Sequence
atgc intronic sequence ATGC exonic sequence...tgtgaatttaagaaaaattagatacaaatacaatcacaattatgcttaaaggctttagttctttgtactgatgttttgtttttataatgctttactggagATGGAATTTTGCTTCTTGAGGCCAACAGGCTCCTGAGGGCGGGTGGCTACTTTGTCTGGGCAGCACAGCCTGTTTACAAACATGAAGAGACCCTTCAAGA
Basic information
species | Glycine max |
transcript | GLYMA13G09520.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA13G09520.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os01g62800.1 (Oryza sativa), 3'ss of exon 3
tgtgaatttaagaaaaattagatacaaatacaatcacaattatgcttaaaggctttagttctt-tgtactgatgttttgtttttataa--tgctttactggagATGGAATTTTGCTTCTTGAGGCCAACAGGCTCCTGAGGGCGGGTGGCTACTTTGTCTGGGCAGCACAGCCTGTTTACAAACATGAAGAGACCCTTCAAGA
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attgttttcaacaaaatatcaacacaaagataactg---ttttttgtagcaccctgacttccaatttgcttaacttttgttgccatgatttgccactttaaagATGGAATCCTGCTTCTGGAGGTTAATAGAATGCTCAGAGCCGGCGGTTATTTTGCTTGGGCAGCACAGCCTGTTTATAAGCATGAAGAGGCTCAGCAAGA
upper sequence: GLYMA13G09520.1 (Glycine max), 3'ss of exon 3
lower sequence: AT1G77260.1 (Arabidopsis thaliana), 3'ss of exon 3
tgtgaatttaagaaaaattagatacaaatacaatcacaattatgcttaaaggctttagttctttgtactgatgttttgtttttataatgctttactggagATGGAATTTTGCTTCTTGAGGCCAACAGGCTCCTGAGGGCGGGTGGCTACTTTGTCTGGGCAGCACAGCCTGTTTACAAACATGAAGAGACCCTTCAAGA
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-gttaatttctggctt-tttgcttctcctctaatgttatttgagctttagcatagtaagtgactaca---gcattttgtttctatga---attac-acagATGGGATACTTCTTCTTGAAGTTAATAGAATGCTTAGAGCAGGAGGCTACTTTGTTTGGGCTGCACAACCCGTTTACAAACATGAGGATAACTTGCAAGA
upper sequence: GLYMA13G09520.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv18s0001g01600.t01 (Vitis vinifera), 3'ss of exon 3
tgtgaatttaagaaaaattagatacaaatacaatcacaattatgcttaaaggctttagttctttgtactgatgttttgtttttataat--gctttactggagATGGAATTTTGCTTCTTGAGGCCAACAGGCTCCTGAGGGCGGGTGGCTACTTTGTCTGGGCAGCACAGCCTGTTTACAAACATGAAGAGACCCTTCAAGA
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--agagggatggaatacttacattcttgatgactaaagctctttaatattgactgtttttcttttttcttttttttcttttgtttgtttggcttgtgataagATGGAATTCTGCTTCTTGAGGTCAACAGGATGCTAAGGGCAGGAGGATACTTTGCTTGGGCTGCACAGCCTGTTTATAAACATGAAGGGAACCTCCAAGA
upper sequence: GLYMA13G09520.1 (Glycine max), 3'ss of exon 3
lower sequence: EFJ24461 (Selaginella moellendorffii), 3'ss of exon 3
tgtgaatttaagaaaaattagatacaaatacaatcacaattatgcttaaaggctttagttctttgtactgatgttttgtttttataatgctttactggagATGGAATTTTGCTTCTTGAGGCCAACAGGCTCCTGAGGGCGGGTGGCTACTTTGTCTGGGCAGCACAGCCTGTTTACAAACATGAAGAGACCCTTCAAGA
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-----------------------------------------gtgagtataagaacatgtctttcct--tgacttctaaggcagtttgtgctatac---agATGGTATACTTCTTGCGGAAGTTAATCGCATAATGCGCGGTGGGGGCTACTTTGCATGGGCAGCTCAGCCTGTTTACAAACACGAGCCAAGTAGTTTGCAMapped 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|208185790|gb|GD983815.1|GD983815EST: ATTTGACCTGATCCATTGTTCAAGATGCAGAATTAATTGGACTCGTGATG ATGGAATTTTGCTTCTTGAGGCCAACAGGCTCCTGAGGGCGGGTGGCTACT
genomic: ATTTGACCTGATCCATTGTTCAAGATGCAGAATTAATTGGACTCGTGATGgtagttcctc ... tttactggagATGGAATTTTGCTTCTTGAGGCCAACAGGCTCCTGAGGGCGGGTGGCTACT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttaaaggctttagttctttgtactgatgttttgtttttataatgctttactggagATGGAATTTTGCTTCTTGAGGCCAACAGGCTCCTGAGGGCGGGTGGCTACTTTGTCTGGGCAGCACAGCCTGTTTACAAACATGAAGAGACCCTTCAAGA
tactgat putative branch site (score: 2)
ctttact putative PPT
ttttgtttttataatg 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tgtgaatttaagaaaaattagatacaaatacaatcacaattatgcttaaaggctttagttctttgtactgatgttttgtttttataatgctttactggagATGGAATTTTGCTTCTTGAGGCCAACAGGCTCCTGAGGGCGGGTGGCTACTTTGTCTGGGCAGCACAGCCTGTTTACAAACATGAAGAGACCCTTCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - -aagaaaa
- - - - - - - - - - gatacaaa
- - - - - - - - - - - - - - - caatcac
- - - - - - - - - - - - - - - - - - - - tatgctt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - actgatg