Sequence
atgc intronic sequence ATGC exonic sequence...ttttccaccttgcctcctaagtacactcttaggcgaacattggaagtttgatctttgtggttgactattagctatttgtgatttgacgtgtcatgattagGTTCAAGTGCATTGATTTGGATGGAAATGGAGTTCTGACACGGAATGAACTGCAATTTTTTTATGAGGAGCAATTGCATCGAATGGAGTGCATGGCCCAA
Basic information
species | Glycine max |
transcript | GLYMA19G43790.1 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA19G43790.1 (Glycine max), 3'ss of exon 9
lower sequence: LOC_Os10g33680.1 (Oryza sativa), 3'ss of exon 9
ttttccaccttgcctcctaagtacactcttaggcgaacattggaagtttgat---ctttgtggttgactat-tagctatttgtgatttgacgtgtca--tgatt----agGTTCAAGTGCATTGATTTGGATGGAAATGGAGTTCTGACACGGAATGAACTGCAATTTTTTTATGAGGAGCAATTGCATCGAATGGAGTGCATGGCCCAA
|||||| | ||| |||| | || | | | | ||| | | ||| | || | | | ||| || | | | ||| ||||| ||||| ||||| | ||||||||||| || | || | |||| |||||||||| ||||||||||||||||| || |||||||||||||| |||
---------ttgcctattgagttttgccttacagtggctttaatattgtagtatattttacaactaattatgttactgtat-tcattgaacatatgaaccaattttacagGTTTAAGTGTATTGACCTTGATGGAAATGGCATTTTAACCACCACTGAAATGCAATTTTTCTATGAGGAGCAATTGCACCGGATGGAGTGCATGGCACAA
upper sequence: GLYMA19G43790.1 (Glycine max), 3'ss of exon 9
lower sequence: GRMZM2G148323_T01 (Zea mays), 3'ss of exon 9
--ttttccaccttgcctcctaagtacactcttag-gcgaacattggaagtttgatctttgtggttgactattagctatttgtgatttgacgtgtcatgattagGTTCAAGTGCATTGATTTGGATGGAAATGGAGTTCTGACACGGAATGAACTGCAATTTTTTTATGAGGAGCAATTGCATCGAATGGAGTGCATGGCCCAA
| || | ||| | | | || |||||| | | | | || | | | | ||| | | || || | | ||||| |||||||| ||| | ||||| ||||| || | || |||||| |||||||||| || |||||||||||||| ||||||||||||||||| |||
gttgttgtgatctattaccttattctatctttgctatacacattgtatatctcaggttacagttgtatttttattgaaatatgg---gaaacaactttcgcagGTTTAAGTGCATCGATCTTGATGGTAATGGTATTTTAACTTTCAATGAAATGCAATTTTTCTACGAGGAGCAATTGCACCGAATGGAGTGCATGGCACAA
upper sequence: GLYMA19G43790.1 (Glycine max), 3'ss of exon 9
lower sequence: AT5G28900.1 (Arabidopsis thaliana), 3'ss of exon 9
ttttccaccttgcctcctaagtacactcttaggcgaacattggaagtttg---atctttgtggttgactattagctatttgtgatttg-acgtgtcatgattagGTTCAAGTGCATTGATTTGGATGGAAATGGAGTTCTGACACGGAATGAACTGCAATTTTTTTATGAGGAGCAATTGCATCGAATGGAGTGCATGGCCCAA
||| | | | | | ||| ||| | | || | ||| || | | | || || |||||| |||||||| || ||||||| |||||| || | || || ||||| ||||||| |||||||| ||||| |||||| |||||||||||||||| |||
--------------------gtaagttgtgatagaagggtccgaaagttgcagacagataccattttaagtcttttatctgacacaagtatacgttg-gactagGTTTAAGTGCATAGACTTGGATGCAAATGGGATTATTACGCGAAATGAGATGCAATTCTTTTATGAAGAGCAGTTGCATAGAATGGAGTGCATGGCGCAA
upper sequence: GLYMA19G43790.1 (Glycine max), 3'ss of exon 9
lower sequence: AT1G54450.1 (Arabidopsis thaliana), 3'ss of exon 9
ttttccaccttgcctcctaagtacactcttaggcgaacattggaagtttg-atctttgtggttgactattagctat-ttgtgat-ttgacgtgtcatgat-tagGTTCAAGTGCATTGATTTGGATGGAAATGGAGTTCTGACACGGAATGAACTGCAATTTTTTTATGAGGAGCAATTGCATCGAATGGAGTGCATGGCCCAA
| || | || | || | |||| || ||| || || |||||| || || | || | || | ||||| |||||||||||||||||||||||||| |||||||||| |||| ||||| || |||||||| ||||| |||||||| | ||| ||||||| |||||||| |||
-----------gtgagaatggtgaatgttttcatacatatagagtctttgtgtcggtgttatttggtaagagctatattctgttattaatgtttgatgatatagGTTCAAGTGCATTGATTTGGATGCAAATGGAGTTTTGACGCGGAACGAGCTGCAATTCTTTTACGAGGAGCAGCTACATAGAATGGAATGCATGGCGCAA
upper sequence: GLYMA19G43790.1 (Glycine max), 3'ss of exon 9
lower sequence: AT5G28850.1 (Arabidopsis thaliana), 3'ss of exon 8
ttttccaccttgcctcctaagtacactcttaggcgaacattggaagtttg---atctttgtggttgactat-tagctatttgtgatttg-acgtgtcatgattagGTTCAAGTGCATTGATTTGGATGGAAATGGAGTTCTGACACGGAATGAACTGCAATTTTTTTATGAGGAGCAATTGCATCGAATGGAGTGCATGGCCCAA
||| | | | | | ||| ||| | | | || | | ||| || | | | || || |||||| |||||||| || ||||||| |||||| || | || || ||||| ||||||| |||||||| ||||| |||||| |||||||||||||||| |||
--------------------gtaagttgtgatataagggtccgaaagttgcagacagatacgattttaagtctttttatctgacacaagtatacgttg-gactagGTTTAAGTGCATAGACTTGGATGCAAATGGGATTATAACGCGAAATGAGATGCAATTCTTTTATGAAGAGCAGTTGCATAGAATGGAGTGCATGGCGCAA
upper sequence: GLYMA19G43790.1 (Glycine max), 3'ss of exon 9
lower sequence: PP1S147_62V6.2 (Physcomitrella patens), 3'ss of exon 9
-----------------------------------------------------------------------------------------------ttttccaccttgcctcctaagtacactcttaggcgaacattggaagtttgatctttgtggttgactattagctatttgtgatttgacgtgtcatgattagGTTCAAGTGCATTGATTTGGATGGAAATGGAGTTCTGACACGGAATGAACTGCAATTTTTTTATGAGGAGCAATTGCATCGAATGGAGTGCATGGCCCAA
| || | | | | | || | | | | | | | | || | | | ||||| | || || | ||| |||||||| || | || ||||| | |||| || | |||| ||||| |||||| |||||||||||||||| | ||||| |||||||||||||| ||
gtacgtacctttatatggcctctaaaatgctctccacttttttggcatgaagttgatgtttttgaatgcaaatcatgtgctttctgacaaaacagtatttaggataaaggattgaattttcactcggattgattagttacataacaacgaggacatcgagtctaatttattttttcttgtacacctgatg--cagGTTCAAATGTGTGGACCTGGATTGTGATGGTGTGATAACACCAAATGAGATGCAATATTTTTATGAGGAGCAACTTCATCGGATGGAGTGCATGGCTCAG
upper sequence: GLYMA19G43790.1 (Glycine max), 3'ss of exon 9
lower sequence: PP1S7_163V6.1 (Physcomitrella patens), 3'ss of exon 9
--------------------------------------------------------------------------------------------ttttccaccttgcctcctaagtacactcttaggcgaacattggaagtttgatctttgtggttgactattagctatttgtgatttgacgtgtcatgattagGTTCAAGTGCATTGATTTGGATGGAAATGGAGTTCTGACACGGAATGAACTGCAATTTTTTTATGAGGAGCAATTGCATCGAATGGAGTGCATGGCCCAA
|| || | | | || | || || | ||| || | ||| | || | ||| ||| | ||| || ||| ||||||||||| | || ||||| | | || | | | || ||||| |||||| |||||| ||||||||| | ||||| |||||||||||||| ||
gtaagtgccttgacatggtctctaaaacattttctgcacctccatatcttaactgtgaatttacatgaatacaaactgtctgctttctgataattgtaacgcggacaatacattagattccgtcacgtatattacaa-taaaatcgaggacattttgt-ttaatgctttcatcctggacacgtgatg--cagGTTCAAGTGTGTAGACCTGGATTGTGACGGGATGATTATACTAAATGAGATGCAATATTTTTACGAGGAGCAACTTCATCGGATGGAGTGCATGGCTCAG
upper sequence: GLYMA19G43790.1 (Glycine max), 3'ss of exon 9
lower sequence: PP1S191_94V6.1 (Physcomitrella patens), 3'ss of exon 10
------------------------------------------------------ttttccaccttgcctcctaagtacactcttaggcgaacattgg-----aagtttgatctttgtggttgactattagctatttgtgatttgacgtgtcatga--------ttagGTTCAAGTGCATTGATTTGGATGGAAATGGAGTTCTGACACGGAATGAACTGCAATTTTTTTATGAGGAGCAATTGCATCGAATGGAGTGCATGGCCCAA
|||| | || || || || | | | | || ||||| ||||| | | || || | | || | || || ||| ||||||||||||| | ||||| ||| | |||| || | || |||||| |||| | |||||||||||||||||| ||||||||||| || ||||| |||
gtaatttttttgtttttttcttattctttttaattttatttattaatttatttattttattatctcccatgtagttatttctttttacaagcttgaattcttaaacatgatcattgtgatatatctatatttaatgattatctaacaagtggtgaaaataaaattagGTTCAAGTGTGTGGATTTAGATTGTGATGGGGTGATCACTGCAAATGAAATGCATTATTTTTATGAGGAGCAATTACATCGAATGGAATGTATGGCACAA
upper sequence: GLYMA19G43790.1 (Glycine max), 3'ss of exon 9
lower sequence: EFJ20642 (Selaginella moellendorffii), 3'ss of exon 9
ttttccaccttgcctcctaagtacactcttaggcgaacattggaagtttgatctttgtggttgactattagctatttgtgatttgacgtgtcatgatt---agGTTCAAGTGCATTGATTTGGATGGAAATGGAGTTCTGACACGGAATGAACTGCAATTTTTTTATGAGGAGCAATTGCATCGAATGGAGTGCATGGCCCAA
| ||| || | | | || | || || | ||||| || || | |||||||| || || ||| ||||| | | ||||| |||| | || || |||| | ||||| ||||||||||||||||| ||||||||| | || |||
-----------------------------------------gtaag--cgacgtcttgaatcttctgtaag--atcgatcgattgacagatcgcgacttccagGTTCAAATGTATCGATCTGGATTGTGACGGAGTGGTGACTCCAAACGAGATGCAGTACTTTTACGAGGAGCAATTGCATCGCATGGAGTGCCTAGCTCAA
upper sequence: GLYMA19G43790.1 (Glycine max), 3'ss of exon 9
lower sequence: EFJ32791 (Selaginella moellendorffii), 3'ss of exon 9
ttttccaccttgcctcctaagtacactcttaggcgaacattggaagtttgatctttgtggttgactattagctatttgtgatttgacgtgtcatgatt---agGTTCAAGTGCATTGATTTGGATGGAAATGGAGTTCTGACACGGAATGAACTGCAATTTTTTTATGAGGAGCAATTGCATCGAATGGAGTGCATGGCCCAA
| ||| || | | | || | || || | ||||| || || | |||||||| || || ||| ||||| | | ||||| |||| | || || |||| | ||||||||||||||||||||||| ||||||||| | || |||
-----------------------------------------gtaag--cgacgtcttgaatcttctgtaag--atcgatcgattgacagatcgcgacttccagGTTCAAATGTATCGATCTGGATTGTGACGGAGTGGTGACTCCAAACGAGATGCAGTACTTTTATGAGGAGCAATTGCATCGCATGGAGTGCCTAGCTCAA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gtttgatctttgtggttgactattagctatttgtgatttgacgtgtcatgattagGTTCAAGTGCATTGATTTGGATGGAAATGGAGTTCTGACACGGAATGAACTGCAATTTTTTTATGAGGAGCAATTGCATCGAATGGAGTGCATGGCCCAA
atttgac putative branch site (score: 4)
actatta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttttccaccttgcctcctaagtacactcttaggcgaacattggaagtttgatctttgtggttgactattagctatttgtgatttgacgtgtcatgattagGTTCAAGTGCATTGATTTGGATGGAAATGGAGTTCTGACACGGAATGAACTGCAATTTTTTTATGAGGAGCAATTGCATCGAATGGAGTGCATGGCCCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA
- ttccacc
- - - - - tgcctcc
- - - - - - - - - - -tacactc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgacgtg