Sequence
atgc intronic sequence ATGC exonic sequence...tctttgttgggtgcatgcctttattacccattttttgaagatctacttttaatgccttcaccaaaaggatcttactggatggtccttatcattttgtcagGTTCGGGATTACATTCATGTTGTTGATTTAGCAGATGGGCACATTGCTGCGTTGCTTAAACTAGATGATCCTAATATAG
Basic information
species | Glycine max |
transcript | GLYMA11G01940.3 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA11G01940.3 (Glycine max), 3'ss of exon 5
lower sequence: AT4G23920.1 (Arabidopsis thaliana), 3'ss of exon 5
---------------------------------------------tctttgttgggtgcatgcctt------tattacccattttttgaagatctacttttaat---gccttcaccaaaaggatcttactggatggtccttatcattttgtcagGTTCGGGATTACATTCATGTTGTTGATTTAGCAGATGGGCACATTGCTGCGTTGCTTAAACTAGATGATCCTAATATAG
| | || | | || ||||| | | | || ||| ||| | || || ||| ||| | || | || | || | ||||||| | |||||||||||||| | |||||||||||||| ||||| ||||| ||| ||| |||||||||| || ||
gtatgtgacttatgatgtcttatagacaacaaaccatttgacagatttacattacaatcttaaattgtgatatattatggagtatgggagataatacaacgaattgtgaattatattaacagatattattc-atctttgttgtgtttctttcagGTTAGAGATTACATTCATGTCATGGATTTAGCAGATGGACACATAGCTGCTCTGCGTAAGCTAGATGATCTCAAAATCA
upper sequence: GLYMA11G01940.3 (Glycine max), 3'ss of exon 5
lower sequence: AT4G10960.1 (Arabidopsis thaliana), 3'ss of exon 5
tctttgttgggtgcatgcctttat-tacccattttttgaagatctacttttaatgccttcaccaaaaggatcttactggatggtccttatcattt-tgtcagGTTCGGGATTACATTCATGTTGTTGATTTAGCAGATGGGCACATTGCTGCGTTGCTTAAACTAGATGATCCTAATATAG
||| ||| | |||| || | | ||| | | || ||| | | | | | || || ||| | | ||||||| ||||||||||||||| |||||||||| ||||| ||||| || || | | ||| ||||| ||| || || |
--------------------gtatgtacttgtctttt----atgttttcataaaac----aagaagaggttttcaacattttgatctcatgttttgttttagGTTCGAGATTACATTCATGTTATTGATTTAGCTGATGGACACATAGCGGCTCTACGTAAGCTAGAAGATTGCAAGATCG
upper sequence: GLYMA11G01940.3 (Glycine max), 3'ss of exon 5
lower sequence: Vv02s0025g01560.t01 (Vitis vinifera), 3'ss of exon 5
tctttgttgggtgcatgcctt-tattacccattttttgaagatctacttttaatgccttcaccaaaaggatcttactggatggtccttatcattttg--tcagGTTCGGGATTACATTCATGTTGTTGATTTAGCAGATGGGCACATTGCTGCGTTGCTTAAACTAGATGATCCTAATATAG
| ||| | | | || || || | | || | | | || | || | || ||| | | || | |||| | || |||||| |||||||||||||||||||| ||||||||||||||||||||||| || |||| || ||| | | | ||||
-ccttggtaa-tataggcattatactgcattccagttttccacttttgatcaaaggtttgatgtcaatgatgt-attgatgcttacttacctattcacatcagGTACGGGATTACATTCATGTTGTGGATTTAGCAGATGGGCACATTGCAGCCTTGCACAAGCTACTCAACTCAGAAATAG
upper sequence: GLYMA11G01940.3 (Glycine max), 3'ss of exon 5
lower sequence: Vv02s0025g01580.t01 (Vitis vinifera), 3'ss of exon 5
tctttgttgggtgcatgcctttattacccatt--ttttgaagatctacttttaatgccttcaccaaaaggatcttactggatggtccttatcattttgtcagGTTCGGGATTACATTCATGTTGTTGATTTAGCAGATGGGCACATTGCTGCGTTGCTTAAACTAGATGATCCTAATATAG
||| | || | |||| | | |||| | | | | ||| | | || || | || ||| ||| ||||| || |||||||| |||||||||||||| ||||||||||||||||| || ||| || ||| | | | ||||
gcttaggtgatataggaattatattgcattctagttttctgcttgtgacctaggttttgatgtcaataatgtgttgatgtttacctattttcacttt--cagGTCCGTGATTACATCCATGTTGTTGATTTGGCAGATGGGCACATTGCAGCTTTGTGCAAGCTATTCAACTCAGAAATAGMapped 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|58025113|gb|CX711854.1|CX711854EST: CTGCACTGACAG-TTTTGGAAATGATTATAATACAACTGATGGCACTGGG GTTCGGGATTACATTCATGTTGTTGATTTAGCAGATGGGCACATTGCTGCG
genomic: CTGCACTGACAGTTTTTGGAAATGATTATAATACAACTGATGGCACTGGGgtatgctctg ... attttgtcagGTTCGGGATTACATTCATGTTGTTGATTTAGCAGATGGGCACATTGCTGCG
EST:
gi|19346921|gb|BM891809.1|BM891809EST: CTGCACTGACAGTTTTTGGAAATGATTATAATACAACTGATGGCACTGGG GTTCGGGATTACATTCATGTTGTTGATTTAGCAGATGGGCACATTGCTGCG
genomic: CTGCACTGACAGTTTTTGGAAATGATTATAATACAACTGATGGCACTGGGgtatgctctg ... attttgtcagGTTCGGGATTACATTCATGTTGTTGATTTAGCAGATGGGCACATTGCTGCG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cttttaatgccttcaccaaaaggatcttactggatggtccttatcattttgtcagGTTCGGGATTACATTCATGTTGTTGATTTAGCAGATGGGCACATTGCTGCGTTGCTTAAACTAGATGATCCTAATATAG
atcttac putative branch site (score: 3)
tcatttt putative PPT
ttatcatttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tctttgttgggtgcatgcctttattacccattttttgaagatctacttttaatgccttcaccaaaaggatcttactggatggtccttatcattttgtcagGTTCGGGATTACATTCATGTTGTTGATTTAGCAGATGGGCACATTGCTGCGTTGCTTAAACTAGATGATCCTAATATAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - tgttggg
- - - - - - -catgcct
- - - - - - - - - - - - - - - - - - - - - - - - - - - -cttcacc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tggatgg