Sequence
atgc intronic sequence ATGC exonic sequence...tcagattgtgtattgataaatcccgtgtatgatacaattgaccttgtgagattatcatttgggctatatgtgctgaagtccttctgtatctgctgatcagATGATCTTATCATTTGAGCTTCCTTTTGCTTTGATTCCACTCCTCAAGTTCACTAGCAGCAAAATCAAGATGGGAGAACATGTCAACTCAATCTCG
Basic information
species | Glycine max |
transcript | GLYMA07G02680.1 |
intron # | 10 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA07G02680.1 (Glycine max), 3'ss of exon 10
lower sequence: LOC_Os06g46310.3 (Oryza sativa), 3'ss of exon 11
---------------------------------------------tcagattgtgtattgataaatcccgtgtatgatacaattgaccttgtgagattatcatttgggctatatgtgctgaagtccttctgtatctgctgatcagATGATCTTATCATTTGAGCTTCCTTTTGCTTTGATTCCACTCCTCAAGTTCACTAGCAGCAAAATCAAGATGGGAGAACATGTCAACTCAATCTCG
|| ||| | ||| || | | || | | |||| | ||| || ||| || | | || | | | | || ||| || |||||||| | ||||||||||||||||||||| | |||||||||| || ||||| ||||||| | || ||||| | || || |||| |
gtaattgctaaaatttactatttcaaagtataatacattcatccttctgataatctataatgaacttcaatgcacatgagaattaaa-ttgctccatc-ccatatgtcaacttttaactaatgccttactttatta--tgcacagATGATACTGTCATTTGAGCTTCCTTTTGCTCTAGTTCCACTCCTAAAATTCACAAGCAGCAGGACAAAAATGGGGCAGCACACAAATTCAAAAGCC
upper sequence: GLYMA07G02680.1 (Glycine max), 3'ss of exon 10
lower sequence: GRMZM2G069198_T01 (Zea mays), 3'ss of exon 12
------------------------------tcagattgtgta---ttgataaatcc--cgtgtatgatacaattgaccttgtgagattatcatttgggct--atatgtgctgaagtccttctgtatctgctg-at-cagATGATCTTATCATTTGAGCTTCCTTTTGCTTTGATTCCACTCCTCAAGTTCACTAGCAGCAAAATCAAGATGGGAGAACATGTCAACTCAATCTCG
| | | || ||| || ||| | || ||| | ||| | | | ||| ||| ||| || | | || || ||| || |||||||| | |||||||| || ||||||||||| |||||||||| || ||||| |||||||||| |||||||| | ||| || ||||| |
gtaatcagtgaactttactgttgtactcttctatacctcaaaaacttaatagttctataatgtttaatctcattactcatgtcaattaaggtttttagctccgtatatgttaactaatgccttgctcggctacatgcagATGATACTGTCATTTGAACTCCCTTTTGCTTTAGTTCCACTCCTTAAATTCACCAGCAGCAAAACAAAGATGGGGCAGCATACAAATTCAATATTC
upper sequence: GLYMA07G02680.1 (Glycine max), 3'ss of exon 10
lower sequence: AT1G15960.1 (Arabidopsis thaliana), 3'ss of exon 11
tcagattgtgtattgataaatcccgtgtatgatacaattgaccttgtgagattatcatttgggctatatgtgctgaagtccttctgtatctgctgatcagATGATCTTATCATTTGAGCTTCCTTTTGCTTTGATTCCACTCCTCAAGTTCACTAGCAGCAAAATCAAGATGGGAGAACATGTCAACTCAATCTCG
| || | | | || | || | | || | ||| || ||| | | || | | ||| | || |||||||||||||| ||||| || || |||||||| | ||||| ||||| ||||| ||||| |||| ||| ||||| ||| | ||| ||| | |
--------------gtataacctcttccataacttaaatccaatctcttaatca-catacatactttattaacatcaatcatcttatatgt-ttg--cagATGATCTTATCCTTTGAACTCCCATTTGCTTTAGTCCCACTTCTCAAATTCACAAGCAGTAAAACCAAAATGGGCTCACACGCCAATTCACTTGTG
upper sequence: GLYMA07G02680.1 (Glycine max), 3'ss of exon 10
lower sequence: AT1G80830.1 (Arabidopsis thaliana), 3'ss of exon 9
tcagattgtgtattgataaatcccgtgtatgatacaattgaccttgtgagattatcatttgggctatatgtgctgaagtccttctgtatctgctgatcagATGATCTTATCATTTGAGCTTCCTTTTGCTTTGATTCCACTCCTCAAGTTCACTAGCAGCAAAATCAAGATGGGAGAACATGTCAACTCAATCTCG
||| | | | | | | | | | | | | | ||| |||| || | | || | |||| || | | |||||||||||||| |||||||| || ||||| ||| |||| || ||||| ||||| || |||||| ||||||||| |||||||||| |||| ||
---------gtactaaaa----tcatttctaactctagttatcatgtatacttat-atatatgacttacttcatgaaatcaaatcatcatcttaaaacagATGATCTTATCCTTTGAGCTCCCGTTTGCGTTGGTTCCTCTTCTCAAATTCACAAGTTGCAAAACCAAGATGGGTTCACATGTCAACCCAATGGCG
upper sequence: GLYMA07G02680.1 (Glycine max), 3'ss of exon 10
lower sequence: Vv09s0070g00210.t01 (Vitis vinifera), 3'ss of exon 12
tcagattgtgtattgata-aatcccgtgtatg---atacaattgaccttgtgagattatcatttgggctatatgtg---ctgaagtccttctgtatctgctgatcagATGATCTTATCATTTGAGCTTCCTTTTGCTTTGATTCCACTCCTCAAGTTCACTAGCAGCAAAATCAAGATGGGAGAACATGTCAACTCAATCTCG
|| | | | | | | | | | | |||| | ||| ||| | || | | || | ||||| || |||||||||||||||||||| || ||||||||| | |||||||| ||||||||||| ||| |||| | |||||||| | | ||||||| || | | |
-------gtttctcaacacggttacatatccacatagagaattttttgctcatgtctattttttagctcttacggaaaacctaacctttgatgtattgtcttggcagATGATCTTATCATTTGAACTCCCTTTTGCTCTCATTCCACTTCTCAAGTTCACCAGCTGCAAGACTAAGATGGGTGCATATGTCAATTCGACCATG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gtgagattatcatttgggctatatgtgctgaagtccttctgtatctgctgatcagATGATCTTATCATTTGAGCTTCCTTTTGCTTTGATTCCACTCCTCAAGTTCACTAGCAGCAAAATCAAGATGGGAGAACATGTCAACTCAATCTCG
attatcattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tcagattgtgtattgataaatcccgtgtatgatacaattgaccttgtgagattatcatttgggctatatgtgctgaagtccttctgtatctgctgatcagATGATCTTATCATTTGAGCTTCCTTTTGCTTTGATTCCACTCCTCAAGTTCACTAGCAGCAAAATCAAGATGGGAGAACATGTCAACTCAATCTCG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- -gattgtg
- - - - - - - - - - -cccgtgt
- - - - - - - - - - - - - - - - - - - - -ccttgtg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgctgaa