Sequence
atgc intronic sequence ATGC exonic sequencegtatgttaaaaatcattagatatctggtggctgtttttgtttcatctttttttctccaactttggcatcctatatttttatgtttaatgcattttttttccctaaaagacattcaattgcttattgccatgccttgaggtcaacaattttatatcatttttcatgtgaacatgttccatagGTTCTGGACCACTTGGTGATTCAAAAACTAAATGCAGAGGGTAGACTGGAGAAGAAAGAAGCCAAAAAAGGAGGAAGTTATTTTGACAAA
Basic information
species | Glycine max |
transcript | GLYMA14G03780.1 |
intron # | 20 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA14G03780.1 (Glycine max), 3'ss of exon 20
lower sequence: LOC_Os07g46590.1 (Oryza sativa), 3'ss of exon 9
gtatgttaaaaatcattagatatctggtggctgtttttgtttcatctttttttctccaactttggcatcctatatttttatgtttaatgcattttttttccctaaaagacattcaattgcttattgccatgccttgaggtcaacaat-tttatatcatttttcatgtgaacatgttccatagGTTCTGGACCACTTGGTGATTCAAAAACTAAATGCAGAGGGTAGACTGGAGAAGAAAGAAGCCAAAAAAGGAGGAAGTTATTTTGACAAA
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--------------------------------------------------------------------------------------------gtgatgagcctgatt--tgtttcatatattgttttaataaatataaacgaataacctctgacttgttctttttctatatatgtc----agGTTCTTGATCACCTAGTGATTCAGAAGCTAAATGCTGAGGGCAGGCTCGAGAAGAAAGAATCAAAAAAAGGTGGTTCCATGTTTGACAAG
upper sequence: GLYMA14G03780.1 (Glycine max), 3'ss of exon 20
lower sequence: GRMZM2G010342_T01 (Zea mays), 3'ss of exon 18
gtatgttaaaaatcattagatatctggtggctgtttttgtttcatctttttttctccaactttggcatcctatatttttatgtttaatgcattttttttccctaaaagacattcaattgcttat-tgccatgccttgaggtcaacaattttatatcatttttcatgtgaacatgttccatagGTTCTGGACCACTTGGTGATTCAAAAACTAAATGCAGAGGGTAGACTGGAGAAGAAAGAAGCCAAAAAAGGAGGAAGTTATTTTGACAAA
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----------------------------------------------------------------------------ggaacgcgcaaagaaaaagatggttgtcaaag----tgcattgttcatgtattctttagtaggattattgaactgttctttttacctattgtttcctatttca--gGTTCTTGATCACTTGGTTATTCAGAAGCTAAATGCTGAGGGCAGGCTTGAGAAGAAAGAATCCAAAAAGGGTGGCTCCATATTTGACAAG
upper sequence: GLYMA14G03780.1 (Glycine max), 3'ss of exon 20
lower sequence: GRMZM2G141258_T01 (Zea mays), 3'ss of exon 22
gtatgttaaaaatcattagatatctggtggctgtttttgtttcatctttttttctccaactttggcatcctatatttttatgtttaatgcattttttttccctaaaagacattcaattgcttattgccatgccttgaggtcaacaatt---ttatatcatttttcatgtgaacatgttccatagGTTCTGGACCACTTGGTGATTCAAAAACTAAATGCAGAGGGTAGACTGGAGAAGAAAGAAGCCAAAAAAGGAGGAAGTTATTTTGACAAA
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---------------------------------------------------------------------------------ttttggaacgcgcaaagaaaaagatggttgtcaaactgcatagt-tcatgtacttagtaggattattgaactgtactttttaccttttttatatatttca--gGTTCTTGATCACTTGGTCATTCAGAAGCTAAACGCTGAGGGCAGGCTTGAGAAGAAAGAATCCAAAAAAGGTGGCCCCATATTTGACAAG
upper sequence: GLYMA14G03780.1 (Glycine max), 3'ss of exon 20
lower sequence: AT2G13370.1 (Arabidopsis thaliana), 3'ss of exon 21
gtatgttaaaaatcattagatatctggtggctgtttttgtttcatctttttttctccaactttggcatcctatatttttatgtttaatgcattttttttccctaaaagacattcaattgcttattgccatgccttgaggtcaacaattttatatcatttttcatgtgaacatgttccatagGTTCTGGACCACTTGGTGATTCAAAAACTAAATGCAGAGGGTAGACTGGAGAAGAAAGAAGCCAAAAAAGGAGGAAGTTATTTTGACAAA
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--------------------------------------------------------------------------agtcaatcacctgtggatgagataggttcaaaa----cccaaatttttacttgtatcactttgttatagcaggctgtaactttttttcgtccac---cattctctagGTTCTTGATCATTTGGTTATTCAAAAACTGAATGCGGAGGGTAGGCTGGAGAAGCGAGAAACTAAAAAAG---GAAGTAATTTTGACAAG
upper sequence: GLYMA14G03780.1 (Glycine max), 3'ss of exon 20
lower sequence: Vv06s0009g03750.t01 (Vitis vinifera), 3'ss of exon 20
gtatgttaaaaatcattagatatctggtggctgtttttgtttcatctttttttctccaactttggcatcctatatttttatgtttaatgcattttttttccctaaaagacattcaattgcttat-tgccatgccttgaggtcaa-caattt-tatatcatttttcatgtgaacatgttcc----atagGTTCTGGACCACTTGGTGATTCAAAAACTAAATGCAGAGGGTAGACTGGAGAAGAAAGAAGCCAAAAAAGGAGGAAGTTATTTTGACAAA
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----------gtaaaccaaacatttctt---tgtctatgcttaaatccttttcttttcatactg----tttatatttaaaagcatg-tctgtttgcacacatggtggattatatggtctctactatttcactaattgaggccaaacaatttacatgttttttcttatgttcccattttttctttatagGTACTTGATCATTTGGTGATTCAAAAACTAAATGCAGAAGGTAGACTGGAGAAGAAAGAATCGAAAAAGG---GGAGTTACTTTGACAAA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ccatgccttgaggtcaacaattttatatcatttttcatgtgaacatgttccatagGTTCTGGACCACTTGGTGATTCAAAAACTAAATGCAGAGGGTAGACTGGAGAAGAAAGAAGCCAAAAAAGGAGGAAGTTATTTTGACAAA
aacaattttatatcat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatgttaaaaatcattagatatctggtggctgtttttgtttcatctttttttctccaactttggcatcctatatttttatgtttaatgcattttttttccctaaaagacattcaattgcttattgccatgccttgaggtcaacaattttatatcatttttcatgtgaacatgttccatagGTTCTGGACCACTTGGTGATTCAAAAACTAAATGCAGAGGGTAGACTGGAGAAGAAAGAAGCCAAAAAAGGAGGAAGTTATTTTGACAAA
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