Sequence
atgc intronic sequence ATGC exonic sequencegtattcatcatcttctttttaatgggtcttcctcaaatttgaaatttgaactctatgtttgacatgaatctgttgacacctgagttttgtgtagtttgtgattttaactctttatttggtggatttgtgtttgaattttgtgaagGCTGATGGGTGGATAGTGGAGATGATTAGTTTACTTGCTAATCCTAATCGAGTGCGTCCAAAGAGGTTTTGGGGTGTCTACACAAAGCTCAAAATATTTA
Basic information
species | Glycine max |
transcript | GLYMA03G40980.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA03G40980.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G166903_T02 (Zea mays), 3'ss of exon 1
gtattcatcatcttctttttaatgggtcttcctcaaatttgaaatttgaactctatgtttgacatgaatctgttgacacctgagttttgtgtagtttgtg--attttaactctttatttggtggatttgtgtttgaattttgtgaagGCTGATGGGTGGATAGTGGAGATGATTAGTTTACTTGCTAATCCTAATCGAGTGCGTCCAAAGAGGTTTTGGGGTGTCTACACAAAGCTCAAAATATTTA----
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-----------------------------------------------agcttttatgtttt-cttgagttcg--gacattcaagtcatgtagatcttgtgccagtctgatgtggtagcgaagctgaccttgcatatatttcatca-ggcagACGGTTGGATCGTGAATCGTATAACGTTACTGGCTAATCCTAATCAATTTAGGCCAAAGAGGTTTTGGGGCGTCTACACCAAGCTGAAGATATTTAACAT
upper sequence: GLYMA03G40980.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G166903_T01 (Zea mays), 3'ss of exon 1
gtattcatcatcttctttttaatgggtcttcctcaaatttgaaatttgaactctatgtttgacatgaatctgttgacacctgagttttgtgtagtttgtg--attttaactctttatttggtggatttgtgtttgaattttgtgaagGCTGATGGGTGGATAGTGGAGATGATTAGTTTACTTGCTAATCCTAATCGAGTGCGTCCAAAGAGGTTTTGGGGTGTCTACACAAAGCTCAAAATATTTA
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-------------------------------------------tagtagcttttatgtttt-cttgagttcg--gacattcaagtcatgtagatcttgtgccagtctgatgtggtagcgaagctgaccttgcatatatttcatca-gGCAGACGGTTGGATCGTGAATCGTATAACGTTACTGGCTAATCCTAATCAATTTAGGCCAAAGAGGTTTTGGGGCGTCTACACCAAGCTGAAGATATTTA
upper sequence: GLYMA03G40980.1 (Glycine max), 3'ss of exon 1
lower sequence: AT5G18480.1 (Arabidopsis thaliana), 3'ss of exon 1
gtattcatcatcttctttttaatgggtcttcctcaaatttgaaatttgaactctatgtttgacatgaatctgttgacacctgagttttgtgtagtttgtgatttta-act-ctttatttggtggatttgtgtttgaattttgtgaagGCTGATGGGTGGATAGTGGAGATGATTAGTTTACTTGCTAATCCTAATCGAGTGCGTCCAAAGAGGTTTTGGGGTGTCTACACAAAGCTCAAAATATTTA
| ||| || | | | || | | | | | | | ||| | | ||||||| | | |||| | ||| |||| ||| | || ||| ||| | | |||||||||| |||| ||| |||| |||||||||||| || ||||| |||| ||| | ||| | ||||| |||||||| || |||||||| || || ||||
--------------------gtttggtttttattgt-ctagttatagtagtttaaagatctaaagagttctcctttcgattgagtttgagcttaaatttgatcacatactgctttgtttaaagttgtttgcttttgattctat--agGCTGATGGATGGAAAGTAGAGAAGATTAGTTTACTGGCAAATCCAAATCAAGTTCATCCGACTAGGTTCTGGGGTGTTTATACAAAGCTTAAGATCTTTA
upper sequence: GLYMA03G40980.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv14s0036g00430.t01 (Vitis vinifera), 3'ss of exon 1
gtattcatcatcttctttttaatgggtcttcctcaaatttgaaatttgaactctatgtttgacatgaatctgttgacacctgagttttgtgtagtttgtgattttaactctttatttgg-tggatttgtgtttgaattttgtgaagGCTGATGGGTGGATAGTGGAGATGATTAGTTTACTTGCTAATCCTAATCGAGTGCGTCCAAAGAGGTTTTGGGGTGTCTACACAAAGCTCAAAATATTTA
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------------------------------------------agagacagttgaatgtttgact----actgctgctattttactgtgattgtttttacttatctaatattctttggggatcggttctggtgaatattgtgtacagGCTGATGGTTGGATTGTGGAGCTTATTAGTTTACTGGCAAACCCTAACCAAGTGCGGCCAAAGAGATTTTGGGGTGTCTACACAAAGCTAAAAATATTTA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gtagtttgtgattttaactctttatttggtggatttgtgtttgaattttgtgaagGCTGATGGGTGGATAGTGGAGATGATTAGTTTACTTGCTAATCCTAATCGAGTGCGTCCAAAGAGGTTTTGGGGTGTCTACACAAAGCTCAAAATATTTA
ttttaac putative branch site (score: 2)
attttaactctttatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtattcatcatcttctttttaatgggtcttcctcaaatttgaaatttgaactctatgtttgacatgaatctgttgacacctgagttttgtgtagtttgtgattttaactctttatttggtggatttgtgtttgaattttgtgaagGCTGATGGGTGGATAGTGGAGATGATTAGTTTACTTGCTAATCCTAATCGAGTGCGTCCAAAGAGGTTTTGGGGTGTCTACACAAAGCTCAAAATATTTA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA