Sequence
atgc intronic sequence ATGC exonic sequence...tacatttcatcaacatagaattatttactaataagtattaagttctattttctggacttgcactgtatctcataagatcttgattggtttcttactgacaGGTGGGCTGGTCAGGCTTTGTTTGGAACTCTTACACCAGATATAATTGTTCTCACACTCCTATACAGCATAGCTGG
Basic information
species | Glycine max |
transcript | GLYMA18G43310.1 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA18G43310.1 (Glycine max), 3'ss of exon 9
lower sequence: GRMZM2G162672_T02 (Zea mays), 3'ss of exon 9
-tacatttcatcaacatagaattatttac-taataagtattaagttctattttctggacttgcactgtatct-cataagatcttgattggtttcttactgacaGGTGGGCTGGTCAGGCTTTGTTTGGAACTCTTACACCAGATATAATTGTTCTCACACTCCTATACAGCATAGCTGG-
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gtatgatcta-cgttgccgatttctcttcatgttgcgcaaacaattttggttttgatgctaccatcatatatgcactaga-cttaaagggttttttttttgcagGTGGGCTGGCCAGGCGTTATTTGGAACTCTTACACCAGATATCATTGTCTTGACTACTTTGTACAGCATAGCTGGG
upper sequence: GLYMA18G43310.1 (Glycine max), 3'ss of exon 9
lower sequence: AT3G51820.1 (Arabidopsis thaliana), 3'ss of exon 9
tacatttcatcaacatagaattatttactaataagtattaagttctattttctggacttgcactgtatctcataagatc-ttgattggtttctt-actgacaGGTGGGCTGGTCAGGCTTTGTTTGGAACTCTTACACCAGATATAATTGTTCTCACACTCCTATACAGCATAGCTGG-
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--------------gtaagatatctcgt------gtatcaa----taatatatggcgttgttct-catctcattgatttgtttcttgctcacttgactgatagGTGGGCTGGCCAAGCATTGTTTGGCACTCTTACGCCAGATGTTGTTGTTCTAACACTCTTGTACAGCATAGCTGGG
upper sequence: GLYMA18G43310.1 (Glycine max), 3'ss of exon 9
lower sequence: Vv08s0105g00590.t01 (Vitis vinifera), 3'ss of exon 9
tacatttcatcaacatagaattatttactaataagtattaagttctattttctggacttgcactgtatctcataagatctt---gatt-ggtttcttactgacaGGTGGGCTGGTCAGGCTTTGTTTGGAACTCTTACACCAGATATAATTGTTCTCACACTCCTATACAGCATAGCTGG-
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---attttctct-tatagttcttattaatgctaataattagcatgaaatttgtttggtt-catcgtgttgagtaactttttttggattcaaatgtttattgatagGTGGGCTGGTCAAGCTTTGTTTGGGACTCTTAATCCTGATATAATTGTTCTCACCCTCTTGTACAGCATAGCTGGGMapped 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|16276277|gb|BI941773.1|BI941773EST: TGGATGGATTGGAAACTTTGCCCTTGGAGCAAGTTACATTAGCTTGCCAT GGTGGGCTGGTCAGGCTTTGTTTGGAACTCTTACACCAGATATAATTGTTC
genomic: TGGATGGATTGGAAACTTTGCCCTTGGAGCAAGTTACATTAGCTTGCCATggtgtggtat ... cttactgacaGGTGGGCTGGTCAGGCTTTGTTTGGAACTCTTACACCAGATATAATTGTTC
EST:
gi|16349016|gb|BI974611.1|BI974611EST: TGGATGGATTGGAAACTTTGCCCTTGGAGCAAGTTACATTAGCTTGCCAT GGTGGGCTGGTCAGGCTTTGTTTGGAACTCTTACACCAGATATAATTGTTC
genomic: TGGATGGATTGGAAACTTTGCCCTTGGAGCAAGTTACATTAGCTTGCCATggtgtggtat ... cttactgacaGGTGGGCTGGTCAGGCTTTGTTTGGAACTCTTACACCAGATATAATTGTTC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tattttctggacttgcactgtatctcataagatcttgattggtttcttactgacaGGTGGGCTGGTCAGGCTTTGTTTGGAACTCTTACACCAGATATAATTGTTCTCACACTCCTATACAGCATAGCTGG
ttcttac putative branch site (score: 2)
tttcttact CT-rich tract
ataagat 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
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tacatttcatcaacatagaattatttactaataagtattaagttctattttctggacttgcactgtatctcataagatcttgattggtttcttactgacaGGTGGGCTGGTCAGGCTTTGTTTGGAACTCTTACACCAGATATAATTGTTCTCACACTCCTATACAGCATAGCTGG
- - - -catcaac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - cttgcac