Sequence
atgc intronic sequence ATGC exonic sequence...tttgaccgtgacatgattttaatttttgttcattctctcacctattctctctctctctcaaattggcgatcgatttttgagcattcttgttttccttcagTGCCTCTTCTTCTAGTTGGATATGGATTTGGTGCCTCCTTTGTTGCACTATTTGCCCAGTTGGGTGGTGGAATATACACAAAGGCCGCTGATGTTGGAGC
Basic information
species | Glycine max |
transcript | GLYMA08G24120.2 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA08G24120.2 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os02g33490.1 (Oryza sativa), 3'ss of exon 6
tttgaccgtgacatgattttaatttttgttcattctctcacctattctctctctctctcaaattggcgatcgatttttgagcattcttgt---tttccttcagTGCCTCTTCTTCTAGTTGGATATGGATTTGGTGCCTCCTTTGTTGCACTATTTGCCCAGTTGGGTGGTGGAATATACACAAAGGCCGCTGATGTTGGAGC
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-tttcctggttgataacactggttatggttatatgtttg--caattagttcttttattcaaatggaatatttcttttgtcaatttcacatttatttcctgtagTGCCTCTTCTCCTTGTGGGATATGGTTTTGGTGCGTCTTTTGTCGCCCTTTTTGCTCAGTTGGGTGGTGGAATATACACCAAAGCTGCTGATGTCGGAGC
upper sequence: GLYMA08G24120.2 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G075900_T01 (Zea mays), 3'ss of exon 6
---------------------------------------------------tttgaccgtgacatgattttaatttttgttcattctctcacctattctctctctctctcaaattggcgatcgatttttgagc-----attcttgttttccttc-------agTGCCTCTTCTTCTAGTTGGATATGGATTTGGTGCCTCCTTTGTTGCACTATTTGCCCAGTTGGGTGGTGGAATATACACAAAGGCCGCTGATGTTGGAGC
||| || | | | |||| || || | | | | | | | | | | | ||| || || |||| | | || || |||||||||||| || || |||||||| ||||||||||| |||||||| || ||||| ||||||||||||||||||||||| || || ||||||||||||||
gtaagtttcttgtacacaatacacctgaaaacacactagattacaatccaacttgtccaccaattatctacttattttattgtttttgcaaattgcaataccattttgttatgtgaaaggaacattattctgctgctgattcatatgttttttttgtgtgtagTGCCTCTTCTCCTTGTGGGATATGGTTTTGGTGCCTCTTTTGTTGCCCTTTTTGCTCAGTTGGGTGGTGGAATATACACGAAAGCTGCTGATGTTGGAGC
upper sequence: GLYMA08G24120.2 (Glycine max), 3'ss of exon 6
lower sequence: AT1G16780.1 (Arabidopsis thaliana), 3'ss of exon 7
-----tttgaccgtgacatgattttaatttttgt-tcattctctcacctattctctctctctctcaaattggcgatcgatttttgagcattcttgttttccttcagTGCCTCTTCTTCTAGTTGGATATGGATTTGGTGCCTCCTTTGTTGCACTATTTGCCCAGTTGGGTGGTGGAATATACACAAAGGCCGCTGATGTTGGAGC
| | || | | || || | | || || | | | | | || || ||||| | | ||||| | |||||||||||||||| || |||||||| |||||||| || |||||||| ||||||| |||||||||||||||||||| || |||| |||||||| || ||
ttgttctcaaatgtttaacgtttgcaaacccgaaattgcatttgcatgtactagtgttactttttagcttaatga------tttgactttcccatttttcttacagTGCCTCTTCTTCTTGTGGGATATGGTTTTGGTGCATCATTTGTTGCCTTATTTGCTCAGTTGGGTGGTGGAATATATACTAAGGGAGCTGATGTCGGGGC
upper sequence: GLYMA08G24120.2 (Glycine max), 3'ss of exon 6
lower sequence: AT1G78920.1 (Arabidopsis thaliana), 3'ss of exon 6
--tttgaccgtgacatgattttaatttttgttcattctctcacctattctctctctctctcaaattggcgatcgattt-ttgagcattcttgttttccttcagTGCCTCTTCTTCTAGTTGGATATGGATTTGGTGCCTCCTTTGTTGCACTATTTGCCCAGTTGGGTGGTGGAATATACACAAAGGCCGCTGATGTTGGAGC
| | | ||| ||||| || | | || | || | | | ||| ||| |||| |||| || || | |||| ||||||||||| || |||||||| |||||||| || |||||||| ||||||| |||||||||||||||||||| || |||| ||||||||||| ||
attctcttgatttattgaccagaatttgcatttgca---tgggcgatagtggagctattaaacttgtaagatttattgattgaattttctgtttctcttacagTACCTCTTCTTCTTGTCGGATATGGTTTTGGTGCTTCGTTTGTTGCCTTATTTGCTCAGTTGGGTGGTGGAATATATACTAAGGGAGCTGATGTTGGGGC
upper sequence: GLYMA08G24120.2 (Glycine max), 3'ss of exon 6
lower sequence: Vv09s0054g00700.t01 (Vitis vinifera), 3'ss of exon 6
tttgaccgtgacatgattttaatttttgttcattctctcacctattctctctctctctcaaattggcg--atcgatttttgagcattcttgttttcctt---cagTGCCTCTTCTTCTAGTTGGATATGGATTTGGTGCCTCCTTTGTTGCACTATTTGCCCAGTTGGGTGGTGGAATATACACAAAGGCCGCTGATGTTGGAGC
| |||| ||| | | || | | || | | | | || ||| | ||| ||| | | | ||| | ||| |||||||||||||||| || |||||||||||||| || || |||||||| || ||||| |||||||||||||||||||| ||||| || || |||||||||||
-----tttttacatctcttttacacctaccattttcttgaattagcatgcacatgtattaatgtggtgtaatctgtttattgacttcaatgtacttctttcccagTGCCTCTTCTTCTTGTGGGATATGGATTTGGAGCTTCATTTGTTGCCCTTTTTGCTCAGTTGGGTGGTGGAATATATACAAAAGCAGCAGATGTTGGAGC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tctctctctctctcaaattggcgatcgatttttgagcattcttgttttccttcagTGCCTCTTCTTCTAGTTGGATATGGATTTGGTGCCTCCTTTGTTGCACTATTTGCCCAGTTGGGTGGTGGAATATACACAAAGGCCGCTGATGTTGGAGC
cattcttgttttcctt CT-rich tract
atttttga 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tttgaccgtgacatgattttaatttttgttcattctctcacctattctctctctctctcaaattggcgatcgatttttgagcattcttgttttccttcagTGCCTCTTCTTCTAGTTGGATATGGATTTGGTGCCTCCTTTGTTGCACTATTTGCCCAGTTGGGTGGTGGAATATACACAAAGGCCGCTGATGTTGGAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG