Sequence
atgc intronic sequence ATGC exonic sequence...gagaatgaggactttcaagtttcataaataacctttgacctccatactttaatatttggttgcattaatctgtacttgtgatattatcgtattcacttagGTGGGCTTCTATAGCATCTCAACTACCTGGAAGAACAGACAATGAGATTAAGAACTTCTGGAACACCCATCTAAAGAAGCGTCTCCTTCGATCATGTCAT
Basic information
species | Glycine max |
transcript | GLYMA20G29730.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA20G29730.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv16s0050g00070.t01 (Vitis vinifera), 3'ss of exon 2
gagaatgaggactttcaagtttcataaa--taacctttgacctccatactttaatatttggttgcattaatctgtacttgtgatattatcgtat--tcacttagGTGGGCTTCTATAGCATCTCAACTACCTGGAAGAACAGACAATGAGATTAAGAACTTCTGGAACACCCATCTAAAGAAGCGTCTCCTTCGATCATGTCAT
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--ggaccctgttgatgcagtcccatcctcctatatttcgaggtcaata--tggaccttccgcattttttgttttcatatgtgaactgaatgtaagatatttcagGTGGGCTGCAATCGCTTCAAAAATACCTGGTAGAACGGACAATGAGATCAAGAACTTCTGGAACACCCATCTAAAGAAGCGCCTCCTGGGCAACCACCAAMapped 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|298188693|gb|HO035386.1|HO035386EST: AGTGAAGAAGAAAGTACAATCGTTCAACTTCATGGCATGCTTGGCAACAG GTGGGCTTCTATAGCATCTCAACTACCTGGAAGAACAGACAATGAGATTAA
genomic: AGTGAAGAAGAAAGTACAATCGTTCAACTTCATGGCATGCTTGGCAACAGgtaccacatt ... attcacttagGTGGGCTTCTATAGCATCTCAACTACCTGGAAGAACAGACAATGAGATTAA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.actttaatatttggttgcattaatctgtacttgtgatattatcgtattcacttagGTGGGCTTCTATAGCATCTCAACTACCTGGAAGAACAGACAATGAGATTAAGAACTTCTGGAACACCCATCTAAAGAAGCGTCTCCTTCGATCATGTCAT
cattaat putative branch site (score: 3)
ttcactt putative PPT
tgatattat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gagaatgaggactttcaagtttcataaataacctttgacctccatactttaatatttggttgcattaatctgtacttgtgatattatcgtattcacttagGTGGGCTTCTATAGCATCTCAACTACCTGGAAGAACAGACAATGAGATTAAGAACTTCTGGAACACCCATCTAAAGAAGCGTCTCCTTCGATCATGTCAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- gaatgag
- - - - - - - - - - - - - - - acctttg
- - - - - - - - - - - - - - - - - - -acctcca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgcatta
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -acttgtg