Sequence
atgc intronic sequence ATGC exonic sequence...cttgctattcagaatcattaattagcaaatgtattatacacgccagttctaattggttggtggtatactgtactgatgtttgtgatgtgtttgtttgcagCGTTTTGCTGCTGTGATTATGAGGATAAGAGATCCCAAAACAACTGCTCTAATTTTTGCTTCTGGCAAGATG
Basic information
species | Glycine max |
transcript | GLYMA03G04500.2 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA03G04500.2 (Glycine max), 3'ss of exon 2
lower sequence: AT3G13445.1 (Arabidopsis thaliana), 3'ss of exon 3
-cttgctattcagaatcattaattagcaaatgtattatacacgccagttctaattggttggtggtatactgtactgatgtttgtgatgtgtt-tgtttgcagCGTTTTGCTGCTGTGATTATGAGGATAAGAGATCCCAAAACAACTGCTCTAATTTTTGCTTCTGGCAAGATG
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aattagaatctaagat-attatctgtttttggcttttgctaaactaatttgccttagctaagctcgtcttatg-taatacctcttgtgttttatgtttccagCGTTTTGCTGCGGTGATAATGAGGATCAGAGAACCGAAGACTACAGCATTAATATTCGCCTCAGGGAAAATG
upper sequence: GLYMA03G04500.2 (Glycine max), 3'ss of exon 2
lower sequence: Vv06s0004g00180.t01 (Vitis vinifera), 3'ss of exon 3
-cttgctattcagaatcattaattagcaaatgtattatacacgccagttctaattggttggtggtatactgtactgatgtttgtgatgtgtt-tgtttgcagCGTTTTGCTGCTGTGATTATGAGGATAAGAGATCCCAAAACAACTGCTCTAATTTTTGCTTCTGGCAAGATG
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gatcaacatcttaaccttgttcctattggaggaatttttttt--ctttccctatttgttgccagttttttttatgtattttaaatttatgatgttcctgcagCGTTTTGCTGCCGTAATCATGAGGATAAGGGACCCAAAAACCACGGCTTTGATATTTGCTTCTGGAAAGATG
upper sequence: GLYMA03G04500.2 (Glycine max), 3'ss of exon 2
lower sequence: EFJ29072 (Selaginella moellendorffii), 3'ss of exon 2
cttgctattcagaatcattaattagcaaatgtattatacacgccagttctaattggttggtggtatactgtactgatgtttgtgatgtgtttgtttgcagCGTTTTGCTGCTGTGATTATGAGGATAAGAGATCCCAAAACAACTGCTCTAATTTTTGCTTCTGGCAAGATG
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------------------------------gt-ttgtttgtgttctttttttttctcttgtgttttatg--acttgtctctctcttctctta---tccagCGTTTTGCTGCTGTGATCATGCGTATAAGAGAACCCAAAACCACGGCTCTCATCTTTGCGTCCGGAAAGATG
upper sequence: GLYMA03G04500.2 (Glycine max), 3'ss of exon 2
lower sequence: EFJ17606 (Selaginella moellendorffii), 3'ss of exon 2
cttgctattcagaatcattaattagcaaatgtattatacacgccagttctaattggttggtggtatactgtactgatgtttgtgatgtgtttgtttgcagCGTTTTGCTGCTGTGATTATGAGGATAAGAGATCCCAAAACAACTGCTCTAATTTTTGCTTCTGGCAAGATG
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------------------------------gt-ttgtttgtgttcttttttttctcttgtttttatgacttgtctctctctctcttctctta---tccagCGTTTTGCTGCTGTGATCATGCGTATAAGAGAACCCAAAACCACGGCTCTCATCTTTGCGTCCGGAAAGATGMapped 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|31461676|gb|CD403704.1|CD403704EST: ACTTCAAGCTCGGAATGCAGAGTACAATCCTAAG CGTTTTGCTGCTGTGATTATGAGGATAAGAGATCCCNAAACAACTGCTCTA
genomic: ACTTCAAGCTCGGAATGCAGAGTACAATCCTAAGgcaagtatca ... ttgtttgcagCGTTTTGCTGCTGTGATTATGAGGATAAGAGATCCCAAAACAACTGCTCTA
EST:
gi|254322493|gb|GR837907.1|GR837907EST: ACCTCAAAACAATTGCACTTCAAGCTCGGAATGCAGAGTACAATCCTAAG CGTTTTGCTGCTGTGATTATGAGGATAAGAGATCCCAAAACAACTGCTCTA
genomic: ACCTCAAAACAATTGCACTTCAAGCTCGGAATGCAGAGTACAATCCTAAGgcaagtatca ... ttgtttgcagCGTTTTGCTGCTGTGATTATGAGGATAAGAGATCCCAAAACAACTGCTCTA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gttctaattggttggtggtatactgtactgatgtttgtgatgtgtttgtttgcagCGTTTTGCTGCTGTGATTATGAGGATAAGAGATCCCAAAACAACTGCTCTAATTTTTGCTTCTGGCAAGATG
tactgat putative branch site (score: 2)
tttgttt putative PPT
tttgttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
cttgctattcagaatcattaattagcaaatgtattatacacgccagttctaattggttggtggtatactgtactgatgtttgtgatgtgtttgtttgcagCGTTTTGCTGCTGTGATTATGAGGATAAGAGATCCCAAAACAACTGCTCTAATTTTTGCTTCTGGCAAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG