Sequence
atgc intronic sequence ATGC exonic sequence...gattcatttattgagaataatggtactcgattgactttactccattctttttctacccggacctgctcaactgactctctctggggttgttcaatttcagCTATTTGATTTTGCTGACAAATACAGAGGCAAATATGACAGCAGCATCACGGTTGCCCAAAAGTATTACAGATCCATCAGTGGTTACAAT
Basic information
species | Glycine max |
transcript | GLYMA08G02610.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA08G02610.1 (Glycine max), 3'ss of exon 3
lower sequence: AT1G64390.1 (Arabidopsis thaliana), 3'ss of exon 3
------gattcatttattgagaataatggtactcgattgacttta-ctccattctttttctacccggacctgctcaactgactctctctggggttgttcaatttcagCTATTTGATTTTGCTGACAAATACAGAGGCAAATATGACAGCAGCATCACGGTTGCCCAAAAGTATTACAGATCCATCAGTGGTTACAAT
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acgaaaacgccactccccacccaaaac--ttgtaaactaaccttgtctttaatgttttactac--ggatttgccaccctaattccatttt---ttgtttggttacagTTGTTTGATTTCGCCGACAAATACAGAGGAAAATACGACAGCAGTATCACTGTTGCCCAGAAATACTACCGATCCGTCAGCGGTTACAAT
upper sequence: GLYMA08G02610.1 (Glycine max), 3'ss of exon 3
lower sequence: AT4G11050.1 (Arabidopsis thaliana), 3'ss of exon 3
gattcatttattg--agaataatggtactcgattgactttactccattctttttctacccggacctgctcaactgactctctctggggttgttcaatttcagCTATTTGATTTTGCTGACAAATACAGAGGCAAATATGACAGCAGCATCACGGTTGCCCAAAAGTATTACAGATCCATCAGTGGTTACAAT
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ttttggctaggtgcaaaaacgtagatagtagaaataaccttctcaactcataatatttacgattgtgct--actgatcctaatgcaattcttatattgccagCTATTTGAATTTGCGGACAAATACAGAGGCAAATATGACAGCAGCATTACCGTGGCACAAAAATATTACCGATCCGTCAGCGGTTACAAT
upper sequence: GLYMA08G02610.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv02s0025g01380.t01 (Vitis vinifera), 3'ss of exon 5
gattcatttattgagaataatggtactcgattgactttactccattctttttctacccggacctgctcaactgactctctctggggttgt------tcaatttcagCTATTTGATTTTGCTGACAAATACAGAGGCAAATATGACAGCAGCATCACGGTTGCCCAAAAGTATTACAGATCCATCAGTGGTTACAAT
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------cttcccctcaacctctcttcccaaactacccttcatgttttatcatatctactgaattacccttcagtcactaacacatgttctaaaatcttattttcagCTGTTCGAGTTTGGAGACAAATACAGGGGCAAATATGACAGCAGCATCACAGTGGCCCAGAAGTACTACCGGTCTTACAGTGGATACGCTMapped 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|209723572|gb|BW682716.1|BW682716EST: GACGCTCTAACCCTGCCTATGCCGGCGAACTTCTCCGCCATGCCTACCAG CTATTTGATTTTGCTGACAAATACAGAGGCAAATATGACAGCAGCATCACG
genomic: GACGCTCTAACCCTGCCTATGCCGGCGAACTTCTCCGCCATGCCTACCAGgtactacact ... tcaatttcagCTATTTGATTTTGCTGACAAATACAGAGGCAAATATGACAGCAGCATCACG
EST:
gi|21888585|gb|BQ741798.1|BQ741798EST: GACGCTCTAACCCTGCCTATGCCGGCGAACTTCTCCGCCATGCCTACCAG CTATTTGATTTTGCTGACAAATACAGAGGCAAATATGACAGCAGCATCACG
genomic: GACGCTCTAACCCTGCCTATGCCGGCGAACTTCTCCGCCATGCCTACCAGgtactacact ... tcaatttcagCTATTTGATTTTGCTGACAAATACAGAGGCAAATATGACAGCAGCATCACG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tctttttctacccggacctgctcaactgactctctctggggttgttcaatttcagCTATTTGATTTTGCTGACAAATACAGAGGCAAATATGACAGCAGCATCACGGTTGCCCAAAAGTATTACAGATCCATCAGTGGTTACAAT
aactgac putative branch site (score: 2)
ttcaattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gattcatttattgagaataatggtactcgattgactttactccattctttttctacccggacctgctcaactgactctctctggggttgttcaatttcagCTATTTGATTTTGCTGACAAATACAGAGGCAAATATGACAGCAGCATCACGGTTGCCCAAAAGTATTACAGATCCATCAGTGGTTACAAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctgctca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctctctc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ggggttg