Sequence
atgc intronic sequence ATGC exonic sequence...atcaagatagaagacatttataatgtttccttttcataaattcttgaattttacttataaaacagaggctaaaactggttcttgggaaatgtgcttgcagAATCTGTGCTGGCTGCAATTCCGAGATTGGCCATGGAAGATTTTTGAGTTGCATGGGAGGTTATTGGCATCCAGAATGTTTTTGTTGCCATGCTTGCAAA
Basic information
species | Glycine max |
transcript | GLYMA16G25750.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA16G25750.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os06g08400.1 (Oryza sativa), 3'ss of exon 4
atcaagatagaagacatttataatgtttccttttcataaattcttgaattttacttataaaacagaggctaaaactggttcttgggaaatgtgcttg------cagAATCTGTGCTGGCTGCAATTCCGAGATTGGCCATGGAAGATTTTTGAGTTGCATGGGAGGTTATTGGCATCCAGAATGTTTTTGTTGCCATGCTTGCAAA
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--ctgcactgatac--ttggggatggtaattggtaagcgagaatgggatgctgcgagttgcttttactctta--ctgtttcttaatatatacgcttatttcctcagGACTTGTGCCGGATGTCACAGTGAGATTGGTCATGGGCGTTTCCTTAGTTGCATGGGAGCTGTTTGGCATCCAGAATGTTTTCGCTGTCATGCTTGTAAT
upper sequence: GLYMA16G25750.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G017845_T04 (Zea mays), 3'ss of exon 4
atcaagat--agaagacatttataatgtttccttttcataaat--tcttgaattttacttataaaacagaggctaaaactggttcttgggaaatgtgcttgcagAATCTGTGCTGGCTGCAATTCCGAGATTGGCCATGGAAGATTTTTGAGTTGCATGGGAGGTTATTGGCATCCAGAATGTTTTTGTTGCCATGCTTGCAAA
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gtaatgctcaagaacacaccaggatgattggcatggaagatatcattttgaccttttttctcttactatttttttatataaact----aacttcttttctgcagAGCATGCGCAGGATGTCACAGAGAGATTGGTCACGGGCGTTTTCTCAGTTGCATGGGAGCTGTTTGGCATCCGGAATGTTTTCGTTGCCATGCATGTAGT
upper sequence: GLYMA16G25750.1 (Glycine max), 3'ss of exon 4
lower sequence: AT4G36860.1 (Arabidopsis thaliana), 3'ss of exon 4
-------------------------atcaagatagaagacattta--taatgtttccttttcataaattcttgaattttacttataaaac-----agaggctaaaactggttcttgggaaatgtgcttgcagAATCTGTGCTGGCTGCAATTCCGAGATTGGCCATGGAAGATTTTTGAGTTGCATGGGAGGTTATTGGCATCCAGAATGTTTTTGTTGCCATGCTTGCAAA
|| | | ||| || | | | | || | ||| ||| | | | | | | | || || ||||| | || | |||| || || |||| || ||| | | ||||| || |||||||| ||| ||||||||||||| || ||||||||| |||||||| |||||| |||| || |
gtaaatggttcaaaaatacattaatgtccatttcttagattttcagacactatcatctctagatagtgatatgatgcatgatcacattagctccaatgagtcaattttgtttctttgtttattttcttggagGATATGTGTCGGTTGCCAAGCTGAGATAGGACATGGAAGGTTTCTGAGTTGCATGGGTGGCGTTTGGCATCCTGAATGTTTCTGTTGCAATGCATGTGAT
upper sequence: GLYMA16G25750.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv04s0023g01040.t01 (Vitis vinifera), 3'ss of exon 8
atcaagatagaagacatttataatgtttccttttcataaattcttgaattttacttataaaacagaggctaaaactggttcttgggaaatgt-gcttgcagAATCTGTGCTGGCTGCAATTCCGAGATTGGCCATGGAAGATTTTTGAGTTGCATGGGAGGTTATTGGCATCCAGAATGTTTTTGTTGCCATGCTTGCAAA
||| | | | | ||| | ||| || | | || || | | | || | | | | || ||| ||| || ||||||||| | ||||| || ||||| |||| |||| |||||| ||||||| | | ||||||||||||||||||| |||| ||||||||
-tcataaatggtgcttctcatattttttgtcattttcctgcatcagtttcatagacatcatatgaaacctcacatggatgattacacaataccatttgtagGATCTGTGCTCGGTGCAACCTTGAAATTGGTCATGAAAGACATTTGAGGCGCATGGGTGCTGTTTGGCATCCAGAATGTTTTCGTTGTCATGCTTGTGGT
upper sequence: GLYMA16G25750.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv04s0023g01030.t01 (Vitis vinifera), 3'ss of exon 5
atcaagatagaagacatttataatgtttccttttcataaatt-cttgaattttacttataaaaca-gaggctaaaactggttc-ttgggaaatgt-gcttgcagAATCTGTGCTGGCTGCAATTCCGAGATTGGCCATGGAAGATTTTTGAGTTGCATGGGAGGTTATTGGCATCCAGAATGTTTTTGTTGCCATGCTTGCAAA
|||| | || | |||||| | | | | | || | | | | | ||| | | ||||| || ||| | |||| || ||||||||||| ||||| | ||||||||| |||||||||| ||||||||||||||| | | ||||||||||||||||||| |||||| ||||||
----tgataaatagggcttctcatgttttatgtcattctcctgcatgtgtgtcatggacttcgtatgagacctcacatggttaattacacaatatcacttgtagGATCTGTGCTGGGTGCAACTGCGAGATTGGTCATGGAAGATATTTGAGTTGCATGGGTGCTGTTTGGCATCCAGAATGTTTTCGTTGCCGTGCTTGTGGG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gaattttacttataaaacagaggctaaaactggttcttgggaaatgtgcttgcagAATCTGTGCTGGCTGCAATTCCGAGATTGGCCATGGAAGATTTTTGAGTTGCATGGGAGGTTATTGGCATCCAGAATGTTTTTGTTGCCATGCTTGCAAA
ggctaaa putative branch site (score: 3)
ttacttataaaaca 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
atcaagatagaagacatttataatgtttccttttcataaattcttgaattttacttataaaacagaggctaaaactggttcttgggaaatgtgcttgcagAATCTGTGCTGGCTGCAATTCCGAGATTGGCCATGGAAGATTTTTGAGTTGCATGGGAGGTTATTGGCATCCAGAATGTTTTTGTTGCCATGCTTGCAAA
- - - - - - - - - - - -tgtttcc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -actggtt