Sequence
atgc intronic sequence ATGC exonic sequencegtgtgcaagttttttccaccctgcatccccaaattaccatattattttttctcatttcactttctatgcgcagAAATCGTCTCCGCTTGCTTACTCAGTTTTTGGAGCATCTTGTAAGTGAGGGAAGCCAGGATGTGCATGTGCATAATGCTCTGGGTAAAATTATCATTGAC
Basic information
species | Glycine max |
transcript | GLYMA02G39360.1 |
intron # | 22 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA02G39360.1 (Glycine max), 3'ss of exon 22
lower sequence: LOC_Os11g01380.1 (Oryza sativa), 3'ss of exon 22
----------------------------------------------gtgtgcaagttttttccaccctgcatccccaaattaccatattattttttctcatttcactttctatgcgcagAAATCGTCTCCGCTTGCTTACTCAGTTTTTGGAGCATCTTGTAAGTGAGGGAAGCCAGGATGTGCATGTGCATAATGCTCTGGGTAAAATTATCATTGAC
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gtatgattctttatattatcttgtattccacaaccagattaagggcatgtgcacacgcacacaaacatatgcttttttgttttgttgctgacctcatcttttata-tttcttttttcagGAACCGCCTACGGCTGCTGACACAATTTTTGGAGCACTTAGTGAGCGAGGGTAGCCAAGATGTCCATGTGCACAATGCTCTTGGAAAAATCATCATTGAC
upper sequence: GLYMA02G39360.1 (Glycine max), 3'ss of exon 22
lower sequence: LOC_Os12g01390.1 (Oryza sativa), 3'ss of exon 22
----------------------------------------------gtgtgcaagttttttccaccctgcatccccaaattaccatattattttttctcatttcactttctatgcgcagAAATCGTCTCCGCTTGCTTACTCAGTTTTTGGAGCATCTTGTAAGTGAGGGAAGCCAGGATGTGCATGTGCATAATGCTCTGGGTAAAATTATCATTGAC
|||||| | | | | | || | | | | | || | ||||| | ||| || || || || |||| || || ||||||||||| | || || ||||| ||||| ||||| |||||||| |||||||| || ||||| |||||||||
gtatgattctttatattatcttgtattccacagccagcttaagggcatgtgcacatgcacacaaacatatgcttttttgtttcgttgctgatctcatcttttata-tttcttttttcagGAACCGCCTACGGCTGCTGACACAATTTTTGGAGCACTTAGTGAGCGAGGGTAGCCAAGATGTCCATGTGCACAATGCTCTTGGAAAAATCATCATTGAC
upper sequence: GLYMA02G39360.1 (Glycine max), 3'ss of exon 22
lower sequence: GRMZM2G057576_T01 (Zea mays), 3'ss of exon 21
gtgtgcaagttttttccaccctgcatccccaaatta-------ccatattattttttc-------tcatttcactttctatgcg-----cagAAATCGTCTCCGCTTGCTTACTCAGTTTTTGGAGCATCTTGTAAGTGAGGGAAGCCAGGATGTGCATGTGCATAATGCTCTGGGTAAAATTATCATTGAC
|| | || ||| || | || |||| | || ||| |||| ||| || ||| || | ||| || || || || ||||||||||| || ||||||||||| || ||||| || ||||| ||||||||||| || |||||||| || ||||| ||||| |||
--gtttgaattctttattcctggggtctgcaaagtgacaagtttcacattccctttttaagtggatcacatctgtttgaatatgtgtatcagGAACCGCCTACGGTTGCTTACTCAATTCTTGGAGCATCTAGTGAGTGAAGGTAGCCAAGATGTGCATGTCCACAATGCTCTTGGGAAAATCATCATCGAC
upper sequence: GLYMA02G39360.1 (Glycine max), 3'ss of exon 22
lower sequence: GRMZM2G111355_T02 (Zea mays), 3'ss of exon 2
----gtgtgcaagttttttccaccctgcatccccaaattaccata-----ttattttttctcatttcactttctatgcgcagAAATCGTCTCCGCTTGCTTACTCAGTTTTTGG-AGCATCTTGTAAGTGAGGGAAGCCAGGATGTGCATGT----GCATAATGCTCTGGGTAAAATTATCATTGAC-----------
|| | | | | ||| | | | || || | | | | | | || | | ||||| || | || || | | | | ||| | | | | || | ||| | ||| | || | ||| | ||
gtttgtttttcatatcctcccagtttacttattcacatgagtgaaggtagccaagatgtgcatgtccataatgctcttggtaaaatcatcattgacagCAACAACAATCCTGAGCATTTCCTTACTACCAACCCATTTTACGACTCTCGTGTTGTGGGTAAATATTGTGAAAAGCGGGATCCTACACTTGCTGTTGTT
upper sequence: GLYMA02G39360.1 (Glycine max), 3'ss of exon 22
lower sequence: Vv06s0004g06860.t01 (Vitis vinifera), 3'ss of exon 22
-------------gtgtgcaagttttttccaccctgcatccccaaattaccatattatt-ttttctcatttcactttctatgcgcagAAATCGTCTCCGCTTGCTTACTCAGTTTTTGGAGCATCTTGTAAGTGAGGGAAGCCAGGATGTGCATGTGCATAATGCTCTGGGTAAAATTATCATTGAC
|| |||||| || || | | | | |||| |||||| || | | |||||||||||||||| || || |||||||| |||||||||||||| |||||||| ||||||||||||||||| |||||||||||||||||||| ||||| |||
gtgcattgtttttacctgtgtaccgtttccatta-atatttttaattcttattgctttcgttttatcattttgtgttttgtttgcagAAATCGTCTCCGTTTACTCACTCAGTTCTTGGAGCATCTTGTGAGTGAGGGTAGCCAGGATGTGCATGTTCATAATGCTCTGGGTAAAATCATCATAGAC
upper sequence: GLYMA02G39360.1 (Glycine max), 3'ss of exon 22
lower sequence: PP1S452_30V6.1 (Physcomitrella patens), 3'ss of exon 22
--------------------------gtgtgcaagttttttccaccctgcatccccaaattaccatattattttttctcatttcactttcta-tgcgcagAAATCGTCTCCGCTTGCTTACTCAGTTTTTGGAGCATCTTGTAAGTGAGGGAAGCCAGGATGTGCATGTGCATAATGCTCTGGGTAAAATTATCATTGAC
||| || |||| | || | || | | | | | | | || |||||||| || || | || || || || |||||| | |||||||| || ||||| |||||||||||||| |||||||| || || || ||||| ||
atattagaactaggttgcgtttttaaatgtctaaacattttagtgtcacgatttaaacatcctgacgtcgtcgagaactgatgagttgtggggtttatagGAATCGTCTGCGACTGTTGACACAATTCTTAGAGCATTTGGTAAGTGAAGGTAGCCAAGATGTGCATGTGCACAATGCTCTTGGGAAGATCATCATAGAT
upper sequence: GLYMA02G39360.1 (Glycine max), 3'ss of exon 22
lower sequence: EFJ24508 (Selaginella moellendorffii), 3'ss of exon 22
gtgtgcaagttttttccaccctgcatccccaaattaccatattattttttctcatttcactttctatgcgcagAAATCGTCTCCGCTTGCTTACTCAGTTTTTGGAGCATCTTGTAAGTGAGGGAAGCCAGGATGTGCATGTGCATAATGCTCTGGGTAAAATTATCATTGAC
|| | | || | | | |||||| | |||| |||| ||| ||||| || | | || ||||||||||||||||| || || || || || ||||| || ||||||||||| ||||| || || ||||||||||| ||
-------------gtctgtttcgttttttcatgt-atctcattattgagcttaattttcttttc------cagTAATCGGCTGAGACTTCTCACTCAGTTTTTGGAGCACCTGGTTAGCGAAGGTAGCCAAGACGTGCATGTGCACAATGCGCTCGGAAAAATTATCATCGAT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ccctgcatccccaaattaccatattattttttctcatttcactttctatgcgcagAAATCGTCTCCGCTTGCTTACTCAGTTTTTGGAGCATCTTGTAAGTGAGGGAAGCCAGGATGTGCATGTGCATAATGCTCTGGGTAAAATTATCATTGAC
ttattttttctcattt CT-rich tract
aaattaccatattatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgtgcaagttttttccaccctgcatccccaaattaccatattattttttctcatttcactttctatgcgcagAAATCGTCTCCGCTTGCTTACTCAGTTTTTGGAGCATCTTGTAAGTGAGGGAAGCCAGGATGTGCATGTGCATAATGCTCTGGGTAAAATTATCATTGAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG