Sequence
atgc intronic sequence ATGC exonic sequence...ttgctgaaatgttaaccaataagtttgtgtctgtatatttcattttctaattgtatatgttctgttgtttcatgattggtatatttaaatctcttttcagGTATTGTGGATCTTTGGAGCCAATGCCTATGCCTGCAGGGAGTGGTGGTATTGCCCATGCCTTGTTTGTCTCCAAAGATCGCAGAATTCCCAAGATTCGA
Basic information
species | Glycine max |
transcript | GLYMA04G39980.1 |
intron # | 8 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA04G39980.1 (Glycine max), 3'ss of exon 8
lower sequence: LOC_Os03g03710.1 (Oryza sativa), 3'ss of exon 8
ttgctgaaat-gttaaccaataagtttgtgtctgtatatttcattttctaattgtatatgttctgt-tgtttcatgattggtatatttaaatctcttttcagGTATTGTGGATCTTTGGAGCCAATGCCTATGCCTGCAGGGAGTGGTGGTATTGCCCATGCCTTGTTTGTCTCCAAAGATCGCAGAATTCCCAAGATTCGA
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gtgcttagattgtcatctaccaaaactat-tcagtctataattgcaatttaccttaactgttttatgtgcttcac-attcatacaatgcctgcaaacggcagGTATTGTGGGTCCTTGGAGCCAATGCCCATGCCTGCTGGTAGTGGAGGCGTTGCTCATGCTCTATTTGTGTCTAAAGATCGACGAATCCCAAAGATTCGA
upper sequence: GLYMA04G39980.1 (Glycine max), 3'ss of exon 8
lower sequence: AT2G17510.2 (Arabidopsis thaliana), 3'ss of exon 9
--ttg-ctgaaatgttaaccaataagtttgtgtctgtatatttcattttctaattgtatatgttctgttgtttcatgattggtatatt-taaatctcttttcagGTATTGTGGATCTTTGGAGCCAATGCCTATGCCTGCAGGGAGTGGTGGTATTGCCCATGCCTTGTTTGTCTCCAAAGATCGCAGAATTCCCAAGATTCGA
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ctttgtctgtgcaattatgctttacttttccttaagtttgtcttctgtttcaagc---catggttt-ctggatgacggttcctaatttgtatgttttcatgcagCTATTGTGGATCTCTTGAACCGATGTCACTACCTGCTGGTAGTGGTGGAACGGCACATGCTTTATTTGTCTCTAAAGATCGCAGAATTCCCAAGATCCGC
upper sequence: GLYMA04G39980.1 (Glycine max), 3'ss of exon 8
lower sequence: Vv07s0031g02190.t01 (Vitis vinifera), 3'ss of exon 8
------ttgctgaaatgttaaccaataagtttgtgtctgtatatttcattttctaattgtatatgttctgttgtttcatg---attggtatatttaaatctcttttcagGTATTGTGGATCTTTGGAGCCAATGCCTATGCCTGCAGGGAGTGGTGGTATTGCCCATGCCTTGTTTGTCTCCAAAGATCGCAGAATTCCCAAGATTCGA
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tgaatcttggaaaattgtttgtggctagagctactggtg-atgattgactctttg--tctataaattcagttgcttgatataagttgctgtggttaaatg------cagTTATTGTGGATCTTTGGAGCCAATGCCTATGCCTGCAGGCAATGGTGGTATTGCCCATGCTTTATTTGTCTCCAAAGATCGCAGAATTCCAAAGATCCGGMapped 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|18735584|gb|BM528847.1|BM528847EST: AGTCGTCCTTCTGGTCGTATTGTTGGCATTATAAAGAGAAACTGGCATTC GTATTGTGGATCTTTGGAGCCAATGCCTATGCCTGCAGGGAGTGGTGGTAT
genomic: AGTCGTCCTTCTGGTCGTATTGTTGGCATTATAAAGAGAAACTGGCATTCgtaagtatct ... ctcttttcagGTATTGTGGATCTTTGGAGCCAATGCCTATGCCTGCAGGGAGTGGTGGTAT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tctaattgtatatgttctgttgtttcatgattggtatatttaaatctcttttcagGTATTGTGGATCTTTGGAGCCAATGCCTATGCCTGCAGGGAGTGGTGGTATTGCCCATGCCTTGTTTGTCTCCAAAGATCGCAGAATTCCCAAGATTCGA
ttctaat putative branch site (score: 2)
tctcttttc putative PPT
tatatttaaatctctt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttgctgaaatgttaaccaataagtttgtgtctgtatatttcattttctaattgtatatgttctgttgtttcatgattggtatatttaaatctcttttcagGTATTGTGGATCTTTGGAGCCAATGCCTATGCCTGCAGGGAGTGGTGGTATTGCCCATGCCTTGTTTGTCTCCAAAGATCGCAGAATTCCCAAGATTCGA
-tgctgaa
- - - - - - - - - - - - - gtgtctg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tctgttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ttcatga