Sequence
atgc intronic sequence ATGC exonic sequencegtaagtttatatgcttcttccatgctgtttacaattaatatacttttaaatagaattctttttcttccatttatattatattattttatttttatgttgttactaaatgtttttcccgggtgcatagGTTACCAGTTATTCAAGCGTTGGCTGCAGAAGTTAGGCTGACTACCCAATCACTTCTTTCTCAGCTTCTACAGAAACTTCGCTCAAATATTCAG
Basic information
species | Glycine max |
transcript | GLYMA16G22880.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA16G22880.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os12g35290.1 (Oryza sativa), 3'ss of exon 4
gtaagtttatatgcttcttccatgctgtttacaattaatatacttttaaatagaattctttttcttccatttatattatattattttatttttatgttgttactaaatgtttttcccgggtgcatagGTTACCAGTTATTCAAGCGTTGGCTGCAGAAGTTAGGCTGACTACCCAATCACTTCTTTCTCAGCTTCTACAGAAACTTCGCTCAAATATTCAG
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-------------------------------------gtaagtcatttgacataatctttattatggcctttgtaatttgcaatt----------aatttaactgtatgccttttc---gattgaagTTTACCTGTTATCCAAGGCTTAGCTGTTGAAGTCAAGAAGACAATACAGTCATTAATTTCTCAGCTTCTCCAGAAGCTTCGATCAAATATTCAG
upper sequence: GLYMA16G22880.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G006781_T03 (Zea mays), 3'ss of exon 4
gtaagtttatatgcttcttccatgctgtttacaattaatatacttttaaatagaattctttttcttccatttatattatattattttatttttatgttgttactaaatgtttttcccgggtgcatagGTTACCAGTTATTCAAGCGTTGGCTGCAGAAGTTAGGCTGACTACCCAATCACTTCTTTCTCAGCTTCTACAGAAACTTCGCTCAAATATTCAG
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-------------------------------------gtatgttgtgtaacataattgcatcacactccctgacatt---------tgctgttatatta--accatttacttttttccaattga-agTTTACCTGTTGTCCAAGGATTAGCCACTGAAGTCAAGAAGACAGTGCAATCATTAGTTTCACAGCTTCTCCAGAAACTTCGATCAAATATTCAG
upper sequence: GLYMA16G22880.1 (Glycine max), 3'ss of exon 3
lower sequence: AT5G11980.1 (Arabidopsis thaliana), 3'ss of exon 4
gtaagtttatatgcttcttccatgctgtttacaattaatatacttttaaatagaattctttttcttcca-tttatattatattattttatttttatgttgttactaaatgtttttcccgggtgcatagGTTACCAGTTATTCAAGCGTTGGCTGCAGAAGTTAGGCTGACTACCCAATCACTTCTTTCTCAGCTTCTACAGAAACTTCGCTCAAATATTCAG
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----------------------------gtgagttttttgtaatctttctcacgatacttttacttaaggcctcaaccatcaagctttagctctaaac----attatatcttctctct--atgtcaagATTGCCAGTTATCCAAGCACTTGCAGCGGAGGTTAGACAAACAACTCAGTCACTTCTCTCACAGCTTCTCCAGAAACTACGCTCAAATATACAG
upper sequence: GLYMA16G22880.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv04s0008g01350.t01 (Vitis vinifera), 3'ss of exon 4
gtaagtttatatgcttcttccatgctgtttac-aattaatatacttttaaatagaattctttttcttccatttatattatattattttatttttatgttgttactaaatgtttttcccgggtgcatagGTTACCAGTTATTCAAGCGTTGGCTGCAGAAGTTAGGCTGACTACCCAATCACTTCTTTCTCAGCTTCTACAGAAACTTCGCTCAAATATTCAG
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gtgagcttttat--ttcttgtatgctacttgccaactaatatttgttttagctg------------tcaaccttgagaaatgtaactcactattgccctgtt---------ttttc----gcttaaagATTGCCAGTCATTCAAGCACTGGCTGCAGAAGTTAGGCAAACAACCCAATCTCTTCTTCATCAGCTTCTCCAGAAACTTCGATCAAATATTCTG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atattatattattttatttttatgttgttactaaatgtttttcccgggtgcatagGTTACCAGTTATTCAAGCGTTGGCTGCAGAAGTTAGGCTGACTACCCAATCACTTCTTTCTCAGCTTCTACAGAAACTTCGCTCAAATATTCAG
tactaaa putative branch site (score: 1)
tttttcccg putative PPT
atattattttattttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagtttatatgcttcttccatgctgtttacaattaatatacttttaaatagaattctttttcttccatttatattatattattttatttttatgttgttactaaatgtttttcccgggtgcatagGTTACCAGTTATTCAAGCGTTGGCTGCAGAAGTTAGGCTGACTACCCAATCACTTCTTTCTCAGCTTCTACAGAAACTTCGCTCAAATATTCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TCAGCT