Sequence
atgc intronic sequence ATGC exonic sequence...agtgcattaaaatgcaaagttgatacagagcaaattcctttgttctcaatggaattttttattaaatctagtatttttacctgcattgatttacatgcagTATTCGGAGGCGTGCTCTAGATTTGCTTTATGGCATGTGTGACGTTTCAAATGCAAAGGATATAGTTGAAGAACTACTGCAG
Basic information
species | Glycine max |
transcript | GLYMA12G30520.1 |
intron # | 10 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA12G30520.1 (Glycine max), 3'ss of exon 10
lower sequence: AT5G22780.1 (Arabidopsis thaliana), 3'ss of exon 10
agtgcattaaaatgcaaagttgatacagagcaaattcct-ttgttctcaatggaattttttattaaatctagtatttttacc--tgcattgatttacatgcagTATTCGGAGGCGTGCTCTAGATTTGCTTTATGGCATGTGTGACGTTTCAAATGCAAAGGATATAGTTGAAGAACTACTGCAG
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---gcttctgtttcacacaatcatatagtttgatttatagttatattctcttggttcttttgctaatggtatcagtttcactattggttgaactttcgtgcagTATTCGTAGACGCGCTCTTGATTTGCTATATGGGATGTGCGATGTGTCAAATGCAAAGGATATAGTTGAAGAGTTGTTGCAG
upper sequence: GLYMA12G30520.1 (Glycine max), 3'ss of exon 10
lower sequence: AT5G22770.2 (Arabidopsis thaliana), 3'ss of exon 11
agtgcattaaaatgcaaagttgatacaga-gcaaattcctttgttctcaatggaattttttattaaatctagtatttttacc--tgcattgatttacatgcagTATTCGGAGGCGTGCTCTAGATTTGCTTTATGGCATGTGTGACGTTTCAAATGCAAAGGATATAGTTGAAGAACTACTGCAG
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---aaatggtggcttccgttttacaaacatatagtttgatttatcatctcttggttcttttgcttatggtgtcagattcactattggttgaactttcctgcagTATTCGTAGGCGTGCTCTTGATTTATTATATGGGATGTGTGATGTGTCAAATGCAAAGGATATAGTCGAAGAGTTGCTGCAG
upper sequence: GLYMA12G30520.1 (Glycine max), 3'ss of exon 10
lower sequence: Vv06s0061g01170.t01 (Vitis vinifera), 3'ss of exon 10
-agtgcattaaaatgcaaa-gttgatacagagcaaattcctttgttctcaatggaattttttattaaatctagtatttttacctgcattgatttaca---tgcagTATTCGGAGGCGTGCTCTAGATTTGCTTTATGGCATGTGTGACGTTTCAAATGCAAAGGATATAGTTGAAGAACTACTGCAG
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ggtttcatgtttgtttaattatctgcaactggcaagatgttttactctaagcaagggactt-----acattagcttgcttactgacaatgattttaaccttgcagTATAAGGAGACGAGCACTTGATCTGCTTTATGGTATGTGTGATATTTCAAATGCAAAGGACATTGTTGAAGAATTACTGCAG
upper sequence: GLYMA12G30520.1 (Glycine max), 3'ss of exon 10
lower sequence: EFJ34224 (Selaginella moellendorffii), 3'ss of exon 10
agtgcattaaaatgcaaagttgatacagagcaaattcctttgttctcaatggaatt-ttttattaaatctagtatttttacctgcattgatttacatgcagTATTCGGAGGCGTGCTCTAGATTTGCTTTATGGCATGTGTGACGTTTCAAATGCAAAGGATATAGTTGAAGAACTACTGCAG
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----------------------------------------------gtttagaattatcttcatcgatct--ccttgttcagtgtatt--tctctttgcagTATTCGAAGGCGATCTCTGGATTTGCTTTATGGAATGTGTGATGTAACAAATGCGAAAGATATTGTTGAGGAGCTTTTGCAG
upper sequence: GLYMA12G30520.1 (Glycine max), 3'ss of exon 10
lower sequence: EFJ21842 (Selaginella moellendorffii), 3'ss of exon 10
agtgcattaaaatgcaaagttgatacagagcaaattcctttgttctcaatggaattttttattaaatctagtatttttacctgcattgatttacatgcagTATTCGGAGGCGTGCTCTAGATTTGCTTTATGGCATGTGTGACGTTTCAAATGCAAAGGATATAGTTGAAGAACTACTGCAG
||| ||| | ||||| | ||| || || || ||| | | ||||||||||| ||||| |||| |||||||||||||| |||||||| || ||||||| || ||||| ||||| || || |||||
-----------------------------------------gtttagaatta---tctttatcga-tct--ccttgttcagtgtatt--tctctttgcagTATTCGAAGGCGATCTCTGGATTTGCTTTATGGAATGTGTGATGTAACAAATGCGAAAGATATTGTTGAGGAGCTTTTGCAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tcaatggaattttttattaaatctagtatttttacctgcattgatttacatgcagTATTCGGAGGCGTGCTCTAGATTTGCTTTATGGCATGTGTGACGTTTCAAATGCAAAGGATATAGTTGAAGAACTACTGCAG
cattgat putative branch site (score: 4)
aattttttattaaatc 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
agtgcattaaaatgcaaagttgatacagagcaaattcctttgttctcaatggaattttttattaaatctagtatttttacctgcattgatttacatgcagTATTCGGAGGCGTGCTCTAGATTTGCTTTATGGCATGTGTGACGTTTCAAATGCAAAGGATATAGTTGAAGAACTACTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG
- tgcatta
- - - - - aatgcaa
- - - - - - - - - - - - - - - - - -tcctttg
- - - - - - - - - - - - - - - - - - - - - - ctcaatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - acctgca