Sequence
atgc intronic sequence ATGC exonic sequencegtaatttatgtccataataggttttaattttgacctaagttcttttgggagggttgcatcatgaacttatgcccatacacattattgatttatttcattatattattagACCCCCTGAGCTGCTGCTTGGGACAACAAGGTATGGGCCAGCTGTAGATATGTGGTCTGTAGGGTGCATTTTTGCAGAGCTTCTTCATGGGAAGCCTATC
Basic information
species | Glycine max |
transcript | GLYMA20G10960.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA20G10960.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os05g32360.1 (Oryza sativa), 3'ss of exon 7
gtaatttatgtccataataggttttaattttgacctaagttcttttgggagggttgcatcatgaacttatgcccatacacattattgatttatttcattatattattagACCCCCTGAGCTGCTGCTTGGGACAACAAGGTATGGGCCAGCTGTAGATATGTGGTCTGTAGGGTGCATTTTTGCAGAGCTTCTTCATGGGAAGCCTATC
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---------gtattgcagaattatgaacttgccattgaattttgcatattgtgttatggtatttagtttttgct-tggatcatgctgaccatttgccaatgattttcagACCTCCAGAGTTGCTGCTCGGAAGCACCAAGTATGGACCAGCAGTTGACATGTGGTCTGTCGGTTGTATTTTTGCAGAGCTTCTCAATGGAAAGCCAATT
upper sequence: GLYMA20G10960.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv06s0009g01800.t01 (Vitis vinifera), 3'ss of exon 8
----gtaatttatgtccataataggttttaattttgacctaagttcttttgggagggttgcatcatgaacttatgcccatacacattattgatttatttcattatattattagACCCCCTGAGCTGCTGCTTGGGACAACAAGGTATGGGCCAGCTGTAGATATGTGGTCTGTAGGGTGCATTTTTGCAGAGCTTCTTCATGGGAAGCCTATC
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gtaagcagttaaactccc--atgggtagaga-----actcagatttcagtagcagcctctttctattccttaaggagcattaac-tgtttaaccaatccca--atttgaacagACCGCCAGAGTTGCTGCTTGGGACCACAAGGTATGGTCCAGCTGTTGATATGTGGTCAGTTGGCTGTATCTTTGCAGAACTTCTGCATGGAAAACCTATC
upper sequence: GLYMA20G10960.1 (Glycine max), 3'ss of exon 6
lower sequence: PP1S121_162V6.1 (Physcomitrella patens), 3'ss of exon 6
------------------------------------------gtaatttatgtccataataggtt--ttaattttgacctaagttcttttgggagggttgcatcatgaacttatgcccata---cacattattgatt--tatttcattatattattagACCCCCTGAGCTGCTGCTTGGGACAACAAGGTATGGGCCAGCTGTAGATATGTGGTCTGTAGGGTGCATTTTTGCAGAGCTTCTTCATGGGAAGCCTATC
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gtaaggcatcagtgttctacttttggccctgctatcattatcttggttcggataggaggggagttagttttctttgactgagcataagtgagcattgctccatagtggacgactactagtaagtcacttgactttctagtatttcttcctgtt-tcagGCCCCCTGAGCTGCTGATGGGCTCCACAAAGTATACTCCAGCTGTGGACATGTGGTCAGTGGGGTGCATTTTTGCTGAGCTTCTTAATGGGAAACCCATC
upper sequence: GLYMA20G10960.1 (Glycine max), 3'ss of exon 6
lower sequence: EFJ34303 (Selaginella moellendorffii), 3'ss of exon 5
gtaatttatgtccataataggttttaattttgacctaagttcttttgggagggttgcatcatgaacttatgcccatacacattattgatttatttcattatattattagACCCCCTGAGCTGCTGCTTGGGACAACAAGGTATGGGCCAGCTGTAGATATGTGGTCTGTAGGGTGCATTTTTGCAGAGCTTCTTCATGGGAAGCCTATC
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-------------------------------------------------------gtacctagtccgtgctttgcagaatgtttctggttacggccgtt-tgttat-agACCTCCTGAGCTACTTCTTGGCTGTACAAAGTATGGGCCAGCAGTAGACATGTGGTCTGTGGGCTGCATCTTTGCAGAGCTTCTCTACGGAAAGCCAGTG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgcatcatgaacttatgcccatacacattattgatttatttcattatattattagACCCCCTGAGCTGCTGCTTGGGACAACAAGGTATGGGCCAGCTGTAGATATGTGGTCTGTAGGGTGCATTTTTGCAGAGCTTCTTCATGGGAAGCCTATC
tattgat putative branch site (score: 3)
atacacattattgatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaatttatgtccataataggttttaattttgacctaagttcttttgggagggttgcatcatgaacttatgcccatacacattattgatttatttcattatattattagACCCCCTGAGCTGCTGCTTGGGACAACAAGGTATGGGCCAGCTGTAGATATGTGGTCTGTAGGGTGCATTTTTGCAGAGCTTCTTCATGGGAAGCCTATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT