Sequence
atgc intronic sequence ATGC exonic sequence...aaggttctgtagaagtcattccaaatattaattatcttaaggtttatttgcatatgcttgattttactgattcttgtttcaatattgctatgttgatcagTTCATTATGAAGGCACACTTGCTGATACTGGTGAAGTTTTTGACACTACACATGAAGATAACACCATCTTCTCTTTCGAGATTGGAAAGGGCAGTGTTAT
Basic information
species | Glycine max |
transcript | GLYMA11G34120.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA11G34120.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os05g38370.2 (Oryza sativa), 3'ss of exon 2
aaggttctgtagaagtcattccaaatattaattatcttaaggtttatttgcatatgcttgattttac-tgattcttgtttca---atattgctatg-ttgatcagTTCATTATGAAGGCACACTTGCTGATACTGGTGAAGTTTTTGACACTACACATGAAGATAACACCATCTTCTCTTTCGAGATTGGAAAGGGCAGTGTTAT
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----atgtgtaaaactatttatgtatattactagtaattgagtatgtgcata-atacaagacataacacaatacttagcccacttacatttatatcctttcacagTTCATTATGAAGGCACACTCGCTGAAAATGGTGAAGTTTTCGACACCACTCATGAAGACAACTCTATTTTCTCATTTGAAATTGGGCAAGGAGCTGTCAT
upper sequence: GLYMA11G34120.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os01g62610.1 (Oryza sativa), 3'ss of exon 4
aaggttctgtagaagtcattccaaatattaattatcttaaggtttatttgcatatgcttgattttactgattcttg-----tttcaatattgctatgttgatcagTTCATTATGAAGGCACACTTGCTGATACTGGTGAAGTTTTTGACACTACACATGAAGATAACACCATCTTCTCTTTCGAGATTGGAAAGGGCAGTGTTAT
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---gtattgcagctatc--tacacatcttggtcttgcttcagtacacctat---tcttcagatttacaaaagcataaaagcttctgcttctaccttgtcta-cagTTCACTATGAAGGAACACTTGCTGAGAACGGGGAAGTGTTTGACACTACTCATGAAGACAACTCCGTCTTCTCATTTGAAATTGGAGAGGGAACTGTCAT
upper sequence: GLYMA11G34120.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G035922_T02 (Zea mays), 3'ss of exon 1
aaggttctgtagaagtcattccaaatattaattatcttaaggtttatttgc-----atatgcttgattttactgattcttgtttcaatattgctatgttgatcagTTCATTATGAAGGCACACTTGCTGATACTGGTGAAGTTTTTGACACTACACATGAAGATAACACCATCTTCTCTTTCGAGATTGGAAAGGGCAGTGTTAT
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-aaagtgagcacccgctgtttcatatcgccaagatttcagatactgtatcccgaataaagtcatgaaaatatgaatacttacc---attttaccttgtctat-agTTCATTACGAAGGTACACTTGCTGAGACTGGTGAAGTTTTCGATACCACCCATGAAGATAACTCTATTTTCTCATTTGAAATTGGACAAGGCGCTGTCAT
upper sequence: GLYMA11G34120.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv13s0019g01900.t01 (Vitis vinifera), 3'ss of exon 2
aaggttctgtagaagtcattccaaatattaattatcttaaggtttatttgcatatgcttgattttactgattcttgtttcaatattgct-atgttgatcagTTCATTATGAAGGCACACTTGCTGATACTGGTGAAGTTTTTGACACTACACATGAAGATAACACCATCTTCTCTTTCGAGATTGGAAAGGGCAGTGTTAT
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cttgttttggatggggaaccttatataa-aatggtgagtggtgctctctgtgatctttatgtattcaagatcattacggtatacttgtttgtgttgtgcagTGCATTATGAAGGCACTCTTGCAGAAACCGGTGGAGTTTTTGACACTACACATGAGGATAATACAGTGTTCTCATTTGAGCTTGGGAAAGGCACTGTAATMapped 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|208087121|gb|GD887169.1|GD887169EST: TTCCT-TTGTTTGTATG TTCATTATGAAGGCACACTTGCTGATACTGGTGAAGTTTTTGACACTACA
genomic: TTCCTCTTG-TTG-ATGgtaagctcgt ... tgttgatcagTTCATTATGAAGGCACACTTGCTGATACTGGTGAAGTTTTTGACACTACA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atttgcatatgcttgattttactgattcttgtttcaatattgctatgttgatcagTTCATTATGAAGGCACACTTGCTGATACTGGTGAAGTTTTTGACACTACACATGAAGATAACACCATCTTCTCTTTCGAGATTGGAAAGGGCAGTGTTAT
tactgat putative branch site (score: 2)
tttcaatatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
aaggttctgtagaagtcattccaaatattaattatcttaaggtttatttgcatatgcttgattttactgattcttgtttcaatattgctatgttgatcagTTCATTATGAAGGCACACTTGCTGATACTGGTGAAGTTTTTGACACTACACATGAAGATAACACCATCTTCTCTTTCGAGATTGGAAAGGGCAGTGTTAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- ggttctg
- - - - - - - - cattcca
- - - - - - - - - - - - - - - - - - - - - - - - tgcatat