Sequence
atgc intronic sequence ATGC exonic sequence...aatatatatttttatcattcttgtacatgaaggactcccaatacatgaccctttaccctttaattctcattttgtacttaattttgccttcataatgtagATAAGTTTATGTGCTATAGGAATTGAATGACAAGAAGAGGTTAGCTACTACTGGAGCAAACTTTGCAAGAGCATACACCGTGGAATTCGGTAGTTGCAAG
Basic information
species | Glycine max |
transcript | GLYMA04G39370.3 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA04G39370.3 (Glycine max), 3'ss of exon 1
lower sequence: AT5G64040.1 (Arabidopsis thaliana), 3'ss of exon 1
aatatatatttttatcattcttgtacatgaaggactcccaatacatgaccctttaccctttaattctcattttgtacttaattttgccttcataatgtagATAAGTTTATGTGCTATAGGAATTGAATGACAAGAAGAGGTTAGCTACTACTGGAGCAAACTTTGCAAGAGCATACACCGTGGAATTCGGTAGTTGCAAG-------------------
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----------------------------gtaagtctttgaatgcctcaatcttgacattgcta----aagatcctaaaaagttttggattttt--------tgaaattttg-attatagGAACTTAATGATAAGAAGAGATTGGCAACAAGTGGAGCAAACTTTGCGAGAGCATTCACTGTTCAATTCGGAAGCTGCAAGTTCCCTGAGAATTTCACTG
upper sequence: GLYMA04G39370.3 (Glycine max), 3'ss of exon 1
lower sequence: Vv04s0044g01410.t01 (Vitis vinifera), 3'ss of exon 1
aatatatatttttatcattcttgtacatgaaggactcccaatacatgaccctttaccctttaattctcattttgtacttaattttgccttcataatgtagATAAGTTTATGTGCTATAGGAATTGAATGACAAGAAGAGGTTAGCTACTACTGGAGCAAACTTTGCAAGAGCATACACCGTGGAATTCGGTAGTTGCAAG-------------------
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------------------gtttgttccaggatccttctttttatgtttttatttttattttgactcctatacaattataaacaatac--ttatactg-aggtcggatcatga---atagGAGTTGAACGACAAGAAAAGGTTGGCTACAAGCGGAGCAAACTTTGCCAGAGCATACACTGTTCAATTTGGAACCTGCAAGTTCCCTGAGAACTTCACTGMapped 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|6951775|gb|AW423843.1|AW423843EST: CCAATGCTGGGATCATTGAAGATTACCTTGAGAGGAGCAAGGCCAACAAG ATAAGTTTATGTGCTATAGGAATTGAATGACAAGAAGAGGTTAGCTACTAC
genomic: CCAATGCTGGGATCATTGAAGATTACCTTGAGAGGAGCAAGGCCAACAAGgtataatcaa ... cataatgtagATAAGTTTATGTGCTATAGGAATTGAATGACAAGAAGAGGTTAGCTACTAC
EST:
gi|207837063|gb|GD808372.1|GD808372EST: CCAATGCTGGGATCATTGAAGATTACCTTGAGAGGAGCAAGGCCAACAAG ATAAGTTTATGTGCTATAGGAATTGAATGACAAGAAGAGGTTAGCTACTAC
genomic: CCAATGCTGGGATCATTGAAGATTACCTTGAGAGGAGCAAGGCCAACAAGgtataatcaa ... cataatgtagATAAGTTTATGTGCTATAGGAATTGAATGACAAGAAGAGGTTAGCTACTAC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgaccctttaccctttaattctcattttgtacttaattttgccttcataatgtagATAAGTTTATGTGCTATAGGAATTGAATGACAAGAAGAGGTTAGCTACTACTGGAGCAAACTTTGCAAGAGCATACACCGTGGAATTCGGTAGTTGCAAG
acttaat putative branch site (score: 4)
ttttgccttc CT-rich tract
tttaattctcattttg 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
aatatatatttttatcattcttgtacatgaaggactcccaatacatgaccctttaccctttaattctcattttgtacttaattttgccttcataatgtagATAAGTTTATGTGCTATAGGAATTGAATGACAAGAAGAGGTTAGCTACTACTGGAGCAAACTTTGCAAGAGCATACACCGTGGAATTCGGTAGTTGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA
- - - - - - - - - -cttgtac
- - - - - - - - - - - -tacatga
- - - - - - - - - - - - - - - - - ctcccaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ttttgcc