTCAAATCT
Basic information
| species | Arabidopsis thaliana |
| transcript | AT3G25980.1 |
| intron # | 2 |
| splice site | 3' |
| intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G25980.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA11G37380.1 (Glycine max), 3'ss of exon 2
--gtgagaattg-gatcggaacttttcaa--tttcagtgtctggaa----atcttcgattctgtgattttttt-----acagtgaaattg----attcgt---tattggtttctgggta------cagTATATTGTATAATCGTGCAGTTTATCCAGAGGAAAGTTTTGTGAAAGTGAAGAAATATGGACTTCCGATGTTGCTTATTGAAGATGAATCCGTCAAATCT
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gtttgatccttgtgtcctgcattttttaaattttttttattttgggccttatttttcgcattgcaattatgtatgtggccggaaaaattgtgatatttataagtatttgaatttgggaatttgatcagCATTCTTTACAACCGTGGAGTTTATCCAGAAGAAAGCTTTGTGAAGGTTAAGAAATATGGCCTCCCCATGTTGCTTACTGAAGATGAGGGTGTCAAAACT
upper sequence: AT3G25980.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA11G37380.3 (Glycine max), 3'ss of exon 2
--gtgagaattggatcg-gaacttttcaa--tttcagtgtctggaa----atcttcgattctgtgattttttta-----cagtgaaattg----attcgt---tattggtttctgggta------cagTATATTGTATAATCGTGCAGTTTATCCAGAGGAAAGTTTTGTGAAAGTGAAGAAATATGGACTTCCGATGTTGCTTATTGAAGATGAATCCGTCAAATCT-----------------------------
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gtttgatccttgtgtcctgcattttttaaattttttttattttgggccttatttttcgcattgcaattatgtatgtggccggaaaaattgtgatatttataagtatttgaatttgggaatttgatcagcattctttacaaccgtggagtttatccagAAGAAAGCTTTGTGAAGGTTAAGAAATATGGCCTCCCCATGTTGCTTACTGAAGATGAGGGTGTCAAAACTTTTTTAGCCAATCTAACTGCTCAGCTCTC
upper sequence: AT3G25980.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA15G34480.1 (Glycine max), 3'ss of exon 1
gtgagaattggatcggaacttttcaatttcagtgtctggaaatcttcgattctgtgatttttttacagtgaaattgattcgttattggtttctgggtacagTATATTGTATAATCGTGCAGTTTATCCAGAGGAAAGTTTTGTGAAAGTGAAGAAATATGGACTTCCGATGTTGCTTATTGAAGATGAATCCGTCAAATCT--------------------
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-------------------tatttttttgcattgcaattatgcatgtggctggaaaatttgtgatatttataagtattttaatat-gataatttgat-caacattctctacaaccgtggagTTTATCCAGAAGAAAGCTTTGTGAAAGTTAAGAAATATGGCCTCCCCATGTTGCTAACGGAAGATGAGGGTGTCAAATCTTTTCTAGCAAATCTAACCGC
upper sequence: AT3G25980.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA18G01350.1 (Glycine max), 3'ss of exon 2
-------------------------------gtgagaattggatcggaacttttcaatttcagtgtctggaaatcttcgattctgtgatttttttacagtgaaattgattcgttattggtttctgggtacagTATATTGTATAATCGTGCAGTTTATCCAGAGGAAAGTTTTGTGAAAGTGAAGAAATATGGACTTCCGATGTTGCTTATTGAAGATGAATCCGTCAAATCT
| | || || ||| | || || || | | | | | || | | || | || ||| || | || ||| || | || || |||| |||||||||||| ||||| |||||||| || ||||||||||| || || |||||||| | |||||||| |||||||||
gtttgatcctcgtgtcctgcattttttatttttttaatttattatgggtcttattttttgcattgcaattatgcatgtggctggaaaagttgtgatatttataagtattttaatatgggaatttgat--cagCATTCTCTACAACCGTGGAGTTTATCCAGAAGAAAGCTTTGTGAAGGTTAAGAAATATGGCCTCCCCATGTTGCTAACGGAAGATGAGGGTGTCAAATCT
upper sequence: AT3G25980.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv01s0010g02430.t01 (Vitis vinifera), 3'ss of exon 2
--gtgagaattggatcggaacttttcaatttcagtgtctggaaatcttcg----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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgagaattggatcggaacttttcaatttcagtgtctggaaatcttcgattctgtgatttttttacagtgaaattgattcgttattggtttctgggtacagTATATTGTATAATCGTGCAGTTTATCCAGAGGAAAGTTTTGTGAAAGTGAAGAAATATGGACTTCCGATGTTGCTTATTGAAGATGAATCCGTCAAATCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
