Sequence
atgc intronic sequence ATGC exonic sequence...caagatgtgtttgacactggtttggaagtcattttgaagtgttgtgcttcctagttatttactatttgtgtcaatgtctcatatcatggtaattacacagTATACGATTGAGGAAAAAGTCATTGAAAGGGCTTACAAAAAGCTTGCTCTTGATGCTCTGGTGATTCAGCAAGGGCGATTAGCTGAACAGAAGA
Basic information
species | Glycine max |
transcript | GLYMA17G02640.1 |
intron # | 12 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA17G02640.1 (Glycine max), 3'ss of exon 12
lower sequence: LOC_Os05g05780.1 (Oryza sativa), 3'ss of exon 12
caagatgtgtttgacactggtttggaagtcattttgaagtgttgtgcttcctagttatttactatttgtgtcaatgtctcatatcatg----gtaat-tacacagTATACGATTGAGGAAAAAGTCATTGAAAGGGCTTACAAAAAGCTTGCTCTTGATGCTCTGGTGATTCAGCAAGGGCGATTAGCTGAACAGAAGA
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---gttttatttaat--ttattttaagatttaaaaacactggtttagcactaagcaatatcttctatttatttatataacagaatatgcttcatattctatgcagTATACAATTGAGGAAAAGGTGATTGAGAGAGCTTATAAGAAGCTTGCCCTGGATGCTTTGGTCATACAACAGGGTCGATTGGCAGAGCAGAAAG
upper sequence: GLYMA17G02640.1 (Glycine max), 3'ss of exon 12
lower sequence: AT5G18620.1 (Arabidopsis thaliana), 3'ss of exon 12
caagatgtgtttgacactggtttggaagtcattttgaagtgttgtgcttcctagttatttactatttgtgtcaatgtctcatatcatggtaattacacagTATACGATTGAGGAAAAAGTCATTGAAAGGGCTTACAAAAAGCTTGCTCTTGATGCTCTGGTGATTCAGCAAGGGCGATTAGCTGAACAGAAGA
| | | | | ||| | | | | | | | | | | ||| ||| ||| |||| ||| ||| || | ||||||| ||||||||||| || |||||||| ||| | || |||||||||||||| |||||||||||| |||| || |||||||| |
---------------gttactcttgtacccatgtgtatgaagtaagaat----gacctggagaacttgaactaattctgcat----tggtc-ttatgcagAATGCTATTGAGGCTAAAGTCATTGAGAGAGCTTACAAGAAGTTGGCACTTGATGCTCTGGTTATTCAGCAAGGGAGATTGGCAGAACAGAAAA
upper sequence: GLYMA17G02640.1 (Glycine max), 3'ss of exon 12
lower sequence: AT3G06400.1 (Arabidopsis thaliana), 3'ss of exon 12
caagatgtgtttgacactggtttggaagtcattttgaagtgttgtgcttcctagttatttactatttgtgtcaatgtctcatatcatggtaattacacagTATACGATTGAGGAAAAAGTCATTGAAAGGGCTTACAAAAAGCTTGCTCTTGATGCTCTGGTGATTCAGCAAGGGCGATTAGCTGAACAGAAGA
||| | | | | | | |||| | | || |||| ||| | || | || | || ||||| | | |||||||| ||||| |||||||| |||||||| ||| | || |||||||||||||| ||||| |||||| |||| || |||||||| |
--------gttggtctcctctccgtga---atttcaagttaaaacagccatgagaggtttaaaattaat----------tatgtgttgtttgtt-tacagTCTGCTATTGAGGAGAAAGTGATTGAAAGAGCTTACAAGAAGTTAGCACTTGATGCTCTGGTTATTCAACAAGGGAGATTGGCAGAACAGAAAA
upper sequence: GLYMA17G02640.1 (Glycine max), 3'ss of exon 12
lower sequence: EFJ32950 (Selaginella moellendorffii), 3'ss of exon 11
caagatgtgtttgacactggtttggaagtcattttgaagtgttgtgcttcctagttatttactatttgtgtcaatgtctcatatcatggtaattacacagTATACGATTGAGGAAAAAGTCATTGAAAGGGCTTACAAAAAGCTTGCTCTTGATGCTCTGGTGATTCAGCAAGGGCGATTAGCTGAACAGAAGA
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----------------------------------------------gtaataagttgattataacttcctttcg-gcctctcaac-tgggagctttgcagTTGACTATCGAGGAAAAAGTTATTGAACGGGCTTACAAAAAACTTGCCTTGGATGCGTTAGTCATACAACAAGGTCGTTTGGCGGAAGAAAAGA
upper sequence: GLYMA17G02640.1 (Glycine max), 3'ss of exon 12
lower sequence: EFJ31365 (Selaginella moellendorffii), 3'ss of exon 12
caagatgtgtttgacactggtttggaagtcattttgaagtgttgtgcttcctagttatttactatttgtgtcaatgtctcatatcatggtaattacacagTATACGATTGAGGAAAAAGTCATTGAAAGGGCTTACAAAAAGCTTGCTCTTGATGCTCTGGTGATTCAGCAAGGGCGATTAGCTGAACAGAAGA
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---------------------------------gtaaaaggatg--------acttgtgtgttatttct-ttgctgactcgttttctg----tttctcagTATACTATTGAAGAGAAAGTCATTGAACGCGCGTACAAAAAGCTTGCACTGGATGCTTTGGTGATCCAACAGGGTCGACTAGCCGAACAGAGAG
upper sequence: GLYMA17G02640.1 (Glycine max), 3'ss of exon 12
lower sequence: EFJ06565 (Selaginella moellendorffii), 3'ss of exon 12
caagatgtgtttgacactggtttggaagtcattttgaagtgttgtgcttcctagttatttactatttgtgtcaatgtctcatatcatggtaattacacagTATACGATTGAGGAAAAAGTCATTGAAAGGGCTTACAAAAAGCTTGCTCTTGATGCTCTGGTGATTCAGCAAGGGCGATTAGCTGAACAGAAGA
| || | || | || | | ||||| | | || ||| | | || || | |||||||| ||||| || |||||||||||| | || |||||||||||||| || |||||| ||||||| || || || ||| ||||||||||||
---------------------------------gtaaaaggatg--------acttgtgtgttatttct-ttgctgactcgttttctg----tttctcagTATACTATTGAAGAGAAAGTCATTGAACGCGCGTACAAAAAGCTTGCACTGGATGCTTTGGTGATCCAACAGGGTCGACTAGCTGAACAGAGAG
upper sequence: GLYMA17G02640.1 (Glycine max), 3'ss of exon 12
lower sequence: EFJ15818 (Selaginella moellendorffii), 3'ss of exon 11
caagatgtgtttgacactggtttggaagtcattttgaagtgttgtgcttcctagttatttactatttgtgtcaatgtctcatatcatggtaattacacagTATACGATTGAGGAAAAAGTCATTGAAAGGGCTTACAAAAAGCTTGCTCTTGATGCTCTGGTGATTCAGCAAGGGCGATTAGCTGAACAGAAGA------
| |||| ||| | || | | ||| | | | | | | |||| || || ||||||||||| |||||| ||||||||||||||||||| | ||||| | || || || ||||| || || || ||| | ||||
----------------------------------------------gtaataagttgattataacttcctttcg-gcctctcaac-taggagctttgcagTTGACTATCGAGGAAAAAGTTATTGAACGGGCTTACAAAAAGCTTGCCTTGGATGCGTTAGTCATACAACAAGGTCGTTTGGCGGAAGAAAAGAGTATGG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gcttcctagttatttactatttgtgtcaatgtctcatatcatggtaattacacagTATACGATTGAGGAAAAAGTCATTGAAAGGGCTTACAAAAAGCTTGCTCTTGATGCTCTGGTGATTCAGCAAGGGCGATTAGCTGAACAGAAGA
tagttatttactattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
caagatgtgtttgacactggtttggaagtcattttgaagtgttgtgcttcctagttatttactatttgtgtcaatgtctcatatcatggtaattacacagTATACGATTGAGGAAAAAGTCATTGAAAGGGCTTACAAAAAGCTTGCTCTTGATGCTCTGGTGATTCAGCAAGGGCGATTAGCTGAACAGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - -tgacact
- - - - - - - - - ggtttgg
- - - - - - - - - - - - - - - - - tgaagtg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tttgtgt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -caatgtc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -catatca