Sequence
atgc intronic sequence ATGC exonic sequence...tagtgcaccccactgatcacctatcacattcactctctcttttattattttctgtttttcatcttctaactttcattgcctttctatttctttctcacagTTAACGAAGCTCAAAGATGGGCTCGCAATGGGCCTAGCGTTCAACCATGCTGTCTTGGACGGGACTGCCACGTGGCAGTTCATGACCTCATGGGCCGAGA
Basic information
species | Glycine max |
transcript | GLYMA09G24900.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA09G24900.1 (Glycine max), 3'ss of exon 1
lower sequence: AT5G23940.1 (Arabidopsis thaliana), 3'ss of exon 1
-tagtgcaccccactgatcacctatcacattcactctctcttttattattttctgtttttcatcttctaactttcattgcctttctatttctttctcacagTTAACGAAGCTCAAAGATGGGCTCGCAATGGGCCTAGCGTTCAACCATGCTGTCTTGGACGGGACTGCCACGTGGCAGTTCATGACCTCATGGGCCGAGA
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accattaacatgaaaaaaaaagcattacactaaaatttaaaagaaaaataaaaacattttcacaagtattaattaaccaacatttt-tcgtttcgcaacagGTGACCAAGCTAAAAGATGGGCTTGCAATGGGCCTAGCTTTCAATCACGCAGTCTTAGACGGGACATCCACGTGGCATTTTATGAGCTCATGGGCCGAGA
upper sequence: GLYMA09G24900.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv16s0050g00830.t01 (Vitis vinifera), 3'ss of exon 1
tagtgcaccccactgatcacctatcacattcactctctcttttattattttctgtttttcatcttctaact-ttcattgcctttctatttctttctcacagTTAACGAAGCTCAAAGATGGGCTCGCAATGGGCCTAGCGTTCAACCATGCTGTCTTGGACGGGACTGCCACGTGGCAGTTCATGACCTCATGGGCCGAGA
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gacaattactcactgttaccgtcccttgaacctccacgtggctccaattttgagtctgttaccgtgagccaactaattatttttctgtcatgatc-cgcagTTCACCAAGCTAAGAGATGGACTCGCACTGGGATGCGCTTTCAACCACGCGATCCTCGACGGTACCTCCACGTGGCACTTCATGACCTCGTGGGCCGAGA
upper sequence: GLYMA09G24900.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv16s0050g00870.t01 (Vitis vinifera), 3'ss of exon 1
------------------------------------------------------------tagtgcaccccactgatcacctatcacattcactctctct---tttattattttctgtttttcatcttctaactttcattgcctttctatttctttctcacagTTAACGAAGCTCAAAGATGGGCTCGCAATGGGCCTAGCGTTCAACCATGCTGTCTTGGACGGGACTGCCACGTGGCAGTTCATGACCTCATGGGCCGAGA
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gtaacaatttatttatttatttattttctattaaaagtggtcatatgactttggtacaaaaggaatgatttcccaatagttgaaaagatggactagaacaaagtttgttgtcccaggttattcaact----gcttcaactgtttttctgtcatgatc-cgcagTTCACCAAGCTAAGAGATGGCCTCGCAATGGGATGCGCGTTCAACCACGCTGTCCTCGACGGTACCTCCACGTGGCACTTCATGAGCTCGTGGGCCGAAAMapped 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|24136952|gb|BU927462.1|BU927462EST: GTGGTATCTTGAATTTGGAAGGCATGCATAGGCCCTTGCTGGCTGTTCAG TTAACGAAGCTCAAAGATGGGCTCGCAATGGGCCTAGCGTTCAACCATGCT
genomic: GTGGTATCTTGAATTTGGAAGGCATGCATAGGCCCTTGCTGGCTGTTCAGgtaaatataa ... tttctcacagTTAACGAAGCTCAAAGATGGGCTCGCAATGGGCCTAGCGTTCAACCATGCT
EST:
gi|298176615|gb|HO023202.1|HO023202EST: GTGGTATCTTGAATTTGGAAGGCATGCATAGGCCCTTGCCGGCTGTTCAG TTAACGAAGCTCAAAGATGGGCTCGCAATGGGCCTAGCGTTCAACCATGCT
genomic: GTGGTATCTTGAATTTGGAAGGCATGCATAGGCCCTTGCTGGCTGTTCAGgtaaatataa ... tttctcacagTTAACGAAGCTCAAAGATGGGCTCGCAATGGGCCTAGCGTTCAACCATGCT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tattttctgtttttcatcttctaactttcattgcctttctatttctttctcacagTTAACGAAGCTCAAAGATGGGCTCGCAATGGGCCTAGCGTTCAACCATGCTGTCTTGGACGGGACTGCCACGTGGCAGTTCATGACCTCATGGGCCGAGA
ttctaac putative branch site (score: 1)
tcttctaactttcatt CT-rich tract
tttctattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tagtgcaccccactgatcacctatcacattcactctctcttttattattttctgtttttcatcttctaactttcattgcctttctatttctttctcacagTTAACGAAGCTCAAAGATGGGCTCGCAATGGGCCTAGCGTTCAACCATGCTGTCTTGGACGGGACTGCCACGTGGCAGTTCATGACCTCATGGGCCGAGA
- - -cacccca
- - - - - - - - - - - - -acattca
- - - - - - - - - - - - - - - - ctctctc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cattgcc