Sequence
atgc intronic sequence ATGC exonic sequencegttagttagattctttgatatccagtccacgggtagagtagtagtatttgttatatagtttggtggtgtgctaaaagcatcttttttttccagGAAATAATGCAACATAAACTTGTCTTTATTGAGACTCAGGATGTGGTAGAGACTACATTGGCTCTTGATAACTATCGCAAGGCTTGTGATTGTGGAAGAG
Basic information
species | Glycine max |
transcript | GLYMA16G28290.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA16G28290.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os05g05260.1 (Oryza sativa), 3'ss of exon 5
-gttagttagattctttgatatccagtccacg-ggtagag---tagtagtatttgttatatagtttggtggtgtgctaaaagcat--cttttttttccagGAAATAATGCAACATAAACTTGTCTTTATTGAGACTCAGGATGTGGTAGAGACTACATTGGCTCTTGATAACTATCGCAAGGCTTGTGATTGTGGAAGAG
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tgcttttactgttctcatgaatacagcattcttggcaaagccttgataacacgcaatgcattagcacctaatatgaaaatcttatgacttcaatttgcagGACATCATGCAGCATAAGTTGGTATTCATTGAAACACCAGATGTTGTTGAGACAACATTGGCTCTTGATAATTACAGAAAGGCATGTGATTGTGGAAGAG
upper sequence: GLYMA16G28290.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G097605_T01 (Zea mays), 3'ss of exon 5
---------gttagttagattctttgatatccagtccacgggtagagtagtagtatttgttatatagtttggtggtgtgctaaaagcatcttttttttccagGAAATAATGCAACATAAACTTGTCTTTATTGAGACTCAGGATGTGGTAGAGACTACATTGGCTCTTGATAACTATCGCAAGGCTTGTGATTGTGGAAGAG
| | | | || | | | || | | | ||| || |||| || || | | | | | | |||| ||||| || |||||||||||| | || ||||| || || | ||||| || ||||| |||||||||||||||||||| | ||||| ||||||||||||||||
ctgtgttatgaaaataaaatacctgtaaatgttatata-gccaagataagatgtatatgcatta-gttccaataacgaaaacctggttttactgtttttcagGACATCATGCAACATAAATTAGTGTTTATCGAAACACCAGATGTCGTTGAGACAACATTGGCTCTTGATAACTACAGAAAGGCATGTGATTGTGGAAGAG
upper sequence: GLYMA16G28290.1 (Glycine max), 3'ss of exon 6
lower sequence: AT1G03190.2 (Arabidopsis thaliana), 3'ss of exon 6
----------------------------------------------------gttagttagattcttt--gatatc-cagtccacgggtaga-gtagtagtatttgttatata---gtttggtggtgtgctaaaagcatcttttttttccagGAAATAATGCAACATAAACTTGTCTTTATTGAGACTCAGGATGTGGTAGAGACTACATTGGCTCTTGATAACTATCGCAAGGCTTGTGATTGTGGAAGAG
| | || || | ||| |||| | || | ||| | || || | |||| |||| || | | || | | | ||| |||||||||||||||| || ||||| || ||||| || || ||||| ||||| || |||||||| || ||||| ||||||| |||||| ||||| |||||||
gtaaggtcttcttcatcgctttaccatgccagtaattttttcagagttttgcatgaattggaatttttatgatacctcaaaatatttttagttgcttcaggcattaatgtatatttgtttactgatattaccaattctcttaatgtttgtagGAAATAATGCAACAGAAGCTTGTTTTCATTGAAACACAAGATGTTGTAGAAACAACATTGGCACTGGATAATTATCGCAGGGCTTGCGATTGCGGAAGAG
upper sequence: GLYMA16G28290.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv07s0104g00060.t01 (Vitis vinifera), 3'ss of exon 6
gttagttagattctttgatatccagtccacgggtagagtagtagtatttgttatatag------tttggtggtg--tgctaaaagcatcttttttttccagGAAATAATGCAACATAAACTTGTCTTTATTGAGACTCAGGATGTGGTAGAGACTACATTGGCTCTTGATAACTATCGCAAGGCTTGTGATTGTGGAAGAG
| || || | | || | | | | || | | || || | | ||| || | | || || || | | ||| || |||||||||||||||||||| ||||||||||||||||||||||||||||| || |||||||| ||||| || || ||||||| |||||||| ||||| ||||
accgtctgtatagttctacacacactttccctgggaattatttttgctttatagaaaaactaattttcttgatagatacttaatgc-tatctttgttgcagGAAATAATGCAACATAAGCTTGTCTTTATTGAGACTCAGGATGTGGTGGAAACTACATTAGCTCTAGACAATTATCGCAGAGCTTGTGACTGTGGGAGAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tagtagtatttgttatatagtttggtggtgtgctaaaagcatcttttttttccagGAAATAATGCAACATAAACTTGTCTTTATTGAGACTCAGGATGTGGTAGAGACTACATTGGCTCTTGATAACTATCGCAAGGCTTGTGATTGTGGAAGAG
tgctaaa putative branch site (score: 2)
catcttttttttcc putative PPT
tatttgttatatagtt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttagttagattctttgatatccagtccacgggtagagtagtagtatttgttatatagtttggtggtgtgctaaaagcatcttttttttccagGAAATAATGCAACATAAACTTGTCTTTATTGAGACTCAGGATGTGGTAGAGACTACATTGGCTCTTGATAACTATCGCAAGGCTTGTGATTGTGGAAGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA