Sequence
atgc intronic sequence ATGC exonic sequence...ttctttaaaagcttgacaagatggactttcaactttcaagttcattctggttatctttactaagcacggcattttgatttttctgcaataaaatccccagGGTCAATACAAGTCAACATTGGTTTGTCCAGTATGTGGCAAAATTTCAATTACTTTCGATCCATTCATGTACTTATCATTACCACTGCCTTCCACTGTCA
Basic information
species | Glycine max |
transcript | GLYMA20G36020.1 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA20G36020.1 (Glycine max), 3'ss of exon 9
lower sequence: GRMZM2G009655_T01 (Zea mays), 3'ss of exon 8
ttctttaaaagcttgacaagatggact-ttcaactttcaagttcattctggttatctttactaagcacggcattttgatttttctgc-----aataaaatccccagGGTCAATACAAGTCAACATTGGTTTGTCCAGTATGTGGCAAAATTTCAATTACTTTCGATCCATTCATGTACTTATCATTACCACTGCCTTCCACTGTCA
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---actatcaatttgataatctggcctatatcaattataattccacctgtgttatgtgtgtaaagcac---actttaatctatcggcttgttggttcatgttgcagGGTCAATACAAGTCCACATTGGTGTGCCCAGTTTGTAACAAAATCTCTGTTACCTTTGATCCATTTATGTATTTGTCGCTACCATTGCCATCAACAGTTT
upper sequence: GLYMA20G36020.1 (Glycine max), 3'ss of exon 9
lower sequence: AT4G10570.1 (Arabidopsis thaliana), 3'ss of exon 8
-----------------------------------ttctttaaaagcttgacaagatggactttcaactttcaagttcattctggttatctttactaagcacggcattttgatttttctgcaata---aaatccc--cagGGTCAATACAAGTCAACATTGGTTTGTCCAGTATGTGGCAAAATTTCAATTACTTTCGATCCATTCATGTACTTATCATTACCACTGCCTTCCACTGTCA
| | || || | | | | || | ||| | ||||| | | | ||| || | | || || || | || | | ||||| |||||||||||||| ||||||||||||| || || ||||| ||||| ||||| ||||| ||||||||||| || |||| |||| || || | |
gtaagtctctctcttaccgtttcctaatcgcttcttccattgaatgttcatctggttgtagttttt-tatacaagt--actacaagtttctctattttattttcccgaccagttcttatgaggtgttcaacttctttcagGGCCAATACAAGTCAACTCTGGTTTGTCCAGTTTGCGGAAAAATATCAATCACTTTTGATCCCTTCATGTACTTGTCTGTACCTTTGCCATCAACACTTA
upper sequence: GLYMA20G36020.1 (Glycine max), 3'ss of exon 9
lower sequence: AT1G32850.1 (Arabidopsis thaliana), 3'ss of exon 8
---------------------------ttctttaaaagcttgacaagatggactttcaac----------tttcaagttcattc----tggttatctttactaagcacggcattttgatttttctgcaataaaatccccagGGTCAATACAAGTCAACATTGGTTTGTCCAGTATGTGGCAAAATTTCAATTACTTTCGATCCATTCATGTACTTATCATTACCACTGCCTTCCACTGTCA
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gtaagcatttcttactctttgtattacttatctaacaagtatccgaggttatagttaaaccaaaaatgtatttgaagttacttcctcttctttgtctgttttaaac---gtacctcatgttgtatgtgttttca-cttcagGGACAATACAAGTCAACATTGGTGTGTCCAGATTGTGGAAAAATCTCAATCACATTTGACCCCTTCATGTACTTATCTTTGCCGTTGCCATCAAGTCGCA
upper sequence: GLYMA20G36020.1 (Glycine max), 3'ss of exon 9
lower sequence: AT4G10590.1 (Arabidopsis thaliana), 3'ss of exon 8
----------------------ttctttaaaagcttgacaagatggactttcaactttcaagttcattctggttatctttactaagcacggcattttgatttttctgcaataa--aatccc---cagGGTCAATACAAGTCAACATTGGTTTGTCCAGTATGTGGCAAAATTTCAATTACTTTCGATCCATTCATGTACTTATCATTACCACTGCCTTCCACTGTCA
||| | || || | | | || | | ||||| | | | ||| || | | || || || | ||| | ||||| ||||||||||| || |||||||||||| || || ||||| ||||| ||||| ||||| ||||||||||| || |||| |||| || || | |
gtaagtatcggttaccatttccttccattgaatgttcatctggttcttgtttttcatacaagt--actacaagtttctctattttattttcccgaccagttcttatgaggtgttcaatttctttcagGGCCAATACAAGTCCACTCTGGTTTGTCCAGCTTGCGGAAAAATATCAATCACTTTTGATCCCTTCATGTACTTGTCTGTACCTTTGCCATCAACACTTA
upper sequence: GLYMA20G36020.1 (Glycine max), 3'ss of exon 9
lower sequence: Vv02s0025g02760.t01 (Vitis vinifera), 3'ss of exon 9
ttctttaaaagcttgacaagatggactttcaactttcaagttcatt--ctggttatctttactaagcacggcattttgatttttctgcaataaaatccccagGGTCAATACAAGTCAACATTGGTTTGTCCAGTATGTGGCAAAATTTCAATTACTTTCGATCCATTCATGTACTTATCATTACCACTGCCTTCCACTGTCA
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-gttttaaagtatttcttttctttactta-aaatatggagtacagaaacttggaattaggcataataatatggtcactaacagtctataaccaaacactcagGGTCAATATAAGTCAACTCTGGTTTGCCCAGTTTGCAGCAAAATTTCAATAACATTTGATCCGTTCATGTATTTGTCATTGCCGCTGCCTTCAACGGTCAMapped 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|10237362|gb|BE806250.1|BE806250EST: GGAAAAATCATATGGCTCGGAATGATTCATTGATTGTTGATGTATGCCAG GGTCAATACAAGTCAACATTGGTTTGTCCAGTATGTGGCAAAATTTCAATT
genomic: GGAAAAATCATATGGCTCGGAATGATTCATTGATTGTTGATGTATGCCAGgtgagaatat ... aaatccccagGGTCAATACAAGTCAACATTGGTTTGTCCAGTATGTGGCAAAATTTCAATT
EST:
gi|8827229|gb|BE210959.1|BE210959EST: GGAATGATTCATTGATTGTTGATGTATGCCAG GGTCAATACAAGTCAACATTGGTTTGTCCAGTATGTGGCAAAATTTCAATT
genomic: GGAATGATTCATTGATTGTTGATGTATGCCAGgtgagaatat ... aaatccccagGGTCAATACAAGTCAACATTGGTTTGTCCAGTATGTGGCAAAATTTCAATT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tctggttatctttactaagcacggcattttgatttttctgcaataaaatccccagGGTCAATACAAGTCAACATTGGTTTGTCCAGTATGTGGCAAAATTTCAATTACTTTCGATCCATTCATGTACTTATCATTACCACTGCCTTCCACTGTCA
ttttgat putative branch site (score: 4)
tcccc putative PPT
attttgatttttct 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttctttaaaagcttgacaagatggactttcaactttcaagttcattctggttatctttactaagcacggcattttgatttttctgcaataaaatccccagGGTCAATACAAGTCAACATTGGTTTGTCCAGTATGTGGCAAAATTTCAATTACTTTCGATCCATTCATGTACTTATCATTACCACTGCCTTCCACTGTCA
- - - - - - -tgacaag
- - - - - - - - - - - - - - - - - - - - - cattctg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctaagca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ggcattt