Sequence
atgc intronic sequence ATGC exonic sequence...tacatagtgtagtgtactctagcttgtgctatttagtgtatttataaatatatgtgtaagaggataatttattaatattgtgttagtttgggtcttgtagGAGGCATGGTTCTTCATAAGGGAGAAATAGCTGAAATGAGGACCGGAGAAGGGAAGACACTGGTTGCTGTTTTGCCAGCTTATTTAAATGCATTGAGTGG
Basic information
species | Glycine max |
transcript | GLYMA02G01060.2 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA02G01060.1 (Glycine max), 3'ss of exon 2
lower sequence: AT4G01800.1 (Arabidopsis thaliana), 3'ss of exon 2
--tacatagtgta-gtgtactctagcttgtgctatttagtgtatttataaatatatgtgtaagaggataatttattaatattgtgttagtttgggtcttgtagGAGGCATGGTTCTTCATAAGGGAGAAATAGCTGAAATGAGGACCGGAGAAGGGAAGACACTGGTTGCTGTTTTGCCAGCTTATTTAAATGCATTGAGTGG
||| ||| | ||| | | | | | | | || ||| | | | | || || | | | | |||| || ||| || | ||| || |||||||||||||| |||||||||||||||||||| || || |||||||| || || |||||| |||| ||||||||||| |||||||| |||||
gtaacacagtctctgtggaatgttattctaatggtctcac-tgttatgaaagacttttttgagtgg--agtctctctatatggttttaatt--------gcagGTGGTATGGTTCTTCATAAAGGAGAAATAGCTGAAATGAGAACTGGTGAAGGGAAAACGCTTGTTGCTATTTTACCAGCTTATTTGAATGCATTAAGTGG
upper sequence: GLYMA02G01060.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv07s0005g02610.t01 (Vitis vinifera), 3'ss of exon 2
---tacatagtgtagtgtactctagcttgtg--ctatttagtgtatttataaatatat-gtgtaagaggataatttattaatattgtgttagtttgggtcttgtagGAGGCATGGTTCTTCATAAGGGAGAAATAGCTGAAATGAGGACCGGAGAAGGGAAGACACTGGTTGCTGTTTTGCCAGCTTATTTAAATGCATTGAGTGG
| | ||| | || | ||| ||| | |||| | ||||| |||| | | | ||| | || || | | || | | || | ||||||| |||||||||||||||||||||||||||||||||||||| || |||||||| ||||| || ||||| |||| ||||||||||| |||||||| |||||
aaatccttagatcatagttgtttagtcagtggattgtttatt-tatttgtaaacagaaagcttaatatgaatatcaagttgaatgatatctgtat-----ttgtagGTGGCATGGTTCTTCATAAGGGAGAAATAGCTGAAATGAGAACTGGAGAAGGAAAGACCCTTGTTGCAATTTTACCAGCTTATTTGAATGCATTAAGTGG
upper sequence: GLYMA02G01060.1 (Glycine max), 3'ss of exon 2
lower sequence: PP1S9_141V6.1 (Physcomitrella patens), 3'ss of exon 2
tacatagtgtagtgtactctagcttgtgctatttagtgtatttataaatatatgtgtaagaggataatttattaatattgtgttagttt--gggtcttgtagGAGGCATGGTTCTTCATAAGGGAGAAATAGCTGAAATGAGGACCGGAGAAGGGAAGACACTGGTTGCTGTTTTGCCAGCTTATTTAAATGCATTGAGTGG
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-cccgaatgtggtatgtacatattcttgccattccgcgtgaat-caagtgaaaacgagtgggacttatcgtctctgctggtggggatttccgaattctgcagGAGGAATGGTTCTACACAAAGGGCAAATTGCAGAAATGAGAACAGGAGAAGGGAAGACACTTGTTGCAGTCCTACCTGCATTTCTGAACTGCTTGACAGGMapped 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|213618218|gb|DB972988.1|DB972988EST: AGCTTCGAAGAGGGTTCTGGGCCTTCGTCCCTTCGATGTCCAGCTCATAG GAGGCATGGTTCTTCATAAGGGAGAAATAGCTGAAATGAGGACCGGAGAAG
genomic: AGCTTCGAAGAGGGTTCTGGGCCTTCGTCCCTTCGATGTCCAGCTCATAGgtaagtcttt ... ggtcttgtagGAGGCATGGTTCTTCATAAGGGAGAAATAGCTGAAATGAGGACCGGAGAAG
EST:
gi|23731923|gb|BU764108.1|BU764108EST: AGCTTCGAAGAGGGTTCTGGGCCTTCGTCCCTTCGATGTCCAGCTCATAG GAGGCATGGTTCTTCATAAGGGAGAAATAGCTGAAATGAGGACCGGAGAAG
genomic: AGCTTCGAAGAGGGTTCTGGGCCTTCGTCCCTTCGATGTCCAGCTCATAGgtaagtcttt ... ggtcttgtagGAGGCATGGTTCTTCATAAGGGAGAAATAGCTGAAATGAGGACCGGAGAAG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aaatatatgtgtaagaggataatttattaatattgtgttagtttgggtcttgtagGAGGCATGGTTCTTCATAAGGGAGAAATAGCTGAAATGAGGACCGGAGAAGGGAAGACACTGGTTGCTGTTTTGCCAGCTTATTTAAATGCATTGAGTGG
tattaat putative branch site (score: 2)
ataatttattaatatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tacatagtgtagtgtactctagcttgtgctatttagtgtatttataaatatatgtgtaagaggataatttattaatattgtgttagtttgggtcttgtagGAGGCATGGTTCTTCATAAGGGAGAAATAGCTGAAATGAGGACCGGAGAAGGGAAGACACTGGTTGCTGTTTTGCCAGCTTATTTAAATGCATTGAGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT