Sequence
atgc intronic sequence ATGC exonic sequence...agaattttgaataaaattaaatgcttgagattgatgataacatccacgggtttcaatttcttctattcttcataaatttgtgctcgaatgccacttgcagACCATCAGTTACATGGCTGAACGTGTTGTTGGCACTGGATCATTCGGAATTGTTTTCCAG
Basic information
species | Glycine max |
transcript | GLYMA13G36570.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA13G36570.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G045330_T02 (Zea mays), 3'ss of exon 2
--aga-attttgaataaaattaaa-tgcttg-agattgatgataacatccacgggtt-tcaatttcttctattcttcataaatttgtgctcgaatgccacttgcagACCATCAGTTACATGGCTGAACGTGTTGTTGGCACTGGATCATTCGGAATTGTTTTCCAG
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tcagatactctgtctgatgccagcctacttctagagtccggttagcctcatctcgtcctcagttactcacgtgct------gttcttattccggccttaatcgcagACCATCAGTTACATGGCAGAACGTGTCGTGGGCACAGGCTCATTTGGGATCGTCTTCCAG
upper sequence: GLYMA13G36570.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G472625_T02 (Zea mays), 3'ss of exon 2
-agaattttgaataaaattaaatgcttgagattgatgataacatccacgggtttcaatttcttctattcttcataaatttgtgctcgaatgccacttgcagACCATCAGTTACATGGCTGAACGTGTTGTTGGCACTGGATCATTCGGAATTGTTTTCCAG
||||| | | |||| || | | | | || || || |||| || | || | ||||||||||||||||||||||| |||||||| || || || || ||||| || || || ||||||
tcgaattccttcctgc-tcagttgctctgacgcctgcctagtttgttaccctcttcgtgtcctcagttgctcatttgttcttcttctggccttaattgcagACCATCAGTTACATGGCAGAACGTGTCGTGGGTACGGGCTCATTTGGGATCGTCTTCCAG
upper sequence: GLYMA13G36570.1 (Glycine max), 3'ss of exon 1
lower sequence: AT1G06390.1 (Arabidopsis thaliana), 3'ss of exon 2
agaattttgaataaaattaaatgcttgagattgatgataacatccacgggtttcaatttcttctattcttcataaatttgtgctcgaat--gccacttgcagACCATCAGTTACATGGCTGAACGTGTTGTTGGCACTGGATCATTCGGAATTGTTTTCCAG
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--catcaaatgctccagcaagtgttactttcccattaaaaccctttttcaagtcaaattaattcatctctcccttacatgatcttcattctgtcccctacagACCATTAGTTACATGGCTGAGCGGGTTGTTGGAACAGGTTCATTCGGGATTGTTTTTCAG
upper sequence: GLYMA13G36570.1 (Glycine max), 3'ss of exon 1
lower sequence: AT2G30980.1 (Arabidopsis thaliana), 3'ss of exon 2
-agaattttgaataaaattaaatgcttgagattgatgataacatccacgggtttcaatttc---ttctattcttcataaatttgtgctcgaatgccacttgcagACCATCAGTTACATGGCTGAACGTGTTGTTGGCACTGGATCATTCGGAATTGTTTTCCAG
| | | |||| || | | |||| | | || ||| | ||||| ||| | | ||| | || | || |||||||| ||||||||||| |||||||||||||| || ||||||||||||||||| ||||||
caaataaataaataggtttttacatctt---ttgactttgtggctccttttttccaactctaagttctactctcta-atgttttcatccctctggcctttacagACCATTAGTTACATGGCCGAACGTGTTGTTGGAACAGGATCATTCGGAATTGTATTCCAG
upper sequence: GLYMA13G36570.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv12s0028g01810.t01 (Vitis vinifera), 3'ss of exon 2
agaattttgaataaaattaaatgcttg--agattgatgataacatccacgggtttcaatttcttctattcttcataaat--------ttgtgctcgaatgccacttgcagACCATCAGTTACATGGCTGAACGTGTTGTTGGCACTGGATCATTCGGAATTGTTTTCCAG
|||||| || || || || |||| ||| ||| | | |||| |||| | | |||| | | | |||| |||||||||||||||||||||||| || || |||| ||||||||||| || ||||||||||| |||
-----tttgaa-aagtagaattgtttattggattcgtga----atctgtgtttcctgatttgttcttcccagtaaaaatgcttaggcctctcttgtgatgcttcttgcagACCATCAGTTACATGGCAGAGCGCATTGTAGGCACTGGATCGTTTGGAATTGTTTTTCAG
upper sequence: GLYMA13G36570.1 (Glycine max), 3'ss of exon 1
lower sequence: PP1S306_43V6.2 (Physcomitrella patens), 3'ss of exon 3
--------agaattttgaataaaattaaatgcttgagattgatgataacatccacgggtttcaatttcttctattcttcataaatttgtgctcgaatgccacttgcagACCATCAGTTACATGGCTGAACGTGTTGTTGGCACTGGATCATTCGGAATTGTTTTCCAG
||| ||| ||| | ||| || || || || | || ||| | | ||| | ||||| || | ||||| ||||||| ||||| || ||| ||||||||||||||||||||||||||||| ||||| ||||||
cttttcctggaagcttg--ccaaaggacatgaatggtgcagac--tatcagctacttattttatctacttattttctttggaacaaacgacatgaatgg----tgcagACGATCAGCTATTCGGCAGAACGTGTTGTTGGCACTGGATCATTCGGGATTGTCTTCCAG
upper sequence: GLYMA13G36570.1 (Glycine max), 3'ss of exon 1
lower sequence: PP1S60_100V6.1 (Physcomitrella patens), 3'ss of exon 3
agaattttgaataaaattaaatgcttgagat--tgatgataacatccacgggtttcaatttcttctattcttcataaatttgtgctcgaatgccacttgcagACCATCAGTTACATGGCTGAACGTGTTGTTGGCACTGGATCATTCGGAATTGTTTTCCAG
| |||| | | | | | || | | ||| | | | || | | || |||| | | ||| || || | ||||| || || ||| || ||||| ||||||||||||||||||||||| || |||||||||
tgcgctttgtcagggctcgactacgtcaggtcctcctgaaagctggtaaaagtgacctgtactgatatttgttgccctgtattgcatgagtgttgc--acagACTATTAGCTACTGTGCAGAACGAGTTGTTGGCACTGGATCATTCGGGATCGTTTTCCAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.acgggtttcaatttcttctattcttcataaatttgtgctcgaatgccacttgcagACCATCAGTTACATGGCTGAACGTGTTGTTGGCACTGGATCATTCGGAATTGTTTTCCAG
tattcttcataaattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
agaattttgaataaaattaaatgcttgagattgatgataacatccacgggtttcaatttcttctattcttcataaatttgtgctcgaatgccacttgcagACCATCAGTTACATGGCTGAACGTGTTGTTGGCACTGGATCATTCGGAATTGTTTTCCAG
- - - - -aataaaa
- - - - - - - - - - -tgcttga
- - - - - - - - - - - - - - - -tgatgat
- - - - - - - - - - - - - - - - - - - - catccac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tttgtgc