Sequence
atgc intronic sequence ATGC exonic sequence...accatctatgttgatgattatttgatttatttctttttgtatttccaccttagattagaaatatatcaccatctgatgttggacatggatctgttaacagACAGGTCCTACAGTTTACCGTAGTAGAACTGTCTTTGATGATGCAACTCCAGAGTTGGTGAGGGATTTCTTCTGGGATGATGACTTTCGTCCTAAATGGG
Basic information
species | Glycine max |
transcript | GLYMA11G01030.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA11G01030.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os07g08760.2 (Oryza sativa), 3'ss of exon 1
accatctatgttgatgattatttgatttatttctttttgtatttccaccttagattagaaatatatcaccatctgatgt-tggacatggatctgttaacagACAGGTCCTACAGTTTACCGTAGTAGAACTGTCTTTGATGATGCAACTCCAGAGTTGGTGAGGGATTTCTTCTGGGATGATGACTTTCGTCCTAAATGGG
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atttcctgtcttttcaatgaatctacgt-ttgatgtgaccaaatcaatagcatataggttatagtgcaacatctaatggactgatcttcctttgcttgtagGTGGGACCTATCATGTACTGTAGTCGCACTATTTTTGAGGATGCTACTCCTGAGCTTGTTAGAGATTTCTTCTGGGATGATGAATTTCGTCTGAAGTGGG
upper sequence: GLYMA11G01030.1 (Glycine max), 3'ss of exon 2
lower sequence: AT3G23080.2 (Arabidopsis thaliana), 3'ss of exon 3
accatctatgttgatgattatttgatttatttctttttgtatttccaccttagattagaaatatatcaccatctgat-gttggacatggatctgttaacagACAGGTCCTACAGTTTACCGTAGTAGAACTGTCTTTGATGATGCAACTCCAGAGTTGGTGAGGGATTTCTTCTGGGATGATGACTTTCGTCCTAAATGGG
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----------------------------gtaaatctaagttttaaagactctaactttatatgacttagttcctgaaaggtggttatg--ttggttgtcagATAGGTCCTGTTGTTTATCGTAGTCGAACTGTTTTTGAGGATGTAACACCAGACATTGTTAGGGATTTCTTCTGGGACGATGAGTTTCGACCTAAATGGG
upper sequence: GLYMA11G01030.1 (Glycine max), 3'ss of exon 2
lower sequence: AT4G14500.1 (Arabidopsis thaliana), 3'ss of exon 2
----accatctatgttga--tgattatttgatttatttctttttgtatttccaccttagattagaaatatatcaccatctgatgttggacatggatctgttaacagACAGGTCCTACAGTTTACCGTAGTAGAACTGTCTTTGATGATGCAACTCCAGAGTTGGTGAGGGATTTCTTCTGGGATGATGACTTTCGTCCTAAATGGG
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gtgttcttgctataatgaaatggggaattc-ttaaatactagatg-atagaaacatttgatcaaattgtgtttgtagcctgata--ggtcgt--attgtttatcagACAGGTCCTGTTATTTATCGCAGCCGGACTGTGTTTGAGGATGCAACTCCAGATATTGTTAGGGATTTCTTCTGGGATGATGAGTTTCGACCTAAATGGG
upper sequence: GLYMA11G01030.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv05s0020g04870.t01 (Vitis vinifera), 3'ss of exon 2
accatctatgttgatgattatttgatttatttctttttgtatttccaccttagattagaaatata--tcaccatctgatgttggacatggatctgttaacagACAGGTCCTACAGTTTACCGTAGTAGAACTGTCTTTGATGATGCAACTCCAGAGTTGGTGAGGGATTTCTTCTGGGATGATGACTTTCGTCCTAAATGGG
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-gtgtgtgtgtgtgtgtgtgtgtattgtgcataattttcaattctcattgtagactgaagataaaattcattagtaaccgataatggtgtttct-ttatcagAATGGCCCCACTGTGTATCGTAGCAGAACTGTATTTGAGGATGCAACTCCCGAGGTGGTTAGAGATTTCTTCTGGGATGATGAGTTTAGACCTAAATGGGMapped 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|254324610|gb|GR834035.1|GR834035EST: AAAGGTCAACACCAAACATGCAATACAAAGCTTGGCGTTACGATCCTGAG ACAGGTCCTACAGTTTACCGTAGTAGAACTGTCTTTGATGATGCAACTCCA
genomic: AAAGGTCAACACCAAACATGCAATACAAAGCTTGGCGTTACGATCCTGAGgttcaatttt ... ctgttaacagACAGGTCCTACAGTTTACCGTAGTAGAACTGTCTTTGATGATGCAACTCCA
EST:
gi|192297133|gb|FG988229.1|FG988229EST: AAAGGTCAACACCAAACATGCAATACAAAGCTTGGCGTTACGATCCTGAG ACAGGTCCTACAGTTTACCGTAGTAGAACTGTCTTTGATGATGCAACTCCA
genomic: AAAGGTCAACACCAAACATGCAATACAAAGCTTGGCGTTACGATCCTGAGgttcaatttt ... ctgttaacagACAGGTCCTACAGTTTACCGTAGTAGAACTGTCTTTGATGATGCAACTCCA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.caccttagattagaaatatatcaccatctgatgttggacatggatctgttaacagACAGGTCCTACAGTTTACCGTAGTAGAACTGTCTTTGATGATGCAACTCCAGAGTTGGTGAGGGATTTCTTCTGGGATGATGACTTTCGTCCTAAATGGG
atctgat putative branch site (score: 4)
tagattagaaatatat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
accatctatgttgatgattatttgatttatttctttttgtatttccaccttagattagaaatatatcaccatctgatgttggacatggatctgttaacagACAGGTCCTACAGTTTACCGTAGTAGAACTGTCTTTGATGATGCAACTCCAGAGTTGGTGAGGGATTTCTTCTGGGATGATGACTTTCGTCCTAAATGGG
-ccatcta
- - - - -gttgatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tcaccat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gatgttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -catggat