Sequence
atgc intronic sequence ATGC exonic sequencegtaagggtgttgcttaaaccaataaaatctttctaattgcttattatagatgcctgattattatttcctaatgatgctcagGTCTGTGCTGGATTGTCATCCCGTCTTCAAGAATACAAATCTGAAAATGCACAGTTGGAGGAACTTCTCACTTCAGAG
Basic information
species | Glycine max |
transcript | GLYMA16G08430.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA16G08430.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os01g54119.1 (Oryza sativa), 3'ss of exon 5
---------gtaagggtgttgcttaaaccaataaaatctttctaattgcttattatagatgcctgattattatttcctaatgatgctcagGTCTGTGCTGGATTGTCATCCCGTCTTCAAGAATACAAATCTGAAAATGCACAGTTGGAGGAACTTCTCACTTCAGAG
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gtaagagcagtataagtttgaccctgcctgttatctatgttgtggctagttcatatgctgacttgtagatttatttgttactaccaatagGTCTGCGCTGGACTTTCATCCCGCCTCCAGGAGTATAAATCTGAGAATGCACAGCTGGAGGAACTTCTTGTTCAGGAG
upper sequence: GLYMA16G08430.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G055219_T01 (Zea mays), 3'ss of exon 5
-------------------------------------------------gtaagggtgttgc-ttaaaccaataaaatctttctaattgcttattatagatgcctgattatt-atttcctaatgatgctcagGTCTGTGCTGGATTGTCATCCCGTCTTCAAGAATACAAATCTGAAAATGCACAGTTGGAGGAACTTCTCACTTCAGAG
|| | | | || | | ||| || | | || || ||| ||| | | | | | |||| ||||||||| | |||||||| || ||||| || || ||||||||||||||| ||||||||||||| | ||||
gtaaggataagcataagctcaattgcctcacaactcacactcgatctatgttggttagctctgtttttttgttcgtttgttttcaacttaccaacatgttcttttgcccatttgttttcaacttacgaatagGTTTGTGCTGGACTTTCATCCCGCCTCCAAGAGTATAAGTCTGAAAATGCACAGCTGGAGGAACTTCTTGTTCAAGAG
upper sequence: GLYMA16G08430.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM5G870802_T01 (Zea mays), 3'ss of exon 3
-----------------------------------------------------gtaagggtgttgcttaaaccaataaaatctttctaattgcttattatagatgcctgattat-tatttcctaatgatgctcagGTCTGTGCTGGATTGTCATCCCGTCTTCAAGAATACAAATCTGAAAATGCACAGTTGGAGGAACTTCTCACTTCAGAG------
|| || | || | | ||| || | || | || || | ||| | | | | | |||| ||||||||| | |||||| | || ||||| || || ||| ||||||||||| ||||||||||||| | ||||
gtaaggataagcataagctcaattgcctcacaactcacacttgatctatgttggttagctctgttttttttttgttcgtttgttttcaacctaccaacatgtttttttgcccatctgttttcaacttacgaatagGTTTGTGCTGGACTTTCATCCTGCCTCCAAGAGTATAAGTCTAAAAATGCACAGCTGGAGGAACTTCTTGTTCAAGAGGTCTAG
upper sequence: GLYMA16G08430.1 (Glycine max), 3'ss of exon 5
lower sequence: AT2G19950.1 (Arabidopsis thaliana), 3'ss of exon 5
--------------------------------gtaagggtgttgcttaaac-caataaaatctttctaattgcttatta-------tagatgcctgattattatttcctaatgatgctc-agGTCTGTGCTGGATTGTCATCCCGTCTTCAAGAATACAAATCTGAAAATGCACAGTTGGAGGAACTTCTCACTTCAGAG
| | | || | || | | || | | ||| || | | ||||| | | || | || | || | ||| |||| ||||||||| | || ||||||||||||||| ||| | ||||||||||||||||| || ||||||||| |||||
gtaagctcaaatatccattgctactttcctgcatcaaatttgtgataaagtactctttcatgcctgtggttggttctgagcaacctcagatgtatccattttttgtcttcattttcctctagGTTTGTGCTGGACTTTCGTCCCGTCTTCAAGAAATTAAAGCGGAAAATGCACAGTTGGAAGAGCTTCTCACTGCAGAG
upper sequence: GLYMA16G08430.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv11s0016g03230.t01 (Vitis vinifera), 3'ss of exon 5
-------------gtaagggtgttgcttaaaccaataaaat--ctttctaattgctta---ttatagatgcctga-ttattatttcctaatgatgctcagGTCTGTGCTGGATTGTCATCCCGTCTTCAAGAATACAAATCTGAAAATGCACAGTTGGAGGAACTTCTCACTTCAGAG
||| | || | | ||| ||| ||| || || || || | || || ||| | | ||| |||| |||||| ||||||||| | | | ||||||||||||||| |||||||||||||||||||||||| |||||||||||| |||||
ttatggcttctatataatcatattttcttatttgatagaattccttgtcaaatgttttgccttttggaagcaaatcttaatgcatgctattgatattcagGTTTGTGCTGGACTTTTAACCCGTCTTCAAGAATGCAAATCTGAAAATGCACAGTTGGAAGAACTTCTCACTGCAGAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atctttctaattgcttattatagatgcctgattattatttcctaatgatgctcagGTCTGTGCTGGATTGTCATCCCGTCTTCAAGAATACAAATCTGAAAATGCACAGTTGGAGGAACTTCTCACTTCAGAG
tcctaat putative branch site (score: 2)
attattatttcctaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagggtgttgcttaaaccaataaaatctttctaattgcttattatagatgcctgattattatttcctaatgatgctcagGTCTGTGCTGGATTGTCATCCCGTCTTCAAGAATACAAATCTGAAAATGCACAGTTGGAGGAACTTCTCACTTCAGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA