Sequence
atgc intronic sequence ATGC exonic sequence...atcatcaggtttgttgaaggttaccacagtatatacaacatatttataataaatcaattttaatgtattgtgtttttatactattgtttcattttctaagGTTGCTGCATGGAAAGACAAGGATGGAGACTGGTACGAGACAGGCCTACACATCTTTT
Basic information
species | Glycine max |
transcript | GLYMA18G00720.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA18G00720.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv09s0002g00100.t01 (Vitis vinifera), 3'ss of exon 4
--atcatcaggtttgttgaaggtt-accacagtatatacaacatatttataataaatcaattttaatgtattgtgtttttatactattgtttcattttctaagGTTGCTGCATGGAAAGACAAGGATGGAGACTGGTACGAGACAGGCCTACACATCTTTT
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gcaatactaattgtataatagatttaacttcctacttaatttccccttttattgttggaagtttctttcatttagtg--aaggctagtctctcttgatata-gGTGGCTGCATGGAAAGATGAGGATGGAGACTGGTATGAGACAGGCCTACATATATTCT
upper sequence: GLYMA18G00720.1 (Glycine max), 3'ss of exon 3
lower sequence: EDP05305 (Chlamydomonas reinhardtii), 3'ss of exon 1
atcatcaggtttgttgaaggttaccacagtatatacaacatatttataataaatcaattttaatgtattgtgttt-ttatactattgtttcattttctaagGTTGCTGCATGGAAAGACAAGGATGGAGACTGGTACGAGACAGGCCTACACATCTTTT------------------------------------------
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-------------gtgagtgtgcacccggcgagcgcca-attcgtgcatcgtagcataaatggacaattgggctaaccgtgccaaccttttgctggt--agGTCGCTGCATGGAAGGATGAGGATGGCGACTGGTACGAGACTGGCTTGCACATCTTCTTCGGCGCGTACCCCAACATGATGAATGTCTTCAAGGAGCTAA
upper sequence: GLYMA18G00720.1 (Glycine max), 3'ss of exon 3
lower sequence: PP1S369_27V6.1 (Physcomitrella patens), 3'ss of exon 2
-------------------------atcatcaggtttgttgaaggttaccacagtatatacaacatatttataataaatcaatt--ttaatgtattgtgtttttatactattgtttcattttctaagGTTGCTGCATGGAAAGACAAGGATGGAGACTGGTACGAGACAGGCCTACACATCTTTT
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gtgataattgtgaacttttgggttaatgtgccattctgcctcagccgaacagaggacgaatattacgctaactataactagactagtcaata-atactggctctaagtgatttttctgaaatgta-gGTTGCGGCATGGAAGGACAAGGATGGGGATTGGTACGAGACTGGTTTGCACATCTTTTMapped 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|209699095|gb|BW664324.1|BW664324EST: CTGGGCATAAACCTATATTGCTGGAAGCAAGAGACGTTCTAGGTGGAAAG GTTGCTGCATGGAAAGACAAGGATGGAGACTGGTACGAGACAGGCCTACAC
genomic: CTGGGCATAAACCTATATTGCTGGAAGCAAGAGACGTTCTAGGTGGAAAGgttttcctgc ... attttctaagGTTGCTGCATGGAAAGACAAGGATGGAGACTGGTACGAGACAGGCCTACAC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ataataaatcaattttaatgtattgtgtttttatactattgtttcattttctaagGTTGCTGCATGGAAAGACAAGGATGGAGACTGGTACGAGACAGGCCTACACATCTTTT
ttttaat putative branch site (score: 3)
ttgtttcattttct putative PPT
aaatcaattttaatgt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
atcatcaggtttgttgaaggttaccacagtatatacaacatatttataataaatcaattttaatgtattgtgtttttatactattgtttcattttctaagGTTGCTGCATGGAAAGACAAGGATGGAGACTGGTACGAGACAGGCCTACACATCTTTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - -tgttgaa
- - - - - - - - - - - accacag