Sequence
atgc intronic sequence ATGC exonic sequencegtgcggatttgaatctatttgagatcttaatatgattgttaaaataaattattattcatcatttaattatcatgctttagatgacttttgtaattcctattgctttaaaaaaaattgttggggctttcatttctctcatgcagtcacaagattatcaatatccttgttacattcatttgattgctgatgcagTTGGTCAGTCCCTTTCCACAAGGCCAGATATCATTGGTGTTGAGATGTCCAAG
Basic information
species | Glycine max |
transcript | GLYMA20G31940.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA20G31940.1 (Glycine max), 3'ss of exon 3
lower sequence: AT2G39190.2 (Arabidopsis thaliana), 3'ss of exon 3
gtgcggatttgaatctatttgagatcttaatatgattgttaaaataaattattattcatcatttaattatcatgctttagatgacttttgtaattcctattgctttaaaaaaaattgttggggctttcatttctctcatgcagtcacaagattatcaatatccttgttacattcatttgattgctgatgcagTTGGTCAGTCCCTTTCCACAAGGCCAGATATCATTGGTGTTGAGATGTCCAAG
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-----------------------------------------------------gtctgtgattagcttattatttttgaagtga-------aa---ctatccatcagtcaccatttacatttactgccatatattagatactttgatctg-ttgtgaatga--ttcttccctctcttc---tgctggttcagTTGGTCAATCGCTTTCCACGAGGCCAGATATCATTGGGACTGAAATCTCCAAG
upper sequence: GLYMA20G31940.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv13s0019g04130.t01 (Vitis vinifera), 3'ss of exon 3
gtgcggatttgaatctatttgagatcttaatatgattgttaaaataaattattattcatcatttaattatcatgctttagatgacttttgtaattcctattgctttaaaaaaaat-tgttggggctttcatttctctcatgcagtcacaagattatcaatatccttgttacattcatttgattgctgatgcagTTGGTCAGTCCCTTTCCACAAGGCCAGATATCATTGGTGTTGAGATGTCCAAG
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gttagcaatatgatgtagttgaaatttgcattcaaacattcaatt--tttggcttttgcttttgtagttgcat-ctttttatttttcttgcatccaatattattctttgaattatctgtctgggccgtttacccttttctgcagtcacaagattacaaatatgctagttacatgcctttgcttgctgatgcagTTGGTCAGTCCATTTCCACAAGACCAGATATCATTGGTCCAGAAATTTCCAAGMapped 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|26268090|gb|CA819153.1|CA819153EST: AATGGTGTTAAAGGAAACATTGCTTAATCTTGGCCCTACCTTTATAAAAG TTGGTCAGTCCCTTTCCACAAGGCCAGATATCATTGGTGTTGAGATGTCCA
genomic: AATGGTGTTAAAGGAAACATTGCTTAATCTTGGCCCTACCTTTATAAAAGgtgcggattt ... gctgatgcagTTGGTCAGTCCCTTTCCACAAGGCCAGATATCATTGGTGTTGAGATGTCCA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atgcagtcacaagattatcaatatccttgttacattcatttgattgctgatgcagTTGGTCAGTCCCTTTCCACAAGGCCAGATATCATTGGTGTTGAGATGTCCAAG
tgctgat putative branch site (score: 3)
aagattatcaatat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgcggatttgaatctatttgagatcttaatatgattgttaaaataaattattattcatcatttaattatcatgctttagatgacttttgtaattcctattgctttaaaaaaaattgttggggctttcatttctctcatgcagtcacaagattatcaatatccttgttacattcatttgattgctgatgcagTTGGTCAGTCCCTTTCCACAAGGCCAGATATCATTGGTGTTGAGATGTCCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG