Sequence
atgc intronic sequence ATGC exonic sequence...agtccttaaaaggcccccagatataattgaatcatcaacttctctgttagtaaattgatatttaaatgatgacaatcactgtcaactttgtttcatgtagGCTACACCGGAGTTGGAGTATGGAAGGATGAACATTGGAAGTCGACCAGCAAAGAGAAAGCCTAGTGGAGGCATTGAAACACTGCGTGCAATACCTTGGA
Basic information
species | Glycine max |
transcript | GLYMA13G34560.1 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA13G34560.1 (Glycine max), 3'ss of exon 9
lower sequence: LOC_Os01g55350.1 (Oryza sativa), 3'ss of exon 10
----agtccttaaaaggcccccagatataattgaatcatcaacttctctgttagtaaattgatatttaaatgatgacaatcactgtcaactttgtttcatgtagGCTACACCGGAGTTGGAGTATGGAAGGATGAACATTGGAAGTCGACCAGCAAAGAGAAAGCCTAGTGGAGGCATTGAAACACTGCGTGCAATACCTTGGA
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cttcactctgtagtcaccttcataaatttgttattttgctaatgattattctaatggtctg---tataaataatctcaatt-ttgcttctttgctgtcaaatagGCAACACCAGAGTTGGAATATGGTAGGATGAATATTGGAAGTAGGCCATCAAAACGAAAGCCTAGTGGAGGCATTGAATCACTTCGTGCAATTCCTTGGA
upper sequence: GLYMA13G34560.1 (Glycine max), 3'ss of exon 9
lower sequence: LOC_Os09g14670.1 (Oryza sativa), 3'ss of exon 8
----agtccttaaaaggcccccagatataatt---gaatcatcaacttctctgttagtaaattgatatttaaatgatgacaatcactgtcaactttgtttcatgtagGCTACACCGGAGTTGGAGTATGGAAGGATGAACATTGGAAGTCGACCAGCAAAGAGAAAGCCTAGTGGAGGCATTGAAACACTGCGTGCAATACCTTGGA
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atggaacagtgtaaactagactaaagataaccttggagccattgaattagac-ttattagact--ttttcaaa--attataatttgtgttgtttgtggttg--gcagGCAACACCTGAGACAGAGTATGGAAGGATGAACATAGGAAGCAGGCCATCCAAGAGGAAGCCGAGTGGAGGCATTGAATCACTCCGTGCGATCCCATGGA
upper sequence: GLYMA13G34560.1 (Glycine max), 3'ss of exon 9
lower sequence: LOC_Os08g27840.1 (Oryza sativa), 3'ss of exon 8
----------------------------agtccttaaaaggccccca-gatataattgaatcatcaacttctctgttagtaaattgatatttaaatgatgacaatcactgtcaactttgtt--tcatg----tagGCTACACCGGAGTTGGAGTATGGAAGGATGAACATTGGAAGTCGACCAGCAAAGAGAAAGCCTAGTGGAGGCATTGAAACACTGCGTGCAATACCTTGGA
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gtgagtgttttgtttcttcataatcatcagacttggaacatttcatataatgcatttaaggcacttagctaaacattgttcatttcaggcaaaacctttgtaaattaattttctttacatttttcatgaaatcagGCAACACCAGAGATGGAGTATGGAAGGATGAATATAGGAAGCAGGCCATCCAAGAGAAAGCCGAGTGGTGGCATCGAGTCACTCCGTGCCATCCCATGGA
upper sequence: GLYMA13G34560.1 (Glycine max), 3'ss of exon 9
lower sequence: Vv19s0014g01390.t01 (Vitis vinifera), 3'ss of exon 8
agtccttaaaaggcccccagatataattgaatcatcaacttctctgttagtaaattgatatttaaatgatgacaatcactgtcaactttgtttcatgtagGCTACACCGGAGTTGGAGTATGGAAGGATGAACATTGGAAGTCGACCAGCAAAGAGAAAGCCTAGTGGAGGCATTGAAACACTGCGTGCAATACCTTGGA
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-----gtaagtatcctgca-atatctttgactc-----tatttaaaccaagtaaaggctgttaccattttaatgatcgtcttgtgctatgatt---gtagGCTACACCAGAGCTGGAGTATGGTAGAATGAACATTGGTAGCCGTCCATCAAAGCGTAAGCCAAGTGGGGGAATTGAATCGCTCCGTGCAATCCCATGGAMapped 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|10236260|gb|BE805148.1|BE805148EST: ACCGTTCCATTGTATTCAAGGAACCACGCTATGTTGAGTATTTCCGCCTG GCTACACCGGAGTTGGAGTATGGAACGATGAACATTGTAAGT
genomic: ACCGTTCCATTGTATTCAAGGAACCACGCTTTGTTGAGTATTTCCGCCTGgtaaggacca ... tttcatgtagGCTACACCGGAGTTGGAGTATGGAAGGATGAACATTGGAAGT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gttagtaaattgatatttaaatgatgacaatcactgtcaactttgtttcatgtagGCTACACCGGAGTTGGAGTATGGAAGGATGAACATTGGAAGTCGACCAGCAAAGAGAAAGCCTAGTGGAGGCATTGAAACACTGCGTGCAATACCTTGGA
aattgat putative branch site (score: 4)
ctttgtttc putative PPT
taaattgatatttaaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
agtccttaaaaggcccccagatataattgaatcatcaacttctctgttagtaaattgatatttaaatgatgacaatcactgtcaactttgtttcatgtagGCTACACCGGAGTTGGAGTATGGAAGGATGAACATTGGAAGTCGACCAGCAAAGAGAAAGCCTAGTGGAGGCATTGAAACACTGCGTGCAATACCTTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - ccccaga
- - - - - - - - - - - - - - - - catcaac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - caatcac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgtcaac