Sequence
atgc intronic sequence ATGC exonic sequence...tccaccttgcctcctaagtacactcttaggcgaacattggaagtttgacctttgtggttgactcttgttagctatttgtgatttgatgtgtcatgattagGTTCAAGTGCATTGATTTGGATGGAAATGGAGTTCTGACACGGAATGAACTGCAATTTTTTTATGAGGAGCAATTGCATCGAATGGAGTGCATGGCCCAA
Basic information
species | Glycine max |
transcript | GLYMA03G41180.1 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA03G41180.1 (Glycine max), 3'ss of exon 9
lower sequence: LOC_Os10g33680.1 (Oryza sativa), 3'ss of exon 9
tccaccttgcctcctaagtacactcttaggcgaacattggaagtttgac---ctttgtggttgactcttgttagctatttgt-gatttgatgtgtcatgatt--agGTTCAAGTGCATTGATTTGGATGGAAATGGAGTTCTGACACGGAATGAACTGCAATTTTTTTATGAGGAGCAATTGCATCGAATGGAGTGCATGGCCCAA
|||||| | ||| |||| | || | | | ||| | | | | | |||| | || ||| || || ||||| ||||| ||||| | ||||||||||| || | || | |||| |||||||||| ||||||||||||||||| || |||||||||||||| |||
------ttgcctattgagttttgccttacagtggctttaatattgtagtatattttacaactaattatgttactgtattcattgaacatatgaaccaattttacagGTTTAAGTGTATTGACCTTGATGGAAATGGCATTTTAACCACCACTGAAATGCAATTTTTCTATGAGGAGCAATTGCACCGGATGGAGTGCATGGCACAA
upper sequence: GLYMA03G41180.1 (Glycine max), 3'ss of exon 9
lower sequence: GRMZM2G148323_T01 (Zea mays), 3'ss of exon 9
-----tccaccttgcctcctaagtacactcttag-gcgaacattggaagtttgacctttgtggttgactcttgttagctatttgtgatttgatgtgtcatgattagGTTCAAGTGCATTGATTTGGATGGAAATGGAGTTCTGACACGGAATGAACTGCAATTTTTTTATGAGGAGCAATTGCATCGAATGGAGTGCATGGCCCAA
| | ||| | | | || |||||| | | | | || |||| | || | | || || || | | || ||||| |||||||| ||| | ||||| ||||| || | || |||||| |||||||||| || |||||||||||||| ||||||||||||||||| |||
gttgttgtgatctattaccttattctatctttgctatacacattgtatatctcaggtt-acagttgtatttttattgaaatatgggaaacaactt-tcgc----agGTTTAAGTGCATCGATCTTGATGGTAATGGTATTTTAACTTTCAATGAAATGCAATTTTTCTACGAGGAGCAATTGCACCGAATGGAGTGCATGGCACAA
upper sequence: GLYMA03G41180.1 (Glycine max), 3'ss of exon 9
lower sequence: AT5G28900.1 (Arabidopsis thaliana), 3'ss of exon 9
tccaccttgcctcctaagtacactcttaggcgaacattggaagtttgacctttgtggttgactcttgttagctatttgtgatttg-atgtgtcatgattagGTTCAAGTGCATTGATTTGGATGGAAATGGAGTTCTGACACGGAATGAACTGCAATTTTTTTATGAGGAGCAATTGCATCGAATGGAGTGCATGGCCCAA
||| | | | | | ||| ||| | | || ||| || | | || || || |||||| |||||||| || ||||||| |||||| || | || || ||||| ||||||| |||||||| ||||| |||||| |||||||||||||||| |||
-----------------gtaagttgtgatagaagggtccgaaagttgcagacagataccattttaagtcttttatctgacacaagtatacgttg-gactagGTTTAAGTGCATAGACTTGGATGCAAATGGGATTATTACGCGAAATGAGATGCAATTCTTTTATGAAGAGCAGTTGCATAGAATGGAGTGCATGGCGCAA
upper sequence: GLYMA03G41180.1 (Glycine max), 3'ss of exon 9
lower sequence: AT1G54450.1 (Arabidopsis thaliana), 3'ss of exon 9
tccaccttgcctcctaagtacactcttaggcgaacattggaagtttgacctttgtggttgactcttgttagctat-ttgtgat-ttgatgtgtcatgat-tagGTTCAAGTGCATTGATTTGGATGGAAATGGAGTTCTGACACGGAATGAACTGCAATTTTTTTATGAGGAGCAATTGCATCGAATGGAGTGCATGGCCCAA
| || | || | |||| ||| | | | ||| | | |||||| || || | || |||| | ||||| |||||||||||||||||||||||||| |||||||||| |||| ||||| || |||||||| ||||| |||||||| | ||| ||||||| |||||||| |||
--------gtgagaatggtgaatgtttt--catacatatagagtctttgtgtcggtgttatttggtaagagctatattctgttattaatgtttgatgatatagGTTCAAGTGCATTGATTTGGATGCAAATGGAGTTTTGACGCGGAACGAGCTGCAATTCTTTTACGAGGAGCAGCTACATAGAATGGAATGCATGGCGCAA
upper sequence: GLYMA03G41180.1 (Glycine max), 3'ss of exon 9
lower sequence: AT5G28850.1 (Arabidopsis thaliana), 3'ss of exon 8
tccaccttgcctcctaagtacactcttaggcgaacattggaagtttg---acctttgtggtt--gactcttgttagctatttgtgatttgatgtgtcatgattagGTTCAAGTGCATTGATTTGGATGGAAATGGAGTTCTGACACGGAATGAACTGCAATTTTTTTATGAGGAGCAATTGCATCGAATGGAGTGCATGGCCCAA
||| | | | | | ||| ||| || | | || | |||| ||| || | || || || |||||| |||||||| || ||||||| |||||| || | || || ||||| ||||||| |||||||| ||||| |||||| |||||||||||||||| |||
-----------------gtaagttgtgatataagggtccgaaagttgcagacagatacgattttaagtctttttatctgacacaagt---atacgttg-gactagGTTTAAGTGCATAGACTTGGATGCAAATGGGATTATAACGCGAAATGAGATGCAATTCTTTTATGAAGAGCAGTTGCATAGAATGGAGTGCATGGCGCAA
upper sequence: GLYMA03G41180.1 (Glycine max), 3'ss of exon 9
lower sequence: PP1S147_62V6.2 (Physcomitrella patens), 3'ss of exon 9
---------------------------------------------------------------------------tccaccttgcctcctaagtacactcttaggcgaacattggaagtttgacctttgt-ggttgact-cttgttagcta---------------tttgtgatttgatgtgt-catgat-tagGTTCAAGTGCATTGATTTGGATGGAAATGGAGTTCTGACACGGAATGAACTGCAATTTTTTTATGAGGAGCAATTGCATCGAATGGAGTGCATGGCCCAA
| | || | | || | | | | || | ||| ||| || | | || | | | | | | ||| | ||| ||| | |||| |||||||| || | || ||||| | |||| || | |||| ||||| |||||| |||||||||||||||| | ||||| |||||||||||||| ||
gtacgtacctttatatggcctctaaaatgctctccacttttttggcatgaagttgatgtttttgaatgcaaatcatgtgcttt-ctgacaaaacagtatttaggataaaggattgaattttcactcggattgattagttacataacaacgaggacatcgagtctaatttattttttcttgtacacctgatgcagGTTCAAATGTGTGGACCTGGATTGTGATGGTGTGATAACACCAAATGAGATGCAATATTTTTATGAGGAGCAACTTCATCGGATGGAGTGCATGGCTCAG
upper sequence: GLYMA03G41180.1 (Glycine max), 3'ss of exon 9
lower sequence: PP1S7_163V6.1 (Physcomitrella patens), 3'ss of exon 9
---------------------------------------------------------------------tccaccttgcctcctaagtac--actcttaggcgaacattgga----agtttgacctttgtggttgactcttgttagctatttgtgatttgatgtgt------------catgat-tagGTTCAAGTGCATTGATTTGGATGGAAATGGAGTTCTGACACGGAATGAACTGCAATTTTTTTATGAGGAGCAATTGCATCGAATGGAGTGCATGGCCCAA
| || || || || | | | | | ||| ||| | | | | | | | | | | | | | | | ||| ||| | | |||| ||||||||||| | || ||||| | | || | | | || ||||| |||||| |||||| ||||||||| | ||||| |||||||||||||| ||
gtaagtgccttgacatggtctctaaaacattttctgcacctccatatcttaactgtgaatttacatgaatacaaactgtctgctttctgataattgtaacgcggacaatacattagattccgtcacgtatattacaataaaatcgaggacattttgtttaatgctttcatcctggacacgtgatgcagGTTCAAGTGTGTAGACCTGGATTGTGACGGGATGATTATACTAAATGAGATGCAATATTTTTACGAGGAGCAACTTCATCGGATGGAGTGCATGGCTCAG
upper sequence: GLYMA03G41180.1 (Glycine max), 3'ss of exon 9
lower sequence: PP1S191_94V6.1 (Physcomitrella patens), 3'ss of exon 10
---------------------------------------------------------tccaccttgcctcctaagtacactcttaggcgaacattgg-----aagtttgacctttgtggttgactcttgtt----agctatttgtgatttgatgtgt-catgattagGTTCAAGTGCATTGATTTGGATGGAAATGGAGTTCTGACACGGAATGAACTGCAATTTTTTTATGAGGAGCAATTGCATCGAATGGAGTGCATGGCCCAA
| | || || || || | | | | || ||| | ||||| | | | || ||| | | || || | |||||||||||||| | ||||| ||| | |||| || | || |||||| |||| | |||||||||||||||||| ||||||||||| || ||||| |||
gtaatttttttgtttttttcttattctttttaattttatttattaatttatttattttattatctcccatgtagttatttctttttacaagcttgaattcttaaacatgatcattgtgatatatctatatttaatgattatctaacaagtggtgaaaataaaattagGTTCAAGTGTGTGGATTTAGATTGTGATGGGGTGATCACTGCAAATGAAATGCATTATTTTTATGAGGAGCAATTACATCGAATGGAATGTATGGCACAA
upper sequence: GLYMA03G41180.1 (Glycine max), 3'ss of exon 9
lower sequence: EFJ20642 (Selaginella moellendorffii), 3'ss of exon 9
tccaccttgcctcctaagtacactcttaggcgaacattggaagtttgacctttgtggttgactcttgttagctatttgtgatttgatgtgtcatgatt---agGTTCAAGTGCATTGATTTGGATGGAAATGGAGTTCTGACACGGAATGAACTGCAATTTTTTTATGAGGAGCAATTGCATCGAATGGAGTGCATGGCCCAA
| | | || |||| |||| | || | |||| || || | |||||||| || || ||| ||||| | | ||||| |||| | || || |||| | ||||| ||||||||||||||||| ||||||||| | || |||
--------------------------------------------gtaagcgacgtc-ttgaatcttctgtaagatcgatcgattgacagatcgcgacttccagGTTCAAATGTATCGATCTGGATTGTGACGGAGTGGTGACTCCAAACGAGATGCAGTACTTTTACGAGGAGCAATTGCATCGCATGGAGTGCCTAGCTCAA
upper sequence: GLYMA03G41180.1 (Glycine max), 3'ss of exon 9
lower sequence: EFJ32791 (Selaginella moellendorffii), 3'ss of exon 9
tccaccttgcctcctaagtacactcttaggcgaacattggaagtttgacctttgtggttgactcttgttagctatttgtgatttgatgtgtcatgatt---agGTTCAAGTGCATTGATTTGGATGGAAATGGAGTTCTGACACGGAATGAACTGCAATTTTTTTATGAGGAGCAATTGCATCGAATGGAGTGCATGGCCCAA
| | | || |||| |||| | || | |||| || || | |||||||| || || ||| ||||| | | ||||| |||| | || || |||| | ||||||||||||||||||||||| ||||||||| | || |||
--------------------------------------------gtaagcgacgtc-ttgaatcttctgtaagatcgatcgattgacagatcgcgacttccagGTTCAAATGTATCGATCTGGATTGTGACGGAGTGGTGACTCCAAACGAGATGCAGTACTTTTATGAGGAGCAATTGCATCGCATGGAGTGCCTAGCTCAA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgacctttgtggttgactcttgttagctatttgtgatttgatgtgtcatgattagGTTCAAGTGCATTGATTTGGATGGAAATGGAGTTCTGACACGGAATGAACTGCAATTTTTTTATGAGGAGCAATTGCATCGAATGGAGTGCATGGCCCAA
tatttgt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tccaccttgcctcctaagtacactcttaggcgaacattggaagtttgacctttgtggttgactcttgttagctatttgtgatttgatgtgtcatgattagGTTCAAGTGCATTGATTTGGATGGAAATGGAGTTCTGACACGGAATGAACTGCAATTTTTTTATGAGGAGCAATTGCATCGAATGGAGTGCATGGCCCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA
-ccacctt
- - - - gcctcct
- - - - - - - - - tacactc
- - - - - - - - - - - - - - - - - - - - - - - - - - -gtggttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgatgtg