Sequence
atgc intronic sequence ATGC exonic sequence...agaatttctctgtattatggagagtgctttcttttctttgttaaatacatgattaattttctatttcttcttcagtggcactgaactaagcattttgtagGTCCTCTTCCAAAATGATTCACCTGCAACATTACTTGCTCGGGTGATTGGGATCATTGATCCAATTGATCAAAGTATGCTTGCAAAAGGACGCGACACAT
Basic information
species | Glycine max |
transcript | GLYMA05G33560.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA05G33560.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os03g51020.1 (Oryza sativa), 3'ss of exon 5
agaatttctctgt--attatggagagtgctttcttttctttgttaaatacatgattaattttctatttcttcttcagtggcactgaactaagcattttgtagGTCCTCTTCCAAAATGATTCACCTGCAACATTACTTGCTCGGGTGATTGGGATCATTGATCCAATTGATCAAAGTATGCTTGCAAAAGGACGCGACACAT
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tgatcttagcaggcaatgtttgcaatttatctatttactgttatacatagagaatgaatatgttagttcatcttgattcaccatggtctatgctcttc--agGTTCTTTTCCAAAATGATTCTCCTGCAACTTTACTTGCACGTGTGATGGGCATCATTGGTTCGATAGAACAAGCTATGCTTGCACAGGGACGTGAAACAT
upper sequence: GLYMA05G33560.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G015073_T01 (Zea mays), 3'ss of exon 5
-agaatttctctgtattatggagagtgctttcttttctttgttaaatacatgattaattttctatttcttcttcagtggcactgaactaagcattttgtagGTCCTCTTCCAAAATGATTCACCTGCAACATTACTTGCTCGGGTGATTGGGATCATTGATCCAATTGATCAAAGTATGCTTGCAAAAGGACGCGACACAT
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ttttttattattatttcaaggtatatattttttacctattttctgtcatatgcttg-tatggtgcatggaagctgatgagtgcgtcctctatgcttttcagGTCCTTTTCCAAAATGATTCTCCTGCAACATTACTTGCTCGCGTGATGGGCATCATTGGCTCCATAGAACAAGCTATGCTTGCACAGGGACGCGACACCT
upper sequence: GLYMA05G33560.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G181002_T01 (Zea mays), 3'ss of exon 5
----agaatttctctgtattatggagagtgct-ttcttttctttgttaaatacatgattaattttctatttcttcttcagtggcactgaactaagcattttgtagGTCCTCTTCCAAAATGATTCACCTGCAACATTACTTGCTCGGGTGATTGGGATCATTGATCCAATTGATCAAAGTATGCTTGCAAAAGGACGCGACACAT
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gaaggtggtgattagaagctatgcagcttgctattttttttgttgttatacgcttgtatggtggacggaagctgatgtgtgcgtcct---ctatgcttttc--agGTTCTTTTCCAAAACGATTCGCCTGCAACATTACTTGCTCGTGTGATGGGCATCATTGGCGCCATAGAACAAGCTATGCTTGCACAGGGACGGGACACCT
upper sequence: GLYMA05G33560.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv01s0011g01590.t01 (Vitis vinifera), 3'ss of exon 11
---agaatttctctgtattatggagagtgctttcttttctttgttaaatacatgattaattttctatttcttcttcagtggcactgaactaagcattttgtagGTCCTCTTCCAAAATGATTCACCTGCAACATTACTTGCTCGGGTGATTGGGATCATTGATCCAATTGATCAAAGTATGCTTGCAAAAGGACGCGACACAT
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agcaagatatct-tacctggtttaatgtggtcattttccttaaaactatcaattatga--ttcctggtgcaaagcgctttacataaagtttgctatgttttagGTCCTCTTCCAAAATGATTCACCAGCGACGTTACTTGCACGGGTGATTGGAATAATAGGTTCAATTGACCAAGGCATGCTTGCTAAAGGACGTGATACATMapped 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|192296155|gb|FG989740.1|FG989740EST: GATATCTGGTCTCTTGGCTGCATCTTGGCAGAACTTTGTACTGGCAAT GTCCTCTTCCGAAATGATTCACCTGCATCATTACTTGCTCGGGTGATTGGG
genomic: GATATCTGGTCTCTTGGCTGCATCTTGGCAGAACTTTGTACTGGCAATgtaaggacca ... cattttgtagGTCCTCTTCCAAAATGATTCACCTGCAACATTACTTGCTCGGGTGATTGGG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tacatgattaattttctatttcttcttcagtggcactgaactaagcattttgtagGTCCTCTTCCAAAATGATTCACCTGCAACATTACTTGCTCGGGTGATTGGGATCATTGATCCAATTGATCAAAGTATGCTTGCAAAAGGACGCGACACAT
gattaat putative branch site (score: 3)
attaattttctatttc 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
agaatttctctgtattatggagagtgctttcttttctttgttaaatacatgattaattttctatttcttcttcagtggcactgaactaagcattttgtagGTCCTCTTCCAAAATGATTCACCTGCAACATTACTTGCTCGGGTGATTGGGATCATTGATCCAATTGATCAAAGTATGCTTGCAAAAGGACGCGACACAT
- - - -ctctgta
- - - - - - - - -tggagag
- - - - - - - - - - - - tgctttc
- - - - - - - - - - - - - - - - - - - - - - -tacatga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cactgaa