Sequence
atgc intronic sequence ATGC exonic sequence...gtcataataactgcatgagcaacatattcttattttcgcaatagaacatgtattttgtggaggcaccaaaatgattattgatctaagttacttttaatagATGATACAGCAATGCTTTGGGGACTTAAGTTCTACAATGATTTTCTCATGCAAGCTGGCCCTCTTGGTAATGTACAATCAGAGCTACTATTCAGAAAGGA
Basic information
species | Glycine max |
transcript | GLYMA13G06660.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA13G06660.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os05g32110.3 (Oryza sativa), 3'ss of exon 3
----------------gtcataataactgcatgagcaacatattcttattttcgcaata-gaacatgtat-tttgtggaggcaccaaaatgattattgatctaagttacttttaat--agATGATACAGCAATGCTTTGGGGACTTAAGTTCTACAATGATTTTCTCATGCAAGCTGGCCCTCTTGGTAATGTACAATCAGAGCTACTATTCAGAAAGGA
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gtaagtcaatttacaaactgttctcctttatttaagaaaattggagtgcacttgtaatacgttcctttatctctctctctctctctctttctctgatgaagtttattccttctattttagATGATACTGCGATGTTCTGGGGAGTTAAGTTCTATAACGATTTGCTCATGCAAGCTGGTCCACTTGGAAATGCACAGTCAGAACTTCTTCTGCGTAAGGA
upper sequence: GLYMA13G06660.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G071970_T01 (Zea mays), 3'ss of exon 5
gtcataataactgcatgagcaacatattcttattttcgcaatagaacatgtattttgtggaggcaccaaaatgattattgatctaagttacttttaatagATGATACAGCAATGCTTTGGGGACTTAAGTTCTACAATGATTTTCTCATGCAAGCTGGCCCTCTTGGTAATGTACAATCAGAGCTACTATTCAGAAAGGA
||| | | | ||| | | | |||| | || | | | ||| | || ||| || | ||| ||||||||| |||||| | ||||| | ||||||||||||||||| || |||||||| ||| ||||| ||||| |||||||| || || || | |||||
------gtaagtaaacttgtcttatagaaa-agaatagaaataaaccaacctacctcccaacctctcctgatg-tagtttgtct--gtcccgttt--cagATGATACGGCAATGTTCTGGGGTGTAAAGTTCTACAATGATTTGCTGATGCAAGCCGGCAAACTTGGGAATGTGCAATCAGAACTGCTTCTCCGCAAGGA
upper sequence: GLYMA13G06660.1 (Glycine max), 3'ss of exon 5
lower sequence: AT3G02210.1 (Arabidopsis thaliana), 3'ss of exon 5
gtcataataactgcatgagcaa-catattcttattttcgcaatagaacatgtattttgtggaggcaccaaaatgattattgatctaagttacttttaatagATGATACAGCAATGCTTTGGGGACTTAAGTTCTACAATGATTTTCTCATGCAAGCTGGCCCTCTTGGTAATGTACAATCAGAGCTACTATTCAGAAAGGA
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---gtaagtacaccatcatctatcagtcccttgtttctatagaaaggaacaaatctt---gatgtgttttttttgtttttgatttgat---------atagATGATACTGGGATTCTCTGGGGAATAAAGTTCTACAATGATCTGTTGATGCAAGCTGGGCCATTTGGTAATGTACAATCTGAGCTACTTTTCCAGAAAGA
upper sequence: GLYMA13G06660.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv14s0083g01160.t01 (Vitis vinifera), 3'ss of exon 5
--gtcataataactgcatgagcaacatattcttattttcgcaatagaacatgtattttgtggaggcaccaaaatgattattg-atctaagttacttttaatagATGATACAGCAATGCTTTGGGGACTTAAGTTCTACAATGATTTTCTCATGCAAGCTGGCCCTCTTGGTAATGTACAATCAGAGCTACTATTCAGAAAGGA
|||| ||||||| ||| || | | | ||| | | | | | | | || || ||| ||| | | || | || ||||||||| || ||||| ||||| ||||||||||||||||| | ||| ||||||||||||||||||| |||||||| ||||||||||| || | |||||
atatcatcgct-ttgcatga-caaaatgtgcatgtttcc-ctttttggtttatgacatattgaaaattgaacatgggtataacaagttcttttttcccaacagATGATACTGCCATGCTATGGGGGGTTAAGTTCTACAATGATCTGCTCGTGCAAGCTGGCCCTCTTGGAAATGTACAGTCAGAGCTACTCTTTCGGAAGGA
upper sequence: GLYMA13G06660.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv17s0000g05070.t01 (Vitis vinifera), 3'ss of exon 5
------------gtcataataactgcatgagcaa------catattcttattttcgcaatagaacatgtat-----tttgtggaggcaccaaaatgattattgatctaagttactttta-atagATGATACAGCAATGCTTTGGGGACTTAAGTTCTACAATGATTTTCTCATGCAAGCTGGCCCTCTTGGTAATGTACAATCAGAGCTACTATTCAGAAAGGA
|| || | || | |||| | | | ||| |||| || | | || || | || || || | || | | || ||| | |||||| || || ||| | |||||| | ||||| ||||||||||| ||| |||||||| |||||||| ||||| || |||||||||||||| |||||||
gtacgtcatatcttctcaagatttggttttgcaaagttgttgtctgccagctttttaaataaaaaacatgcaactgttcgtcttaatcctaacatc-ttgtgaatatgaattttggttatacagATGACACTGCCATGTTATGGGGAGTCAAGTTTTACAATGATTTGCTCTCTCAAGCTGGTCCTCTTGGGAATGTGCAGTCAGAGCTACTATTTCGAAAGGA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.acatgtattttgtggaggcaccaaaatgattattgatctaagttacttttaatagATGATACAGCAATGCTTTGGGGACTTAAGTTCTACAATGATTTTCTCATGCAAGCTGGCCCTCTTGGTAATGTACAATCAGAGCTACTATTCAGAAAGGA
tattgat putative branch site (score: 3)
ttactttt putative PPT
taagttacttttaata 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtcataataactgcatgagcaacatattcttattttcgcaatagaacatgtattttgtggaggcaccaaaatgattattgatctaagttacttttaatagATGATACAGCAATGCTTTGGGGACTTAAGTTCTACAATGATTTTCTCATGCAAGCTGGCCCTCTTGGTAATGTACAATCAGAGCTACTATTCAGAAAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT
- - - - - -tgcatga
- - - - - - - - - - - - - - - - - - - - - - - catgtat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - gtggagg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -caccaaa