Sequence
atgc intronic sequence ATGC exonic sequence...ttgcactttgaatgtgttaagatgtcattcatcattaattaatcatagacagctctttcctgctgaacgttagtaatatattcattttcaattttgacagAGAATCTGAACCTAATTCATGGGAAGATACAATGAAAGATGAATTAGAACGTGAAAAATATCCTCGTATGCCTTGGCATGATGTTCATTGTGCCCTTTGG
Basic information
species | Glycine max |
transcript | GLYMA15G16270.1 |
intron # | 10 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA15G16270.1 (Glycine max), 3'ss of exon 10
lower sequence: LOC_Os05g29050.2 (Oryza sativa), 3'ss of exon 11
ttgcactttgaatgtgttaagatgtcattcatcattaattaatcatagacagctctttcctgctgaacgttagtaatatattcattttcaattttgacagAGAATCTGAACCTAATTCATGGGAAGATACAATGAAAGATGAATTAGAACGTGAAAAATATCCTCGTATGCCTTGGCATGATGTTCATTGTGCCCTTTGG
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-------gtaactatggta---tttcgtttatgatgg--tatttatgtaggattattcccaaattattcttacctgagttttcctgctgtacata---agGGAATCTGAGCCAAATTCCTGGGAGGACACAATGAAAGATGAGCTGGACCGAACGAAATATCCTCGCATGCCTTGGCATGATGTTCAGTGTGCTCTCTAC
upper sequence: GLYMA15G16270.1 (Glycine max), 3'ss of exon 10
lower sequence: LOC_Os01g20860.1 (Oryza sativa), 3'ss of exon 8
-------------------------ttgcactttgaatgtgttaagat-gtcattcatcattaattaatcatagacagctctttcc-----tgctgaa--------cgttagtaatata--ttcatttt-caattttgac--agAGAATCTGAACCTAATTCATGGGAAGATACAATGAAAGATGAATTAGAACGTGAAAAATATCCTCGTATGCCTTGGCATGATGTTCATTGTGCCCTTTGG
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gtaatgttttgtgctctcatcatatttttatctcaagatttataggatagtgtttcctaatttaccgaacacgattaatgtttcctaatgattctaaaacctttttttttgcctatctaattgcattttactatcttgtttaagGGAATCTGAGCCAAATTCTTGGGAGGACACCATGAAAGATGAGCTTGATCGTACTAAATATCCTCGCATGCCCTGGCATGATGTTCAGTGTGCTCTTTAT
upper sequence: GLYMA15G16270.1 (Glycine max), 3'ss of exon 10
lower sequence: GRMZM2G066485_T01 (Zea mays), 3'ss of exon 9
ttgcactttgaatgtgttaagatgtcattcatcattaattaatcatagacagctctttcctgctgaacgttagtaatatattcattttcaattttgacagAGAATCTGAACCTAATTCATGGGAAGATACAATGAAAGATGAATTAGAACGTGAAAAATATCCTCGTATGCCTTGGCATGATGTTCATTGTGCCCTTTGG
|| || | ||| || | ||| | || | | | || || || | | |||| | | | || ||||||||||| ||||| ||||| || || ||||||||||| | || ||||| |||||||| || |||||||||||||||||||| ||||| || |
-------------gtattttgttgttatcttctacccattcag-atgtatggggcaaagtccctaaatgtcact-------tcatctctg---taaatagGGAATCTGAACCCAATTCCTGGGAGGACACCATGAAAGATGAGCTGGACCGTGATAAATATCCCCGCATGCCTTGGCATGATGTTCAGTGTGCTCTCTAT
upper sequence: GLYMA15G16270.1 (Glycine max), 3'ss of exon 10
lower sequence: AT3G16785.1 (Arabidopsis thaliana), 3'ss of exon 10
----ttgcactttgaatgtgttaagatgtcattcatcattaattaatcatagacagctctttcctgctgaacgttagtaatatattcattttcaattttgacagAGAATCTGAACCTAATTCATGGGAAGATACAATGAAAGATGAATTAGAACGTGAAAAATATCCTCGTATGCCTTGGCATGATGTTCATTGTGCCCTTTGG
||| | | | | |||||| ||| | | ||| | | | | || |||| || | | | | || |||||| |||||| |||||||| ||| | ||||| ||| | |||||||||||||||| ||| |||| |||| || ||||||||||||||||| |||||||| | |||
aattttgtattaaatacaaaccaggatgtc---cattagtcatttcacctttccgaattcaaccctctgattttttggtttgaacgtacttaaaattttc-cagAGAGTCTGAACCCAATACTTGGGAGGATGCTCTGAAAGATGAATTAGAGCGTAAAAAGCATCCACGGATGCCTTGGCATGATGTGCATTGTGCTTTATGG
upper sequence: GLYMA15G16270.1 (Glycine max), 3'ss of exon 10
lower sequence: Vv05s0077g01830.t01 (Vitis vinifera), 3'ss of exon 11
ttgcactttgaatgtgttaagatgtcattcatcattaattaatcatagacagctctttcctgctgaacgttagtaatatat---tcattttcaattttga----cagAGAATCTGAACCTAATTCATGGGAAGATACAATGAAAGATGAATTAGAACGTGAAAAATATCCTCGTATGCCTTGGCATGATGTTCATTGTGCCCTTTGG
| | || || | | ||| | ||| |||| | | || || | | || | | || | | | |||||| | ||| ||||||||||| ||||| |||||||||||||||||||||||||| || |||| |||||||||||||||||| |||||||| || ||||||||||| |||
--gtgtgagaacattgacaatagtttcttcttttctaagtaattgcaagtttgttttcactctggctctttcacattggataacttgtaatgaattttcaatttcagGGAATCTGAACCAAATTCTTGGGAAGATACAATGAAAGATGAATTGGATCGTGGAAAATATCCTCGTATGCCATGGCATGACGTCCATTGTGCCCTATGG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tagacagctctttcctgctgaacgttagtaatatattcattttcaattttgacagAGAATCTGAACCTAATTCATGGGAAGATACAATGAAAGATGAATTAGAACGTGAAAAATATCCTCGTATGCCTTGGCATGATGTTCATTGTGCCCTTTGG
ttagtaatatattcat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttgcactttgaatgtgttaagatgtcattcatcattaattaatcatagacagctctttcctgctgaacgttagtaatatattcattttcaattttgacagAGAATCTGAACCTAATTCATGGGAAGATACAATGAAAGATGAATTAGAACGTGAAAAATATCCTCGTATGCCTTGGCATGATGTTCATTGTGCCCTTTGG
-tgcactt
- - - - -gaatgtg
- - - - - - - - - - - - -cattcat