Sequence
atgc intronic sequence ATGC exonic sequencegtattcgaaagtgcatccccaaaatgatttctgagcgatatgacttacatttatgtatttaatgcattttagcctcttgaaaatcatctgcatctgctaggctaatacatattctttatataccagTGTGCTTATAATTCTGCAAAATCTAAAAACAAGTTTCACCTTTGGGGGAGTCATTGGAGACATGGAGATTCATTGCTGTTTGCCCTTGCTTGTGCACAG
Basic information
species | Glycine max |
transcript | GLYMA20G34070.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA20G34070.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os07g31260.1 (Oryza sativa), 3'ss of exon 3
gtattcgaaagtgcatccccaaaatgatttctgagcgatatgacttacatttatgtatttaatgcattttagcctcttgaaaatcatctgcatctgctaggctaatacatattctttatataccagTGTGCTTATAATTCTGCAAAATCTAAAAACAAGTTTCACCTTTGGGGGAGTCATTGGAGACATGGAGATTCATTGCTGTTTGCCCTTGCTTGTGCACAG
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---------------------------------gtcaccaactgctaaactgttgcattttatatggtgaagatgcatgtatggc-ccttttcctcatgtattgatgcttggttttta-----cagTGTGCATATAATTCTGCAAAGTCTAAGAACAGATTTCACTTTTGGGGAAGCCATTGGAGGCATGGAGATGCATTACTTTTTTCACTTGCGTCTGCCCAG
upper sequence: GLYMA20G34070.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G175799_T02 (Zea mays), 3'ss of exon 3
gtattcgaaagtgcatccccaaaatgatttctgagcgatatgacttacatttatgtatttaatgcattttagcctcttgaaaatcatctgcatctgctaggctaatacata--ttctttatataccagTGTGCTTATAATTCTGCAAAATCTAAAAACAAGTTTCACCTTTGGGGGAGTCATTGGAGACATGGAGATTCATTGCTGTTTGCCCTTGCTTGTGCACAG
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-----------------------gtcattaac-agctaaacagtttgttcatatggagaaaatggatagaa--ctatagaagaccaattatacatgaagtattgattcattactgcttaatattgcagTGTGCATATAATTCTGCAAAATCTAAGAACAAATTTCATTTTTGGGGAAGCCATTGGAGACATGGAGATGCATTGCTTTTTTCATTAGCATGTGCCCAG
upper sequence: GLYMA20G34070.1 (Glycine max), 3'ss of exon 3
lower sequence: AT5G51150.1 (Arabidopsis thaliana), 3'ss of exon 3
gtattcgaaagtgcatccccaaaatgatttctgagcgatatgacttacatttatgtatttaatgcattttagcctcttgaaaatcatctgcatctgctaggctaatacatattctttatataccagTGTGCTTATAATTCTGCAAAATCTAAAAACAAGTTTCACCTTTGGGGGAGTCATTGGAGACATGGAGATTCATTGCTGTTTGCCCTTGCTTGTGCACAG
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------------------------------gtacatctaatgg-tcatagtattgtctgtcgtacagagtaatatcaccaca--cagatgtttttttcggagtctgattttttctcttattaatagGCGGCTTATAATTCCGCTAAGTCAAAGAACAAGTTCCATCTTTGGGGTAGCCATTGGAGACATGGAGATTCGTTACTTTTTTCTCTTGCATGTGCTCAG
upper sequence: GLYMA20G34070.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv16s0039g02700.t01 (Vitis vinifera), 3'ss of exon 3
-----gtattcgaaagtgcatccccaaaatgatttctgagcgatatgacttacatttatgtatttaatgcattttagcctcttgaaaatcatctgcatctgctaggctaatacatattctttatataccagTGTGCTTATAATTCTGCAAAATCTAAAAACAAGTTTCACCTTTGGGGGAGTCATTGGAGACATGGAGATTCATTGCTGTTTGCCCTTGCTTGTGCACAG
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gtaaattaatatattttttattgcctcaattacttttcaaagcta-aattgaatcgcaagagttaggggtttgctggtcatgctaatagggttcctttttctt----tttcctttttcctcccctcatcagTGTGCTTACAATTCTGCAAAGTCTAAGAACAAGTTTCACCTCTGGGGAAGCCATTGGAGACATGGAGATTCCTTACTCTTTGCTTTGGCATGTGCCCAGMapped 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|151398679|gb|EV268550.1|EV268550EST: GAGACGTACACTGGCTATATACCTGTTGGCTAGGCTAGCCCAG TGTGCTTATAATTCTGCAAAATCTAAAAACAAGTTTCACCTTTGGGGGAGT
genomic: GAGACGTACACTGGCTTTATACCTGTTGGCTAGGCTAGCCCAGgtattcgaaa ... tatataccagTGTGCTTATAATTCTGCAAAATCTAAAAACAAGTTTCACCTTTGGGGGAGT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gcctcttgaaaatcatctgcatctgctaggctaatacatattctttatataccagTGTGCTTATAATTCTGCAAAATCTAAAAACAAGTTTCACCTTTGGGGGAGTCATTGGAGACATGGAGATTCATTGCTGTTTGCCCTTGCTTGTGCACAG
ggctaat putative branch site (score: 3)
tattcttt putative PPT
taatacatattcttta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtattcgaaagtgcatccccaaaatgatttctgagcgatatgacttacatttatgtatttaatgcattttagcctcttgaaaatcatctgcatctgctaggctaatacatattctttatataccagTGTGCTTATAATTCTGCAAAATCTAAAAACAAGTTTCACCTTTGGGGGAGTCATTGGAGACATGGAGATTCATTGCTGTTTGCCCTTGCTTGTGCACAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
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- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT