Sequence
atgc intronic sequence ATGC exonic sequence...ttgagcttgcactgctgataagtccattgacttgtgatacgtggaaatcaaacaattgtgaagtttttggaatattacatatttattttgtgaaatttagGTTGAGGATGCTCAATCACGTGAAGCACCTGTACAAAGGCTTGCAGATTCAATAGCAGGGCCATTTGTATACAGTGTAATGACTTTGTCAGCAGCAACAT
Basic information
species | Glycine max |
transcript | GLYMA04G05900.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA04G05900.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os03g08070.1 (Oryza sativa), 3'ss of exon 7
-----ttgagcttgcactgctgataagtccattgacttgtgatacgtggaaatcaaacaattgt--gaagtttttggaatattacatatttattttgtgaaatttagGTTGAGGATGCTCAATCACGTGAAGCACCTGTACAAAGGCTTGCAGATTCAATAGCAGGGCCATTTGTATACAGTGTAATGACTTTGTCAGCAGCAACAT
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gtaggtatactcttttctcttgataa--caaagaaactaaaagaagtttttttttctcgaccaaaagaagtttttataatact-tgtattgttcttgaa-----cagGTTGAGGATGCACAAGCACGTGAAGCTCCCGTTCAAAGGCTTGCAGATTCAATTGCAGGGCCATTTGTTTATACTGTTATGACATTGTCTGCAGCAACAT
upper sequence: GLYMA04G05900.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM5G855347_T02 (Zea mays), 3'ss of exon 2
ttgagcttgcactgctgataagtccattgacttgtgatacgtggaaatcaaacaattgtgaagtttttggaatattacatatttattttgtgaaatttagGTTGAGGATGCTCAATCACGTGAAGCACCTGTACAAAGGCTTGCAGATTCAATAGCAGGGCCATTTGTATACAGTGTAATGACTTTGTCAGCAGCAACAT
| || || || | || | | | ||| | || | | | | || | ||| |||| ||| | |||| ||||||||||||| ||| |||||||||| ||||| |||||||| |||||||| || ||||| |||||||| || | ||| ||||| ||| | ||| |||| |
-------------gttgtgaaacacaccctttgctgttgagagtaaagcgaagggtgaaaagggtgtttaactat---atatgtatcct-tgaa---cagGTTGAGGATGCCCAAGCACGTGAAGCTCCTGTTCAAAGGCTCGCAGATTCCATCGCAGGACCATTTGTGTATACTGTTATGACGTTGGCTGCAACAACCT
upper sequence: GLYMA04G05900.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv04s0008g01960.t01 (Vitis vinifera), 3'ss of exon 8
ttgagcttgcactgctgataagtccattgacttgt-gatacgtggaaa--tcaaacaattgtgaagttttt--ggaatattacatatttattttgtgaaatttagGTTGAGGATGCTCAATCACGTGAAGCACCTGTACAAAGGCTTGCAGATTCAATAGCAGGGCCATTTGTATACAGTGTAATGACTTTGTCAGCAGCAACAT
|| | ||| || ||||| ||||| || | | ||| || | ||||| | || ||| | | ||| | | | || ||||||||||||||||| |||| |||||| |||||||||||||||||||||| || || |||||||| || | ||| |||||||| ||||||||||| |
-----tttaaagaatctatatacttgatggcttgttgatacatgaggagtttaaatgttttagtagtttctacggtttatgaaaccttttgctcataatcttcagGTTGAGGATGCTCAAGGCCGTGCAGCACCCATACAAAGGCTTGCAGATTCAATTGCTGGACCATTTGTCTATATTGTGATGACTTTATCAGCAGCAACTT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aatcaaacaattgtgaagtttttggaatattacatatttattttgtgaaatttagGTTGAGGATGCTCAATCACGTGAAGCACCTGTACAAAGGCTTGCAGATTCAATAGCAGGGCCATTTGTATACAGTGTAATGACTTTGTCAGCAGCAACAT
tttttggaatattaca 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttgagcttgcactgctgataagtccattgacttgtgatacgtggaaatcaaacaattgtgaagtttttggaatattacatatttattttgtgaaatttagGTTGAGGATGCTCAATCACGTGAAGCACCTGTACAAAGGCTTGCAGATTCAATAGCAGGGCCATTTGTATACAGTGTAATGACTTTGTCAGCAGCAACAT
- gagcttg
- - - - -cactgct
- - - - - - - - - - - - - - -acttgtg
- - - - - - - - - - - - - - - - - - - - - - - -tcaaaca