Sequence
atgc intronic sequence ATGC exonic sequence...cgctactgtgagacgcagttaaatcatgtgtttatgcactgatttttttatgtatgcgtgtagtggaagatttgatgttgagtttttgcttggtgttcagATTCTAGTCCTATGCTCAGAAATGGAGAGACTGGAGATTGGATTGGAACATTTGAAGGGCACAAAGGTGCTGTGTGGAGTTGCTGCTTGGATACCAGTGC
Basic information
species | Glycine max |
transcript | GLYMA17G12770.3 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA17G12770.2 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os02g11060.1 (Oryza sativa), 3'ss of exon 1
-cgctactgtgagacgcagttaaatcatgtgtttatgcactgatttttttatgtatgcgtgtagtggaagat--ttgatgttgagtttttgcttggtgttcagATTCTAGTCCTATGCTCAGAAATGGAGAGACTGGAGATTGGATTGGAACATTTGAAGGGCACAAAGGTGCTGTGTGGAGTTGCTGCTTGGATACCAGTGC
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gttagaatcttccatttatatgcttcacttcttgttggattaattcttctac-tctttatgtcgttgatattgattgatatta--tctttcatttctttccagACTCAAACCCAATGATTCGCAATGGTGATACTGGAGATTGGATTGGGACCTTTGAAGGTCACAAAGGTGCTGTTTGGAGCTGTTGCCTTGACACCAATGC
upper sequence: GLYMA17G12770.2 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os06g39760.1 (Oryza sativa), 3'ss of exon 1
cgctactgtgagacgcagttaaatcatgtgtttatgcactgatttttttatgtatgcgtgtagtggaagatttgatgttg----agtttttgcttggtgttcagATTCTAGTCCTATGCTCAGAAATGGAGAGACTGGAGATTGGATTGGAACATTTGAAGGGCACAAAGGTGCTGTGTGGAGTTGCTGCTTGGATACCAGTGC
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tatta-tacaaaaactaatttgggtataaatcta---attgttttttagattgatgtttattatacaaacactaatttggtaatattgtatgttttgatcttagATGGGAATCCAATGCTTCGTAATGGTGAGACTGGAGATTGGATTGGGACTTTCCAAGGTCATAAAGGGGCTGTCTGGAGCTGCTGCCTAGACACAAATGC
upper sequence: GLYMA17G12770.2 (Glycine max), 3'ss of exon 1
lower sequence: Vv11s0016g04710.t01 (Vitis vinifera), 3'ss of exon 1
----------------------------------------------------------------------------------------cgctactgtgagacgcagttaaatcatgtgtttatgcactgatttttttatgtatgcgt-gtagtggaagatttgatgttgagtttttgct---------tggtgttcagATTCTAGTCCTATGCTCAGAAATGGAGAGACTGGAGATTGGATTGGAACATTTGAAGGGCACAAAGGTGCTGTGTGGAGTTGCTGCTTGGATACCAGTGC
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gtatgtgtgcatttcttatcaatgtcaattttctatgtgaagggaaaaattgtgaaatttgatatgtatttgcctcattttttgtttacga-attgatggctttggttgattgttttgttgatattggagtcaaattattgctggattatattacattgctctttattgggtatgcgatgttcatttatgatgttcagATTCTAGCCCCATGCTTAGAAATGGAGAGACTGGAGATTGGATTGGAACATTTGAAGGACACAAGGGTGCAGTATGGAGTTGCTGCTTGGATACGAATGC
upper sequence: GLYMA17G12770.2 (Glycine max), 3'ss of exon 1
lower sequence: PP1S25_22V6.1 (Physcomitrella patens), 3'ss of exon 1
--cgctactgtgagacgcagttaaatc-atgtgtttatgcactgattttt-ttatgtatgcgtgtagtggaagat-ttgatgttgagtttttgcttggtgttcagATTCTAGTCCTATGCTCAGAAATGGAGAGACTGGAGATTGGATTGGAACATTTGAAGGGCACAAAGGTGCTGTGTGGAGTTGCTGCTTGGATACCAGTGC
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tatcctctttctagaagaaatcagatttatggatgtagttgttgatttgtgtcatggtttcctttaattaaatttattcgttctgggcgattt-----tgtgcagATGGGAAGCCAATGCTCCGAAATGGTGAGACAGGTGATTGGATTGGAACTTTTGACGGCCACAAAGGAGCCGTATGGGCAGCATGTCTCGACACTCCAGC
upper sequence: GLYMA17G12770.2 (Glycine max), 3'ss of exon 1
lower sequence: EFJ21886 (Selaginella moellendorffii), 3'ss of exon 1
cgctactgtgagacgcagttaaatcatgtgtttatgcactgatttttttatgtatgcgtgtagtggaagatttgatgttgagtttttgcttggtgttcagATTCTAGTCCTATGCTCAGAAATGGAGAGACTGGAGATTGGATTGGAACATTTGAAGGGCACAAAGGTGCTGTGTGGAGTTGCTGCTTGGATACCAGTGC
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-------------------------------------------------gtagatctttctctcgcgatctcttggtttcaattgcggct---gccacagATGGAAAGCCAATGCTAAGAAATGGGGGCACTGGCGATTGGATTGGAACGTTCGAGGGACACAAGGGTGCTGTGTGGGCTGCCTGCCTCGACACACCCGCMapped 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|15815353|gb|BI787628.1|BI787628EST: CTACAGTCCCGTTACGCCCGATGGGTTTTTCCTCATCAGTGCCAGCAAGG ATTCTAGTCCTATGCTCAGAAATGGAGAGACTGGAGATTGGATTGGAACAT
genomic: CTACAGTCCCGTTACGCCCGATGGGTTTTTCCTCATCAGTGCCAGCAAGGgtaactttta ... tggtgttcagATTCTAGTCCTATGCTCAGAAATGGAGAGACTGGAGATTGGATTGGAACAT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttttatgtatgcgtgtagtggaagatttgatgttgagtttttgcttggtgttcagATTCTAGTCCTATGCTCAGAAATGGAGAGACTGGAGATTGGATTGGAACATTTGAAGGGCACAAAGGTGCTGTGTGGAGTTGCTGCTTGGATACCAGTGC
atttgat putative branch site (score: 5)
tttttgctt putative PPT
aagattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
cgctactgtgagacgcagttaaatcatgtgtttatgcactgatttttttatgtatgcgtgtagtggaagatttgatgttgagtttttgcttggtgttcagATTCTAGTCCTATGCTCAGAAATGGAGAGACTGGAGATTGGATTGGAACATTTGAAGGGCACAAAGGTGCTGTGTGGAGTTGCTGCTTGGATACCAGTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT