Sequence
atgc intronic sequence ATGC exonic sequence...gatttttgtatgtcttgaatatggggcagtggcaattattttaaagcagcaccaatttgaaattaatccgatgtgtgaatgcctaatttgacaactgtagGGATGCGGATACTGTAGCAGATGCTGTAGAGTTCGTGCTCCAAAATTTCACTGAAATGAACAAACTTTGGGTGCGAATGCAACATCAG
Basic information
species | Glycine max |
transcript | GLYMA01G36870.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA01G36870.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os03g58700.1 (Oryza sativa), 3'ss of exon 4
--gatttttgtatgtcttgaatatggggcagtggcaattat-tttaaagcagcaccaatttgaaattaatccgatgtgtgaatgcctaatttgacaactgtagGGATGCGGATACTGTAGCAGATGCTGTAGAGTTCGTGCTCCAAAATTTCACTGAAATGAACAAACTTTGGGTGCGAATGCAACATCAG
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ttttgtcctgaaagtatatgctacttcacatttatgttcttctcttttacagtacctaattgt--ttctttatacctgccttttgcaactttcatcac-acagGGATGCTGACAGCATTAACGTCGCAGTTGAGTTTGTTCTTCAGAATTTCATAGAAATGAACAAACTCTGGGTCCGAATGCAACATCAG
upper sequence: GLYMA01G36870.1 (Glycine max), 3'ss of exon 4
lower sequence: AT3G51310.1 (Arabidopsis thaliana), 3'ss of exon 4
gatttttgtatgtcttgaatatggggcagtggcaattattttaaagcagcaccaatttgaaattaat-ccgatgtgtgaatgcctaatttgacaactgtagGGATGCGGATACTGTAGCAGATGCTGTAGAGTTCGTGCTCCAAAATTTCACTGAAATGAACAAACTTTGGGTGCGAATGCAACATCAG
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-------gtaaggccacacgacctgctgttag--atgattttgtttaagc-----tatgaaacacatgttaagaggcaagtgttttgcttttct-ctccagAGATGGTGATGCACACATGAATGCTTTAGAGTTCGTGCTTCAAAATTTTACCGAGATGAACAAATTATGGGTTCGAATGCAACATCAG
upper sequence: GLYMA01G36870.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv04s0023g03870.t01 (Vitis vinifera), 3'ss of exon 4
----gatttttgtatgtcttgaatatggggcagtggcaattattttaaagcagcaccaatttgaaattaatccgatgtgtgaatgcctaatttgacaactgtagGGATGCGGATACTGTAGCAGATGCTGTAGAGTTCGTGCTCCAAAATTTCACTGAAATGAACAAACTTTGGGTGCGAATGCAACATCAG
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gaaatagtaaaaaatgagttattaattcaaaagta-tgattgttctct--ccttagcctactggtattgatt-gagctgtgtatggcttccttgacttgtgcagGGGTGCTGACACTGTCATGGATGCTGTAGAGTTTTTACTCCAAAACTTCACAGAGATGAACAAACTTTGGGTGCGGATGCAACATCAG
upper sequence: GLYMA01G36870.1 (Glycine max), 3'ss of exon 4
lower sequence: PP1S313_104V6.1 (Physcomitrella patens), 3'ss of exon 4
--gatttttgtatgtcttgaatatggggcagtggcaattattttaaagcagcaccaatttgaaattaatccgatgtg-tgaatgcctaatttgacaactgtagGGATGCGGATACTGTAGCAGATGCTGTAGAGTTCGTGCTCCAAAATTTCACTGAAATGAACAAACTTTGGGTGCGAATGCAACATCAG
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tggaggaggggatttgtttgatattttg-attcgttgtgaaattcatgtttcgagtttcccgcacgagtcggctgtgcttgactttgaagttga--atttcagGGAGGGTGGCAACGTGATGGACGCGGTGGAGTTTGTGCTCCAGAATTTTACGGAGATGAACAAATTGTGGGTGCGGATGCAACATCAGMapped 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|193547605|gb|FK504566.1|FK504566EST: TCTCAAGTTAGTAGGGATAAATTGCCAGATATTGGTTCAGAGTACGAAGG GGATGCGGATACTGTAGCAGATGCTGTAGAGTTCGTGCTCCAAAATTTCAC
genomic: TCTCAAGTTAGTAGGGATAAATTGCCAGATATTGGTTCAGAGTACGAAGGgtgagtaagc ... acaactgtagGGATGCGGATACTGTAGCAGATGCTGTAGAGTTCGTGCTCCAAAATTTCAC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gcagcaccaatttgaaattaatccgatgtgtgaatgcctaatttgacaactgtagGGATGCGGATACTGTAGCAGATGCTGTAGAGTTCGTGCTCCAAAATTTCACTGAAATGAACAAACTTTGGGTGCGAATGCAACATCAG
aatttgaaattaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gatttttgtatgtcttgaatatggggcagtggcaattattttaaagcagcaccaatttgaaattaatccgatgtgtgaatgcctaatttgacaactgtagGGATGCGGATACTGTAGCAGATGCTGTAGAGTTCGTGCTCCAAAATTTCACTGAAATGAACAAACTTTGGGTGCGAATGCAACATCAG
- - - tgtatgt
- - - - - - - - - - - ggggcag
- - - - - - - - - - - - - - - - - - - - - - - - -caccaat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - gaaattaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gaatgcc