Sequence
atgc intronic sequence ATGC exonic sequence...acaatgctcttgtcaggatgtcttcctttacatggtcattttttccctttccttgtgtgaattctcggttttactatgttcctttcatctctgacaacagTCCAATATGAGAATTCTGGTTACTGGAGGAGCTGGATTTATTGGCTCTCACCTAGTTGACAAATTGATGGAAAATGAAAAAAATGAG
Basic information
species | Glycine max |
transcript | GLYMA12G06980.3 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA12G06980.3 (Glycine max), 3'ss of exon 2
lower sequence: AT2G28760.1 (Arabidopsis thaliana), 3'ss of exon 2
acaatgct--cttgtcaggatgtcttcctttacatggtcattttttccctttccttgtgtgaattctcggttttactatgttcctttcatctctgacaacagTCCAATATGAGAATTCTGGTTACTGGAGGAGCTGGATTTATTGGCTCTCACCTAGTTGACAAATTGATGGAAAATGAAAAAAATGAG-------------
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acattcattacccgtggtgatg-caacaactatactaacacaaatcactatgatccatgt-agtggtagaaattgatttgttgaatgattttgaaaatacagTCGAATATGAGGATCTTGGTGACCGGAGGAGCTGGATTCATTGGTTCACATCTCGTTGATAAATTGATGCAAAACGAAAAGAATGAAGTAATCGTTGCGG
upper sequence: GLYMA12G06980.3 (Glycine max), 3'ss of exon 2
lower sequence: AT3G46440.1 (Arabidopsis thaliana), 3'ss of exon 2
acaatgctcttgtcagg--atgtcttcctttacatggtcattttttccctt-tccttgtgtgaattctcggttttactatgttcctttcatctctgacaacagTCCAATATGAGAATTCTGGTTACTGGAGGAGCTGGATTTATTGGCTCTCACCTAGTTGACAAATTGATGGAAAATGAAAAAAATGAG
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--tctgcatctggttgtctatgatttagtttgtatagtaaagttgtactatgttcttaataagatgtttaaagtgagtgc-ttttttttttttcattttgcagTCAAATATGAGGATTTTGATCTCAGGAGGAGCTGGATTCATTGGTTCTCACCTTGTTGATAAGCTGATGGAAAACGAAAAGAATGAG
upper sequence: GLYMA12G06980.3 (Glycine max), 3'ss of exon 2
lower sequence: Vv06s0004g04390.t01 (Vitis vinifera), 3'ss of exon 2
-------acaatgctcttgtcaggatgtcttcctttacatggtcattttttccctttccttgtgtgaattctcggttttactatgttcctttcatctctgacaacagTCCAATATGAGAATTCTGGTTACTGGAGGAGCTGGATTTATTGGCTCTCACCTAGTTGACAAATTGATGGAAAATGAAAAAAATGAG
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tccaatcatcacattcatgccaacacatcat--tgcactagatcattacttttattatctttaactaattcc----tacagta-attcctttcactcttgatggcagTCCAATATGAGAATATTGGTCACTGGAGGAGCTGGATTCATTGGTTCACATTTGGTGGACAAGCTGATGGAAAATGAAAAGAATGAGMapped 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|207697729|gb|GD681214.1|GD681214EST: CAAAGCAACCTCCCATGCCATCTCCCTTGCGGTTTTCCAAGTTCTTTCAG TCCAATATGAGAATTCTGGTTACTGGAGGAGCTGGATTTATTGGCTCTCAC
genomic: CAAAGCAACCTCCCATGCCATCTCCCTTGCGGTTTTCCAAGTTCTTTCAGgtgaactctc ... ctgacaacagTCCAATATGAGAATTCTGGTTACTGGAGGAGCTGGATTTATTGGCTCTCAC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cctttccttgtgtgaattctcggttttactatgttcctttcatctctgacaacagTCCAATATGAGAATTCTGGTTACTGGAGGAGCTGGATTTATTGGCTCTCACCTAGTTGACAAATTGATGGAAAATGAAAAAAATGAG
ctctgac putative branch site (score: 3)
tgttcctttcatctct CT-rich tract
ttttactat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
acaatgctcttgtcaggatgtcttcctttacatggtcattttttccctttccttgtgtgaattctcggttttactatgttcctttcatctctgacaacagTCCAATATGAGAATTCTGGTTACTGGAGGAGCTGGATTTATTGGCTCTCACCTAGTTGACAAATTGATGGAAAATGAAAAAAATGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA