Sequence
atgc intronic sequence ATGC exonic sequence...tctctcttttttctttttctttactcacgttgtctcacttcattcaccatgtgtacgtgtattttctgcccctcatctcctttttgttgttgattttcagATGGGCTGCAGCTTCTAATGATATTTCACTAAATGGAATGATTCTTCCAGCTGCTTTGTATTTTTGGCAAATACCACATTTTATGGCCCTAGCCTATTTG
Basic information
species | Glycine max |
transcript | GLYMA20G38710.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA20G38710.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os01g34390.1 (Oryza sativa), 3'ss of exon 4
-------tctctcttttttctttttctttactcacgttgtctcacttcattcaccatgtgtacgtgtattttctgcccctcatctcctttttgttgttgattttcagATGGGCTGCAGCTTCTAATGATATTTCACTAAATGGAATGATTCTTCCAGCTGCTTTGTATTTTTGGCAAATACCACATTTTATGGCCCTAGCCTATTTG
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atcagtatgtgtcaatgtcctatctgttgaatgccaatgagggacctttttttccattgccacatga--tctcagtccttaatttcatcttcttc-----tgtacagGTGGGCAGCAGCTTCGTCTGAACTGTCACTGAATGCTATGATTCTCCCTGCTGCATTGTACTATTGGCAAATACCACATTTTATGGCCCTTGCATACTTA
upper sequence: GLYMA20G38710.1 (Glycine max), 3'ss of exon 4
lower sequence: AT2G44520.1 (Arabidopsis thaliana), 3'ss of exon 4
----------tctctcttttttctttttctttactcacgttgtctcact------------tcattcaccatgtgtacgtgtattttctgcccctcatctcctttttgttgttgattttcagATGGGCTGCAGCTTCTAATGATATTTCACTAAATGGAATGATTCTTCCAGCTGCTTTGTATTTTTGGCAAATACCACATTTTATGGCCCTAGCCTATTTG
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gtaaatttttgttccttttcttctttattttagcagattctgttttgttggatactgcttttaattcaaaatgtagtcatg-gttcaccaattctatgcttatctattttgtgtgttgtcagGTGGGCGGCAGCGTCTGGTCAGATTTCATACAATTCGATGATTCTTCCAGCTGCTCTTTACTTTTGGCAGATACCTCATTTTATGGCCCTTGCACATCTC
upper sequence: GLYMA20G38710.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv15s0021g00430.t01 (Vitis vinifera), 3'ss of exon 4
-tctctcttttttctttttctttactcacgttgt-ctcacttcattcaccatgtgtacgtgtattttctgcccctcatctcctttttgttgttgattttcagATGGGCTGCAGCTTCTAATGATATTTCACTAAATGGAATGATTCTTCCAGCTGCTTTGTATTTTTGGCAAATACCACATTTTATGGCCCTAGCCTATTTG
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gtatcaaatgcatgcatgtgcatacaaacattctgcatatcatatccactggctatatatctgatctgacatgctcatg-cctatctgtt-ttgggttttagGTGGGCTGCAGCTGCCGGACAGGTTTCACTCAATGGAATGATTCTTCCTGCTGCCCTCTATTTTTGGCAAATACCCCATTTTATGGCCCTAGCATACTTGMapped 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|5820336|gb|AI988542.1|AI988542EST: ATAAATACATGGGTGGGAGCTGTTGTCGGTGCTATTCCACCACTTTTGGG ATGGGCTGCAGCTTCTAATGATATTTCACTAAATGGAATGATTCTTCCAGC
genomic: ATAAATACATGGGTGGGAGCTGTTGTCGGTGCTATTCCACCACTTTTGGGgtaaaattat ... tgattttcagATGGGCTGCAGCTTCTAATGATATTTCACTAAATGGAATGATTCTTCCAGC
EST:
gi|13252104|gb|BG363007.1|BG363007EST: ATAAATACATGGGTGGGAGCTGTTGTCGGTGCTATTCCACCACTTTTGGG ATGGGCTGCAGCTTCTAATGATATTTCACTAAATGGAATGATTCTTCCAGC
genomic: ATAAATACATGGGTGGGAGCTGTTGTCGGTGCTATTCCACCACTTTTGGGgtaaaattat ... tgattttcagATGGGCTGCAGCTTCTAATGATATTTCACTAAATGGAATGATTCTTCCAGC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.accatgtgtacgtgtattttctgcccctcatctcctttttgttgttgattttcagATGGGCTGCAGCTTCTAATGATATTTCACTAAATGGAATGATTCTTCCAGCTGCTTTGTATTTTTGGCAAATACCACATTTTATGGCCCTAGCCTATTTG
tgttgat putative branch site (score: 4)
ttttctgcccctcatc CT-rich tract
tgtatttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tctctcttttttctttttctttactcacgttgtctcacttcattcaccatgtgtacgtgtattttctgcccctcatctcctttttgttgttgattttcagATGGGCTGCAGCTTCTAATGATATTTCACTAAATGGAATGATTCTTCCAGCTGCTTTGTATTTTTGGCAAATACCACATTTTATGGCCCTAGCCTATTTG
- - - - - - - - - - - - - - - - - -cacttca
- - - - - - - - - - - - - - - - - - - - - -tcaccat