Sequence
atgc intronic sequence ATGC exonic sequencegtatggcaagagatttggaatgtttgttcatgattcttcttgatgagtgatcataccaaatggttgttgtatgttatttttcttcagGAAACTGTTGTTGAGGGAACTATACAAAAGTTATTTGAAGGACACCATATGAATTACATTGAATGCATCAATGTAGACTACAAATCAACTAGAAAGGAGT
Basic information
species | Glycine max |
transcript | GLYMA20G11300.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA20G11300.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os01g56490.1 (Oryza sativa), 3'ss of exon 6
gtatggcaagagatttggaatgtttgttcatgat-tcttcttgatgagtgatcataccaaatggttgt-tgtatgttatttttcttcagGAAACTGTTGTTGAGGGAACTATACAAAAGTTATTTGAAGGACACCATATGAATTACATTGAATGCATCAATGTAGACTACAAATCAACTAGAAAGGAGT
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--------------gttggacatttatttttgttatatgtaagataataaatagtgtttcatcaatgtacaactactctctcgattcagGGAACTACTGTGGAAGGGACAATTCAACAGCTATTTGAAGGTCATCATATGAATTATATTGAGTGCATTAATGTTGACTACAAATCTACAAGGAAAGAAT
upper sequence: GLYMA20G11300.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv06s0009g00960.t01 (Vitis vinifera), 3'ss of exon 6
gtatggcaagagatttggaatgtttgttcatgattcttcttgatgagtgatcata--ccaaatggttgttgtatgttatttttcttcagGAAACTGTTGTTGAGGGAACTATACAAAAGTTATTTGAAGGACACCATATGAATTACATTGAATGCATCAATGTAGACTACAAATCAACTAGAAAGGAGT
|| ||||| | || ||| || | || | | | || || || | |||| ||||||||| ||||| |||||||| ||||||||||||| ||||||||||| |||||||||||||||||||| ||||||||||| || || |||||||
---------------------gtacaaacatgactgttgttgtggaattatttcagttctgacaattattaagtgct------tgccagGGAACTGTTGTGGAGGGCACTATACAGCAGTTATTTGAAGGGCACCATATGAACTACATTGAATGCATCAATGTGGACTACAAATCTACAAGGAAGGAGT
upper sequence: GLYMA20G11300.1 (Glycine max), 3'ss of exon 6
lower sequence: PP1S104_2V6.1 (Physcomitrella patens), 3'ss of exon 6
---------gtatggcaagagatttggaatgtttgttcatgattcttcttgatgagtgatcataccaaatggttg----ttgtatgttatttttcttcagGAAACTGTTGTTGAGGGAACTATACAAAAGTTATTTGAAGGACACCATATGAATTACATTGAATGCATCAATGTAGACTACAAATCAACTAGAAAGGAGT
| | | | | | | | || || || | || || | | | | | | || || | || ||| || | || ||||| || |||||||| | |||||||| || ||||||||||| || |||||||||||||| || | || || ||| | |||||||
gcgttctcggcgttgtggcggttgttgtgcgcgtgaattcagttattgtgcttgggtcaatttgtgagaagtctaaaatttcgatttccgacttacgtagGGCACGGCAGTGGAGGGGACGATACAAAATCTTTTTGAAGGCCATCATATGAATTATATCGAATGCATCAATGTCGATTTTAAGTCCACTCGGAAGGAGT
upper sequence: GLYMA20G11300.1 (Glycine max), 3'ss of exon 6
lower sequence: EFJ14291 (Selaginella moellendorffii), 3'ss of exon 4
gtatggcaagagatttggaatgtttgttcatgattcttcttgatgagtgatcataccaaatggttgttg-tatgttatttttcttcagGAAACTGTTGTTGAGGGAACTATACAAAAGTTATTTGAAGGACACCATATGAATTACATTGAATGCATCAATGTAGACTACAAATCAACTAGAAAGGAGT
||| | | || | ||| ||||| || | | | || ||| |||| |||||| || || ||||| || | || ||||| || ||||||||||| ||||||||||||||||| ||||| || || ||| ||||||| |
-------------------------gtttactgctattttct--------tcacgttaaatgttttctaacaccaagctccactacagAGTACTGCTGTTGAAGGTACCATACAGCAGCTTTTCGAAGGCCATCATATGAATTATATTGAATGCATCAATGTGGACTATAAGTCCACTCGAAAGGAAT
upper sequence: GLYMA20G11300.1 (Glycine max), 3'ss of exon 6
lower sequence: EFJ18164 (Selaginella moellendorffii), 3'ss of exon 4
gtatggcaagagatttggaatgtttgttcatgattcttcttgatgagtgatcataccaaatggttgttg-tatgttatttttcttcagGAAACTGTTGTTGAGGGAACTATACAAAAGTTATTTGAAGGACACCATATGAATTACATTGAATGCATCAATGTAGACTACAAATCAACTAGAAAGGAGT
||| | | || | ||| ||||| || | | | || ||| |||| |||||| || || ||||| || | || ||||| |||||||||||||| ||||||||||||||||| |||||||| || ||| ||||||| |
-------------------------gtttactgctattttct--------tcacgttaaatgttttctaacaccaagctccactacagAGTACTGCTGTTGAAGGTACCATACAGCAGCTTTTCGAAGGCCACCATATGAATTATATTGAATGCATCAATGTGGACTACAAGTCCACTCGAAAGGAAT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.attcttcttgatgagtgatcataccaaatggttgttgtatgttatttttcttcagGAAACTGTTGTTGAGGGAACTATACAAAAGTTATTTGAAGGACACCATATGAATTACATTGAATGCATCAATGTAGACTACAAATCAACTAGAAAGGAGT
tcttgat putative branch site (score: 4)
tgttatttttcttc putative PPT
ttgtatgttattttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatggcaagagatttggaatgtttgttcatgattcttcttgatgagtgatcataccaaatggttgttgtatgttatttttcttcagGAAACTGTTGTTGAGGGAACTATACAAAAGTTATTTGAAGGACACCATATGAATTACATTGAATGCATCAATGTAGACTACAAATCAACTAGAAAGGAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG