Sequence
atgc intronic sequence ATGC exonic sequence...ttctttcatcttaagaaaagaaaacttattattttgtactattttggtttagtaaatctatgcacaatatgatttatgttcctatttcacatcttcttagACGACCTGTACTGGATGGTGATAACTGGTGGCGAGGTCATGCTGCAGCCTTTCTAAAGTACGTCAATTTGCCTCCAGAAGCGCTTAGACATGGGCGAGTC
Basic information
species | Glycine max |
transcript | GLYMA20G39210.4 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA20G39210.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os04g41200.1 (Oryza sativa), 3'ss of exon 6
ttctttcatcttaagaaaagaaaacttattattttgt-actattttggtttagtaaatctatgcacaatatgatttatgttcctatttcacatcttctt--agACGACCTGTACTGGATGGTGATAACTGGTGGCGAGGTCATGCTGCAGCCTTTCTAAAGTACGTCAATTTGCCTCCAGAAGCGCTTAGACATGGGCGAGTC
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--taatcctccttgaactggaccaactgttacattgagataagtttgaacatcttatgctgttcttgccttatatgacatccacatattg-gtcttcatgcagGCGCCCTGCACTTGATGGTGACAACTGGTGGCGAGGGCATGCTGCCGCTTTCCTTCGATTTGTTCACATACCAGCTGCAGCACTTCTACGGGGCCGTGTT
upper sequence: GLYMA20G39210.1 (Glycine max), 3'ss of exon 5
lower sequence: AT1G05790.2 (Arabidopsis thaliana), 3'ss of exon 6
----------------------------------------------------ttctttcatcttaagaaaagaaaacttattattttgtactattttggtttagtaaatctatgcacaatat-gatttatgttcctatttcacatcttctt--agACGACCTGTACTGGATGGTGATAACTGGTGGCGAGGTCATGCTGCAGCCTTTCTAAAGTACGTCAATTTGCCTCCAGAAGCGCTTAGACATGGGCGAGTC
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gtatactatacctggttagctcgtttgaagaaactcaacttgtttctttgaagtttactctttccagttttcatacctttcccttgtgtctgatcttgatacggacaaa-tacatattatatcaatgtaagaaacttccttgcaattatttgcagGCGGCCTAAACTTGATGGTGATAATTGGTGGCGAGGTCATGCAGCTGCCTTCCTTAAGTTCATAAATTTTCCTGCTCATGTTCTTCGACGAGGCCGAATT
upper sequence: GLYMA20G39210.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv05s0124g00140.t01 (Vitis vinifera), 3'ss of exon 4
------------------------------------------------ttctttcatcttaagaaaagaaaacttattat--tttgtact---attttggtttagtaaatctatgcacaatatgatttat-gttcctatttcaca-tcttcttagACGACCTGTACTGGATGGTGATAACTGGTGGCGAGGTCATGCTGCAGCCTTTCTAAAGTACGTCAATTTGCCTCCAGAAGCGCTTAGACATGGGCGAGTC
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gtagttaatttatgggcatctttctttatgtgcatgtattccatatctgatactaatctagaaccaactacatttaatgtagttgagatttaaagctttcttaaattaatttggttactattttttttttcatttttgttttcctctttttttagGCAACCTGTACTTCAGGGTGATAACTGGTGGCGAGGTCATGCAGCAGCCTTTCTGAAATATGTTCGTTTATCCCCAGAAGTACTTCGACTAGGTCGTGTT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ggtttagtaaatctatgcacaatatgatttatgttcctatttcacatcttcttagACGACCTGTACTGGATGGTGATAACTGGTGGCGAGGTCATGCTGCAGCCTTTCTAAAGTACGTCAATTTGCCTCCAGAAGCGCTTAGACATGGGCGAGTC
tttcacatcttctt CT-rich tract
aatatgatttatgtt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttctttcatcttaagaaaagaaaacttattattttgtactattttggtttagtaaatctatgcacaatatgatttatgttcctatttcacatcttcttagACGACCTGTACTGGATGGTGATAACTGGTGGCGAGGTCATGCTGCAGCCTTTCTAAAGTACGTCAATTTGCCTCCAGAAGCGCTTAGACATGGGCGAGTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC