Sequence
atgc intronic sequence ATGC exonic sequencegtactcttttcctttgccaattgtattattgcggaacgagaaatgaaaaatttctgatcactttatattaaatttgatattaatgtttcatttgacatgaatcctaaattttgttagttataacttattttaagtgatattgttgattatagacctcgtgggtagggtaaagggttttatgattgctttttgtgtagGCTGATGGGTGGATAGTTGAGAAGATTAGTTTACTGGCAAATCCTAATCAAGTACGTCCAAAGAGATTTTGGGGTGTCTATACAAAGCTCAAAATATTTA
Basic information
species | Glycine max |
transcript | GLYMA20G37000.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA20G37000.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os04g43700.1 (Oryza sativa), 3'ss of exon 1
gtactcttttcctttgccaattgtattattgcggaacgagaaatgaaaaatttctgatcactttatattaaatttgatattaatgtttcatttgacatgaatcctaaattttgttagttataact-tattttaagtgatattgttgattatagacctcgtgggtagggtaaagggttttatgattgctttttgtgtagGCTGATGGGTGGATAGTTGAGAAGATTAGTTTACTGGCAAATCCTAATCAAGTACGTCCAAAGAGATTTTGGGGTGTCTATACAAAGCTCAAAATATTTA
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-----------------------------------------------------------------------------------------gcatgcagtaaacatcaggatgtgcgatgactagctacatcctcag----atttttttttactagtctaatcagttagttaatctggccttacactaatttc-----agGCAGATGGTTGGATTGTGAGTCATATAACGTTACTGGCCAATCCTAATCAAGTGAGGCCAAAGAGATTTTGGGGCGTCTACACCAAGCTTAAGATATTCA
upper sequence: GLYMA20G37000.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G166903_T02 (Zea mays), 3'ss of exon 1
gtactcttttcctttgccaattgtattattgcggaacgagaaatgaaaaatttctgatcactttatattaaatttgatattaatgtttcatttgacatgaatcctaaattttgtt-agttataacttattttaagtgatattgttgat-tatagacctcgtg-ggtagggtaaagggttttatgattgctttttgtgtagGCTGATGGGTGGATAGTTGAGAAGATTAGTTTACTGGCAAATCCTAATCAAGTACGTCCAAAGAGATTTTGGGGTGTCTATACAAAGCTCAAAATATTTA----
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--------------------------------------------------------------------------------------------------agcttttatgttttcttgagttcggacat---tcaagtcatgtagatcttgtgccagtctgatgtggtagcgaagctgaccttgcatatatttcat---caggcagACGGTTGGATCGTGAATCGTATAACGTTACTGGCTAATCCTAATCAATTTAGGCCAAAGAGGTTTTGGGGCGTCTACACCAAGCTGAAGATATTTAACAT
upper sequence: GLYMA20G37000.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G166903_T01 (Zea mays), 3'ss of exon 1
gtactcttttcctttgccaattgtattattgcggaacgagaaatgaaaaatttctgatcactttatattaaatttgatattaatgtttcatttgacatgaatcctaaattttgtt-agttataacttattttaagtgatattgttgat-tatagacctcgtg-ggtagggtaaagggttttatgattgctttttgtgtagGCTGATGGGTGGATAGTTGAGAAGATTAGTTTACTGGCAAATCCTAATCAAGTACGTCCAAAGAGATTTTGGGGTGTCTATACAAAGCTCAAAATATTTA
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----------------------------------------------------------------------------------------------tagtagcttttatgttttcttgagttcggacat---tcaagtcatgtagatcttgtgccagtctgatgtggtagcgaagctgaccttgcatatatttcat---cagGCAGACGGTTGGATCGTGAATCGTATAACGTTACTGGCTAATCCTAATCAATTTAGGCCAAAGAGGTTTTGGGGCGTCTACACCAAGCTGAAGATATTTA
upper sequence: GLYMA20G37000.1 (Glycine max), 3'ss of exon 1
lower sequence: AT5G18480.1 (Arabidopsis thaliana), 3'ss of exon 1
gtactcttttcctttgccaattgtattattgcggaacgagaaatgaaaaatttctgatcactttatattaaatttgatattaatgtttcatttgacatgaatcctaaattttgttagttataacttattttaagtgatattgttgattatagacctcgtgggtagggtaaagggttttatgattgctttttgtgtagGCTGATGGGTGGATAGTTGAGAAGATTAGTTTACTGGCAAATCCTAATCAAGTACGTCCAAAGAGATTTTGGGGTGTCTATACAAAGCTCAAAATATTTA
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-----------------------------------------------------------------gtttggtttttattgtctagttatagtagtttaaagatctaaagagttctcctttcgattgagtttgagct-taaatttgatcacatactgctttgtt----taaagttgtttgcttttgattct---atagGCTGATGGATGGAAAGTAGAGAAGATTAGTTTACTGGCAAATCCAAATCAAGTTCATCCGACTAGGTTCTGGGGTGTTTATACAAAGCTTAAGATCTTTA
upper sequence: GLYMA20G37000.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv14s0036g00430.t01 (Vitis vinifera), 3'ss of exon 1
gtactcttttcctttgccaattgtattattgcggaacgagaaatgaaaaatttctgatcactttatattaaatttgatattaatgtttcatttgacatgaatcctaaattttgttagttataacttattttaagtgatattgttgattatagacctcgtgggtagggtaaagggttttatgattgctttttgtgtagGCTGATGGGTGGATAGTTGAGAAGATTAGTTTACTGGCAAATCCTAATCAAGTACGTCCAAAGAGATTTTGGGGTGTCTATACAAAGCTCAAAATATTTA
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----------------------------------------------------------------------------------------------agagacagttgaatgtttgactactgctgctattttactgtgattgtttttact-tatctaatattctttggggatcggttctggtgaata--ttgtgtacagGCTGATGGTTGGATTGTGGAGCTTATTAGTTTACTGGCAAACCCTAACCAAGTGCGGCCAAAGAGATTTTGGGGTGTCTACACAAAGCTAAAAATATTTAMapped EST sequences
Showing partial alignments of ESTs and genomic sequences. See full alignments
ATGC EST sequence
ATGC genomic sequence (exon)
ATGC genomic sequence (truncated intron)
EST:
gi|208238519|gb|GE039467.1|GE039467EST: TCGTTTTGGTCTCTGATGGTGTCTCTGATTATGCCAATACCCTTCTCCAG GCTGATGGGTGGAT
genomic: TCGTTTTGGTCTCTGATGGTGTCTCTGATTATGCCAATACCCTTCTCCAGgtactctttt ... ttttgtgtagGCTGATGGGTGGAT
EST:
gi|193423125|gb|FK390570.1|FK390570EST: ATGGTGTCTCTGATTATGCCAATACCCTTCTCCAG GCTGATGGGTGGATAGTTGAGAAGATTAGTTTACTGGCAAATCCTAATCAA
genomic: ATGGTGTCTCTGATTATGCCAATACCCTTCTCCAGgtactctttt ... ttttgtgtagGCTGATGGGTGGATAGTTGAGAAGATTAGTTTACTGGCAAATCCTAATCAA
EST:
gi|193390757|gb|FK355515.1|FK355515EST: GTCTCTGATGGTGTCTCTGATTATGCCAATACCCTTCTCCAG GCTGATGGGTGGATAGTTGAGAAGATTAGTTTACTGGCAAATCCTAATCAA
genomic: GTCTCTGATGGTGTCTCTGATTATGCCAATACCCTTCTCCAGgtactctttt ... ttttgtgtagGCTGATGGGTGGATAGTTGAGAAGATTAGTTTACTGGCAAATCCTAATCAA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttgattatagacctcgtgggtagggtaaagggttttatgattgctttttgtgtagGCTGATGGGTGGATAGTTGAGAAGATTAGTTTACTGGCAAATCCTAATCAAGTACGTCCAAAGAGATTTTGGGGTGTCTATACAAAGCTCAAAATATTTA
tgttgat putative branch site (score: 4)
ttgcttttt putative PPT
ttttatgatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtactcttttcctttgccaattgtattattgcggaacgagaaatgaaaaatttctgatcactttatattaaatttgatattaatgtttcatttgacatgaatcctaaattttgttagttataacttattttaagtgatattgttgattatagacctcgtgggtagggtaaagggttttatgattgctttttgtgtagGCTGATGGGTGGATAGTTGAGAAGATTAGTTTACTGGCAAATCCTAATCAAGTACGTCCAAAGAGATTTTGGGGTGTCTATACAAAGCTCAAAATATTTA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA