Sequence
atgc intronic sequence ATGC exonic sequenceCAGTGGAAGACATCTGATGTGGCAAAATTCACTAGGTCACTGTGTCTTGAAGGCAGAGTTTCCCAAAGGAAGAAAGGAGTTGGCTGTGTCCCTTTTTCAGgtttcaaaaaccattatttaaaatgttaaaatctccatttgtttttgcagtctatcttagcatcttttattgcacaaatttccatttttttaaattaattctgcatgcctggctgtcctctag
Basic information
species | Glycine max |
transcript | GLYMA08G10180.1 |
intron # | 12 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA08G10180.1 (Glycine max), 5'ss of exon 12
lower sequence: LOC_Os03g57290.1 (Oryza sativa), 5'ss of exon 12
CAGTGGAAGACATCTGATGTGGCAAAATTCACTAGGTCACTGTGTCTTGAAGGCAGAGTTTCCCAAAGGAAGAAAGGAGTTGGCTGTGTCCCTTTTTCAGgtttcaaaaaccattatttaaaatgttaaaatctccatttgtttttgcagtctatcttagcatcttttattgcacaaatttccatttttttaaattaattctgcatgcctggctgtcctctag
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TAGTGGAAGGCGTTTGATGTGGCAAAACTCATTGGGTCACTGTGTATTAAAAGCAGAGTTCCCAAAAGGTAAAAAGGAACTTGCGGTGTCACTATTTCAGgt----agggttatttttcccaatttctt--tggtggtttattgtagctgtaactgtctg-atcaataattagaaaatcactgatttattctgttt--ttcag--------------------
upper sequence: GLYMA08G10180.1 (Glycine max), 5'ss of exon 12
lower sequence: AC155496.2_FGT009 (Zea mays), 5'ss of exon 12
CAGTGGAAGACATCTGATGTGGCAAAATTCACTAGGTCACTGTGTCTTGAAGGCAGAGTTTCCCAAAGGAAGAAAGGAGTTGGCTGTGTCCCTTTTTCAGgt---ttcaaaaaccattatttaaaatgttaaaatctccatttgtttttgcagtctatcttagcatcttttattgcacaaatttccatttttttaaattaattctgcatgcctggctgtcctctag
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CAGTGGAAGGCGTTTAATGTGGCAGAATTCTTTGGGACACTGTGTCTTGAAAGCAGACTTTCCCAAAGGCAAAAAGGAACTTGCAGTATCATTGTTCCAGgtgcattttcatctcattttttggtgc-ttatcagttgaaaccatct--gagatcaatagttataattttgctta-acgtattgctgccatcag--------------------------------
upper sequence: GLYMA08G10180.1 (Glycine max), 5'ss of exon 12
lower sequence: AT5G46210.1 (Arabidopsis thaliana), 5'ss of exon 12
CAGTGGAAGACATCTGATGTGGCAAAATTCACTAGGTCACTGTGTCTTGAAGGCAGAGTTTCCCAAAGGAAGAAAGGAGTTGGCTGTGTCCCTTTTTCAGgtttcaaaaaccattatttaaaatgttaaaatctccatttgtttttgcagtctatcttagcatcttttattgcacaaatttccatttttttaaattaattctgcatgcctggctgtcctctag
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CAGTGGTAGGAGGTTAATGTGGCAAAATTCATTAGGCCACTGTGTTTTAAAGGCAGATTTCTCCAAAGGTAAAAAGGAGCTGGCTGTTTCCCTGTTTCAGgtcagtcaaattttttttcccccccccccccttttaagct--ctttcctgtcttcccgaggttacagtgttaatcaattgctcttttcttt---ttgtctcag--------------------
upper sequence: GLYMA08G10180.1 (Glycine max), 5'ss of exon 12
lower sequence: Vv10s0003g03710.t01 (Vitis vinifera), 5'ss of exon 12
CAGTGGAAGACATCTGATGTGGCAAAATTCACTAGGTCACTGTGTCTTGAAGGCAGAGTTTCCCAAAGGAAGAAAGGAGTTGGCTGTGTCCCTTTTTCAGgtttcaaaaaccattatttaaaatgttaaaatctccatttgtttttgcagtctatcttagcatcttttat-----tgcacaaatttccatttttttaaattaa---ttctgcatgcctggctgtcctctag
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CAGTGGGAGGCGATTAATGTGGCAAAACTCATTAGGACACTGTGTTTTGAAAGCAGAGTTTCCAAAAGGTAAAAAGGAGCTGGCAGTTTCTCTATTTCAGgtt------ggtcttttctagacacttgtttattctttttctttccatgtttttcctgagttttattaatccctgtgcacaatgctttagtgctcaagttttagcattttgggggtgtgtctgcag-----Mapped 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|21285971|gb|BQ473842.1|BQ473842EST: AGGCAGAGTTTCCCAAAGGAAGAAAGGAGTTGGCTGTGTCCCTATTTCAG ACTGTTGTTCTAATGTTATTCAATGATGCTGAGAAGCTAAGTCTTCAAGAT
genomic: AGGCAGAGTTTCCCAAAGGAAGAAAGGAGTTGGCTGTGTCCCTTTTTCAGgtttcaaaaa ... tgtcctctagACTGTTGTTCTAATGTTATTCAATGATGCTGAGAAGTTAAGTCTTCAAGAT
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
CAGTGGAAGACATCTGATGTGGCAAAATTCACTAGGTCACTGTGTCTTGAAGGCAGAGTTTCCCAAAGGAAGAAAGGAGTTGGCTGTGTCCCTTTTTCAGgtttcaaaaaccattatttaaaatgttaaaatctccatttgtttttgcagtctatcttagcatcttttattgcacaaatttccatttttttaaattaattctgcatgcctggctgtcctctag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG