Sequence
atgc intronic sequence ATGC exonic sequencegtatagaatgatatccatcaccgtgcttatttgtggaattgtcttagagacacctattaattcctttttgggtaattttatttttgctagGTTGAAGCCACAGAAGTTTTCTTTGCTGTGACTAAGCTTTTCCAGTCTAAAGATACGGGATTAAGGAGAATGGTCTACCTGATGATAAAGGAGATCTCTC
Basic information
species | Glycine max |
transcript | GLYMA04G01470.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA04G01470.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os03g12590.1 (Oryza sativa), 3'ss of exon 3
gtatagaatgatatccatcaccgtgcttatttgtggaattgtcttagagacacctattaattcctttttgggtaattttatttttgctagGTTGAAGCCACAGAAGTTTTCTTTGCTGTGACTAAGCTTTTCCAGTCTAAAGATACGGGATTAAGGAGAATGGTCTACCTGATGATAAAGGAGATCTCTC
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--gtaggatacta--catc-tcgtgcaacc----aaacttgccttatg-----ctctcaatgccctgatggat--ttgcttctgatgtagGTTGAGGCCACAGAAGTTTTCTTTGCAGTAACAAAGCTGTTCCAGTCCAAGGATGCTGGTCTTAGGCGGCTGGTGTATTTAATGATCAAAGAGCTTTCAC
upper sequence: GLYMA04G01470.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G178618_T01 (Zea mays), 3'ss of exon 3
gtatagaatgatatccatcaccgtgcttatttgtggaattgtcttagagacac---ctattaatt-cctttttgggtaattttatttttgc-------tagGTTGAAGCCACAGAAGTTTTCTTTGCTGTGACTAAGCTTTTCCAGTCTAAAGATACGGGATTAAGGAGAATGGTCTACCTGATGATAAAGGAGATCTCTC
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-tacttgatagttttctatgagtggaaaaattgcaggttggccattgtgctatagtccatgacttgtgctacttgatagttttatgagtggaaaattgtagGTTGAGGCTACAGAGGTCTTCTTTGCAACGACCAAGCTGTTCCAGTCTAAAGATGCGGGCCTTAGGAGGATGGTGTACCTCATGATCAAGGAACTCTCAC
upper sequence: GLYMA04G01470.1 (Glycine max), 3'ss of exon 3
lower sequence: AT4G34450.1 (Arabidopsis thaliana), 3'ss of exon 2
----------------gtatagaatgatatccatcaccgtgcttatttgtggaattgtcttagagacacctattaattcctttttgggtaattttatttttgctagGTTGAAGCCACAGAAGTTTTCTTTGCTGTGACTAAGCTTTTCCAGTCTAAAGATACGGGATTAAGGAGAATGGTCTACCTGATGATAAAGGAGATCTCTC
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gtcagttaatttttttgcttatactgat--tcgatgtcatgcttat--ggagaattgaattattgtgttcttatcctctcgcgatggttgtttgtttcatatgcagGTTGAAGCAACGGAAGTTTTCTTTTCAGTTACAAAGCTTTTTCAATCAAAAGACACGGGTTTGAGGAGAATGGTCTACTTGATCATTAAGGAGTTATCTC
upper sequence: GLYMA04G01470.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv03s0063g02450.t01 (Vitis vinifera), 3'ss of exon 3
-------gtatagaat---gatatccatcacc-------gtgcttatttgtggaat-tgtcttagagacacctattaattcctttttgggtaattttatttttgc----------tagGTTGAAGCCACAGAAGTTTTCTTTGCTGTGACTAAGCTTTTCCAGTCTAAAGATACGGGATTAAGGAGAATGGTCTACCTGATGATAAAGGAGATCTCTC
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gtgaattttatagtgttttaattttcttcattttgaggtatgttaatttacatgatgcatcatggaaacataggtccttccttttataaatgatct-atttttgcacaaaatttacagATTGAAGCCACAGAAGTGTTCTTTGCTGTCACGAAACTTTTTCAGTCTAGAGACACTGGTTTAAGGAGAATGGTGTATTTAATGATAAAGGAGCTTTCTC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gaattgtcttagagacacctattaattcctttttgggtaattttatttttgctagGTTGAAGCCACAGAAGTTTTCTTTGCTGTGACTAAGCTTTTCCAGTCTAAAGATACGGGATTAAGGAGAATGGTCTACCTGATGATAAAGGAGATCTCTC
tattaat putative branch site (score: 2)
ttttattttt putative PPT
tttttgggtaatttta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatagaatgatatccatcaccgtgcttatttgtggaattgtcttagagacacctattaattcctttttgggtaattttatttttgctagGTTGAAGCCACAGAAGTTTTCTTTGCTGTGACTAAGCTTTTCCAGTCTAAAGATACGGGATTAAGGAGAATGGTCTACCTGATGATAAAGGAGATCTCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC