Sequence
atgc intronic sequence ATGC exonic sequence...tcctgtcgtgtgttgactatgaaaagtcagtcaaagctgtatattgttgaatgtgtgattttttttgtgttcatttgacttctaatatgtaactattcagGTTGGATTGGCAATGGTTGTGGTGGAAAGTGCTGTTACATCCATATATATCTGCTATGCTGAAGACCCGTTATTGATTCAGAGATGGGATGCTGAATTTT
Basic information
species | Glycine max |
transcript | GLYMA20G24760.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA20G24760.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM5G801651_T01 (Zea mays), 3'ss of exon 1
-------------------------tcctgtcgtgtgttgactatgaaaagtca------gtcaaagctgtatattgttgaatgtgtgattttttttgtgttcatttgacttctaatatgt--aactattcagGTTGGATTGGCAATGGTTGTGGTGGAAAGTGCTGTTACATCCATATATATCTGCTATGCTGAAGACCCGTTATTGATTCAGAGATGGGATGCTGAATTTT
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gtaagtgccaatatctcgatatgaatttgcatgactagtaactaaggaaaggaaaaccgtgtccaagttttctttctcatacagtacaatctctgctagttctgtcaagattgacgtctgctcaattttgcagGTTGGACTAACTGTTGTGGTTGTGGAAAGTGCTGTTACATCAATATACATATGCTATGCCGAGGATCCCCTTTTGATTCAGAGATGGGATCCCGAATTTT
upper sequence: GLYMA20G24760.1 (Glycine max), 3'ss of exon 6
lower sequence: AT1G25500.2 (Arabidopsis thaliana), 3'ss of exon 6
---tcctgtcgtgtgttgactatgaaaagtcagtcaaagctgtatattgttgaatgtgtgattttttttgtgttcatttgacttctaatatgtaactattcagGTTGGATTGGCAATGGTTGTGGTGGAAAGTGCTGTTACATCCATATATATCTGCTATGCTGAAGACCCGTTATTGATTCAGAGATGGGATGCTGAATTTT
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gtgagttttcttttgtgcactctttta-gtcacccaaaaaattacatgaccaact------tgttcactttgtttcattga--tccaatgtgg---tgttcagGTGGGTTTAGGAATGGTGGTAGTCGAAAGCGCTGTGACATCGATATACATATGTTTTGCTGAAGATCCTTTGTTGATTCAGAGATGGGATGCTGATTTCT
upper sequence: GLYMA20G24760.1 (Glycine max), 3'ss of exon 6
lower sequence: AT1G25500.1 (Arabidopsis thaliana), 3'ss of exon 6
---tcctgtcgtgtgttgactatgaaaagtcagtcaaagctgtatattgttgaatgtgtgattttttttgtgttcatttgacttctaatatgtaactattcagGTTGGATTGGCAATGGTTGTGGTGGAAAGTGCTGTTACATCCATATATATCTGCTATGCTGAAGACCCGTTATTGATTCAGAGATGGGATGCTGAATTTT----------
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gtgagttttcttttgtgcactctttta-gtcacccaaaaaattacatgaccaact------tgttcactttgtttcattga--tccaatgtgg---tgttcaggtgggtttagGAATGGTGGTAGTCGAAAGCGCTGTGACATCGATATACATATGTTTTGCTGAAGATCCTTTGTTGATTCAGAGATGGGATGCTGATTTCTACACTGAGAT
upper sequence: GLYMA20G24760.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv01s0011g03220.t01 (Vitis vinifera), 3'ss of exon 6
tcctgtcgtgtgttgactatgaaaagtcagtcaaagctgtatattgttgaatgtgtgattttttttgtgttcatt------tgacttctaatatgtaactattcagGTTGGATTGGCAATGGTTGTGGTGGAAAGTGCTGTTACATCCATATATATCTGCTATGCTGAAGACCCGTTATTGATTCAGAGATGGGATGCTGAATTTT
|| | | | | ||||||| | | | ||| | | | | | | || ||| ||| || | ||| || | ||| | || | | |||| ||| |||||||||||||||||||||||||||||||||||||||| || |||||||| |||||||| |||||||| || |||||||||||||| || |
-actcttgggagatgactatatataacc--tcattattttgttggggtct-tatgaagtttatttgatgcttattatgggatgggatggaatgtacaattgt--agGTGGGACTGGCAATGGTTGTGGTGGAAAGTGCTGTTACATCCATATACATTTGCTATGCAGAAGACCCCTTATTGATCCATAGATGGGATGCTGAGTTCT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gttgaatgtgtgattttttttgtgttcatttgacttctaatatgtaactattcagGTTGGATTGGCAATGGTTGTGGTGGAAAGTGCTGTTACATCCATATATATCTGCTATGCTGAAGACCCGTTATTGATTCAGAGATGGGATGCTGAATTTT
taatatgtaactatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tcctgtcgtgtgttgactatgaaaagtcagtcaaagctgtatattgttgaatgtgtgattttttttgtgttcatttgacttctaatatgtaactattcagGTTGGATTGGCAATGGTTGTGGTGGAAAGTGCTGTTACATCCATATATATCTGCTATGCTGAAGACCCGTTATTGATTCAGAGATGGGATGCTGAATTTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- -tgtcgtg
- - - - - tgttgac
- - - - - - - - - - - - - - - - - agctgta
- - - - - - - - - - - - - - - - - - - - - - tgttgaa
- - - - - - - - - - - - - - - - - - - - - - - - - -tgtgtga