Sequence
atgc intronic sequence ATGC exonic sequence...atatccatactcattttgtattgtcatctggtatgcgtttgtgcagcttcaaccaaggtataatgatcaataatacttacacactagactgactttgcagGTTGCAATATCAGTGAAACCATTGAAAGTGCAAAACTGGATTCTTCCAGAAATGCCTGGGCTTATAACTGATTTTCTGATATCTCTTGATGATCGGTTTC
Basic information
species | Glycine max |
transcript | GLYMA08G11400.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA08G11400.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os01g68770.1 (Oryza sativa), 3'ss of exon 5
----------atatccatactcat-tttgtattgtcatctggtatgcgtttgtgcagcttcaaccaaggtataatgatcaataatacttacac--actagac-tgactttgcagGTTGCAATATCAGTGAAACCATTGAAAGTGCAAAACTGGATTCTTCCAGAAATGCCTGGGCTTATAACTGATTTTCTGATATCTCTTGATGATCGGTTTC
| ||||| | || || | | | ||| |||| | | ||| || || | | | | |||| | | ||| |||| | |||||||| ||||| | |||||||||||||||| ||||||||||| || |||||||| || || |||||||||||| | || ||||| |||||||| | ||
gtttgtccataactccatgccaatgttcttgctattttcttgtataaagccctatttgtccaattt--gtttagttgtttactctccttatgcttgcatgacatgacatgacagGTTGCTATATCTATAAAACCATTGAAAGTGCGCAACTGGATTCTGCCTGAAATGCCAGGACTGATAACTGATTTTGTTATCTCTCTGGATGATCGCTATC
upper sequence: GLYMA08G11400.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM5G837351_T01 (Zea mays), 3'ss of exon 4
-atatccatactcattttgtattgtcatctggtatgcgtttgtgcagcttcaaccaaggtataatgatcaataatacttaca-cacta-gactg-actttgcagGTTGCAATATCAGTGAAACCATTGAAAGTGCAAAACTGGATTCTTCCAGAAATGCCTGGGCTTATAACTGATTTTCTGATATCTCTTGATGATCGGTTTC
| ||| ||| | || || || | | || | | | || || |||| || | ||||| | | ||| ||||| |||||| ||||||| || || | ||||||||||| || | |||||| |||| ||||||||||| || | |||||||||||| | || |||||||||||||| | ||
tggagccacgag-gtttgctcatgacacatgacaggatttccccccacct-aatgaa--cttaattttccaactcacttagaaccctatgactgtactttgtagGTTGCTATCTCCATAAAACCATTGAAGGTTCGCAACTGGTTTCTGCCAGAAATGCCAGGATTGATAACTGATTTTGTTATCTCTCTTGATGATCGTTATC
upper sequence: GLYMA08G11400.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G103812_T02 (Zea mays), 3'ss of exon 5
atatccatactcattttgtattgtcatctggtatgcgtttgtgcagcttcaaccaaggtataatgatcaataatacttacacactag--actgactttgcagGTTGCAATATCAGTGAAACCATTGAAAGTGCAAAACTGGATTCTTCCAGAAATGCCTGGGCTTATAACTGATTTTCTGATATCTCTTGATGATCGGTTTC
||| | || | || || | || || | || || | || || | | |||||| | ||| ||||||||||| || || ||||||||| |||| || | ||||||||||| || |||||||| || | ||||||||||| | || ||||||||||| || | ||
------------gtttgttcatgctacatgataagttctttccca--cttaat--gggcttgattttccaacttgcttacattcctattgctgtgcttgcagGTTGCTATCTCTGTGAAACCACTGAAGGTCCGCAACTGGATTCTGCCGGAAATGCCAGGATTGATAACTGATTTCGTCATCTCTCTTGATGACCGTTATC
upper sequence: GLYMA08G11400.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G180331_T01 (Zea mays), 3'ss of exon 1
atatccatactcattttgtattgt---catctggtatgcgtttgtgcagcttcaaccaaggtataatgatcaataatacttacacacta-gactg---actttgcagGTTGCAATATCAGTGAAACCATTGAAAGTGCAAAACTGGATTCTTCCAGAAATGCCTGGGCTTATAACTGATTTTCTGATATCTCTTGATGATCGGTTTC
| ||| | | | |||| | ||| | | | || | | | | || | | || ||| ||||| |||||| ||||||| || || | ||||||||||| || | ||||||||||| ||||||| ||| || | |||||||||||| | || ||||||||||| || | ||
------gtgctctggtaagaatccgcgtatctatcaaaattttctactaata-aatagggctggagttgacattttagttagaaccctatgactgtgtactttgtagGTTGCTATCTCCATAAAACCATTGAAGGTTCGCAACTGGATTCTGCCAGAAACGCCAGGATTGATAACTGATTTTGTTATCTCTCTTGATGACCGTTATC
upper sequence: GLYMA08G11400.1 (Glycine max), 3'ss of exon 5
lower sequence: AT4G14040.1 (Arabidopsis thaliana), 3'ss of exon 4
atatccatactcattttgtattgtcatctggtatgcgtttgtgcagcttcaaccaaggtataatgatcaataatacttacacactagactgactttgcagGTTGCAATATCAGTGAAACCATTGAAAGTGCAAAACTGGATTCTTCCAGAAATGCCTGGGCTTATAACTGATTTTCTGATATCTCTTGATGATCGGTTTC
|| || ||| || ||| | | | | | | | || |||| || | | ||| | || || |||||| ||||| || ||||| |||||||| |||||||||| |||||||||||||| |||||||| || || || |||| || || ||||| ||||||
-------------gcaagtgaagtt-tctaa-atctttttcttttgtcttatctcaaatcta-tgattaacttgtgatttaaactgg--tgttgttttagGTTGTTATATCGGTTAAACCGTTGAAAGTCGAAAACTGGATACTTCCAGAAATGCCGGGGCTTATCACCGACTTCTTGATCTCCCTCGATGACCGGTTTT
upper sequence: GLYMA08G11400.1 (Glycine max), 3'ss of exon 5
lower sequence: AT3G23800.1 (Arabidopsis thaliana), 3'ss of exon 5
atatccatactcattttgtattgtcatctggtatgcgtttgtgcagcttcaaccaaggtataatgatcaataatacttacacactagactgactttgcagGTTGCAATATCAGTGAAACCATTGAAAGTGCAAAACTGGATTCTTCCAGAAATGCCTGGGCTTATAACTGATTTTCTGATATCTCTTGATGATCGGTTTC
| ||| | | | | | | | ||| | | | | || | | ||| | || || | || |||| |||| || |||||||| |||| ||||||| ||||||||||||| ||||||||||| |||||||| || || ||||| || || ||||| || || || |
--gtatataatgaatct---tctctacttattattcttcatttctttttgatttttgtcctaacaacaaacaacctctccaa-----------tttgaagGTGGCTATATCAGTTGAACCTCTGAAAGTTGAAAACTGGATTCTCCCAGAAATGCCAGGGCTTATCACCGACTTTCTAATCTCACTTGACGACCGATTCC
upper sequence: GLYMA08G11400.1 (Glycine max), 3'ss of exon 5
lower sequence: AT4G14030.1 (Arabidopsis thaliana), 3'ss of exon 5
atatccatactcattttgtattgtcatctggtatgcgtttgtgcagcttcaaccaaggtataatgatcaataatacttacacactagactgactttgcagGTTGCAATATCAGTGAAACCATTGAAAGTGCAAAACTGGATTCTTCCAGAAATGCCTGGGCTTATAACTGATTTTCTGATATCTCTTGATGATCGGTTTC
| | ||| | | | | | |||| | ||| | | |||| || | || || ||| ||| |||||| ||||| || ||||| |||||||| |||||||||| |||||||||||||| ||||| || || || || |||| || || ||||| || |||
----gtaagtgtagtttctgattcattttcattacttcttgttttggttc--ttataattctatgactaacca-accagcaataacaacttgtttt--agGTTGTTATATCGGTTAAACCGTTGAAAGTCGAAAACTGGATACTTCCAGAAATGCCGGGGCTAATCACCGACTTCTTGATCTCCCTCGATGACCGATTTA
upper sequence: GLYMA08G11400.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv05s0029g00240.t01 (Vitis vinifera), 3'ss of exon 5
-----------------atatccatactcattttgtattgtcatctggtatgc--gtttgtgc-agcttcaaccaaggtataatgatcaataatac----ttacacactagactgactttgcagGTTGCAATATCAGTGAAACCATTGAAAGTGCAAAACTGGATTCTTCCAGAAATGCCTGGGCTTATAACTGATTTTCTGATATCTCTTGATGATCGGTTTC
| || | | ||||| ||| | || | || |||| || || | |||| || | ||| | |||| | || | ||| | | || |||||||||||||||| |||||| |||| |||||||||||||||||||| || ||||| |||||||||||||||||||| ||||| ||||| || | ||
gtatgcggataatatgtgtttcttcaattcctttgt-ttgaaaccttgcattttgaattgtattagtctctattaaggcatgacaatccacaatatataatcactccctaatttacttatgaagGTTGCAATATCAGTAAAACCACTGAAGGTGCAAAACTGGATTCTTCCTGACATGCCGTCTCTTATAACTGATTTTCTGATCTCTCTCGATGACCGTTATC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gcttcaaccaaggtataatgatcaataatacttacacactagactgactttgcagGTTGCAATATCAGTGAAACCATTGAAAGTGCAAAACTGGATTCTTCCAGAAATGCCTGGGCTTATAACTGATTTTCTGATATCTCTTGATGATCGGTTTC
tataatgatcaataat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
atatccatactcattttgtattgtcatctggtatgcgtttgtgcagcttcaaccaaggtataatgatcaataatacttacacactagactgactttgcagGTTGCAATATCAGTGAAACCATTGAAAGTGCAAAACTGGATTCTTCCAGAAATGCCTGGGCTTATAACTGATTTTCTGATATCTCTTGATGATCGGTTTC
- - -catactc
- - - - - - - - - - -tgtcatc
- - - - - - - - - - - - - - - gtatgcg
- - - - - - - - - - - - - - - - - - - - -tgcagct
- - - - - - - - - - - - - - - - - - - - - - - - -caaccaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tacacac