Sequence
atgc intronic sequence ATGC exonic sequenceggtatgcgtttttctctcttgtttgatgtgcaattgttcttggtaacaatgaggagaaaaattatatgcagaggtctataacagctaatcaacaatagaaacgagaatgcatgttggaactgccactttttttgctagtgatttgtatacatcattttttttgtgttttgatgcttaaacttacttgtgatgaaGATGGGATACTGCTTCTTGAAGTTAATAGGATGCTAAGAGCAGGAGGGTACTTTGTCTGGGCTGCCCAGCCAGTTTATAAGCATGAAGAAGTTTTAGAAG
Basic information
species | Glycine max |
transcript | GLYMA18G03890.2 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA18G03890.2 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os01g62800.1 (Oryza sativa), 3'ss of exon 3
ggtatgcgtttttctctcttgtttgatgtgcaattgttcttggtaacaatgaggagaaaaattatatgcagaggtctataacagctaatcaacaatagaaacgagaatgcatgttggaactgccactttttttgctagtgatttgtatacatcattttttttgtgttttgatgcttaaacttacttgtgatgaaGATGGGATACTGCTTCTTGAAGTTAATAGGATGCTAAGAGCAGGAGGGTACTTTGTCTGGGCTGCCCAGCCAGTTTATAAGCATGAAGAAGTTTTAGAAG-
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------------------------------------------------------------------------------------------attgttttcaacaaaatatcaacacaaagata--actgttttttgtagcaccctgacttc--caatttgcttaacttttgttgccatgatttgccactt-taaagATGGAATCCTGCTTCTGGAGGTTAATAGAATGCTCAGAGCCGGCGGTTATTTTGCTTGGGCAGCACAGCCTGTTTATAAGCATGAAGAGGCTCAGCAAGA
upper sequence: GLYMA18G03890.2 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G092120_T02 (Zea mays), 3'ss of exon 3
ggtatgcgtttttctctcttgtttgatgtgcaattgttcttggtaacaatgaggagaaaaattatatgcagaggtctataacagctaatcaacaatagaaacgagaatgcatgttggaactgccactttttttgctagtgatttgtatacatcattttttttgtgttttgatgcttaaacttacttgtgatgaaGATGGGATACTGCTTCTTGAAGTTAATAGGATGCTAAGAGCAGGAGGGTACTTTGTCTGGGCTGCCCAGCCAGTTTATAAGCATGAAGAAGTTTTAGAAG-
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-----------------------------------------------------------------------------------tttcatttaaacttgatctcaaag-gtatgt-gcacttatctatgtactttccaa--atttgcctaagt-------tttgtacttttgttatcatatttgtttatt-tgaagATGGTATCCTGCTCCTGGAGGTTAATAGATTGCTTAGAGCTGGAGGCTACTTTGCTTGGGCAGCCCAACCTGTTTATAAGCATGAAGAGGCCCAACAAGA
upper sequence: GLYMA18G03890.2 (Glycine max), 3'ss of exon 3
lower sequence: Vv13s0019g02250.t01 (Vitis vinifera), 3'ss of exon 3
ggtatgcgtttttctctcttgtttgatgtgcaattgttcttggtaacaatgaggagaaaaattatatgcagaggtctataacagctaatcaacaatagaaacgagaatgcatgttggaactgccactttttttgctagtgatttgta-tacatcattttttttgtgttttgatgcttaaacttacttgtgatgaaGATGGGATACTGCTTCTTGAAGTTAATAGGATGCTAAGAGCAGGAGGGTACTTTGTCTGGGCTGCCCAGCCAGTTTATAAGCATGAAGAAGTTTTAGAAG-
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---------------------------------------------------------------------------------------------aagagaaa-gagaaagctcacttaagatttttttttgtttaattgttaaatttactaggggacactttctg-atcatgctttttcctttcattt-tgatgaagATGGAATCTTGCTGCTTGAGGTAAATAGAATGCTTCGGGCAGGAGGATACTTTGCTTGGGCAGCACAGCCAGTTTATAAGCATGAAGAAAACCTAGAAGAMapped 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|193511024|gb|FK468937.1|FK468937EST: CTTTTGACTTGGTACATTGTTCACGATGTAGAATTAATTGGACTAGAGAT GATGGGATACTGCTTCTTGAAGTTA-TAGGATGCTAAGAGCAGGAGGGTAC
genomic: CTTTTGACTTGGTACATTGTTCACGATGTAGAATTAATTGGACTAGAGATggtatgcgtt ... ttgtgatgaaGATGGGATACTGCTTCTTGAAGTTAATAGGATGCTAAGAGCAGGAGGGTAC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gatttgtatacatcattttttttgtgttttgatgcttaaacttacttgtgatgaaGATGGGATACTGCTTCTTGAAGTTAATAGGATGCTAAGAGCAGGAGGGTACTTTGTCTGGGCTGCCCAGCCAGTTTATAAGCATGAAGAAGTTTTAGAAG
aacttac putative branch site (score: 2)
cttactt CT-rich tract
tatacatcattttttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ggtatgcgtttttctctcttgtttgatgtgcaattgttcttggtaacaatgaggagaaaaattatatgcagaggtctataacagctaatcaacaatagaaacgagaatgcatgttggaactgccactttttttgctagtgatttgtatacatcattttttttgtgttttgatgcttaaacttacttgtgatgaaGATGGGATACTGCTTCTTGAAGTTAATAGGATGCTAAGAGCAGGAGGGTACTTTGTCTGGGCTGCCCAGCCAGTTTATAAGCATGAAGAAGTTTTAGAAG
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