Sequence
atgc intronic sequence ATGC exonic sequence...gacttttgtaaaatcttacgattctatttatgttttttaccccctttttgatcgaaggtaaatccatattttgactaccttgctatttacatcattacagAGCAGATCTTGCAAACCTAGTAAATGAGGCTGCTTTACTGGCTGGAAGACAAAATAAAGTTGTGGTGGAGAAACTTGATTTCATCCAAGCTGTAGAGAGA
Basic information
species | Glycine max |
transcript | GLYMA0028S00210.2 |
intron # | 8 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA0028S00210.1 (Glycine max), 3'ss of exon 8
lower sequence: GRMZM2G163193_T02 (Zea mays), 3'ss of exon 8
gacttttgtaaaatcttacgattctatttatgttttttaccccctttttgatcgaaggtaaatccatattttgactaccttgctatttacatcattacagAGCAGATCTTGCAAACCTAGTAAATGAGGCTGCTTTACTGGCTGGAAGACAAAATAAAGTTGTGGTGGAGAAACTTGATTTCATCCAAGCTGTAGAGAGA
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-------gtaaaactt----attctaccaatttcttgatcttgaccctgtagggatttcaaattgacgtgttaaataattt------tatgctat-acagAGCAGACCTTGCAAACTTGGTAAATGAAGCTGCTTTGTTGGCTGGGCGATTAAATAAAGAAATTGTGGAAAAGATTGACTTCATCCATGCGGTTGAGCGA
upper sequence: GLYMA0028S00210.1 (Glycine max), 3'ss of exon 8
lower sequence: AT3G47060.1 (Arabidopsis thaliana), 3'ss of exon 8
gacttttgtaaaatcttacgattctatttatgttttttacccccttt--ttgatcgaaggtaaatccatattttgactaccttgctatttacatcattacagAGCAGATCTTGCAAACCTAGTAAATGAGGCTGCTTTACTGGCTGGAAGACAAAATAAAGTTGTGGTGGAGAAACTTGATTTCATCCAAGCTGTAGAGAGA
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-------gtacgcttttgt-atattatcaatgatttgaagtttattcagttatacgtttttgggtgtatatctcataaactcttttgtcc---tatttgcagGGCAGATCTTGCAAACTTGGTAAATGAGGCTGCCTTGCTAGCTGGAAGAAAGAACAAGACGAACGTTGAGAAAATTGACTTCATTCAAGCTGTGGAGCGA
upper sequence: GLYMA0028S00210.1 (Glycine max), 3'ss of exon 8
lower sequence: Vv06s0004g06120.t01 (Vitis vinifera), 3'ss of exon 8
-------gacttttgtaaaatcttacgattctatttatgttttttaccccctttttgatcgaaggtaaatccatattttgactaccttgctatttacatcattacagAGCAGATCTTGCAAACCTAGTAAATGAGGCTGCTTTACTGGCTGGAAGACAAAATAAAGTTGTGGTGGAGAAACTTGATTTCATCCAAGCTGTAGAGAGA
|| | || | || | | | | | ||| | || || ||| | | || | || || ||||| | ||| | | ||| ||||| || ||||| |||| ||||| |||||||| | ||||||||||||||||||||||| ||||||||| ||||||| | || || |||||| |
cccattcaggttctatatatgtatatgtgtgtgtgtgtgtgtgttttcctaatttctagctaacattgata-attttttgttgattttggatgctg------tgcagGGCAGACCTAGCAAATTTAGTGAATGAAGCTGCTTTGTTAGCTGGAAGACAAAATAAAGTTGTCGTGGAGAAAATTGATTTTGTTCATGCAGTAGAGCGG
upper sequence: GLYMA0028S00210.1 (Glycine max), 3'ss of exon 8
lower sequence: EFJ33021 (Selaginella moellendorffii), 3'ss of exon 8
gacttttgtaaaatcttacgattctatttatgttttttaccccctttttgatcgaaggtaaatccatattttgact-accttgctatttacatcattacagAGCAGATCTTGCAAACCTAGTAAATGAGGCTGCTTTACTGGCTGGAAGACAAAATAAAGTTGTGGTGGAGAAACTTGATTTCATCCAAGCTGTAGAGAGA
| || | | | |||||||| || || || | ||| |||||| |||||||||||||| ||||| ||||||||| |||| ||||| ||| ||||||| ||| || | |||| | || || | ||||| ||| |
---------------------------------------------gtaagagtgtggattg-caaatattttggcttacgaccctgtatacg------cagAGCGGATCTTGCAAACCTTGTAAACGAGGCTGCTCTACTAGCTGGTAGAGAAAATAAGCTTGAAGTCGGGAAAGTGGAGTTTTCGCGTGCTGTTGAGCGT
upper sequence: GLYMA0028S00210.1 (Glycine max), 3'ss of exon 8
lower sequence: EFJ30338 (Selaginella moellendorffii), 3'ss of exon 8
gacttttgtaaaatcttacgattctatttatgttttttaccccctttttgatcgaaggtaaatccatattttgact-accttgctatttacatcattacagAGCAGATCTTGCAAACCTAGTAAATGAGGCTGCTTTACTGGCTGGAAGACAAAATAAAGTTGTGGTGGAGAAACTTGATTTCATCCAAGCTGTAGAGAGA
| || | || | |||||||| || || || | ||| |||||| |||||||||||||| ||||| ||||||||| |||| ||||| ||| ||||||| ||| || | |||| | || || | ||||| ||| |
---------------------------------------------gtaagagtgtagattg-caaatattttggcttacgaccctgtatacg------cagAGCGGATCTTGCAAACCTTGTAAACGAGGCTGCTCTACTAGCTGGTAGAGAAAATAAGCTTGAAGTCGGGAAAGTGGAGTTTTCGCGTGCTGTTGAGCGT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttttgatcgaaggtaaatccatattttgactaccttgctatttacatcattacagAGCAGATCTTGCAAACCTAGTAAATGAGGCTGCTTTACTGGCTGGAAGACAAAATAAAGTTGTGGTGGAGAAACTTGATTTCATCCAAGCTGTAGAGAGA
ttttgac putative branch site (score: 3)
taaatccatatttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gacttttgtaaaatcttacgattctatttatgttttttaccccctttttgatcgaaggtaaatccatattttgactaccttgctatttacatcattacagAGCAGATCTTGCAAACCTAGTAAATGAGGCTGCTTTACTGGCTGGAAGACAAAATAAAGTTGTGGTGGAGAAACTTGATTTCATCCAAGCTGTAGAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ccttgct