Sequence
atgc intronic sequence ATGC exonic sequencegtatgttcatgcaatatatctacaaggagatattgtttaatttgtgaaaattgttaacttgggtatccaatattcttcatttcttttcatcagtttgatttgtcattttatatcacaaataatatacctcctttttctttgcagAGTATTGCAATAGAATTACAGAGCGAGCCTAAATGGAAGCAGTTGGGAGAATTAACTATGTCTACTGGAAAG
Basic information
species | Glycine max |
transcript | GLYMA15G01680.1 |
intron # | 18 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA15G01680.1 (Glycine max), 3'ss of exon 18
lower sequence: AT3G15980.2 (Arabidopsis thaliana), 3'ss of exon 18
gtatgttcatgcaatatatctacaaggagatattgtttaatttgtgaaaattgttaacttgggtatccaatattcttcatttcttttcatcagtttgatttgtcattttatatcacaaataatatacctcctttttctttgcagAGTATTGCAATAGAATTACAGAGCGAGCCTAAATGGAAGCAGTTGGGAGAATTAACTATGTCTACTGGAAAG
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-------------------------------gtaatatcatatgtgatgcttaattgcttagacatt--actttactctactctttttggaagtagaattttttttcttatctt------------tgttttccatgcttgtagGAAATTGCTGAAGAAGTACAGAGCGAGTCTAAATGGAAGCAGTTAGGAGAGTTAGCCATGTCCTCGGGGAAG
upper sequence: GLYMA15G01680.1 (Glycine max), 3'ss of exon 18
lower sequence: Vv09s0002g04810.t01 (Vitis vinifera), 3'ss of exon 18
-----gtatgttcatgcaatatatctacaaggagatattgtttaatttgtgaaaa--ttgttaacttgggtatccaa---tattcttcatttcttttca-------tcagtttgatttgtca-ttttatatcacaaataatatacctcctttttctttgcagAGTATTGCAATAGAATTACAGAGCGAGCCTAAATGGAAGCAGTTGGGAGAATTAACTATGTCTACTGGAAAG
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gtaaattatgttgattt--tatgtcagtatagggatataaactagttctttgacagtttgttgacttgaacatttaagcacatctttattttcttctgaggaatgattagtcctctgtgacaattttatctgaaatatagcatga-tcttctttgctttcagGACATTGCTACAGAAGTGCAAAGTGAGTCAAAATGGAAGCAATTGGGAGAATTAGCTATGTCCACTGGAAAG
upper sequence: GLYMA15G01680.1 (Glycine max), 3'ss of exon 18
lower sequence: Vv11s0016g04180.t01 (Vitis vinifera), 3'ss of exon 18
----gtatgttcatgcaa-tatatctacaaggagatattgtttaatttgtgaaaattgttaacttgggtatccaatattcttcatttcttttcatcagtttgatttgtcattttatatcacaaataatatacctcctttttctttgcagAGTATTGCAATAGAATTACAGAGCGAGCCTAAATGGAAGCAGTTGGGAGAATTAACTATGTCTACTGGAAAG
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gtaagaatttttatttatctttagttaggtgtataaacc-ttcaattggcatttaacacctatgtaagtgagtgagttcatcaaaatcaactcttttcttataattgtttgtttccattatgaaagatgtttcttctcttc--ttgcagGAAATAGCTTCAGAAGTACAGAGTGAAACCAAATGGAAGCAGTTGGGAGAATTAGCTATGTCCAATGGAAAGMapped 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|193368490|gb|FK337544.1|FK337544EST: TACAGATTTGATCTATCAATACAGCTTGGAAAACTAGATGTTGCAAAG AGTATTGCAATAGAATTACAGAGCGAGCCTAAATGGAAGCAGTTGGGAGAA
genomic: TACAGATTTGATCTATCAATACAGCTTGGAAAACTAGATGTTGCAAAGgtatgttcat ... ttctttgcagAGTATTGCAATAGAATTACAGAGCGAGCCTAAATGGAAGCAGTTGGGAGAA
EST:
gi|7145778|gb|AW507700.1|AW507700EST: ACTACAGATTTGATCTAGCAATACAGCTTGGAAAACTAGATGTTGCAAAG AGTATTGCAATAGAATTGCAGAGCGAGCCTAAATGGAAGCAGTTGGGAGAA
genomic: AGTACAGATTTGATCTATCAATACAGCTTGGAAAACTAGATGTTGCAAAGgtatgttcat ... ttctttgcagAGTATTGCAATAGAATTACAGAGCGAGCCTAAATGGAAGCAGTTGGGAGAA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tcagtttgatttgtcattttatatcacaaataatatacctcctttttctttgcagAGTATTGCAATAGAATTACAGAGCGAGCCTAAATGGAAGCAGTTGGGAGAATTAACTATGTCTACTGGAAAG
gtttgat putative branch site (score: 5)
tatacctcctttttct putative PPT
atttgtcattttatat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatgttcatgcaatatatctacaaggagatattgtttaatttgtgaaaattgttaacttgggtatccaatattcttcatttcttttcatcagtttgatttgtcattttatatcacaaataatatacctcctttttctttgcagAGTATTGCAATAGAATTACAGAGCGAGCCTAAATGGAAGCAGTTGGGAGAATTAACTATGTCTACTGGAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA