Sequence
atgc intronic sequence ATGC exonic sequencegtaagttcttgtagataatcaatacaatatgaagttatcctcttgatagtggaggaatgaaaaatacatgctattattctctttactttttgtgaaataagcaatgcacaaattgatgtggctctcgttcatgagtagGTAATTGTCTCGGCAAACAAACCAGAATTCTTCCAAATGTCACACCCCATGTATGAGGTGGTGACAGAAGAGGGCCTGATGCGTCCATGCTTTAAGGCTC
Basic information
species | Glycine max |
transcript | GLYMA15G21240.1 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA15G21240.1 (Glycine max), 3'ss of exon 9
lower sequence: AT5G48960.1 (Arabidopsis thaliana), 3'ss of exon 10
gtaagttcttgtagataatcaatacaatatgaagttatcctcttgatagtggaggaatgaaaaatacatgctattattctctttactttttgtgaaataagcaatgcacaaattgatgtggctctcgttcatgagtagGTAATTGTCTCGGCAAACAAACCAGAATTCTTCCAAATGTCACACCCCATGTATGAGGTGGTGACAGAAGAGGGCCTGATGCGTCCATGCTTTAAGGCTC
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-----------------gtgagca-aacgtaaatttgtt-tctgcattttg-----attgtaaatc--tgttgtttttcagagagtagtttgc--attagactttactgtttttga----attcatgtttccacatagGTGATAGTTTCTGCGAGGAAACCAGAGTTCTTCCAGATGTCGCACCCTCTATATGAGGTTGTGACTGGAGAGGGTTTGATGCGTCCATGCTTCAAGGCTG
upper sequence: GLYMA15G21240.1 (Glycine max), 3'ss of exon 9
lower sequence: Vv05s0020g00880.t01 (Vitis vinifera), 3'ss of exon 10
gtaagttcttgtagataatcaatacaatatgaagttatcctcttgatagtggaggaatgaaaaatacatgctattattctctttactttttgtgaaataagcaatgcacaaattgatgtggctctcgttcatgagtagGTAATTGTCTCGGCAAACAAACCAGAATTCTTCCAAATGTCACACCCCATGTATGAGGTGGTGACAGAAGAGGGCCTGATGCGTCCATGCTTTAAGGCTC
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-------------------ggctaaattataaag--aatgcctaaacaatgtaggagtca----catgtgctttgcacttctggcagttttgttgcc-------ttcatgtgttcacgttgttcttgt------gtagGTTATAGTCTCTGCGAGGAAGCCAGAGTTCTTCCAAATGTCACACCCATTGTATGAGGTGGTGACAGATGAGGGTCTAATGCGTCCATGCTTCAAGGCTT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tactttttgtgaaataagcaatgcacaaattgatgtggctctcgttcatgagtagGTAATTGTCTCGGCAAACAAACCAGAATTCTTCCAAATGTCACACCCCATGTATGAGGTGGTGACAGAAGAGGGCCTGATGCGTCCATGCTTTAAGGCTC
aattgat putative branch site (score: 4)
ctctcgttc putative PPT
tgaaataa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagttcttgtagataatcaatacaatatgaagttatcctcttgatagtggaggaatgaaaaatacatgctattattctctttactttttgtgaaataagcaatgcacaaattgatgtggctctcgttcatgagtagGTAATTGTCTCGGCAAACAAACCAGAATTCTTCCAAATGTCACACCCCATGTATGAGGTGGTGACAGAAGAGGGCCTGATGCGTCCATGCTTTAAGGCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG