Sequence
atgc intronic sequence ATGC exonic sequence...ttgtaaaatagcaaatgcctccctttgtttaaaatggattgttttatgagttcacaaagtggattcttttcattgttaaatagcattctgctctttgcagGAGAAGGATATTACTCTAAGTGGCGAGCATGTGAGAGAGGGTCTAACATGTGTTGTCTCAGTCAAGGTCCCAAATCCTGAGTTTGAAGGACAAACAAAG
Basic information
species | Glycine max |
transcript | GLYMA03G28290.1 |
intron # | 11 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA03G28290.1 (Glycine max), 3'ss of exon 11
lower sequence: LOC_Os01g16290.1 (Oryza sativa), 3'ss of exon 11
ttgtaaaatagcaaatgcctccctttgtttaaaatggattgttttatgagttcacaaagtggattcttttcat------tgttaaatagcattctgctctttgcagGAGAAGGATATTACTCTAAGTGGCGAGCATGTGAGAGAGGGTCTAACATGTGTTGTCTCAGTCAAGGTCCCAAATCCTGAGTTTGAAGGACAAACAAAG
|| | ||||| | | | | || | ||| | ||| ||| || | | | | ||| |||| | | | | || |||| ||| |||| || ||||||| | ||||| |||||||| |||||||| | || || || | |||| |||||||| ||||| ||||||||||| |||||||||
tttt----tagcatacttattcatctgatcaaatggtatt-tttaattaact-gtattggtaatttttttagtgggatttatcttaacatataatgctttttatagGATAAAGATATTAGCTTGAGTGGGGAGCATGTAAGAGAGGGAATGACCTGCATTATTGCAGTGAAGGTCCCTAATCCAGAGTTTGAAGGGCAAACAAAG
upper sequence: GLYMA03G28290.1 (Glycine max), 3'ss of exon 11
lower sequence: AT5G04130.2 (Arabidopsis thaliana), 3'ss of exon 11
ttgtaaaatagcaaatgcctccctttgtttaaaatggattgttttatgagttcacaaagtggattcttttcattgttaaatagcattctgctct--ttgcagGAGAAGGATATTACTCTAAGTGGCGAGCATGTGAGAGAGGGTCTAACATGTGTTGTCTCAGTCAAGGTCCCAAATCCTGAGTTTGAAGGACAAACAAAG
| || | || | | |||| | |||| | || | || || ||| | | ||| || | ||| | || |||||||| ||||||| ||||||| || ||||| |||||||| | || ||| | |||||||||||||| || ||||||||||||||||| |||||||||
gtaaaacgttcttgattcataccttcaat--aaataatatacttccttcatttcttttttgtatttataattattttatatttttgttggctgtgttttcagGAGAAAGATATTAGCTTAAGTGGGGAACATGTTAGAGAGGGATTGACCTGTATCGTCTCAGTCAAGGTTCCTAATCCTGAGTTTGAAGGTCAAACAAAG
upper sequence: GLYMA03G28290.1 (Glycine max), 3'ss of exon 11
lower sequence: AT3G10270.1 (Arabidopsis thaliana), 3'ss of exon 12
-----------------ttgtaaaata--------gcaaatgcctccctttgtttaaaatgga----ttgtttta---tgagttcacaaagtggattcttttcattgttaaatagcatt-ctgctc---tttgcagGAGAAGGATATTACTCTAAGTGGCGAGCATGTGAGAGAGGGTCTAACATGTGTTGTCTCAGTCAAGGTCCCAAATCCTGAGTTTGAAGGACAAACAAAG
||| ||| | | | | |||| ||| | | | || | || || | | || || | | | | ||| | || || || | ||| ||||| |||||||||| ||||||| || ||||| || || || | || || |||||||||||||||| || || |||||||||||||| |||||||||
gtactaccatgattgaactgtgaaacatgccagttatagaggttgttttttgcttacatttaagcatttatcttgacctgttctgaaaaggttgctaactcatagtgtaacttattgttgttggttatgttttcagGAAAAGGATATTAGCTTAAGTGGGGAACATGTTAGGGAAGGATTGACCTGCATTGTCTCAGTCAAGGTTCCGAACCCTGAGTTTGAAGGTCAAACAAAG
upper sequence: GLYMA03G28290.1 (Glycine max), 3'ss of exon 11
lower sequence: Vv08s0007g05120.t01 (Vitis vinifera), 3'ss of exon 11
--ttgtaaaatagcaaatgcctccctttgtttaaaatggattgttttatgagttcacaaagtggattcttttcattgttaaatagcattctgctctttgcagGAGAAGGATATTACTCTAAGTGGCGAGCATGTGAGAGAGGGTCTAACATGTGTTGTCTCAGTCAAGGTCCCAAATCCTGAGTTTGAAGGACAAACAAAG
|| || | | ||| | | ||||| | || | |||||| | ||| | |||| || ||| || || | | |||||||||||||||||| |||||||||| ||||| |||||||| ||||||||||| ||||||| || || |||||||| || ||||||||||| || |||
tattttattagacttgatgaactcgt--agttaaatttgaataaaaaatgagtggaagcagtagtaactttcagcagtaaaagtttgttttgtttcattcagGAGAAGGATATTACTTTAAGTGGCGAACATGTAAGAGAGGGATTAACATGTGTTATCTCAGTAAAAGTTCCAAATCCAGAATTTGAAGGACAGACGAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atgagttcacaaagtggattcttttcattgttaaatagcattctgctctttgcagGAGAAGGATATTACTCTAAGTGGCGAGCATGTGAGAGAGGGTCTAACATGTGTTGTCTCAGTCAAGGTCCCAAATCCTGAGTTTGAAGGACAAACAAAG
ttctgctcttt CT-rich tract
ttttcattgttaaata 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttgtaaaatagcaaatgcctccctttgtttaaaatggattgttttatgagttcacaaagtggattcttttcattgttaaatagcattctgctctttgcagGAGAAGGATATTACTCTAAGTGGCGAGCATGTGAGAGAGGGTCTAACATGTGTTGTCTCAGTCAAGGTCCCAAATCCTGAGTTTGAAGGACAAACAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - -caaatgc
- - - - - - - - - ctccctt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gcattct