Sequence
atgc intronic sequence ATGC exonic sequence...tattctcttaactacatgacactgttggggattcatagtaatgatttgtttattttttatttttatttgtatgtggtggtggttggggtcatacaagcagACCGTTCAACATAATGCTTATGATCAAGATCCTTATGCAAAGGAATTTGGAATTAAAATCAGTGAAAAGCTAGCTTCTGTTGAAGCACGAATTCTTCCTG
Basic information
species | Glycine max |
transcript | GLYMA20G28970.1 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA20G28970.1 (Glycine max), 3'ss of exon 9
lower sequence: LOC_Os06g39640.1 (Oryza sativa), 3'ss of exon 8
tattctcttaactacatgacactgttggggat-tcatagtaatgatttgtttattttttatttttatttgtatgtggtggtggttggggtcatacaa--gcagACCGTTCAACATAATGCTTATGATCAAGATCCTTATGCAAAGGAATTTGGAATTAAAATCAGTGAAAAGCTAGCTTCTGTTGAAGCACGAATTCTTCCTG
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tgttcaat-agctaccc-acccaataagtgctactagggtttctcttcacttgatcagcactcttgttataatg-gttcaagactaaaaaaatttctttccagACAGTTCAACAAAATGGATATGAGCAAGACCCTTATGCAAAAGAATTTGGAATCAACATTAGTGAGAAGCTAACCTCAGTTGAAGCTCGGGTCCTTCCTG
upper sequence: GLYMA20G28970.1 (Glycine max), 3'ss of exon 9
lower sequence: GRMZM2G079080_T01 (Zea mays), 3'ss of exon 8
tattctcttaactaca--tgacactgttggggattcata-gtaatgattt-gtttattttttatttttatttgtatgtggtggtggttggggtcatacaa--gcagACCGTTCAACATAATGCTTATGATCAAGATCCTTATGCAAAGGAATTTGGAATTAAAATCAGTGAAAAGCTAGCTTCTGTTGAAGCACGAATTCTTCCTG
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------cataaatacagctaggatttttcactttttataagtgatggttttaattaatcaaaagatttgttaaaatggctcaagaaacaacattatttgttttcagACAGTTCATCAAAATGATTATGAGCAAGATCCATATGCGAAGGAATTTGGGATCAACATTAGTGAGAAGCTAACCTCTGTTGAAGCCCGAGTCCTTCCTG
upper sequence: GLYMA20G28970.1 (Glycine max), 3'ss of exon 9
lower sequence: AT5G43810.1 (Arabidopsis thaliana), 3'ss of exon 8
-tattctcttaactacatgacactgttggggattcatagtaatgatttgtttattttttatttttatttgtatgtggtggtggttggggtcatacaagcagACCGTTCAACATAATGCTTATGATCAAGATCCTTATGCAAAGGAATTTGGAATTAAAATCAGTGAAAAGCTAGCTTCTGTTGAAGCACGAATTCTTCCTG
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gtatttttttagtcatgt---atcttatatggttctttgtgagttagaacttagaagtgaggatta-----atcttgttgtcaaaaatgttttata----gACTGTCCAACACAACGCATATGATCAAGATCCATATGCAAAGGAGTTTGGCATGAACATAAGCGAAAAGTTAGCTTCTGTTGAAGCTCGTATTCTTCCAG
upper sequence: GLYMA20G28970.1 (Glycine max), 3'ss of exon 9
lower sequence: Vv05s0020g04190.t01 (Vitis vinifera), 3'ss of exon 8
----tattctcttaactacatgacactgttggggattcatagtaatgatttgtttattttttatttttatttgtatgtggtggtggttggggtcatacaagcagACCGTTCAACATAATGCTTATGATCAAGATCCTTATGCAAAGGAATTTGGAATTAAAATCAGTGAAAAGCTAGCTTCTGTTGAAGCACGAATTCTTCCTG
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tgtttgatcttggattgacatgattctgt-gatgtttttgggtcttggtttagtttgagctaataacatcttatgctttttaaacttcaaa---aaataaccagACGGTTCAACATAATGCTTATGATCAAGATCCATATGCAAAGGAGTTTGGGATCAAAATCAGTGAAAAATTAGCTTCTGTTGAGGCTCGGATTCTTCCTGMapped 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|193476564|gb|FK442169.1|FK442169EST: AATGACATTTTACGG ACCGTTCAACATAATGCTTATGATCAAGATCCTTATGCAAAGGAATTTGGA
genomic: AATGACATTTTACGGgtgtttaatt ... atacaagcagACCGTTCAACATAATGCTTATGATCAAGATCCTTATGCAAAGGAATTTGGA
EST:
gi|24136288|gb|BU926798.1|BU926798EST: TGAAAGTTACTTGCCAGAGGCCTCGCGATCGGGAAAATGACATTTTACGG ACCGTTCAACATAATGCTTATGATCAAGATCCTTATGCAAAGGAATTTGGA
genomic: TGAAAGTTACTTGCCAGAGGCCTCGCGATCGGGAAAATGACATTTTACGGgtgtttaatt ... atacaagcagACCGTTCAACATAATGCTTATGATCAAGATCCTTATGCAAAGGAATTTGGA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttgtttattttttatttttatttgtatgtggtggtggttggggtcatacaagcagACCGTTCAACATAATGCTTATGATCAAGATCCTTATGCAAAGGAATTTGGAATTAAAATCAGTGAAAAGCTAGCTTCTGTTGAAGCACGAATTCTTCCTG
tattttttatttttat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tattctcttaactacatgacactgttggggattcatagtaatgatttgtttattttttatttttatttgtatgtggtggtggttggggtcatacaagcagACCGTTCAACATAATGCTTATGATCAAGATCCTTATGCAAAGGAATTTGGAATTAAAATCAGTGAAAAGCTAGCTTCTGTTGAAGCACGAATTCTTCCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - -acatgac
- - - - - - - - - - - tgttggg
- - - - - - - - - - - - - - - - - - - - -tgatttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ttgtatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tggtggt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ggttggg