Sequence
atgc intronic sequence ATGC exonic sequence...ttaattatattggatttgtgtactttgccctgatgttgaatttgtagtgggaattttgtaggaggtatattgcattctgacactttggttttgcttttagTGTCAAAGAGAGGGTTATGTGCAAAGGGTAAAGGATGAAGAAGGTGAAGGATGCAATCTTCAAGGATCTCTTGAAGTTAATAAAGTAGCAGGAAATTTTC
Basic information
species | Glycine max |
transcript | GLYMA08G07840.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA08G07840.1 (Glycine max), 3'ss of exon 6
lower sequence: AT1G22200.1 (Arabidopsis thaliana), 3'ss of exon 6
------------------------------------------------------------------------------tta--attatattggatttgtgtactttgccct--gatgttgaatttgtagtgggaattttgtagg-----aggtatattgcattctgacactttggttttgcttttagTGTCAAAGAGAGGGTTATGTGCAAAGGGTAAAGGATGAAGAAGGTGAAGGATGCAATCTTCAAGGATCTCTTGAAGTTAATAAAGTAGCAGGAAATTTTC
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gtatactgacgttccttcactaacaacaaaattgggttgatcttggtacttagtttgaaacaaatagtgacaccttgtttggcactaaaatggatatatctaaagaaaccatgggtatctggtctttcgtttcagctatccccacatctagttgtatgatattcttactcatca--tttcatttcagTGTAAAAGAGAAGGCTTTGTGCAAAAGGTAAAAGATGAAGAAGGTGAAGGTTGTAATGTTCACGGTTTCTTGGAAGTTAACAAAGTTGCTGGGAACTTTC
upper sequence: GLYMA08G07840.1 (Glycine max), 3'ss of exon 6
lower sequence: AT1G36050.2 (Arabidopsis thaliana), 3'ss of exon 6
ttaattatattggatttgtgtactttgccctgatgttgaatttgtagtggga--attttgtag----gaggtatattgcattctgacactttggttttgcttttagTGTCAAAGAGAGGGTTATGTGCAAAGGGTAAAGGATGAAGAAGGTGAAGGATGCAATCTTCAAGGATCTCTTGAAGTTAATAAAGTAGCAGGAAATTTTC
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-----agtatgcacttgggaggctcttaactgaactatgcttcaaagagtttccatcttccaactgcgagctgaaatac-ttttcacttatctgtttgtgattcagTGTAAACGAGAAGGTTTTCTACAAAGAGTAAAGGATGAAGAAGGTGAAGGGTGTAATATATATGGGTTCTTGGAGGTCAATAAGGTGGCTGGGAACTTCCMapped 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|192326043|gb|FK016915.1|FK016915EST: CATATAGGAAAAAAGGCTGGGCAATGACAAATATGGATTTGATTGATCAG TGTCAAAGAGAGGGTTATGTGCAAAGGGT
genomic: CATATAGGAAAAAAGGCTGGGCAATGACAAATATGGATTTGATTGATCAGgttgacttca ... ttgcttttagTGTCAAAGAGAGGGTTATGTGCAAAGGGT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.agtgggaattttgtaggaggtatattgcattctgacactttggttttgcttttagTGTCAAAGAGAGGGTTATGTGCAAAGGGTAAAGGATGAAGAAGGTGAAGGATGCAATCTTCAAGGATCTCTTGAAGTTAATAAAGTAGCAGGAAATTTTC
ttctgac putative branch site (score: 2)
ttttgctttt putative PPT
aattttgta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttaattatattggatttgtgtactttgccctgatgttgaatttgtagtgggaattttgtaggaggtatattgcattctgacactttggttttgcttttagTGTCAAAGAGAGGGTTATGTGCAAAGGGTAAAGGATGAAGAAGGTGAAGGATGCAATCTTCAAGGATCTCTTGAAGTTAATAAAGTAGCAGGAAATTTTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - -ggatttg
- - - - - - - - - - - ctttgcc
- - - - - - - - - - - - - - - -gatgttg
- - - - - - - - - - - - - - - - - - - - - -gtagtgg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gcattct