Sequence
atgc intronic sequence ATGC exonic sequencegttttatatgcatttctatgaagtttgagtgtgcaattgttggaagagttcaagtattgcataacctgcttgtgtgttttcttttgtagGTTGTTGAAGATGGATATGAATTTTTTTCCAATAGACAACTTGTGACTATCTTTTCTGCACCTAACTACTGTGGAGAATTTGACAATGCTGGAGCAATGA
Basic information
species | Glycine max |
transcript | GLYMA02G00850.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA02G00850.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G112240_T01 (Zea mays), 3'ss of exon 2
gttttatatgcatttctatgaagtttgagtgtgcaattgttggaagagttcaa-gtat-tgcataacctgcttgtgtgttttcttt-------tgtagGTTGTTGAAGATGGATATGAATTTTTTTCCAATAGACAACTTGTGACTATCTTTTCTGCACCTAACTACTGTGGAGAATTTGACAATGCTGGAGCAATGA
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--gttgt-tgtgttcttaaagatgtgacctacttattaccttataaactacaaagtgtatcaatagtttacttatgcttttgcattgttgaaattcagGTTGTCGAAGATGGATACGAGTTTTTCGCTAGCCGTCAACTCGTAACAATATTTTCAGCCCCTAACTACTGTGGAGAATTCGACAACGCTGGTGCCATGA
upper sequence: GLYMA02G00850.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G390076_T03 (Zea mays), 3'ss of exon 2
gttttatatgcatttctatgaagtttgag-tgtgcaattgttggaagagttcaagtattgcataacc-tgcttgtgtgttttcttttgtagGTTGTTGAAGATGGATATGAATTTTTTTCCAATAGACAACTTGTGACTATCTTTTCTGCACCTAACTACTGTGGAGAATTTGACAATGCTGGAGCAATGA
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--gttgc-tgtgctctgaaagagtgtgacctacttattcccttataaagtgtatcaaccgtttactcatgtttttgccctgttaaattcagGTTGTCGAAGATGGATATGAGTTTTTCGCTAGCCGCCAACTCGTAACAATGTTTTCAGCCCCTAACTACTGTGGAGAATTTGATAACGCTGGTGCCATGA
upper sequence: GLYMA02G00850.1 (Glycine max), 3'ss of exon 2
lower sequence: EFJ20637 (Selaginella moellendorffii), 3'ss of exon 2
gttttatatgcatttctatgaagtttgagtgtgcaattgttggaagagttcaagtattgcataacctgcttgtgtgttttcttttgtagGTTGTTGAAGATGGATATGAATTTTTTTCCAATAGACAACTTGTGACTATCTTTTCTGCACCTAACTACTGTGGAGAATTTGACAATGCTGGAGCAATGA
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---------------gtatgatgctcgtgagttctttcttt--------ctcgttgctttgagccccatgtctgcaataacaataacagGTGGTGGAAGACGGATACGAGTTTTTCGCCAACAGACAACTTGTGACGATATTTTCGGCACCCAACTATTGTGGGGAGTTCGACAATTCAGGCGCTATGA
upper sequence: GLYMA02G00850.1 (Glycine max), 3'ss of exon 2
lower sequence: EFJ32796 (Selaginella moellendorffii), 3'ss of exon 2
gttttatatgcatttctatgaagtttgagtgtgcaattgttggaagagttcaagtattgcataacctgcttgtgtgttttcttttgtagGTTGTTGAAGATGGATATGAATTTTTTTCCAATAGACAACTTGTGACTATCTTTTCTGCACCTAACTACTGTGGAGAATTTGACAATGCTGGAGCAATGA
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---------------gtatgatgctcgtgagttctttcttt------attgttgctttgagc--cccatgtctgcaataacaataacagGTGGTGGAAGACGGATACGAGTTTTTCGCCAACAGACAACTTGTGACGATATTTTCGGCACCCAACTATTGTGGGGAGTTCGACAATTCAGGCGCTATGAMapped 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|16345727|gb|BI971322.1|BI971322EST: CAGAATTTCTTGGAAAGCATGATCTTGACCTGATTTGTAGAGCACACCAG N
genomic: CAGAATTTCTTGGAAAGCATGATCTTGACCTGATTTGTAGAGCACACCAGgttttatatg ... tcttttgtag-
EST:
gi|16345727|gb|BI971322.1|BI971322EST: CAGAATTTCTTGGAAAGCATGATCTTGACCTGATTTGTAGAGCACACCAG N
genomic: CAGAATTTCTTGGAAAGCATGATCTTGACCTGATTTGTAGAGCACACCAGgttttatatg ... tcttttgtag-
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aattgttggaagagttcaagtattgcataacctgcttgtgtgttttcttttgtagGTTGTTGAAGATGGATATGAATTTTTTTCCAATAGACAACTTGTGACTATCTTTTCTGCACCTAACTACTGTGGAGAATTTGACAATGCTGGAGCAATGA
gcataac putative branch site (score: 3)
tgttttctttt putative PPT
ttttctttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttttatatgcatttctatgaagtttgagtgtgcaattgttggaagagttcaagtattgcataacctgcttgtgtgttttcttttgtagGTTGTTGAAGATGGATATGAATTTTTTTCCAATAGACAACTTGTGACTATCTTTTCTGCACCTAACTACTGTGGAGAATTTGACAATGCTGGAGCAATGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA