Sequence
atgc intronic sequence ATGC exonic sequencegtaatgccttctttatattagtttgatggaatgcttatattcttgccattaggtctcctggaacattggagttttcacaatcttaatttcttttcccgtatttcatggtactcccttatgttttttcttaccattctctttgctgtgaaaagACAAGGTTAGGAAATCCAGAGGTGCGAAAAGTGGTTGATCAATCTATTCAAGAATATCTTACTGAGTATTTAGAATTGCATCCAGATGTTCTTGATTCAG
Basic information
species | Glycine max |
transcript | GLYMA03G28290.1 |
intron # | 12 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA03G28290.1 (Glycine max), 3'ss of exon 12
lower sequence: LOC_Os01g16290.1 (Oryza sativa), 3'ss of exon 12
gtaatgccttctttatattagtttgatggaatgcttatattcttgccattaggtctcctggaacattggagttttcacaatcttaatttcttttcccgtatttcatggtactcccttatgttttttcttaccattctctttgctgtgaaaagACAAGGTTAGGAAATCCAGAGGTGCGAAAAGTGGTTGATCAATCTATTCAAGAATATCTTACTGAGTATTTAGAATTGCATCCAGATGTTCTTGATTCAG
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----------------------gtaacagcttgctcctgatacagaca---aatgtgccagaagaatga---ttcgataacttttgtctttt-------aagtgctgatgattggctaaatcttgttt--cttttctcttttc-----acagACGAGGTTGGGAAATCCAGAAGTCCGAAGAATAGTTGAACAATCTGTTCAAGAAAATTTAACTGAGTACTTAGAGTTACATCCAGATGTTTTAGATTCGA
upper sequence: GLYMA03G28290.1 (Glycine max), 3'ss of exon 12
lower sequence: AT5G04130.1 (Arabidopsis thaliana), 3'ss of exon 12
gtaatgccttctttatattagtttgatggaatgcttatattcttgccattaggtctcctggaacattggagttttcacaatcttaatttcttttcccgtatttcatggtactcccttatgt--tttttcttaccattctctttgctgtgaaaagACAAGGTTAGGAAATCCAGAGGTGCGAAAAGTGGTTGATCAATCTATTCAAGAATATCTTACTGAGTATTTAGAATTGCATCCAGATGTTCTTGATTCAG
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--------------------gtacgtgatgatgattgcctctttagtgttga---tctatgtatggtcaacatgaagcaatttcttctgtcatatttgtggaaatttaccccaactaatataattcgtctactaatcccacttccaccttgcagACAAGATTAGGAAATCCAGAGGTGAGAAAAATTGTTGACCAATCAGTTCAGGAATATCTCACAGAGTTTTTGGAATTGCATCCAGATATTCTTGAGAGCA
upper sequence: GLYMA03G28290.1 (Glycine max), 3'ss of exon 12
lower sequence: AT3G10270.1 (Arabidopsis thaliana), 3'ss of exon 13
gtaatgccttctttatattagtttgatggaatgcttatattcttgccattaggtctcctggaacattggagttt-tcacaatcttaatttcttttcccgtatttcatg-gtactcccttatgttttt--tcttaccattctctttgctgtgaaaagACAAGGTTAGGAAATCCAGAGGTGCGAAAAGTGGTTGATCAATCTATTCAAGAATATCTTACTGAGTATTTAGAATTGCATCCAGATGTTCTTGATTCAG
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------------------------------------------gtactagggagcataatgatatgttgaccctcatttttgtcaacaatctctggtcagcaggccataagttttcttggattctgttgatcattttaatttttttgtgtcccaaagACAAGACTAGGAAATCCAGAGGTGAGAAAAATTGTTGACCAATCAGTCCAGGAGTACCTCACGGAGTACTTGGAATTGCATCCGGATGTACTTGAAAGCA
upper sequence: GLYMA03G28290.1 (Glycine max), 3'ss of exon 12
lower sequence: Vv08s0007g05120.t01 (Vitis vinifera), 3'ss of exon 12
gtaatgccttctttatattagtttg-atggaatgcttatattcttgccattaggtctcctggaacattggagttttcacaatcttaa-tttcttttcccgtatttcatggtactcccttatgttttttcttaccattctctttgctgtgaaaagACAAGGTTAGGAAATCCAGAGGTGCGAAAAGTGGTTGATCAATCTATTCAAGAATATCTTACTGAGTATTTAGAATTGCATCCAGATGTTCTTGATTCAG
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---gtattgtgtttagctttgtgtacatgaattgattt--tttgggtcatcaacaattctctagc--tgg----ctcaaaattgaaactttctcttcccttttctttttatggctgatagcttaccattctgccacttatattattattggaagACAAGGTTAGGAAATCCAGAGGTGCGCAAAGTGGTTGATCAGACTGTTCAAGAGTTTCTTACTGAGTACTTGGAGTTGCATCCGGATGTTCTTGATTTGA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gtatttcatggtactcccttatgttttttcttaccattctctttgctgtgaaaagACAAGGTTAGGAAATCCAGAGGTGCGAAAAGTGGTTGATCAATCTATTCAAGAATATCTTACTGAGTATTTAGAATTGCATCCAGATGTTCTTGATTCAG
ttcttac putative branch site (score: 2)
ctcccttatgtttttt CT-rich tract
ttatgttttttctta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaatgccttctttatattagtttgatggaatgcttatattcttgccattaggtctcctggaacattggagttttcacaatcttaatttcttttcccgtatttcatggtactcccttatgttttttcttaccattctctttgctgtgaaaagACAAGGTTAGGAAATCCAGAGGTGCGAAAAGTGGTTGATCAATCTATTCAAGAATATCTTACTGAGTATTTAGAATTGCATCCAGATGTTCTTGATTCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG