Sequence
atgc intronic sequence ATGC exonic sequence...agagtaataatattagttgagttttagttcagctgaagttgtagtgaattttctcttgagactattacctgaatatttttttcttattattttcattcagGGTTCTTATTAGGCCACATCCTGCAATTTGGCGCTTGGTTCATGGAATGGCTGTTGTTTACCTTGTTGCCCTCACATTTTTGCTTTTTCAG
Basic information
species | Glycine max |
transcript | GLYMA10G41430.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA10G41430.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os01g02890.1 (Oryza sativa), 3'ss of exon 3
agagtaataatattagttgagttttagttcagctgaagttgtagtgaattttctcttgagactatt--acctgaatatttttttcttattattttcattcagGGTTCTTATTAGGCCACATCCTGCAATTTGGCGCTTGGTTCATGGAATGGCTGTTGTTTACCTTGTTGCCCTCACATTTTTGCTTTTTCAG
||| | | | | | || | | | | | | | || | | | || || | | | | ||| || || | | |||||| || |||||||| ||||||||||| |||||||| |||| || || ||||| ||||||||||||||||| || || ||||||||||| |||
-aagtga-ggcactgttccatttcctaaaaatataacctcattgggggcttctctgtaattttgtttaacatttacttatatttatttatactatgattcagTGTACTTATTAGACCACATCCTGCCATTTGGCGGCTGGTCCACGGGATGGCAGTTGTTTACCTTGTTGCTCTAACTTTTTTGCTTTTCCAG
upper sequence: GLYMA10G41430.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G095757_T02 (Zea mays), 3'ss of exon 3
-----agagtaataatattagttgagttt-tag-ttcagctg--aagttgtagtgaattttctcttgagactattacctgaatatttttttcttattattttcattcagGGTTCTTATTAGGCCACATCCTGCAATTTGGCGCTTGGTTCATGGAATGGCTGTTGTTTACCTTGTTGCCCTCACATTTTTGCTTTTTCAG
| | | | | | | ||| | ||| || || | ||| | || ||| ||| | | ||| |||| ||| ||| ||| | | ||| || | || ||||| ||||||||||| |||||| | | |||||||| ||| | |||||||||||||| |||||||| || ||||||||||||
tgaacaaaacagttacttccttgaagtatatagatttagttattaaggtatattgagtttatgc---aaactgttac-tgacaattatttc-----tgctacgatttagTGGACTCATTAGACCACATCCTGCCATTTGGAGGCTTGTTCATGGGATGACAGTTGTTTACCTTGTCGCCCTCACTTTCTTGCTTTTTCAG
upper sequence: GLYMA10G41430.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G110834_T02 (Zea mays), 3'ss of exon 3
----agagtaataata-ttagttgagttttagttcagctgaagttgtagtgaattttctcttg-agactattacctgaatatttttttcttattattttcattcagGGTTCTTATTAGGCCACATCCTGCAATTTGGCGCTTGGTTCATGGAATGGCTGTTGTTTACCTTGTTGCCCTCACATTTTTGCTTTTTCAG
||| | || || |||| | || | || || ||| | ||| | ||| |||| |||| || | | | |||| || || || ||||| ||||||||||| |||||| | | |||||||| ||||| |||||||||||||| |||||||| || |||||||| |||
ctgaagaaaagagttacttccttgaagtctatagagttagttattaaggtatattgagtattgcaaactgttactgacatatacttctgctgtgattt------agTGTACTCATTAGACCACATCCTGCCATTTGGAGGCTAGTTCATGGGATGGCAGTTGTTTACCTTGTCGCCCTCACTTTCTTGCTTTTCCAG
upper sequence: GLYMA10G41430.1 (Glycine max), 3'ss of exon 4
lower sequence: AT1G15110.1 (Arabidopsis thaliana), 3'ss of exon 4
--------------agagtaataatattagttgagttttagttcagctgaagttgtagtgaattttctcttgagact-attacctgaatatttttttcttattattttcattcagGGTTCTTATTAGGCCACATCCTGCAATTTGGCGCTTGGTTCATGGAATGGCTGTTGTTTACCTTGTTGCCCTCACATTTTTGCTTTTTCAG
|| | ||||| || ||| || || | | || || | ||| ||| | | || | | | | ||| || || ||||||||| || ||||| ||||||||||| |||||||| |||||||||||||| || ||||| | ||||| || || |||||||| ||||||
gtttgtttaccatctcagctgttttattaatttgctttctcttttat--aatgtagattgtggttgttggtgatacttgtgatgtgtctttaatcaagtaatttgctttatgcagGGTTCTAATCAGGCCCCATCCTGCAATCTGGCGCTTAGTTCATGGAATGGCCGTCATTTACTTAGTTGCACTTACTTTTTTGCTCTTTCAG
upper sequence: GLYMA10G41430.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv01s0011g04370.t01 (Vitis vinifera), 3'ss of exon 4
agagtaataatattag--ttgagttttagttcagctgaagttgtagtgaattttctcttgagactattacctgaatatttttttcttattattttcatt--cagGGTTCTTATTAGGCCACATCCTGCAATTTGGCGCTTGGTTCATGGAATGGCTGTTGTTTACCTTGTTGCCCTCACATTTTTGCTTTTTCAG
| | | | || | | |||| | | | || ||| || | || ||| ||| | | ||| | || | |||| || |||||| ||||||||||||||||| ||||||||||| | |||||||| ||||| || ||||||||||| ||||||||||||||||| |||
----tgctgacaccagaatgggattttgatgttgatactactgaagttcataaacatttccagttatgcactgtaaaatttgtagttgtcttttttttttacagGGTACTTATTAGGCCACATCCAGCAATTTGGCGACTAGTTCATGGGATGGCGGTCATTTACCTTGTTTGTCTCACATTTTTGCTTTTCCAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gaattttctcttgagactattacctgaatatttttttcttattattttcattcagGGTTCTTATTAGGCCACATCCTGCAATTTGGCGCTTGGTTCATGGAATGGCTGTTGTTTACCTTGTTGCCCTCACATTTTTGCTTTTTCAG
tttttttcttattatt CT-rich tract
tattacctgaatattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
agagtaataatattagttgagttttagttcagctgaagttgtagtgaattttctcttgagactattacctgaatatttttttcttattattttcattcagGGTTCTTATTAGGCCACATCCTGCAATTTGGCGCTTGGTTCATGGAATGGCTGTTGTTTACCTTGTTGCCCTCACATTTTTGCTTTTTCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT
- - - - - - - - - - - - - - -cagctga
- - - - - - - - - - - - - - - - - - - -tgtagtg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - acctgaa