Sequence
atgc intronic sequence ATGC exonic sequence...tctatctgcatatggtgttttcttggctttcattttcaatgtttggtgctcagatgtcacatatatcctaattgcaattttttacttgtttttacactagTGTGGCTCGTTTCCTGGAATCACGAGGGATGATAGAGGATGCTCTTGAAGTAGCTACTGACCCTGACTATAGGTTTGATCTAGCCATACAGCTTGGAAGA
Basic information
species | Glycine max |
transcript | GLYMA07G03890.1 |
intron # | 17 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA07G03890.2 (Glycine max), 3'ss of exon 6
lower sequence: AT1G79990.1 (Arabidopsis thaliana), 3'ss of exon 21
----------------------------------------------------------------tctatctgcatatggtgttttcttggctttcattttcaatgtttggtgctcagatgtcacatatatcctaattgcaattttttacttgtttttacactagTGTGGCTCGTTTCCTGGAATCACGAGGGATGATAGAGGATGCTCTTGAAGTAGCTACTGACCCTGACTATAGGTTTGATCTAGCCATACAGCTTGGAAGA
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gtatgagaatgtgctttccctcgcattatggttacagctggattatggtgttagtaaacatgtatccaaggtcacataatggttt---aaattgttttcctaaattcacgcattcctacttttctgat-tctcgacttcaaaatcctgttcgtttt---gtcagCGTGGCACACTTTTTGGAGTCACGTGGCATGACAGAAGATGCTCTAGAAGTAGCAACTGATCCTGACTACAGATTTGAGTTGGCCATACAGCTCGGTAGA
upper sequence: GLYMA07G03890.2 (Glycine max), 3'ss of exon 6
lower sequence: Vv11s0016g04180.t01 (Vitis vinifera), 3'ss of exon 17
tctatctgcatatggtgttttcttggcttt--cattttcaatgtttggtgctcagatgtcacatatatcctaattgcaattttttacttgtttttacactagTGTGGCTCGTTTCCTGGAATCACGAGGGATGATAGAGGATGCTCTTGAAGTAGCTACTGACCCTGACTATAGGTTTGATCTAGCCATACAGCTTGGAAGA
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--tgaccgcattttttttccacttattcttgttgtttcaattcctttttccatagttctgaaatttgactgagatgtgatgaagatatattttacttgctagTGTGGCTCGTTTCTTGGAAGCTCGAGGTATGCTGGAGGATGCACTGGAAGTTGCCACAGATCCTGACTATAGATTTGATCTAGCTATACAGCTAGGCAGA
upper sequence: GLYMA07G03890.2 (Glycine max), 3'ss of exon 6
lower sequence: Vv09s0002g04810.t01 (Vitis vinifera), 3'ss of exon 17
tctatctgca-tatggtgttttcttggctttcattttcaatgtttggtgctcagatgtcacatatatcctaattgcaattttttac--ttgtttttac-actagTGTGGCTCGTTTCCTGGAATCACGAGGGATGATAGAGGATGCTCTTGAAGTAGCTACTGACCCTGACTATAGGTTTGATCTAGCCATACAGCTTGGAAGA
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----tctgaacttttatacccgctgaaaatgaaacaaagatgaattattttgcagtcttttaagtttcttgcatgctaataagaaaagttgtttgaattgctagTGTGGCTCGTTTCTTGGAATCACGGGGTATGATAGAGGATGCCCTGGAAGTAGCTACTGACCCTGATTACCGATTTGAGCTAGCAATGCAGCTTGGCAGAMapped 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|254341657|gb|GR852794.1|GR852794EST: GAAAGGGCCAATGAAATTCTACCATCAATTCCTAAAGAGTATCATAACAG TGTGGCTCGTTTCCTGGAATCACGAGGGATGATAGAG-ATGCTCT-GAAGT
genomic: GAAAGGGCCAATGAAATTCTACCATCAATTCCTAAAGAGTATCATAACAGgtagtagtta ... tttacactagTGTGGCTCGTTTCCTGGAATCACGAGGGATGATAGAGGATGCTCTTGAAGT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gtgctcagatgtcacatatatcctaattgcaattttttacttgtttttacactagTGTGGCTCGTTTCCTGGAATCACGAGGGATGATAGAGGATGCTCTTGAAGTAGCTACTGACCCTGACTATAGGTTTGATCTAGCCATACAGCTTGGAAGA
tcctaat putative branch site (score: 2)
ttttttacttgttttt putative PPT
aattttttacttgttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tctatctgcatatggtgttttcttggctttcattttcaatgtttggtgctcagatgtcacatatatcctaattgcaattttttacttgtttttacactagTGTGGCTCGTTTCCTGGAATCACGAGGGATGATAGAGGATGCTCTTGAAGTAGCTACTGACCCTGACTATAGGTTTGATCTAGCCATACAGCTTGGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA