Sequence
atgc intronic sequence ATGC exonic sequence...ctattatggatatgctttagaagtgtgaattctcctgtgtttgttttagagatatatattgttgaagtcagtatttattaatgaaaagtgtggtatccagGTATCTGAGGCAGGCGAGAACTTCAGTGTTGGACAAAGACAACTGTTGAGTCTTTCTCGGGCTTTATTGCGTAGATCAAAGATATTAGTACTTGACGAAG
Basic information
species | Glycine max |
transcript | GLYMA13G29180.1 |
intron # | 24 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA13G29180.1 (Glycine max), 3'ss of exon 24
lower sequence: AT1G30400.1 (Arabidopsis thaliana), 3'ss of exon 25
ctattatggatatgctttagaagtgtgaattctcctgtgtttgttttagagatatatattgttgaagtcagtatttattaatgaaaagtgtggtatccagGTATCTGAGGCAGGCGAGAACTTCAGTGTTGGACAAAGACAACTGTTGAGTCTTTCTCGGGCTTTATTGCGTAGATCAAAGATATTAGTACTTGACGAAG
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------------------------gtacttaattaaatatttccatttggga-aagtctcat-gtattcagtaataataactcagtctttt--tggtcagGTAACTGAGGCAGGAGAGAATTTCAGTGTTGGACAGAGACAGTTGTTGAGTCTTGCACGTGCATTGTTACGAAGATCTAAGATACTTGTTCTTGATGAAG
upper sequence: GLYMA13G29180.1 (Glycine max), 3'ss of exon 24
lower sequence: AT2G34660.2 (Arabidopsis thaliana), 3'ss of exon 24
ctattatggatatgctttagaagtgtgaattctcctgtgtttgttttagagatatatattgttgaagtcagtatttattaatgaaaagtgtggtatccagGTATCTGAGGCAGGCGAGAACTTCAGTGTTGGACAAAGACAACTGTTGAGTCTTTCTCGGGCTTTATTGCGTAGATCAAAGATATTAGTACTTGACGAAG
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----------------------gtattcagt-tgctgcctatattgatatgaagtctcatttttaagt-ggtaataactgattttcaatctt-tgttcagGTCTCTGAGGCAGGAGAGAATTTCAGCGTGGGACAGAGGCAATTGTTGAGTCTTTCACGTGCGCTGTTACGGAGATCTAAGATACTCGTCCTTGATGAAG
upper sequence: GLYMA13G29180.1 (Glycine max), 3'ss of exon 24
lower sequence: Vv10s0003g04390.t01 (Vitis vinifera), 3'ss of exon 24
ctattatggatatgctttagaag--tgtgaattctcctgtgtt----tgttttagagatatatattgttga-agtcagtatttattaatgaaaagtgtggtatccagGTATCTGAGGCAGGCGAGAACTTCAGTGTTGGACAAAGACAACTGTTGAGTCTTTCTCGGGCTTTATTGCGTAGATCAAAGATATTAGTACTTGACGAAG
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-tag-gtaaatgggccctgatatgttgtcaattctgttgttttgaactaattcagagtaacaacttttaaatagaaacaattcttccatgtggtatgtga-----agGTTTCCGAGGCCGGAGAGAATTTCAGTGTTGGACAGAGGCAACTTTTAAGTCTTGCTCGAGCATTGCTGCGGAGATCAAAGATTCTTGTTCTTGATGAAGMapped 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|13480707|gb|BG510050.1|BG510050EST: CACATTTGAAGGATGTGATACGGAGGAATTCTCTGGGGCTGGACGCTGAG GTATCTGAGGCAGGCGAGAACTTCAGTGTTGGACAAAGACAACTGTTGAGT
genomic: CACATTTGAAGGATGTGATACGGAGGAATTCTCTGGGGCTGGACGCTGAGgtaaatgcta ... tggtatccagGTATCTGAGGCAGGCGAGAACTTCAGTGTTGGACAAAGACAACTGTTGAGT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttagagatatatattgttgaagtcagtatttattaatgaaaagtgtggtatccagGTATCTGAGGCAGGCGAGAACTTCAGTGTTGGACAAAGACAACTGTTGAGTCTTTCTCGGGCTTTATTGCGTAGATCAAAGATATTAGTACTTGACGAAG
tattaat putative branch site (score: 2)
agtatttattaatgaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ctattatggatatgctttagaagtgtgaattctcctgtgtttgttttagagatatatattgttgaagtcagtatttattaatgaaaagtgtggtatccagGTATCTGAGGCAGGCGAGAACTTCAGTGTTGGACAAAGACAACTGTTGAGTCTTTCTCGGGCTTTATTGCGTAGATCAAAGATATTAGTACTTGACGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA
- - - - gatatgc
- - - - - - - - - - aagtgtg
- - - - - - - - - - - - - - - -ctcctgt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgttgaa