Sequence
atgc intronic sequence ATGC exonic sequence...cagttgagtgaattatgatttttgtttttcattgtgttactataaaatctatagttgcattgacatggataatttgtttttcctccatctgtgcatgcagGTTCCTTTATCCAATATATCCACTTATTTGTGTAGCTGCTTCAGCTGTCATTGAGAGCTTCCCTGATTTTTTCCGTAGCAAATATAATCCATACGATCGT
Basic information
species | Glycine max |
transcript | GLYMA12G35830.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA12G35830.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os01g11070.1 (Oryza sativa), 3'ss of exon 5
cagttgagtgaattatgatttttgtttttca--ttgtgttactataaaatctatagttgcattgac-atggataatttgtttttcctccatctgtgcatgcagGTTCCTTTATCCAATATATCCACTTATTTGTGTAGCTGCTTCAGCTGTCATTGAGAGCTTCCCTGATTTTTTCCGTAGCAAATATA-ATCCATACGATCGT
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---ctgatattctcctagttttttttttatggttaatgctactctacagatgagaactacaaaaactgaccattttttttctttcctctatctgtttatgcagGTTTCTTTATCCAATTTACCCATTGATATGTGTTGCAGCTGCAGCTGTTATTGACACCTTTCCAGATTTTTTCCATGACAAATATTCATCTGAACAGTCT-
upper sequence: GLYMA12G35830.1 (Glycine max), 3'ss of exon 2
lower sequence: AT1G16900.1 (Arabidopsis thaliana), 3'ss of exon 5
----------------------------------------------------cagttgagtgaattatgatttttgtttttcattgtgttactataaaatctatagttgcattgacatggataatttgtttttcctccatctg--tgcatgcagGTTCCTTTATCCAATATATCCACTTATTTGTGTAGCTGCTTCAGCTGTCATTGAGAGCTTCCCTGATTTTTTCCGTAGCAAATATAATCCATACGATCGT
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gtgattttctaagatctttcatcttgtaattttttgagcattcgtatggtggcttctatatcgttgaggaaaccagtttt--atgatacttttacaaaatc----acggtattca-acaaacaatgtttttgattgtcaattaattgactgcagGTTCCTTTATCCTATATACCCTCTTATTTGTGTCTCTGCTTCTGCTGTTATTGAGAACATCCCTGAGCTGTTCCGGGAAAAGTATAGCTCACGTGAAAGT
upper sequence: GLYMA12G35830.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv19s0014g01410.t01 (Vitis vinifera), 3'ss of exon 5
-cagttgagtgaattatgatttttgtttttcattgtgttactataaaatctatagttgcattgacatggataatttgtttt-tcctccatctgtgcatgcagGTTCCTTTATCCAATATATCCACTTATTTGTGTAGCTGCTTCAGCTGTCATTGAGAGCTTCCCTGATTTTTTCCGTAGCAAATATAATCCATACGATCGT
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gacgatgatcagaagat--cctttaatcccaagtatagggcactttattattgactgccagtgagcaaaatgactgataatatattcccattacccttgcagGTTCCTCTATCCAATATATCCACTTGTCTGTGTTGCTGCTTCAGCTGTCATTGAGAGCTTTCCAGATCTTTTTCGAGACCCATACTATCCCAATGCTAACMapped 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|192332079|gb|FK024567.1|FK024567EST: ATATATATTTGGCTGGGGTTTATGTCTTTGCAGCCACACAAAGAAGAAAG GTTCCTTTATCCAATATATCCACTTATTTGTGTAGCTGCTTCAGCTGTCAT
genomic: ATATATATTTGGCTGGGGTTTATGTCTTTGCAGCCACACAAAGAAGAAAGgtctggctaa ... gtgcatgcagGTTCCTTTATCCAATATATCCACTTATTTGTGTAGCTGCTTCAGCTGTCAT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aatctatagttgcattgacatggataatttgtttttcctccatctgtgcatgcagGTTCCTTTATCCAATATATCCACTTATTTGTGTAGCTGCTTCAGCTGTCATTGAGAGCTTCCCTGATTTTTTCCGTAGCAAATATAATCCATACGATCGT
cattgac putative branch site (score: 3)
tttttcctccatctgt putative PPT
ataatttgttttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
cagttgagtgaattatgatttttgtttttcattgtgttactataaaatctatagttgcattgacatggataatttgtttttcctccatctgtgcatgcagGTTCCTTTATCCAATATATCCACTTATTTGTGTAGCTGCTTCAGCTGTCATTGAGAGCTTCCCTGATTTTTTCCGTAGCAAATATAATCCATACGATCGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT
- - tgagtga
- - - - - - - - - - - - - - - - - - - - - - - - - - - -tgcattg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -catggat