Sequence
atgc intronic sequence ATGC exonic sequencegtatgacattcttttacacaactgaaccaaaccaagttttatgtttctctctcttttttttctttaagattatttgaagttaataaaattgtattattctgtttgtagGGAATTGACACAATGGTTGGAGGGCATGGAACTCAACTTTCTGGTGGGCAAAAACAAAGAATAGCAATTGCAAGGGCAATTTTGAAGAACCCAAGAATCC
Basic information
species | Glycine max |
transcript | GLYMA13G29380.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA13G29380.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os02g21750.1 (Oryza sativa), 3'ss of exon 1
-------------------gtatgacattcttt-tacacaactgaaccaaaccaa---gttttatgtttctctctcttttttttctttaagattatttgaagttaataaaattgtattatt--------ctgtttgtagGGAATTGACACAATGGTTGGAGGGCATGGAACTCAACTTTCTGGTGGGCAAAAACAAAGAATAGCAATTGCAAGGGCAATTTTGAAGAACCCAAGAATCC
| | ||||| | | | | || | || | | | | | ||| || | | ||||| | || || || || || ||| ||||| | || ||||||||||| | |||||| || || || |||||||| || ||||||||||| ||||||||||| |||||||||||| |||| || || |
gtacactcatctattcaaacaacccctctctttctgcccttttagctttgacttatggattctgcgatctctttttagcatttatttcatcttaatttggggcccatgaatcatgatcataagtgataactattttcagGGACTAGATACAATGGTTGGTGAGCATGGCACACAGCTATCTGGTGGACAGAAACAAAGAATTGCAATTGCAAGAGCAATTTTGAAGGACCCTAGGATAC
upper sequence: GLYMA13G29380.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G412276_T01 (Zea mays), 3'ss of exon 5
-----gtatgacattcttttacacaactgaaccaaaccaagttttatgtttctctctcttttttttctttaagattatttgaagttaataaaattgtattattctgtttgtagGGAATTGACACAATGGTTGGAGGGCATGGAACTCAACTTTCTGGTGGGCAAAAACAAAGAATAGCAATTGCAAGGGCAATTTTGAAGAACCCAAGAATCC
| || |||| | | | | | | |||| | | |||| | | | ||| || | | | || | | | | | | | | |||| ||||||||||||| || | ||||||||||| || ||||| ||||| ||||| |||||||||||||| || ||||| | |||||||| | |||
gtataactcaatgaactattacgtccgtaatgctatttatttattatatagatgctaattttctgccactcccattgtt---aatcagtacatct-tgtgaaac-atccgcagGGTCTTGACACAATGGTGGGGGAACATGGAACTCAGCTGTCTGGAGGGCAGAAACAGAGAATAGCAATTGCTAGAGCAATCATAAAGAACCCTAAGATCT
upper sequence: GLYMA13G29380.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G082385_T01 (Zea mays), 3'ss of exon 6
gtatgacattcttttacacaactgaaccaaaccaagttttatgtttctctctcttttttttctttaagat-tatttgaagttaataaaattgtattattctgtttgtagGGAATTGACACAATGGTTGGAGGGCATGGAACTCAACTTTCTGGTGGGCAAAAACAAAGAATAGCAATTGCAAGGGCAATTTTGAAGAACCCAAGAATCC
| | | |||| || || | | | || | || | || | | || | | |||| || | || | || |||| | ||||||||||| || | ||||||| | ||| | || || ||||||||||||||||| ||||| |||||||||| |||| ||||| | |||
-----------------gtatgtagattaaacaaaattgtttcatacttgtgcaaagttacatatatgttataactaaccataattaatcgagaactttgttatttcagGGCCTAGACACAATGGTCGGTGAGCATGGAGCACAATTGTCAGGAGGGCAAAAACAAAGAATTGCAATCACAAGGGCAATACTGAAAAACCCCAAGATCT
upper sequence: GLYMA13G29380.1 (Glycine max), 3'ss of exon 6
lower sequence: AT4G18050.1 (Arabidopsis thaliana), 3'ss of exon 6
gtatgacattcttttacacaactgaaccaaaccaagttttatgtttctctctcttttttttctttaagattatttgaagttaataaaattgtattattctgtttgtagGGAATTGACACAATGGTTGGAGGGCATGGAACTCAACTTTCTGGTGGGCAAAAACAAAGAATAGCAATTGCAAGGGCAATTTTGAAGAACCCAAGAATCC
| | || | | | || || | | | ||| | | | || || ||| | ||| || || ||||| ||||||||||||| | || |||||||| |||| ||| || || ||| | ||||| ||||| ||||| ||| ||||||| || ||||| |||||||| ||||| | |||
-------gtaccttcaaatttcaatacagaaactactattagaagaatttgtattcgttgcattt----tcttttaaa----atgaaatta------tctgtttgtagGGTTTGGATACAATGGTAGGAGAGCACGGGACACAAATGTCTGGCGGGCAGAAACAGAGACTAGCAATCGCTAGGGCGATTTTGAAAAACCCTAAAATAT
upper sequence: GLYMA13G29380.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv10s0003g02580.t01 (Vitis vinifera), 3'ss of exon 6
--------------------------------------------------------------------------------------gtatgacattcttttacacaactgaaccaaaccaagttttatgtttctctctcttttttttctttaagattatttgaagttaataaaattgtattattctgtttgtagGGAATTGACACAATGGTTGGAGGGCATGGAACTCAACTTTCTGGTGGGCAAAAACAAAGAATAGCAATTGCAAGGGCAATTTTGAAGAACCCAAGAATCC
| || || || | || || | || ||| | | | | || || |||| || | ||| | ||| | | | ||||| |||| | ||||||||||| || | |||||||| || | ||||| || || || |||||||| ||||||||||| || ||||||||||| ||||||||||
gtgagcctatgattcattcatattcaggtcacagttgaaagagggttcaaatatacatgtctgttagaatgagtccatgaatcactgcatttcaacctcacagacctttgtaataataagagtcatgcaat-caaacaaattcttctcttc----ttttcatcagtattttgaatcatggtggtgtgtttacagGGGCTGGACACAATGGTGGGTGAACATGGAACGCAGTTATCTGGAGGACAGAAGCAAAGAATTGCAATTGCAAGAGCCATTTTGAAGAATCCAAGAATCC
upper sequence: GLYMA13G29380.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv10s0003g02540.t01 (Vitis vinifera), 3'ss of exon 6
---------------------------------gtatgacattcttttacaca-actgaaccaaaccaagttttatgt-ttctctctctt-----------------ttttttctttaagattatttgaagttaataaaattgtattattctgtttgtagGGAATTGACACAATGGTTGGAGGGCATGGAACTCAACTTTCTGGTGGGCAAAAACAAAGAATAGCAATTGCAAGGGCAATTTTGAAGAACCCAAGAATCC
||| |||| || | | | | | | ||||| | | |||| | | || || |||| ||| | || | | | ||| || | | ||| | |||| | ||||||||||| || | ||||||||||| || ||||| || || || |||||||| ||||||||||| || ||||||||||||||| ||||||
gtaagcctattttctttctttctccttttattatggtgaaattccttcatattcagcatgctagaaaaagttacaaatcttctatttgttaaatagagaaacaattcttctttccttataaaggcctgcaatatttggaatggttgtggtgtgtatacagGGGCTAGACACAATGGTGGGTGAACATGGAACTCAGCTATCTGGGGGACAGAAGCAAAGAATTGCAATTGCAAGAGCCATTTTGAAGAACCCACGAATCC
upper sequence: GLYMA13G29380.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv10s0003g02570.t01 (Vitis vinifera), 3'ss of exon 7
--------------------------------------------------gtatgacattcttttaca-caactgaacca-aaccaagttttatgtttctctctcttttttttctttaagattatttgaag--ttaataaaattgtattat--tctgtttgtagGGAATTGACACAATGGTTGGAGGGCATGGAACTCAACTTTCTGGTGGGCAAAAACAAAGAATAGCAATTGCAAGGGCAATTTTGAAGAACCCAAGAATCC
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gtgagccattctttcttaagtgaattcaaggtcatattcaggtcacagatccctgacagatctctgcagcattcaaaccataattaccgtgtagcctaataaattcttcttttccttttaatggtctaaacatctggaatggttgtggtgtgatttaattacagGGACTTGACACAATGGTGGGTGAGCATGGAACTCAGCTATCTGGGGGACAGAAGCAAAGAATTGCAATTGCAAGAGCCATTTTGAAGAACCCAAGAATCC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttttttttctttaagattatttgaagttaataaaattgtattattctgtttgtagGGAATTGACACAATGGTTGGAGGGCATGGAACTCAACTTTCTGGTGGGCAAAAACAAAGAATAGCAATTGCAAGGGCAATTTTGAAGAACCCAAGAATCC
agttaat putative branch site (score: 4)
ttctgttt putative PPT
tttctttaagattatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatgacattcttttacacaactgaaccaaaccaagttttatgtttctctctcttttttttctttaagattatttgaagttaataaaattgtattattctgtttgtagGGAATTGACACAATGGTTGGAGGGCATGGAACTCAACTTTCTGGTGGGCAAAAACAAAGAATAGCAATTGCAAGGGCAATTTTGAAGAACCCAAGAATCC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC