Sequence
atgc intronic sequence ATGC exonic sequencegttttttgtctgcctcatttgatattcctgttttctgtttatctttcaatgcttgttgtaatttgtgaatcttaggcactgtggtcgtttgttacagGTTTTGTTGGTGAAGTTCCTGTTTTCCTTGCAAAGCCTCAAACTTACATGAATCTCAGTGGTGAATCG
Basic information
species | Glycine max |
transcript | GLYMA08G12110.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA08G12110.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os03g22610.1 (Oryza sativa), 3'ss of exon 3
-----gtt--ttttgtctgcctcatttga-----tattcctgttttctg-----tttatctttcaatgctt--gttgtaatttgtgaatcttaggcactgt--ggtcgtt----tgttacagGTTTTGTTGGTGAAGTTCCTGTTTTCCTTGCAAAGCCTCAAACTTACATGAATCTCAGTGGTGAATCG
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gtctggttcattacatctgatcccatagagaatgtatttttatattttgagcaatatatactctgttctctcggttgaaagggctgaattgaaactgttgtcttgtctttccattgatgcagGAATGGTCGAAGGTGTACCTGTTTTGCTTGCTAAGCCTCAAACATATATGAATCTCAGTGGTGAATCT
upper sequence: GLYMA08G12110.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv05s0124g00260.t01 (Vitis vinifera), 3'ss of exon 1
gttttttgtctgcctcatttgatattcctgttttctgtttatctttcaatgcttgttgtaatttgtgaatcttaggcactgtggtcgtttgttacagGTTTTGTTGGTGAAGTTCCTGTTTTCCTTGCAAAGCCTCAAACTTACATGAATCTCAGTGGTGAATCG
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---gtctgtcaacttcattt--cattcatgcttttcataaatattccattacattatggcaattatca---ttaaattttgtttatttatatctcagGTTTTGTTGGTGATGTTCTTGTTTTTCTTGCAAACCCTCATACTTACATGAATTTGAGTGGTGAATCA
upper sequence: GLYMA08G12110.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv06s0004g00560.t01 (Vitis vinifera), 3'ss of exon 2
gttttttgtctgcctcatttgatattcctgttttctgtttatctttcaatgcttgttgtaatttgtgaatcttaggcactgtggtcgtttgttacagGTTTTGTTGGTGAAGTTCCTGTTTTCCTTGCAAAGCCTCAAACTTACATGAATCTCAGTGGTGAATCG
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---gtctgtcagcttcattc--cactcatgctcttcataaatattccagtacataattgcatttatca---ttaaattttgtttatttatgtctcagGTTTTGTTGATGCTGTTCCTGTTTTCCTCGCAAAGCCTCAGACTTACATGAATTTGAGTGGTGAATCAMapped 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|192327645|gb|FK020664.1|FK020664EST: ACAGGGGATTCCTATGGACACTGTTCACTCCAAAGCTATTTTTGGAAAAG GTTTTGTTGGTGAAGTTCCTGTTTTCCTTGCAAAGCCTCAAACTTACATGA
genomic: ACAGGGGATTCCTATGGACACTGTTCACTCCAAAGCTATTTTTGGAAAAGgttttttgtc ... tttgttacagGTTTTGTTGGTGAAGTTCCTGTTTTCCTTGCAAAGCCTCAAACTTACATGA
EST:
gi|192326838|gb|FK015110.1|FK015110EST: ACAGGGGATTCCTATGGACACTGTTCACTCCAAAGCTATTTTTGGAAAAG GTTTTGTTGGTGAAGTTCCTGTTTTCCTTGCAAAGCCTCAAACTTACATGA
genomic: ACAGGGGATTCCTATGGACACTGTTCACTCCAAAGCTATTTTTGGAAAAGgttttttgtc ... tttgttacagGTTTTGTTGGTGAAGTTCCTGTTTTCCTTGCAAAGCCTCAAACTTACATGA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ctttcaatgcttgttgtaatttgtgaatcttaggcactgtggtcgtttgttacagGTTTTGTTGGTGAAGTTCCTGTTTTCCTTGCAAAGCCTCAAACTTACATGAATCTCAGTGGTGAATCG
ttgtaattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttttttgtctgcctcatttgatattcctgttttctgtttatctttcaatgcttgttgtaatttgtgaatcttaggcactgtggtcgtttgttacagGTTTTGTTGGTGAAGTTCCTGTTTTCCTTGCAAAGCCTCAAACTTACATGAATCTCAGTGGTGAATCG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG