Sequence
atgc intronic sequence ATGC exonic sequence...ttctttatttgaatttcaactacatgcgctgcttgctttgttttggtaagctactttttatttattttgtgaacccccctctttggcttgatttgttcagGTCATTAGACATTTTGATGGTTGCAAGGCTGACCTGGTTGTGTGTGATGGTGCTCCTGATG
Basic information
species | Glycine max |
transcript | GLYMA13G31380.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA13G31380.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os06g49140.1 (Oryza sativa), 3'ss of exon 5
ttctttatttgaatttcaactacatgcgctgcttgctttgttttggtaagctac-tttttatttattttgtgaacccccctctttggcttgattt-gtt--cagGTCATTAGACATTTTGATGGTTGCAAGGCTGACCTGGTTGTGTGTGATGGTGCTCCTGATG
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-----------------------gtacttttctcatatggatttggcttgctgtattttctcccatggtttgtcttgctgcaactgatataattttgttactagGTTATTAGGCATTTTGATGGATGCAAAGCAGATTTGGTTGTCTGCGATGGTGCTCCTGATG
upper sequence: GLYMA13G31380.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G083745_T03 (Zea mays), 3'ss of exon 5
ttctttatttgaatttcaactacatgcgctgcttgctttgttttggtaagctactttttatttattttgtgaacccccctctttggcttgatttgttcagGTCATTAGACATTTTGATGGTTGCAAGGCTGACCTGGTTGTGTGTGATGGTGCTCCTGATG
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--------gtgagacagaagtaaaagacgtg-tagcttttttgttgtt-gccgcagttagctggctgtg---actaactagtatggatt--tcctgtcagGTCATTAGGCATTTTGATGGATGCAAAGCAGACTTGGTTGTTTGCGATGGAGCCCCGGATG
upper sequence: GLYMA13G31380.1 (Glycine max), 3'ss of exon 6
lower sequence: AT5G01230.2 (Arabidopsis thaliana), 3'ss of exon 6
---------------ttctttatttgaatttcaactacatgcgctgcttgctttgttttggtaagctactttt-tatttatttt-gtgaacccccctctttggcttgatttgttcagGTCATTAGACATTTTGATGGTTGCAAGGCTGACCTGGTTGTGTGTGATGGTGCTCCTGATG---------------------------------------
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gtaaaatttctcgactcctatctcataaatttttctacatctctttcttcctctttaattatgcttcaagtttgtgtttgtttccatggcttaccttttccggtgttttttttcaagGTCATTAGACACTTTGACGGCTGCAAAGCGGACCTGGTTGTCTGTGATGGTGCTCCAGATGGTAAAACAGTAGATAAAGTGTCTGTCTCGCCGTTCAATA
upper sequence: GLYMA13G31380.1 (Glycine max), 3'ss of exon 6
lower sequence: AT5G01230.1 (Arabidopsis thaliana), 3'ss of exon 6
---------------ttctttatttgaatttcaactacatgcgctgcttgctttgttttggtaagctactttt-tatttatttt-gtgaacccccctctttggcttgatttgttcagGTCATTAGACATTTTGATGGTTGCAAGGCTGACCTGGTTGTGTGTGATGGTGCTCCTGATG
| || | | || || |||||| | ||| || | | | | | ||| | ||| ||| || || | | || | ||| | ||||||||||||| ||||| || ||||| || ||||||||||| |||||||||||||| ||||
gtaaaatttctcgactcctatctcataaatttttctacatctctttcttcctctttaattatgcttcaagtttgtgtttgtttccatggcttaccttttccggtgttttttttcaagGTCATTAGACACTTTGACGGCTGCAAAGCGGACCTGGTTGTCTGTGATGGTGCTCCAGATG
upper sequence: GLYMA13G31380.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv08s0007g01960.t01 (Vitis vinifera), 3'ss of exon 5
--ttctttatttgaatttcaactacatgcgctgcttgctttgttttggtaagctactttttatttattttgtgaacccccctctttggcttgatttgttcagGTCATTAGACATTTTGATGGTTGCAAGGCTGACCTGGTTGTGTGTGATGGTGCTCCTGATG
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gtatttgtgtgctattttaaatcatttttgctctcagtttttggctgtgtaaaaatgatatatctga--cattatccttatttatcatcttctgttcttcagGTCATTAGGCATTTTGATGGATGCAAGGCTGACCTGGTTGTGTGTGATGGTGCTCCTGATGMapped 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|151401979|gb|EV271792.1|EV271792EST: GTGTCATCCAGGTGCAGGGTGATATAACTAATGCTCGGACAGCTGAAGTG GTCATTAGACATTTTGATGGTTGCAAG-CTGACCTGGTTGTGTGTGATG-T
genomic: GTGTCATCCAGGTGCAGGGTGATATAACTAATGCTCGGACAGCTGAAGTGgtatatatta ... atttgttcagGTCATTAGACATTTTGATGGTTGCAAGGCTGACCTGGTTGTGTGTGATGGT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gtaagctactttttatttattttgtgaacccccctctttggcttgatttgttcagGTCATTAGACATTTTGATGGTTGCAAGGCTGACCTGGTTGTGTGTGATGGTGCTCCTGATG
gcttgat putative branch site (score: 5)
tttgttc CT-rich tract
tactttttatttattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttctttatttgaatttcaactacatgcgctgcttgctttgttttggtaagctactttttatttattttgtgaacccccctctttggcttgatttgttcagGTCATTAGACATTTTGATGGTTGCAAGGCTGACCTGGTTGTGTGTGATGGTGCTCCTGATG
- - - - - - - - - - - catgcgc
- - - - - - - - - - - - - - - gcttgct
- - - - - - - - - - - - - - - - - - - tgttttg
- - - - - - - - - - - - - - - - - - - - - - - - -gctactt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ttttgtg