Sequence
atgc intronic sequence ATGC exonic sequence...ttgccttttgccactaatatgctttcattttttgtgtgtgtttctattctactactttacggttaaattgttaaattgatatatttattattcgctgcagAAGCACTAGGGAATCCACACCTTGCAGTTTGATAAGGGACTCGGATACTGTCAGGACTCCGGGTTCAACTACCAGGCCTACTTGTTCAGCTGAAGCTTAT
Basic information
species | Glycine max |
transcript | GLYMA20G34090.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA20G34090.1 (Glycine max), 3'ss of exon 1
lower sequence: AT2G32710.1 (Arabidopsis thaliana), 3'ss of exon 1
---ttgccttttgccactaatatgctttcattttttgtgtgtgtttctattctactactttacggttaaattgttaaattgatatatttattattcgctgc------agAAGCACTAGGGAATCCACACCTTGCAGTTTGATAAGGGACTCGGATACTGTCAGGACTCCGGGTTCAACTACCAGGCCTACTTGTTCAGCTGAAGCTTAT
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gcaataaagtttgcttgcttttgctgctaattaaggaaacacggttatgtgctttttccttgagagcattgtatgaaagtaacatattacttactctcagCTTCAACAGGACCACAAGGGAATCCACACCATGCAGTTTGATAAGAAGGCCTGAAATCATGACAACCCCGGGATCGTCTACAAAGCTTAACATTTGTGTA---------
upper sequence: GLYMA20G34090.1 (Glycine max), 3'ss of exon 1
lower sequence: AT2G32710.2 (Arabidopsis thaliana), 3'ss of exon 1
ttgccttttgccactaatatgctttcattttttgtgtgtgtttctattctactactttacggttaaattgttaaattgatatatttattattcgctgc------agAAGCACTAGGGAATCCACACCTTGCAGTTTGATAAGGGACTCGGATACTGTCAGGACTCCGGGTTCAACTACCAGGCCTA---CTTGTTCAGCTGAAGCTTAT
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------tttgcttgcttttgctgctaattaaggaaacacggttatgtgctttttccttgagagcattgtatgaaagtaacatattacttactctcagcttcaacagGACCACAAGGGAATCCACACCATGCAGTTTGATAAGAAGGCCTGAAATCATGACAACCCCGGGATCGTCTACAAAGCTTAACATTTGTGTAAGTGAAAGC---
upper sequence: GLYMA20G34090.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv05s0029g00040.t01 (Vitis vinifera), 3'ss of exon 1
ttgccttttgccactaatatgctttcattttttgtgtgtgtttctattctactactt-tacggttaaattgttaaattgatatatt-tattattcgctgcagAAGCACTAGGGAATCCACACCTTGCAGTTTGATAAGGGACTCGGATACTGTCAGGACTCCGGGTTCAACTACCAGGCCTACTTGTTCAGCTGAAGCTTAT
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tgatacagagctcttactttagttctgcaattcttat-tgtcctggtgatagtgtcgatattgttttcttat-gaatggattcattgtctttataaaaacagGAGCACTAGGGAAACCACACCTTGCAGTTTGATAAGAGATCCAGAAACCATAAGAACCCCTGGTTCTACTACTAAGCCTGCCAGCTCGTCTGGCATTAACMapped 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|22540112|gb|BU089955.1|BU089955EST: CAGGAAGCGTCGTTCGGGGAAAATGTTTTGGATTTTGAAGGTAGAGAGAG AAGCACTACGGAATCCACACCTTGCAGTTTGATAAGGGACTCGGATACTGT
genomic: CAGGAAGCGTCGTTCGGGGAAAATGTTTTGGATTTTGAAGGTAGAGAGAGgtgagttttc ... ttcgctgcagAAGCACTAGGGAATCCACACCTTGCAGTTTGATAAGGGACTCGGATACTGT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.attctactactttacggttaaattgttaaattgatatatttattattcgctgcagAAGCACTAGGGAATCCACACCTTGCAGTTTGATAAGGGACTCGGATACTGTCAGGACTCCGGGTTCAACTACCAGGCCTACTTGTTCAGCTGAAGCTTAT
aattgat putative branch site (score: 4)
tttacggttaaattgt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttgccttttgccactaatatgctttcattttttgtgtgtgtttctattctactactttacggttaaattgttaaattgatatatttattattcgctgcagAAGCACTAGGGAATCCACACCTTGCAGTTTGATAAGGGACTCGGATACTGTCAGGACTCCGGGTTCAACTACCAGGCCTACTTGTTCAGCTGAAGCTTAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
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- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
-tgccttt
- - - - tgccact
- - - - - - - - - -tgctttc
- - - - - - - - - - - - - - - - -gtgtgtg