Sequence
atgc intronic sequence ATGC exonic sequence...atcactctttttcttttccttgttgaataactatatgatgatatatctgcataaattcattagctaaagtccattctgcttcattttttatttatttcagATGATACCCGTGGCAGCAAATGATGTTGCTTTCTCAGCCCATGCTGTTCTGTTGACAGCAATTTCCTTGTTCCAGATTGCAATCTATGAT
Basic information
species | Glycine max |
transcript | GLYMA19G23610.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA19G23610.1 (Glycine max), 3'ss of exon 2
lower sequence: AT5G40670.1 (Arabidopsis thaliana), 3'ss of exon 2
atcactctttttcttttccttgttgaataactatatgatgatatatctgcataaattca-ttagctaaagtccattctgcttcattttttatttatttcagATGATACCCGTGGCAGCAAATGATGTTGCTTTCTCAGCCCATGCTGTTCTGTTGACAGCAATTTCCTTGTTCCAGATTGCAATCTATGAT
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-ttgttcctttctaagtttcagcaaaaaaaaaacgctttagattgttcgagctggtttaattttttttgagtcgttttgttataattgttgcttatttcagATGATACCTGTGGCTGCAAATGATGTTGCATTCTCGATCCATGCAGTTGTAATGACAGCTGTTACACTGTTCCAGATCTTTATCTATGAA
upper sequence: GLYMA19G23610.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv14s0219g00130.t01 (Vitis vinifera), 3'ss of exon 2
atcactctttttcttttccttgttgaataactatatgatgatatatctgcataaattcattagctaaagtccattctgcttcattttttatttatttcagATGATACCCGTGGCAGCAAATGATGTTGCTTTCTCAGCCCATGCTGTTCTGTTGACAGCAATTTCCTTGTTCCAGATTGCAATCTATGAT
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------------gtttttattttcgggtc----tttcaggttttccctcctctttttggatttttaatatg-----tggtgaaatgttttcttgttgcagATGATACCTGTGGCTGCAAATGATGTTGCTTTCTCAATTCATGCTGTTGTCTTGATAGCATTTACTTGGTTCCAAATTGCAATCTATGAG
upper sequence: GLYMA19G23610.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv14s0219g00120.t01 (Vitis vinifera), 3'ss of exon 2
atcactctttttcttttcct----tgttgaataactatatgatgatatatctgcataaattcattagctaaagtccattctgcttcattttttatttatttcagATGATACCCGTGGCAGCAAATGATGTTGCTTTCTCAGCCCATGCTGTTCTGTTGACAGCAATTTCCTTGTTCCAGATTGCAATCTATGAT
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-ttactttgcttatgttaaaagggtggaagagaacaagttgtttaagtgt-tccattttttcctttttttacaaatatgtgg--tgatacgctttttattacagATGATACCTGTGGCTGCAAATGATGTTGCTTTCTCAATTCATGCTGTTATCTTGACAGCATTTACTTTGTTTCAAATTGCAATCTATGAGMapped 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|209718452|gb|BW666250.1|BW666250EST: TCAGTTCTGCTGTTCAGAAGCAGTACAGAGACAAATACGGTCAGAATGAG ATGATACCCGTGGCAGCAAATGATGTTGCTTTCTCAGCCCATGCTGTTCTG
genomic: TCAGTTCTGCTGTTCAGAAGCAGTACAGAGACAAATACGGTCAGAATGAGgtttgttcct ... tttatttcagATGATACCCGTGGCAGCAAATGATGTTGCTTTCTCAGCCCATGCTGTTCTG
EST:
gi|192331771|gb|FK024875.1|FK024875EST: TCAGTTCTGCTGTTCAGAAGCAGTACAGAGACAAATACGGTCAGAATGAG ATGATACCCGTGGCAGCAAATGATGTTGCTTTCTCAACCCATGCTGTTCTG
genomic: TCAGTTCTGCTGTTCAGAAGCAGTACAGAGACAAATACGGTCAGAATGAGgtttgttcct ... tttatttcagATGATACCCGTGGCAGCAAATGATGTTGCTTTCTCAGCCCATGCTGTTCTG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tctgcataaattcattagctaaagtccattctgcttcattttttatttatttcagATGATACCCGTGGCAGCAAATGATGTTGCTTTCTCAGCCCATGCTGTTCTGTTGACAGCAATTTCCTTGTTCCAGATTGCAATCTATGAT
agctaaa putative branch site (score: 3)
cttcattttttattt putative PPT
ttcattttttatttat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
atcactctttttcttttccttgttgaataactatatgatgatatatctgcataaattcattagctaaagtccattctgcttcattttttatttatttcagATGATACCCGTGGCAGCAAATGATGTTGCTTTCTCAGCCCATGCTGTTCTGTTGACAGCAATTTCCTTGTTCCAGATTGCAATCTATGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT
- - - - - - - - - cttgttg
- - - - - - - - - - - - - - - - - -tgatgat
- - - - - - - - - - - - - - - - - - - - - - - -tgcataa