Sequence
atgc intronic sequence ATGC exonic sequence...atgctatttggtaaacagtggatatttgacattgtggttgacttgttttctgatttttaagtcgtcaaagtacgagctgacttgaaaatgtcactattagGTTCAAGTGCATAGATTTGGATGGAAATGGAGTTCTGACAAGGAATGAACTGCAATTTTTTTATGAGGAACAATTGCATCGGATGGAGTGCATGGCCCAA
Basic information
species | Glycine max |
transcript | GLYMA20G36530.1 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA20G36530.1 (Glycine max), 3'ss of exon 9
lower sequence: LOC_Os10g33680.1 (Oryza sativa), 3'ss of exon 9
-------atgctatttggtaaacagtggatatttgacattgtggttgacttgttttctgatttttaagtcgtcaaagtacgagctga-cttgaaaatgtcactattagGTTCAAGTGCATAGATTTGGATGGAAATGGAGTTCTGACAAGGAATGAACTGCAATTTTTTTATGAGGAACAATTGCATCGGATGGAGTGCATGGCCCAA
|| |||| ||||||| | || | ||||| || | || || ||| | || | ||| ||| | | || | ||||| ||||| || || | ||||||||||| || | || | | |||| |||||||||| |||||||| |||||||| ||||||||||||||||| |||
ttgcctattgagttttgccttacagtggct--ttaatattgtagtatattttacaactaattat------gttactgtattcattgaacatatgaaccaattttacagGTTTAAGTGTATTGACCTTGATGGAAATGGCATTTTAACCACCACTGAAATGCAATTTTTCTATGAGGAGCAATTGCACCGGATGGAGTGCATGGCACAA
upper sequence: GLYMA20G36530.1 (Glycine max), 3'ss of exon 9
lower sequence: AT1G54450.1 (Arabidopsis thaliana), 3'ss of exon 9
atgctatttggtaaacagtggatatttgacattgtggttgacttgttttctgatttttaagtcgtcaaag-tacgagctgacttgaaaatgtcactat-tagGTTCAAGTGCATAGATTTGGATGGAAATGGAGTTCTGACAAGGAATGAACTGCAATTTTTTTATGAGGAACAATTGCATCGGATGGAGTGCATGGCCCAA
| || ||| || ||| ||| | || | || | | | ||| | || | || || ||| | || | | | || ||||||||||||||| |||||||||| |||||||||| |||| |||| || |||||||| ||||| ||||| || | ||| | ||||| |||||||| |||
--------gtgagaatggtgaatgtttt-catacatatagagtctttgtgtcggtgttatttggtaagagctatattctgttattaatgtttgatgatatagGTTCAAGTGCATTGATTTGGATGCAAATGGAGTTTTGACGCGGAACGAGCTGCAATTCTTTTACGAGGAGCAGCTACATAGAATGGAATGCATGGCGCAA
upper sequence: GLYMA20G36530.1 (Glycine max), 3'ss of exon 9
lower sequence: PP1S147_62V6.2 (Physcomitrella patens), 3'ss of exon 9
-------------------------------------------------------------------------------------------atgctatttggtaaacagtggatatttgacattgtggttgacttgttttctgatttttaagtcgtcaa----agtacgagctgacttgaaaatgtcactattagGTTCAAGTGCATAGATTTGGATGGAAATGGAGTTCTGACAAGGAATGAACTGCAATTTTTTTATGAGGAACAATTGCATCGGATGGAGTGCATGGCCCAA
| ||||| | | | || | || || | | |||| | ||| | | | | | || | | | | |||| | | | | |||||||| || | || ||||| | |||| || | ||| ||||| |||||| |||||||||||| ||| | |||||||||||||||||||| ||
gtacgtacctttatatggcctctaaaatgctctccacttttttggcatgaagttgatgtttttgaatgcaaatcatgtgctttctgacaaaacagtatttaggataaaggattgaattttcactcggattgattagttacataacaacgaggacatcgagtctaatttattttttcttgtacacctgat--gcagGTTCAAATGTGTGGACCTGGATTGTGATGGTGTGATAACACCAAATGAGATGCAATATTTTTATGAGGAGCAACTTCATCGGATGGAGTGCATGGCTCAG
upper sequence: GLYMA20G36530.1 (Glycine max), 3'ss of exon 9
lower sequence: PP1S7_163V6.1 (Physcomitrella patens), 3'ss of exon 9
--------------------------------------------------------------------------------------atgctatttggtaaacagtggatatttgacattgtggttgacttgttttc-tgatttttaagtcgtcaaagtacgagct---gacttgaaaatgtcactattagGTTCAAGTGCATAGATTTGGATGGAAATGGAGTTCTGACAAGGAATGAACTGCAATTTTTTTATGAGGAACAATTGCATCGGATGGAGTGCATGGCCCAA
|| || ||| | | | ||| | | ||| | | || | | | | | | | | ||| | || | | || | ||||||||||| |||| ||||| | | || | | | | ||||| |||||| |||||| ||||| ||| | |||||||||||||||||||| ||
gtaagtgccttgacatggtctctaaaacattttctgcacctccatatcttaactgtgaatttacatgaatacaaactgtctgctttctgataattgtaacgcggacaatacattagattccgtcacgtatattacaataaaatcgaggacattttgtttaatgctttcatcctggacacgtgat--gcagGTTCAAGTGTGTAGACCTGGATTGTGACGGGATGATTATACTAAATGAGATGCAATATTTTTACGAGGAGCAACTTCATCGGATGGAGTGCATGGCTCAG
upper sequence: GLYMA20G36530.1 (Glycine max), 3'ss of exon 9
lower sequence: EFJ32791 (Selaginella moellendorffii), 3'ss of exon 9
atgctatttggtaaacagtggatatttgacattgtggttgacttgttttctgatttttaagtcgtcaaagtacgagctgacttgaaaatgtcactattagGTTCAAGTGCATAGATTTGGATGGAAATGGAGTTCTGACAAGGAATGAACTGCAATTTTTTTATGAGGAACAATTGCATCGGATGGAGTGCATGGCCCAA
| | | ||| | || || ||| ||| | | | | ||| |||||||| || || ||| ||||| | | ||||| |||| || || |||| | ||||||||||| ||||||||||| ||||||||| | || |||
-------------------------------------gtaagcgacgtcttgaatcttctgt-----aagatcgatcgattgacagatcgcgacttccagGTTCAAATGTATCGATCTGGATTGTGACGGAGTGGTGACTCCAAACGAGATGCAGTACTTTTATGAGGAGCAATTGCATCGCATGGAGTGCCTAGCTCAA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttttctgatttttaagtcgtcaaagtacgagctgacttgaaaatgtcactattagGTTCAAGTGCATAGATTTGGATGGAAATGGAGTTCTGACAAGGAATGAACTGCAATTTTTTTATGAGGAACAATTGCATCGGATGGAGTGCATGGCCCAA
agctgac putative branch site (score: 3)
tgatttttaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
atgctatttggtaaacagtggatatttgacattgtggttgacttgttttctgatttttaagtcgtcaaagtacgagctgacttgaaaatgtcactattagGTTCAAGTGCATAGATTTGGATGGAAATGGAGTTCTGACAAGGAATGAACTGCAATTTTTTTATGAGGAACAATTGCATCGGATGGAGTGCATGGCCCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
-tgctatt
- - - - - - - - - - - - - - - - -gtggttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gctgact