Sequence
atgc intronic sequence ATGC exonic sequence...gtgtaattcctgagctaatctataggttcagttggggtcattatatcaataggaccagtcaatttaacatatctgtatgttttccctatgatttctgcagATTTTCTTTAATCCTGAGATATATAGTAGTGACTTTACTACCCCTTTGCCAGTTGTAATAGACAAATGCATTCAGTCTGCGCCAATTGACACAAGGAGAT
Basic information
species | Glycine max |
transcript | GLYMA08G13780.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA08G13780.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os08g03440.1 (Oryza sativa), 3'ss of exon 6
-gtgtaattcctgagctaa-tctataggttcagttggggtcattatatcaataggaccagtcaatttaacata--tctgtatgttttccctatgatttctgcagATTTTCTTTAATCCTGAGATATATAGTAGTGACTTTACTACCCCTTTGCCAGTTGTAATAGACAAATGCATTCAGTCTGCGCCAATTGACACAAGGAGAT
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cattttattgacatttggactcttcaccttgaaatga---cattaaaaggagaaaaaca-tgaatttgatgtaatttactaaccttctactagcgcaaatgcagATCTTCTTCCATCCCGAGATTTACTCTGCCGACTTCTCCACTCCTCTACCTGAACTAATTGATAGCTGTGTTCAATCTGCGCCAATTGACACAAGGAGAG
upper sequence: GLYMA08G13780.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G305332_T01 (Zea mays), 3'ss of exon 1
-gtgtaattcctgagctaatctataggttcagttggg-gtcattatatcaataggaccagtcaatttaacatatctgtatgttttccctatgatttctgcagATTTTCTTTAATCCTGAGATATATAGTAGTGACTTTACTACCCCTTTGCCAGTTGTAATAGACAAATGCATTCAGTCTGCGCCAATTGACACAAGGAGAT
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tttgttagaataaacttttaacttgttttcagttggtcatgattttttttaagaagtcag--aatttggtgtgcgtctctaatcatctagcaacaaatgcagATCTTCTTCAATCCTGAGATTTACTCTGCCGACTTCTCCACTCCTTTACCTGAGTTGATTGATAACTGTGTTCAGTCTGCACCAATTGACACAAGGAGAG
upper sequence: GLYMA08G13780.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G136662_T01 (Zea mays), 3'ss of exon 5
gtgtaattcctgag-ctaatcta-taggttca-gttggggtcattatatcaataggaccagtcaatttaacatatctgtatgttttccctatgatttctgcagATTTTCTTTAATCCTGAGATATATAGTAGTGACTTTACTACCCCTTTGCCAGTTGTAATAGACAAATGCATTCAGTCTGCGCCAATTGACACAAGGAGAT
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-taacttgcttgggactaaaagactatgttgatgtacagttggtcatgttttttaggtcag--aattaggtgtgcatctctaatcatttaccaacaaatgcagATCTTCTTCAATCCTGAGATTTACTCTGCCGATTTCTCCACTCCTTTGCCCGAGTTGATTGACAACTGTGTTCAGTCTGCACCAATTGACACAAGGAGAG
upper sequence: GLYMA08G13780.1 (Glycine max), 3'ss of exon 5
lower sequence: AT1G13180.1 (Arabidopsis thaliana), 3'ss of exon 5
-----gtgtaattcctgagctaatctataggttcagttggggtcattatatcaataggaccagtcaatttaacatatctgta-tgttttccctatgatttctgcagATTTTCTTTAATCCTGAGATATATAGTAGTGACTTTACTACCCCTTTGCCAGTTGTAATAGACAAATGCATTCAGTCTGCGCCAATTGACACAAGGAGAT
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caagagagtaactggaaagtggaac-ataatttcctttattgttcttgcgttttt--gttctgctatt---accgatgagtaatgttgagattttgtgtgttacagGTGTTCTTTAATCCAGAGATATACAGCAATGACTTCACAACTACTTTACCAGCTGTGATAGACAAATGTATTCAGTCTGCACCAATTGACACACGAAGAG
upper sequence: GLYMA08G13780.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv01s0137g00280.t01 (Vitis vinifera), 3'ss of exon 5
-gtgtaattcctgagctaatctataggttcagttggggtcattata--tcaataggaccagtcaatttaacatatctgtatgttttccctatgatttctgcagATTTTCTTTAATCCTGAGATATATAGTAGTGACTTTACTACCCCTTTGCCAGTTGTAATAGACAAATGCATTCAGTCTGCGCCAATTGACACAAGGAGAT
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tgtttacttgtgcattgcatttcatctactagatgatgctttgataagtcttttaaaaaaaggaattt---gtttttgatgattaatctggctgattatgcagATTTTCTTCAATCCTGAGATCTACAGCAGCGATTTTGCAACCCCTTTACCAGCTGTAATAGACAAGTGTATTCAGTCTGCACCAATTGACACAAGAAGGGMapped 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|10238544|gb|BE807432.1|BE807432EST: GGGCACCATATTCATGTGATATTGGCTATGAGCGATTTCTTGGCCCTGAG ATTTTCTTTAATCCTGAGATATATAGTAGTGACTTTACTACCCCTTTGCCA
genomic: GGGCACCATATTCATGTGATATTGGCTATGAGCGATTTCTTGGCCCTGAGgtttgttcta ... atttctgcagATTTTCTTTAATCCTGAGATATATAGTAGTGACTTTACTACCCCTTTGCCA
EST:
gi|208073296|gb|GD869929.1|GD869929EST: CTTGGCCCTGAG ATTTTCTTTAATCCTGAGATATATAGTAGTGACTTTACTACCCCTTTGCCA
genomic: CTTGGCCCTGAGgtttgttcta ... atttctgcagATTTTCTTTAATCCTGAGATATATAGTAGTGACTTTACTACCCCTTTGCCA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tcaataggaccagtcaatttaacatatctgtatgttttccctatgatttctgcagATTTTCTTTAATCCTGAGATATATAGTAGTGACTTTACTACCCCTTTGCCAGTTGTAATAGACAAATGCATTCAGTCTGCGCCAATTGACACAAGGAGAT
atttaac putative branch site (score: 3)
tttctgc putative PPT
tcaatttaacatat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgtaattcctgagctaatctataggttcagttggggtcattatatcaataggaccagtcaatttaacatatctgtatgttttccctatgatttctgcagATTTTCTTTAATCCTGAGATATATAGTAGTGACTTTACTACCCCTTTGCCAGTTGTAATAGACAAATGCATTCAGTCTGCGCCAATTGACACAAGGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - -attcctg
- - - - - - - - - - - - - - - gttgggg
- - - - - - - - - - - - - - - - - - - - - - - - - - - ccagtca