Sequence
atgc intronic sequence ATGC exonic sequence...aatgaagtttgaaaagattacaggtgtcattaagatgataaatgatgcttggtcacaatccacatttttttattgccatgctccttcttgcttgatacagGTGCAAAAGTAACTCTGTCCTGTGCTGACAGTAATGGACAAATTACAATGTCAAGAGAAGAAACAACAAACTGGTTTGGAAGCTATACAATGAGGTTCGA
Basic information
species | Glycine max |
transcript | GLYMA04G00680.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA04G00680.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv03s0038g01960.t01 (Vitis vinifera), 3'ss of exon 1
aatgaagtttgaaaagattacaggtgtcattaagatgataaatgatgcttggtcacaatccacatttttttattgccatgctccttcttgcttga-tacagGTGCAAAAGTAACTCTGTCCTGTGCTGACAGTAATGGACAAATTACAATGTCAAGAGAAGAAACAACAAACTGGTTTGGAAGCTATACAATGAGGTTCGA
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-aagaatttgtttctgtttccttcaatttcttagcaatcaaacagggagatgaaagaatggattagggttcaaaagaatttaacagctaccttttctgcagGAATAAAGGTTACCATGGCATGTGCCAACAGTAATGGACAAATCACAATGTGGAGGGAAGAGACTACAAATTGGTTTGGAACCTATGCAATGAGGTTTGAMapped 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|18041186|gb|BM309480.1|BM309480EST: TGACCAATGCAAAGACGGACAGAGATCCCTTTTCGATTATCCTATTAATG GTGCAAAAGTAACTCTGTCCTGTGCTGACAGTAATGGACAAATTACAATGT
genomic: TGACCAATGCAAAGACGGACAGAGATCCCTTTTCGATTATCCTATTAATGgtgagatcta ... cttgatacagGTGCAAAAGTAACTCTGTCCTGTGCTGACAGTAATGGACAAATTACAATGT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgcttggtcacaatccacatttttttattgccatgctccttcttgcttgatacagGTGCAAAAGTAACTCTGTCCTGTGCTGACAGTAATGGACAAATTACAATGTCAAGAGAAGAAACAACAAACTGGTTTGGAAGCTATACAATGAGGTTCGA
gcttgat putative branch site (score: 5)
tgctccttcttgctt CT-rich tract
acatttttttatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
aatgaagtttgaaaagattacaggtgtcattaagatgataaatgatgcttggtcacaatccacatttttttattgccatgctccttcttgcttgatacagGTGCAAAAGTAACTCTGTCCTGTGCTGACAGTAATGGACAAATTACAATGTCAAGAGAAGAAACAACAAACTGGTTTGGAAGCTATACAATGAGGTTCGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
aatgaag
- - - - - gaaaagat
- - - - - - - - - - - - - - - - - - - - - tgatgct
- - - - - - - - - - - - - - - - - - - - - - - - - - - -caatcca