Sequence
atgc intronic sequence ATGC exonic sequence...ggagtcttgttgtgtttaagagatgttatatggtttactgaaagatgagtgaacaacatacgtgtgtgttaatgcatgagtatttgaaattggggtgtagGTTTTCTCATTTAAGCTTCGTGGAGCTTATAATATGATGGCAAAGCTTCCGACGGAATTGTTGGAAAAGGGGGTTATCTGCTCGTCTGCTGGGAACCATG
Basic information
species | Glycine max |
transcript | GLYMA13G21230.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA13G21230.1 (Glycine max), 3'ss of exon 1
lower sequence: AT3G10050.1 (Arabidopsis thaliana), 3'ss of exon 1
--------------------------ggagtcttgttg-tgtttaagagatgttatatggtttactgaaagatgagtgaacaacatacgtgt-gtgttaatgcatgagtatttgaaattggggtgtagGTTTTCTCATTTAAGCTTCGTGGAGCTTATAATATGATGGCAAAGCTTCCGACGGAATTGTTGGAAAAGGGGGTTATCTGCTCGTCTGCTGGGAACCATG
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gtaagtaatgaagcttctccctttatacattttggttgattttttaggtgaattatgtatggaattgagactacatctgaggttttatgtgttgttgtactgagtg-gtgactggaattgt--tttagGTATTCTCGTTTAAGCTTCGTGGAGCTTACAATATGATGGTGAAACTTCCAGCAGATCAATTGGCAAAAGGAGTTATCTGCTCTTCAGCTGGAAACCATG
upper sequence: GLYMA13G21230.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv08s0007g04310.t01 (Vitis vinifera), 3'ss of exon 1
-ggagtcttgttgtgtttaagagatgttatatggttt--actgaaagatgagtgaacaacatacgtgtgtgttaatgcatgagtatttgaaattggggtgtagGTTTTCTCATTTAAGCTTCGTGGAGCTTATAATATGATGGCAAAGCTTCCGACGGAATTGTTGGAAAAGGGGGTTATCTGCTCGTCTGCTGGGAACCATG
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gacacacgtttcttttttggttggtttagaagagtttgaattggaaattggtgtcttaggtcaacttagtcttgat-cattatga--tggatttggtttgtagGTATTTTCCTTCAAGCTCCGTGGTGCTTATAATATGATGGCAAAAATTCCAAAAGAACAGTTGGAAAGAGGGGTTATCTGCTCTTCAGCAGGAAATCATGMapped 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|213600342|gb|DB955882.1|DB955882EST: CTGCGAGACTCGGGGTTAAGGTTTGGCTCAAGAGAGAGGATTTGCAACCC GTTTTCTCATTTAAGCTTCGTGGAGCTTATAATATGATGGCAAAGCTTCCG
genomic: CTGCGAGACTCGGGGTTAAGGTTTGGCTCAAGAGAGAGGATTTGCAACCCgtaagttcgt ... tggggtgtagGTTTTCTCATTTAAGCTTCGTGGAGCTTATAATATGATGGCAAAGCTTCCG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgagtgaacaacatacgtgtgtgttaatgcatgagtatttgaaattggggtgtagGTTTTCTCATTTAAGCTTCGTGGAGCTTATAATATGATGGCAAAGCTTCCGACGGAATTGTTGGAAAAGGGGGTTATCTGCTCGTCTGCTGGGAACCATG
tgttaat putative branch site (score: 3)
tatttgaaatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ggagtcttgttgtgtttaagagatgttatatggtttactgaaagatgagtgaacaacatacgtgtgtgttaatgcatgagtatttgaaattggggtgtagGTTTTCTCATTTAAGCTTCGTGGAGCTTATAATATGATGGCAAAGCTTCCGACGGAATTGTTGGAAAAGGGGGTTATCTGCTCGTCTGCTGGGAACCATG
- - -cttgttg
- - - - - - - - - - - - - - - - - - -ctgaaag
- - - - - - - - - - - - - - - - - - - - - - -tgagtga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gtgtgtg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgcatga