Sequence
atgc intronic sequence ATGC exonic sequence...aaatacatgaaggaagatggagtgcttttagacaaatttttttgtgtaatctagagtgaatattttttgcttttctaataactctgattctgatttgtagGTATTTGAGGCCTCTTGTGGCTGATGTAGCTGTAGTTGCCAAATGCCATTTAAGTGCACTCTATAGGCATGAAAAGGGGAAACTTTTTGCGCAGTTGGTT
Basic information
species | Glycine max |
transcript | GLYMA20G00260.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA20G00260.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os03g26960.1 (Oryza sativa), 3'ss of exon 6
aaatacatgaaggaagatggagtgcttttagacaaatttttttgtgtaatctagagtgaatatt-ttttgcttttctaataactctgattc-tgatttgtagGTATTTGAGGCCTCTTGTGGCTGATGTAGCTGTAGTTGCCAAATGCCATTTAAGTGCACTCTATAGGCATGAAAAGGGGAAACTTTTTGCGCAGTTGGTT
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--ctgctctagcggtgatattatgttattaccaagagctagcttctcatcataaaatgcatattatgtttgctctcaacttatgctgattaacaatgtgcagATTTTTAAGGCCCCTTGTTGCCGATGTAGCTGTTGTTGCTAAGTGTCACTTAAGTGCACTGTATACCCATGAAAAGGGGCGTCTTTTTGCGCAGTTGGTT
upper sequence: GLYMA20G00260.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G410479_T01 (Zea mays), 3'ss of exon 8
----aaatacatgaaggaagatggagtgcttttagacaaatttttttgtgtaatctagagtgaatattttttgcttttctaataactctgattctgatttgtagGTATTTGAGGCCTCTTGTGGCTGATGTAGCTGTAGTTGCCAAATGCCATTTAAGTGCACTCTATAGGCATGAAAAGGGGAAACTTTTTGCGCAGTTGGTT
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attcagttaaatatcgtttacaagtggcattgctaacaaaccttagcttgcattt----gtttatgccttatctttgcctacttatgctggttataatctgcagATTTTTGAGGCCCCTGGTTGCTGATGTTGCTGTTGTTGCCAAGTGCCACTTAAGTGCACTCTACACTCATGAAAAGGGACGGCTTTTTGCACAGTTGGTC
upper sequence: GLYMA20G00260.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv13s0019g00880.t01 (Vitis vinifera), 3'ss of exon 6
--aaatacatgaaggaagatggagtgcttttagacaaatttttttgtgt-aatctagagtgaatattttttgcttttctaataactctgattctgatt-tgtagGTATTTGAGGCCTCTTGTGGCTGATGTAGCTGTAGTTGCCAAATGCCATTTAAGTGCACTCTATAGGCATGAAAAGGGGAAACTTTTTGCGCAGTTGGTT
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tgcaatg-atcaagggatgcttactgtccttcttctcccttctctctcttaatattcag---gtttcttttggttttttattcctttttctcattttcatacagATATCTGAGACCTATTGTATCGGATGTGGCTGTGGTTGCCAAATGCCATTTGAGTGCTCTTTATACTCATGAAAAGGGGAAACTCTTTGCACAATTGGTT
upper sequence: GLYMA20G00260.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv08s0056g01110.t01 (Vitis vinifera), 3'ss of exon 6
aaataca-tgaaggaagatggagtgcttttagacaaatttttttgtgtaatctagagtgaatattttttgcttttctaataactctgattctgatttgta--gGTATTTGAGGCCTCTTGTGGCTGATGTAGCTGTAGTTGCCAAATGCCATTTAAGTGCACTCTATAGGCATGAAAAGGGGAAACTTTTTGCGCAGTTGGTT
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---cacaatgatcaagggatgcttgctgccctccttttcccttctctttcttaatagtcaggtttgttttgttttttaattcctttttctcattttcatacagATATCTGAGACCTATTGTATCAGATGTGGCTGTAGTTGCCAAATGTCATTTGAGTGCTCTTTATACTCATGAAAAGGGGAAACTCTTTGCACAATTGGTT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gtaatctagagtgaatattttttgcttttctaataactctgattctgatttgtagGTATTTGAGGCCTCTTGTGGCTGATGTAGCTGTAGTTGCCAAATGCCATTTAAGTGCACTCTATAGGCATGAAAAGGGGAAACTTTTTGCGCAGTTGGTT
aatattttttgctttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
aaatacatgaaggaagatggagtgcttttagacaaatttttttgtgtaatctagagtgaatattttttgcttttctaataactctgattctgatttgtagGTATTTGAGGCCTCTTGTGGCTGATGTAGCTGTAGTTGCCAAATGCCATTTAAGTGCACTCTATAGGCATGAAAAGGGGAAACTTTTTGCGCAGTTGGTT
- -tacatga
- - - - - - - -gatggag
- - - - - - - - - - - tgctttt
- - - - - - - - - - - - - - - - - - - -ttttgtg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctgattc