Sequence
atgc intronic sequence ATGC exonic sequencegtttttataatattaacacttaatctaacttggtaattctcctgaagttacttgtgtctttttgtttgactatttgattttatattttgcagCAAGTATATATGTACTTCCGTGGCAGTGGCAAGGCTACAGTTTTAAAACGTGAGGCTGCCAGAGGCACAATGATGGCAGCTCTATGACATGGCACTTACA
Basic information
species | Glycine max |
transcript | GLYMA12G11820.2 |
intron # | 12 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA12G11820.2 (Glycine max), 3'ss of exon 12
lower sequence: LOC_Os05g42330.1 (Oryza sativa), 3'ss of exon 11
--gtttt-tataatattaacacttaatctaacttggtaattctcctgaagttacttgtgtctttttgtt--tgactat---ttgattttatattttgcagCAAGTATATATGTACTTCCGTGGCAGTGGCAAGGCTACAGTTTTAAAACGTGAGGCTGCCAGAGGCACAATGATGGCAGCTCTATGACATGGCACTTACA
||| ||| || ||| | | || | ||| | ||| | | | |||| | | |||| || ||| | | ||||||||||||| |||||||||||||| ||||| || || ||| | ||||||||||| || | || | ||| | || | ||| ||
aggttcaacatagcatggacattcttacatacatttcaatcgtttcttagtcaaattttcattttagatcatgaccattgattgctcactcaacatgcagCAAGTATACATGTACTTCCGTGGAAGTGGAAAAGCCGCAGAGATGAAACGTGAGGCGGCACGTGGTGCTCTGAGCTCCGCATTCTGATGAAACATGCCTT
upper sequence: GLYMA12G11820.2 (Glycine max), 3'ss of exon 12
lower sequence: LOC_Os01g57220.1 (Oryza sativa), 3'ss of exon 11
------gtttttataatattaacacttaatctaacttggtaattct-cctgaagttact--tgtgtctttttgtttgactatttgattttatattttgcagCAAGTATATATGTACTTCCGTGGCAGTGGCAAGGCTACAGTTTTAAAACGTGAGGCTGCCAGAGGCACAATGATGGCAGCTCTATGACATGGCACTTACA
| |||| | | | || | || | | | ||| || || | || || || | | | || | ||| | | ||||||||||||| ||||| |||||||| ||||| |||||| | | | ||||||||||| || | || | |||| | || | ||| | || | |
ccctaagattttgttcttgttgcaataaaatttccgctgcaatgctgtcttcattttctcctgggagatgtcattctga-acttggccgtttgaaatgcagCAAGTATACATGTATTTCCGTGGAAGTGGGAAGGCTGCTGAGATGAAACGTGAGGCAGCTCGTGGTGCTATGAGATCGGCCTTTTGATAGAGCTGCTTCG
upper sequence: GLYMA12G11820.2 (Glycine max), 3'ss of exon 12
lower sequence: GRMZM2G041181_T01 (Zea mays), 3'ss of exon 12
gtttttataatattaacacttaatctaacttggtaattctcctgaagttacttgtgtctttt-tgtttgactatttgattttatattttgcagCAAGTATATATGTACTTCCGTGGCAGTGGCAAGGCTACAGTTTTAAAACGTGAGGCTGCCAGAGGCACAATGATGGCAGCTCTATGA-CATGGCACTTACA
| | || | | ||| | | | ||||| ||||||| |||| || | | |||| || || | |||||||||| || |||||||||||||| ||||| |||||| ||| | || ||||| || | || || |||||| || || | | | ||| | |
------gtcagttttctatt--atcaaccgttctaattttcctgaaccaacttcagtgtgacatacttgagcccttt-ttggaccgcgtgcagCAAGTGTACATGTACTTCCGTGGAAGTGGAAAGGCTGCAGAGATGAAGCGTGATGCGACGAGGGGTGCAATGAGAGCCGCATTTTAAGTGTGGTG-TGGTA
upper sequence: GLYMA12G11820.2 (Glycine max), 3'ss of exon 12
lower sequence: Vv12s0059g01930.t01 (Vitis vinifera), 3'ss of exon 11
--------gtttttataatattaacacttaatctaactt-ggtaattctcctgaagttacttgtgtctttttgtt-tgactatttgattttatattttgcagCAAGTATATATGTACTTCCGTGGCAGTGGCAAGGCTACAGTTTTAAAACGTGAGGCTGCCAGAGGCACAATGATGGCAGCTCTATGACATGGCACTTACA
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gttcagtagtctgatttctagttcttctgcttctatctccagcacttctactgca--tcttggtttcttctaactctctttgttctcaatcccaatatgcagCAAGTTTACATGTACTTCCGAGGCAGTGGCAAGGCTCAAGAGATAAAGCGTGATGCGGCAAGAGGGACTGTAATGCAAGCATTTTGATGTGCCACGGATGMapped 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|10231650|gb|BE800538.1|BE800538EST: GATTTGGCNNNNNNNGTCTCGAGTCAGTGCTGAGCATCTGGGTTATACAG CAAGTATATATGTACTTCCGTGGCAGTGGCAAGGCTACAGTTTTAAAACGT
genomic: GATTTGGCTTTTTTTGTCTCGAGTCAGTGCTGAGCATCTGGGTTATACAGgtttttataa ... tattttgcagCAAGTATATATGTACTTCCGTGGCAGTGGCAAGGCTACAGTTTTAAAACGT
EST:
gi|22929729|gb|BU546868.1|BU546868EST: GATTTGGCNNNNNNNGTCTCGAGTCAGTGCTGAGCATCTGGGTTATACAG CAAGTATATATGTACTTCCGTGGCAGTGGCAAGGCTACAGTTTTAAAACGT
genomic: GATTTGGCTTTTTTTGTCTCGAGTCAGTGCTGAGCATCTGGGTTATACAGgtttttataa ... tattttgcagCAAGTATATATGTACTTCCGTGGCAGTGGCAAGGCTACAGTTTTAAAACGT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tctcctgaagttacttgtgtctttttgtttgactatttgattttatattttgcagCAAGTATATATGTACTTCCGTGGCAGTGGCAAGGCTACAGTTTTAAAACGTGAGGCTGCCAGAGGCACAATGATGGCAGCTCTATGACATGGCACTTACA
tttttgtttgactatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtttttataatattaacacttaatctaacttggtaattctcctgaagttacttgtgtctttttgtttgactatttgattttatattttgcagCAAGTATATATGTACTTCCGTGGCAGTGGCAAGGCTACAGTTTTAAAACGTGAGGCTGCCAGAGGCACAATGATGGCAGCTCTATGACATGGCACTTACA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTC