Sequence
atgc intronic sequence ATGC exonic sequencegtacagtacctttcctattttttgatcccctatttttgccaataaagatttagttttgtggtgacaaattatcagtataaatcttaaatatgactgcaaacaaatttgaacaagctctagtctatcattggtaaaactttggtcattttggtgactactgactaaaattctctgaactaatctgattactaaattacagGATTATTTTGCTGATGAAATTGGAGTTTTATCTCCCAGTCAACTACAAGTTGAAGAATTGTATGCTGGTGAG
Basic information
species | Glycine max |
transcript | GLYMA06G16700.1 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA06G16700.1 (Glycine max), 3'ss of exon 9
lower sequence: LOC_Os02g06300.1 (Oryza sativa), 3'ss of exon 9
gtacagtacctttcctattttttgatcccctatttttgccaataaagatttagttttgtggtgacaaattatcagtataaatcttaaatatgactgcaaacaaatttgaacaagctctagtctatcattggtaaaactttggtcattttggtgactactgacta---aaattctctgaactaatctgattactaaatta-cagGATTATTTTGCTGATGAAATTGGAGTTTTATCTCCCAGTCAACTACAAGTTGAAGAATTGTATGCTGGTGAG
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-------------------------------------------------------------------------------------------------------tttataattaactcttctaaaaatcaaatgctacacccatcatcttcatcatccttatctatgtagagacaccatgctgagtttttttttaaataaacagGAATATGTTGCAGATGAAATTGGAGTATTATCTCCCAATCAGATGCAAGTTAGTGAACTTTACGCTGGCGAG
upper sequence: GLYMA06G16700.1 (Glycine max), 3'ss of exon 9
lower sequence: AT5G08650.1 (Arabidopsis thaliana), 3'ss of exon 9
gtacagtacctttcctattttttgatcccctatttttgccaataaagatttagttttgtggtgacaaattatcagtataaatcttaaatatgactgcaaacaaatttgaacaagctctagtctatcattggtaaaactttggtcattttggtgactactgactaaaattctctgaactaatctgattactaaattacagGATTATTTTGCTGATGAAATTGGAGTTTTATCTCCCAGTCAACTACAAGTTGAAGAATTGTATGCTGGTGAG
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------------------------------------------------------------------------------------taattctttcaggaa--aaatttgagaatgtttaagcttttaa-----gaacgcttacttgtgtt--tcactagtatccttcatgttctcagtt--ttgcatca----attgcagGATTATTTTGCGGATGAAGTCGGAGTTCTATCTCCAAATCAAATTCAAGTGGATGAATTATATGCGGGTGAG
upper sequence: GLYMA06G16700.1 (Glycine max), 3'ss of exon 9
lower sequence: Vv07s0031g03050.t01 (Vitis vinifera), 3'ss of exon 9
gtacagtacctttcctattttttgatcccctatttttgccaataaagatttagttttgtggtgacaaattatcagtataaatcttaaatatgactgcaaacaaatttgaacaagctctagtctatcattggtaaaactttggtcattttggtgactactgactaaaattctctgaactaatctgattactaaattacagGATTATTTTGCTGATGAAATTGGAGTTTTATCTCCCAGTCAACTACAAGTTGAAGAATTGTATGCTGGTGAG
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----------------------------------------------------------------------------------------------tctttagtggtctttatgatcactgttttg--gtttgaaagattctaaatattcgtgacatcctttatgctaatt-tcttaactg--cttaatcttaaattgcagGATTATTTTGCTGATGAAATTGGAGTTTTATCTCCCAATCAGTTGCAGGCTGATGAATTATATGCTGGTGAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.attttggtgactactgactaaaattctctgaactaatctgattactaaattacagGATTATTTTGCTGATGAAATTGGAGTTTTATCTCCCAGTCAACTACAAGTTGAAGAATTGTATGCTGGTGAG
tactaaa putative branch site (score: 1)
tgattactaaatta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtacagtacctttcctattttttgatcccctatttttgccaataaagatttagttttgtggtgacaaattatcagtataaatcttaaatatgactgcaaacaaatttgaacaagctctagtctatcattggtaaaactttggtcattttggtgactactgactaaaattctctgaactaatctgattactaaattacagGATTATTTTGCTGATGAAATTGGAGTTTTATCTCCCAGTCAACTACAAGTTGAAGAATTGTATGCTGGTGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG