Sequence
atgc intronic sequence ATGC exonic sequence...aatcttctcaatttccttcagctttgtgcatattctcttgcatgaaagcttgagaagaaataaggctttattatctttctaattaatcttttttaaccagTTATTGTGAGTGCTTTGCTGCTGGAGTCTACTGCATAGAACCTTGTGCATGCCATGATTGCTTCAATAAACCTATTCATGTTGAGACTGTTCTTCAAACT
Basic information
species | Glycine max |
transcript | GLYMA10G39080.1 |
intron # | 11 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA10G39080.1 (Glycine max), 3'ss of exon 11
lower sequence: GRMZM2G701689_T01 (Zea mays), 3'ss of exon 5
--aatcttctcaatttccttcagctttgtgcatattctctt-gcatgaaagcttgagaagaaataaggctt-tattatctttctaattaatcttttttaaccagTTATTGTGAGTGCTTTGCTGCTGGAGTCTACTGCATAGAACCTTGTGCATGCCATGATTGCTTCAATAAACCTATTCATGTTGAGACTGTTCTTCAAACT
| | ||| || ||| | | |||| || | | | || | | | || ||| | ||||| || | |||||| |||||||| ||||||||||||||||| || || |||||| | || | || | || || | | |||| || |||||||| ||
agggagaagggatctgtgttctatttctggcaaactgtctttacactgatacattgtctgatttctgttacatgataaatttttgcttaat----ttcatgcagTTACTGTGAGTGTTTTGCTGCTGGAGTCTATTGTTCTGAGCCTTGTTCGTGTATCGGCTGTATGAACAACCAGAGTCATACGGAAACTGTTCTATCTACG
upper sequence: GLYMA10G39080.1 (Glycine max), 3'ss of exon 11
lower sequence: GRMZM2G322090_T01 (Zea mays), 3'ss of exon 6
------aatcttctcaatttccttcagctttgtgcatattctcttgcatgaaagcttgagaagaaa-taaggctttattatctttctaattaatcttttttaaccagTTATTGTGAGTGCTTTGCTGCTGGAGTCTACTGCATAGAACCTTGTGCATGCCATGATTGCTTCAATAAACCTATTCATGTTGAGACTGTTCTTCAAACT
|| ||| | | ||| | | ||| | ||| || ||| | | | | || || ||| | ||||| || | |||||| |||||||| ||||||||||||||||| || || |||||| | || | || || || | | |||| | || || ||||| ||
gggagaaaggatctgtagtatattc---ctggcaagctatctttacactgatagattgtctcgtttctgttacatgataatttttttgcttaat----ttcatgcagTTACTGTGAGTGTTTTGCTGCTGGAGTCTATTGTTCTGAGCCTTGTTCGTGTATCGGCTGTCAGAACAACCAGAGTCATATGGAAACAGTTCTGTCTACA
upper sequence: GLYMA10G39080.1 (Glycine max), 3'ss of exon 11
lower sequence: AT4G14770.1 (Arabidopsis thaliana), 3'ss of exon 4
aatcttctcaatttccttcagctttgtgcatattctcttgcatgaaagcttgagaagaaataaggctttattatctttctaattaatcttttttaaccagTTATTGTGAGTGCTTTGCTGCTGGAGTCTACTGCATAGAACCTTGTGCATGCCATGATTGCTTCAATAAACCTATTCATGTTGAGACTGTTCTTCAAACT
| || || || ||| || | | | | || || | || || | | |||| || | | | | |||||| ||||| |||||||||||||||||||| |||||||| || ||| |||| || ||||||||||||||||| |||| || ||| || |||
----------gtaagctccaaagttccacatttt---tgatctttggcccttcaaaaaagtttggtgttttgagtcttctgat--gtttgtgtggtgcagTTACTGTGAATGCTTTGCTGCTGGAGTCTATTGCATAGAGCCATGTTCATGTATAGACTGCTTCAATAAACCTATCCATGAAGACGTTGTCCTGGCGACT
upper sequence: GLYMA10G39080.1 (Glycine max), 3'ss of exon 11
lower sequence: AT3G22780.1 (Arabidopsis thaliana), 3'ss of exon 5
--------aatcttctcaatttccttcagctttgtgcatattctcttgcatgaaagcttgagaagaaataaggc--tttattatctttctaattaatcttttttaaccagTTATTGTGAGTGCTTTGCTGCTGGAGTCTACTGCATAGAACCTTGTGCATGCCATGATTGCTTCAATAAACCTATTCATGTTGAGACTGTTCTTCAAACT
| | | | || || | | | ||| || ||| ||| | | | | || | || || | | | || ||| |||||| ||||| |||||||||||||| || || |||||||| || ||| |||| ||||||||||| |||||||| |||| || |||||| | ||
gtaagctcataccccctagcatctcgttaattcctacctgttca---aaataaaaaactgaattgccttgaagtagttaaccattgtttgactcccttttctttctgcagTTACTGTGAATGCTTTGCTGCTGGGGTTTATTGCATAGAGCCATGTTCATGTATAGATTGCTTCAACAAACCTATCCATGAAGAAACTGTTTTGGCTACC
upper sequence: GLYMA10G39080.1 (Glycine max), 3'ss of exon 11
lower sequence: Vv05s0020g03880.t01 (Vitis vinifera), 3'ss of exon 6
aatcttctcaatttccttcagctttgtgcatattctcttgcatgaaagcttgagaagaaataaggctttattatctttctaattaatcttttttaaccagTTATTGTGAGTGCTTTGCTGCTGGAGTCTACTGCATAGAACCTTGTGCATGCCATGATTGCTTCAATAAACCTATTCATGTTGAGACTGTTCTTCAAACT
|||| | || | | | | | | || | | |||| || | | |||| ||| || | |||||| ||||| |||||||||||||| |||||||| |||| || ||| ||||||| || ||||| || ||||||||||||| || ||||||||| ||||
tgtctttgaatctttgaggggggcaaaggaaaattagaaatttattttatttccttctgttttgttcttatgatttgaccttttaagcttcttcatgcagTTACTGTGAATGCTTTGCTGCTGGTGTCTACTGTGTAGAGCCATGTTCATGCCAAGAATGCTTTAACAAACCTATTCATGAAGATACTGTTCTTGCAACT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aagcttgagaagaaataaggctttattatctttctaattaatcttttttaaccagTTATTGTGAGTGCTTTGCTGCTGGAGTCTACTGCATAGAACCTTGTGCATGCCATGATTGCTTCAATAAACCTATTCATGTTGAGACTGTTCTTCAAACT
tctttttt CT-rich tract
tttattatctttctaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
aatcttctcaatttccttcagctttgtgcatattctcttgcatgaaagcttgagaagaaataaggctttattatctttctaattaatcttttttaaccagTTATTGTGAGTGCTTTGCTGCTGGAGTCTACTGCATAGAACCTTGTGCATGCCATGATTGCTTCAATAAACCTATTCATGTTGAGACTGTTCTTCAAACT
- - - - - - -tccttca
- - - - - - - - - - - - - tgcatat
- - - - - - - - - - - - - - - - - - - -gcatgaa
- - - - - - - - - - - - - - - - - - - - - - - -gcttgag
- - - - - - - - - - - - - - - - - - - - - - - - - - - aagaaata