Sequence
atgc intronic sequence ATGC exonic sequence...ttattagattaattatcacttaatgaatcatattgcactggtgatttgatcaacatttatttgttatttcattcagacctaagttatgagttcattttagGTCTCTGCAATAGTATCATTCTTGCTGGGACCTGAGAGAGCAGAAAAAATCAAGATATTTGCCGGAGACGTGGTTCCCCGTAAAAAGCCTGATCCA
Basic information
species | Glycine max |
transcript | GLYMA06G18320.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA06G18320.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os03g36750.1 (Oryza sativa), 3'ss of exon 4
ttattagattaattatcacttaatgaatcatattgcactggtgat--ttgatcaacatttatttgttatttcattcagacctaagttatgagttcattttagGTCTCTGCAATAGTATCATTCTTGCTGGGACCTGAGAGAGCAGAAAAAATCAAGATATTTGCCGGAGACGTGGTTCCCCGTAAAAAGCCTGATCCA
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atgtactatttttca-cactttttaaatagtagtaca-tgttgatagtagctgtgaacttgtatgccagatagctcacatatttatgcttgactgaatgcagGTTTCGGCAATAGTTTCATGTTTACTGGGCCCTGATCGTGCAGAAAAAATTACCATATTTGCTGGAGATGTGGTTCCTCGTAAAAAACCTGATCCA
upper sequence: GLYMA06G18320.1 (Glycine max), 3'ss of exon 5
lower sequence: AT3G48420.1 (Arabidopsis thaliana), 3'ss of exon 4
------------------------------------------------------------------------------------ttattagattaattatcacttaatgaatcatat-----tgcactggtgatttgatc----aacatttatttgttatttcattcagacctaagttatgagttcattttagGTCTCTGCAATAGTATCATTCTTGCTGGGACCTGAGAGAGCAGAAAAAATCAAGATATTTGCCGGAGACGTGGTTCCCCGTAAAAAGCCTGATCCA
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gtatgatcaatcaggttctactacttcagtttcctgagaccataaccatatatctcaaaatcttgtatcctgatgagttttcgtaaacaagactacgcgcagctgcatcgttaacatgaatatgcgagcatcgtcttagcttagaagaactgtataatcggaaatacttttctcatttcttgcctgatttcagGTTTCTGCTATAGTTTCATGCTTGCTTGGACCAGAACGAGCAGAGAAAATCAAGATATTCGCAGGAGACGTAGTCCCCAAAAAGAAACCTGATCCA
upper sequence: GLYMA06G18320.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv17s0000g09910.t01 (Vitis vinifera), 3'ss of exon 4
-------ttattagattaattatcacttaatgaatcatattgcactggtgatttgatcaacatttatttgttatttcattcagacctaagttatgagttcattttagGTCTCTGCAATAGTATCATTCTTGCTGGGACCTGAGAGAGCAGAAAAAATCAAGATATTTGCCGGAGACGTGGTTCCCCGTAAAAAGCCTGATCCA
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tcttgctttgtcattgtctgatttccttggcgaat--tatgatattggttttctgatctaattctcattttgata--actgaattatatgtgctaa---tatcccagGTCTCTGCAATAGTTTCATGCTTGCTGGGGCCTGAGCGAGCAGAAAAAATCAAGATATTTGCAGGCGACGTGGTTCCTCGAAAAAAGCCTGATCCAMapped 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|12688994|gb|BG155330.1|BG155330EST: TTGCTCAAGGAGTCCAAGTTGCAGTTTGCAGCACTTCCAATGAGAAGGCG GTCTCTGCAATAGTATCATTCTTGCTGGGACCTGAGAGAGCAGAAAAAATC
genomic: TTGCTCAAGGAGTCCAAGTTGCAGTTTGCAGCACTTCCAATGAGAAGGCGgtatgcataa ... ttcattttagGTCTCTGCAATAGTATCATTCTTGCTGGGACCTGAGAGAGCAGAAAAAATC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttgatcaacatttatttgttatttcattcagacctaagttatgagttcattttagGTCTCTGCAATAGTATCATTCTTGCTGGGACCTGAGAGAGCAGAAAAAATCAAGATATTTGCCGGAGACGTGGTTCCCCGTAAAAAGCCTGATCCA
atttgat putative branch site (score: 5)
ttcatttt putative PPT
aacatttatttgttat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttattagattaattatcacttaatgaatcatattgcactggtgatttgatcaacatttatttgttatttcattcagacctaagttatgagttcattttagGTCTCTGCAATAGTATCATTCTTGCTGGGACCTGAGAGAGCAGAAAAAATCAAGATATTTGCCGGAGACGTGGTTCCCCGTAAAAAGCCTGATCCA
- - - - - - - - - - - - - - - - -tgcactg
- - - - - - - - - - - - - - - - - - - - -tgatttg
- - - - - - - - - - - - - - - - - - - - - - - - atcaaca