Sequence
atgc intronic sequence ATGC exonic sequence...tgaaatatgcagttagatgattcattttgcatatttgatgagtgttagagaacatttacatgtttcatatgcatcatgatataccattatttgtgtgcagGCAGAAAAGGAGCCAATTTTGAGTAGCTTCTTCTATGCCACTATTCTGTCTCATGATTGCTTGGAGCAAGCATTGGCTTTTGCTCTTGCCAACCGACTCC
Basic information
species | Glycine max |
transcript | GLYMA16G22630.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA16G22630.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G048740_T03 (Zea mays), 3'ss of exon 1
tgaaatatgcagttagatgattcattttgcatatttgatg-agtgttagaga-acatttacatgtt--tcatatgcatcatgatataccattatttgtgt---gcagGCAGAAAAGGAGCCAATTTTGAGTAGCTTCTTCTATGCCACTATTCTGTCTCATGATTGCTTGGAGCAAGCATTGGCTTTTGCTCTTGCCAACCGACTCC
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------gtctcacctctttatgcatggt-catgtttgtcatagttttactgttatattggtaaactgatggccggcagtgtgatggactgatggtcatgctccacagGCAGAAAAGGAACCTATTTTGAGTAGCTTCTTGTATGCCAGTGTGCTGTCTCATGATTGCCTAGAGCGTGCATTGAGCTTCGTCCTTGCAAATAGGCTTG
upper sequence: GLYMA16G22630.1 (Glycine max), 3'ss of exon 2
lower sequence: AT2G17640.1 (Arabidopsis thaliana), 3'ss of exon 1
tgaaatatgcagttagatgattcattttgcatatttgatgagtgttagagaacattt----acatgtttcatatgcatcatgatataccattatttgtgtg-cagGCAGAAAAGGAGCCAATTTTGAGTAGCTTCTTCTATGCCACTATTCTGTCTCATGATTGCTTGGAGCAAGCATTGGCTTTTGCTCTTGCCAACCGACTCC
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--agccttgatatttaat--ccaaccaaacataggacaagaaagtttgagtacagtttgtgaaatgttgaatct-tataatggtgaatcttgttgtgcgtttcagGCAGAGAAAGAGCCTATTTTGAGTAGCTTCTTGTATGCTGGTATCTTAGCACATGATTGTTTAGAGCAAGCTTTAGGGTTTGTTCTAGCCAACCGTCTCC
upper sequence: GLYMA16G22630.1 (Glycine max), 3'ss of exon 2
lower sequence: AT4G35640.1 (Arabidopsis thaliana), 3'ss of exon 1
tgaaatatgcagt-tagatgattcattttgcatatttgatgagtgttagagaaca---tttacatgt-ttcatatgcatc--atgat--ataccattatttgtgt-gcagGCAGAAAAGGAGCCAATTTTGAGTAGCTTCTTCTATGCCACTATTCTGTCTCATGATTGCTTGGAGCAAGCATTGGCTTTTGCTCTTGCCAACCGACTCC
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----------agcgtcaatttttcattaactacacgaaggacaagttaaggaacagagtttgtgtgtgtttatgttcctttaatggtgaatattgttgtgtgttttacagGCAGAAGAGGAGCCGGTTTTGAGTAGCTTCTTGTATGCTAGTATCTTGTCGCATGACTGTTTAGAGCAAGCATTGAGTTTTGTTCTAGCTAACCGTCTCC
upper sequence: GLYMA16G22630.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv04s0210g00190.t01 (Vitis vinifera), 3'ss of exon 1
tgaaatatgcagttagatgattcattttgcatatttgatgagtgttagagaacatttacatgtttcatat--gcatcatgata--taccattatttgtgtgcagGCAGAAAAGGAGCCAATTTTGAGTAGCTTCTTCTATGCCACTATTCTGTCTCATGATTGCTTGGAGCAAGCATTGGCTTTTGCTCTTGCCAACCGACTCC
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--ggtggtggtgtcggggtgttgggctggaagaga-atttcgtttggaagaataatttgttatctgatcttgacatatttgttgctaccatgcaatgttt-cagGCGGAGAAGGAGCCAATTCTAAGTAGCTTCTTGTATGCCAGTATTTTGTCCCATGACTGTTTAGAGCAAGCATTGGCATTTGTTCTTGCAAATCGACTTCMapped 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|254348430|gb|GR852109.1|GR852109EST: ATTGTCTTGATCCTATTTGGGATGCTGTCAGAGAAGAAGCCAAGTTAGAG GCAGAAAAGGAGCCAATTTTGAGTAGCTTCTTCTATGCCACTATTCTGTCT
genomic: ATTGTCTTGATCCTATTTGGGATGCTGTCAGAGAAGAAGCCAAGTTAGAGgtacccataa ... ttgtgtgcagGCAGAAAAGGAGCCAATTTTGAGTAGCTTCTTCTATGCCACTATTCTGTCT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tagagaacatttacatgtttcatatgcatcatgatataccattatttgtgtgcagGCAGAAAAGGAGCCAATTTTGAGTAGCTTCTTCTATGCCACTATTCTGTCTCATGATTGCTTGGAGCAAGCATTGGCTTTTGCTCTTGCCAACCGACTCC
atataccattattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tgaaatatgcagttagatgattcattttgcatatttgatgagtgttagagaacatttacatgtttcatatgcatcatgatataccattatttgtgtgcagGCAGAAAAGGAGCCAATTTTGAGTAGCTTCTTCTATGCCACTATTCTGTCTCATGATTGCTTGGAGCAAGCATTGGCTTTTGCTCTTGCCAACCGACTCC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - -tgcagtt
- - - - - - - - - - - - - -tgcatat
- - - - - - - - - - - - - - - - - - - tgagtgt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - tacatgt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tatgcat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - catgata