Sequence
atgc intronic sequence ATGC exonic sequencegtattttcttagttttttactttcttttatctccattgtaggtggccttaaaacaacatatacaagtgtgtgtgtgtgtgcgcgtgtgtgtgtgtgtgtgcgcgtgtgcacgcatgcgtggggttttctgatgagcagtgtttcagGAACGTCTAGAAGCAGCAAATGCTTTAAAAAAGCAGATGTGGGCAGAAGCACAGCTTGATAAACGCCGTATCAAAGAGGATTACTTTGCTAAGATGCAGT
Basic information
species | Glycine max |
transcript | GLYMA06G44290.1 |
intron # | 17 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA06G44290.1 (Glycine max), 3'ss of exon 17
lower sequence: LOC_Os05g48820.1 (Oryza sativa), 3'ss of exon 13
gtattttcttagttttttactttcttttatctccattgtaggtggccttaaaacaacatatacaagtgtgtgtgtgtgtgcgcgtgtgtgtgtgtgtgtgcgcgtgtgcacgcatgcgtggggttttctgatgagcagtgtttcagGAACGTCTAGAAGCAGCAAATGCTTTAAAAAAGCAGATGTGGGCAGAAGCACAGCTTGATAAACGCCGTATCAAAGAGGATTACTTTGCTAAGATGCAGT
|| | || || || | ||| || | | | | | || | || |||||||| || || ||||||| |||||| |||||||| ||||||||||||||||| ||||||||| | ||| | ||||| | | | ||| ||||| |
---------------------------------------------------------------------------gtaattatct-tgcatgatcttgatatcttgt-cattttcccatcatctgaaccaa-aaggatctttgcagGAACGGCTGGAGGCAGCAAGTGCTTTGAAAAAGCAAATGTGGGCAGAAGCACAACTTGATAAAAGACGTTCGAGGGAGGAATTTTCTAGTAAAATGCAAT
upper sequence: GLYMA06G44290.1 (Glycine max), 3'ss of exon 17
lower sequence: LOC_Os01g48180.1 (Oryza sativa), 3'ss of exon 12
gtattttcttagttttttactttcttttatctccattgtaggtggccttaaaacaacatatacaagtgtgtgtgtgtgtgcgcgtgtgtgtgtgtgtgtgcgcgtgtgcacgcatgcgtggggttttctgatgagcagtgtttcagGAACGTCTAGAAGCAGCAAATGCTTTAAAAAAGCAGATGTGGGCAGAAGCACAGCTTGATAAACGCCGTATCAAAGAGGATTACTTTGCTAAGATGCAGT
|| | | | | | | | | ||| | | | | || | ||||| | || |||||||||||||| ||| |||||||||| |||||||| || ||| |||||| ||||| |||||||| | ||| ||| || || | || | |||| |
-----------------------------------------------------------------gtaataatcttacttaaaatatccttcaatctttgctatttttctcat-tggataacac---ctgatcacttgtctttcagGAACGTCTGGAATCAGCAAATGCCTTAAAAAAACAAATGCTGGCAGAGGCACAACTTGATAAGAGGCGTTCCAAGGAAGAGTTTGCTGGCAGAGTGCAAT
upper sequence: GLYMA06G44290.1 (Glycine max), 3'ss of exon 17
lower sequence: GRMZM2G122750_T01 (Zea mays), 3'ss of exon 13
gtattttcttagttttttactttcttttatctccattgtaggtggccttaaaacaacatatacaagtgtgtgtgtgtgtgcgcgtgtgtgtgtgtgtgtgcgcgtgtgcacgcatgcgtggggttttctgatgagcagtgttt-cagGAACGTCTAGAAGCAGCAAATGCTTTAAAAAAGCAGATGTGGGCAGAAGCACAGCTTGATAAACGCCGTATCAAAGAGGATTACTTTGCTAAGATGCAGT
|| ||| | |||| | ||| | | | | | | ||||| | ||| ||| |||||||| ||||||||||||| |||||| ||||| || |||||||| || ||||| |||||||| | ||| |||| | ||| ||||| ||| |
-----------------------------------------------------------------------gta-atgtttatat-tgtgattttgttatcttgc-tattttcctattgaacatcatctgaacaacagACTTTACAGGAACGCCTAGAAGCAGCAAGTGCTTTGAAAAAACAAATGTGGGCTGAGGCACAACTTGATAAGAGGCGT-TCAAGG--GATGACTTTACTAGTA------
upper sequence: GLYMA06G44290.1 (Glycine max), 3'ss of exon 17
lower sequence: GRMZM2G125294_T01 (Zea mays), 3'ss of exon 13
gtattttcttagttttttactttcttttatctccattgtaggtggccttaaaacaacatatacaagtgtgtgtgtgtgtgcgcgtgtgtgtgtgtgtgtgcgcgtgtgcacgcatgcgtggggttttctgatgagcagtgtttcagGAACGTCTAGAAGCAGCAAATGCTTTAAAAAAGCAGATGTGGGCAGAAGCACAGCTTGATAAACGCCGTATCAAAGAGGATTACTTTGCTAAGATGCAGT
|| ||| | || | | ||| || | | | ||| | | | || ||||||||||| ||||||||||| | |||||| ||||| || ||||||| || ||||| |||||||| | ||||| | || || | | |||||||||||
---------------------------------------------------------------------gta-atgtttctat-tgcgattttgttatcttgc-tattttcccat-tgaacatcatctgaacaagagacttttcagGAACGCCTAGAAGCAGCGAGTGCTTTGAAAAAACAATTGTGGGCTGAGGCACAACTTGATAAGAGGCGTATAAGGGATGACTTTACTAGTAAGATGCAGT
upper sequence: GLYMA06G44290.1 (Glycine max), 3'ss of exon 17
lower sequence: GRMZM2G159357_T01 (Zea mays), 3'ss of exon 13
gtattttcttagttttttactttcttttatctccattgtaggtggccttaaaacaacatatacaagtgtgtgtgtgtgtgcgcgtgtgtgtgtgtgtgtgcgcgtgtgcacgcatgcgtggggttttctgatgagcagtgtttcagGAACGTCTAGAAGCAGCAAATGCTTTAAAAAAGCAGATGTGGGCAGAAGCACAGCTTGATAAACGCCGTATCAAAGAGGATTACTTTGCTAAGATGCAGT
|| | | | || | || | | | ||| | || ||||| | ||| || ||||| ||| | || ||||||||| ||||| ||||| |||||||||||||| || ||||| || | ||| |||| || || | | | | || |
---------------------------------------------------------------------gtatatat-tgtgatcctgctaaactattctatcttgtcattcctcattgggaaacacctgatcaagagtcttgcagGAGCGTTTGGAGTTAGCAAATGCCTTAAAGAAGCAAATGTGGGCAGAAGCGCAACTTGACAAGAGGCGTTTCAAGGAAGAATTTACTAGCAGAGTACAAT
upper sequence: GLYMA06G44290.1 (Glycine max), 3'ss of exon 17
lower sequence: Vv12s0028g03090.t01 (Vitis vinifera), 3'ss of exon 10
gtattttcttagttttttactttcttttatctccattgtaggtggccttaaaacaacatatacaagtgtgtgtgtgtgtgcgcgtgtgtgtgtgtgtgtgcgcgtgtgcacgcatgcgtggggttttctgatgagcagtgtttcagGAACGTCTAGAAGCAGCAAATGCTTTAAAAAAGCAGATGTGGGCAGAAGCACAGCTTGATAAACGCCGTATCAAAGAGGATTACTTTGCTAAGATGCAGT
|| | || ||| ||| | |||| | | | ||||| || || || || | | | | || ||| | | | | || ||| | ||||||||| | ||||| ||||||||| | || ||||| ||||||||||| || || ||||||||||| || || ||||| || || | |||||||| |
-------------gttgcatcttttttcctcttc-ttgttgat--ctataaaataatttagtaaattgcatttcttttggc-----------------------tgtaatctgaaacaagaggcttt--------------tccagGAACGTTTGGAAGCGGCAAATGCTCTGAAGAAGCAAATGTGGGCAGAGGCTCAACTTGATAAACGGCGCATGAAAGAAGAGTATGTCATGAAGATGCATT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gtgtgtgtgcgcgtgtgcacgcatgcgtggggttttctgatgagcagtgtttcagGAACGTCTAGAAGCAGCAAATGCTTTAAAAAAGCAGATGTGGGCAGAAGCACAGCTTGATAAACGCCGTATCAAAGAGGATTACTTTGCTAAGATGCAGT
ttctgat putative branch site (score: 3)
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtattttcttagttttttactttcttttatctccattgtaggtggccttaaaacaacatatacaagtgtgtgtgtgtgtgcgcgtgtgtgtgtgtgtgtgcgcgtgtgcacgcatgcgtggggttttctgatgagcagtgtttcagGAACGTCTAGAAGCAGCAAATGCTTTAAAAAAGCAGATGTGGGCAGAAGCACAGCTTGATAAACGCCGTATCAAAGAGGATTACTTTGCTAAGATGCAGT
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