Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGATGGAAAGAGCTTCACATACAACAGTAATATCAACATTGCAGTGGCTGTGGCAATTGATGGTGGCCTTATTACACCTGTCCTTCAGGATGCAGACAAGgtatatagtatctttgtgataaatttggcttcactccggagttcggagttttagcaaacaagttcaccaaacagtttgttgaatgttacactgtag

Basic information

species Zea mays
transcript GRMZM2G117786_T01
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G117786_T01 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os08g33440.1 (Oryza sativa), 5'ss of exon 2
GGATGGAAAGAGCTTCACATACAACAGTAATATCAACATTGCAGTGGCTGTGGCAATTGATGGTGGCCTTATTACACCTGTCCTTCAGGATGCAGACAAGgtatatagtatctttgtgataaatttggcttcactccggagttcggagttttagcaaacaagttcaccaaacagtttgttgaatgttacactgtag
|||||| ||||||||||| |||||||  || |||||||| || |||||||| ||||| |||||||| || ||||||||||| ||  ||||||| || |||||| |   ||||| |||| | ||| | | |||| |  ||| ||  || |     || |  |||||||  || || |||   ||||  |   || ||
GGATGGGAAGAGCTTCACTTACAACACCAACATCAACATCGCGGTGGCTGTCGCAATCGATGGTGGGCTCATTACACCTGTTCTGGAGGATGCTGATAAGgtacaggatatctgtgtgtttaatgtcgtttcatttaggaatt--gaat-----catatgagttcactgaatagcttgagcaatggcatgatgcag

upper sequence: GRMZM2G117786_T01 (Zea mays), 5'ss of exon 2
lower sequence: GLYMA01G20720.1 (Glycine max), 5'ss of exon 2
GGATGGAAAGAGCTTCACATACAACAGTAATATCAACATTGCAGTGGCTGTGGCAATTGATGGTGGCCTTATTACACCTGTCCTTCAGGATGCAGACAAGgtatatagt-----------atctttgtgataaatttggct--tcactccggagttcggagttttagcaaacaagttcaccaaacagtttgttgaat-gttacactgtag
 ||||| |||| |||  | || || ||||| || |||||||| || ||||||||||   |||||||  | |||||||| || |||||||||||||| ||||||| |  |           ||  ||||  | |||  |     | | |   || | |  | || |     |     | |   ||  ||||| | | | |||    |  ||
AGATGGGAAGAACTTTGCCTATAATAGTAACATTAACATTGCTGTTGCTGTGGCAACCAATGGTGGTTTGATTACACCGGTTCTTCAGGATGCAGATAAGgtatgtgattagtgaattggataattgttctgaatcagaacagtaattggagaatacaaaattgtgtttcagttccttagttaattgtttgcttacttgttttgttacag

upper sequence: GRMZM2G117786_T01 (Zea mays), 5'ss of exon 2
lower sequence: AT3G25860.1 (Arabidopsis thaliana), 5'ss of exon 2
GGATGGAAAGAGCTTCACATACAACAGTAATATCAACATTGCAGTGGCTGTGGCAATTGATGGTGGCCTTATTACACCTGTCCTTCAGGATGCAGACAAGgtatata------gtatctttgtgataaat--ttggcttcactccggagtt---------cggagttttagcaaacaagttcaccaaacagtttgt-tgaatgttac--actgtag------
 || || ||||| || |  ||||| ||||  || |||||||||||||| || || ||  |||||||||| ||||| ||||| || || |||||||| ||||||   |       ||   ||||   ||||   | || |      | | |          |   || |||  |  |  |||     ||| |  ||| ||| |  |      |||        
AGACGGGAAGAGTTTTAGTTACAATAGTAGCATTAACATTGCAGTGGCGGTTGCTATCAATGGTGGCCTGATTACGCCTGTTCTACAAGATGCAGATAAGgtaagcataagcaataaagttgtagaaaatagctagcgtgtgagtgaattaacacacacacttggtattattaggctggtttctttaactgaatgtgtgagtcgtgttggttgttttgatag

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|5895843|gb|AW037089.1|AW037089
EST:     TGGCAATTGATGGTGGCCTTATTACACCTGTCCTTCAGGATGCAGACAAG                         CTGGATATTTATTTGCTCTCGCAAAATTGGAAGGACCTAGTCAAGAAAGCA
genomic: TGGCAATTGATGGTGGCCTTATTACACCTGTCCTTCAGGATGCAGACAAGgtatatagta ... tacactgtagCTGGATATTTATTTGCTCTCGCAAAATTGGAAGGACCTAGTCAAGAAAGCA
EST: gi|91049207|gb|EB159625.1|EB159625
EST:     AGGATGCAGACAAG                         CTGGATATTTATTTGCTCTCGCAAAATTGGAAGGACCTAGTCAAGAAAGCA
genomic: AGGATGCAGACAAGgtatatagta ... tacactgtagCTGGATATTTATTTGCTCTCGCAAAATTGGAAGGACCTAGTCAAGAAAGCA
EST: gi|5936720|gb|AW059988.1|AW059988
EST:     CTGTCCTTCAGGATGCAGCCAAG                         CTGGATATTTATTTGCTCTCGCAAAATTGGAAGGACCTAGTCAAGAAAGCA
genomic: CTGTCCTTCAGGATGCAGACAAGgtatatagta ... tacactgtagCTGGATATTTATTTGCTCTCGCAAAATTGGAAGGACCTAGTCAAGAAAGCA
EST: gi|5770188|gb|AI973362.1|AI973362
EST:     TGGCAATTGATGGTGGCCTTATTACACCTGTCCTTCAGGATGCAGACAAG                         CTGGATATTTATTTGCTCTCGCAAAATTGGAAGGACCTAGTCAAGAAAGCA
genomic: TGGCAATTGATGGTGGCCTTATTACACCTGTCCTTCAGGATGCAGACAAGgtatatagta ... tacactgtagCTGGATATTTATTTGCTCTCGCAAAATTGGAAGGACCTAGTCAAGAAAGCA
EST: gi|91869380|gb|EB400357.1|EB400357
EST:     TGGCAATTGATGGTGGCCTTATTACACCTGTCCTTCAGGATGCAGACAAG                         CTGGATATTTATTTGCTCTCGCAAAATTGGAAGGACCTAGTCAAGAAAGCA
genomic: TGGCAATTGATGGTGGCCTTATTACACCTGTCCTTCAGGATGCAGACAAGgtatatagta ... tacactgtagCTGGATATTTATTTGCTCTCGCAAAATTGGAAGGACCTAGTCAAGAAAGCA
EST: gi|32932202|gb|CF037014.1|CF037014
EST:     TGGCAATTGATGGTGGCCTTATTACACCTGTCCTCCAGGATGCTGACAAG                         CTGGATATTTATTTGCTCTCGCAAAATTGGAAGGACCTAGTCAAGAAAGCA
genomic: TGGCAATTGATGGTGGCCTTATTACACCTGTCCTTCAGGATGCAGACAAGgtatatagta ... tacactgtagCTGGATATTTATTTGCTCTCGCAAAATTGGAAGGACCTAGTCAAGAAAGCA
EST: gi|110529248|gb|EE033432.1|EE033432
EST:     TGGCAATTGATGGTGGCCTTATTACACCTGTCCTTCAGGATGCAGACAAG                         CTGGATATTTATTTGCTCTCGCAAAATTGGAAGGACCTAGTCAAGAAAGCA
genomic: TGGCAATTGATGGTGGCCTTATTACACCTGTCCTTCAGGATGCAGACAAGgtatatagta ... tacactgtagCTGGATATTTATTTGCTCTCGCAAAATTGGAAGGACCTAGTCAAGAAAGCA
EST: gi|4885756|gb|AI676876.1|AI676876
EST:     TGGCAATTGATGGTGGCCTTATTACACCTGTCCTTCAGGATGCAGACAAG                         CTGGATATTTATTTGCTCTCGCAAAATTGGAAGGACCTAGTCAAGAAAGCA
genomic: TGGCAATTGATGGTGGCCTTATTACACCTGTCCTTCAGGATGCAGACAAGgtatatagta ... tacactgtagCTGGATATTTATTTGCTCTCGCAAAATTGGAAGGACCTAGTCAAGAAAGCA
EST: gi|149108974|gb|EE189934.2|EE189934
EST:     TGGCAATTGATGGTGGCCTTATTACACCTGTCCTTCAGGATGCAGACAAG                         CTGGATATTTATTTGCTCTCGCAAAATTGGAAGGACCTAGTCAAGAAAGCA
genomic: TGGCAATTGATGGTGGCCTTATTACACCTGTCCTTCAGGATGCAGACAAGgtatatagta ... tacactgtagCTGGATATTTATTTGCTCTCGCAAAATTGGAAGGACCTAGTCAAGAAAGCA
EST: gi|32932221|gb|CF037033.1|CF037033
EST:     TGGCAATTGATGGTGGCCTTATTACACCTGTCCTCCAGGATGCTGACAAG                         CTGGATATTTATTTGCTCTCGCAAAATTGGAAGGACCTAGTCAAGAAAGCA
genomic: TGGCAATTGATGGTGGCCTTATTACACCTGTCCTTCAGGATGCAGACAAGgtatatagta ... tacactgtagCTGGATATTTATTTGCTCTCGCAAAATTGGAAGGACCTAGTCAAGAAAGCA
EST: gi|71767883|gb|DR965820.1|DR965820
EST:     TGGCAATTGATGGTGGCCTTATTACACCTGTCCTTCAGGATGCAGACAAG                         CTGGATATTTATTTGCTCTCGCAAAATTGGAAGGACCTAGTCAAGAAAGCA
genomic: TGGCAATTGATGGTGGCCTTATTACACCTGTCCTTCAGGATGCAGACAAGgtatatagta ... tacactgtagCTGGATATTTATTTGCTCTCGCAAAATTGGAAGGACCTAGTCAAGAAAGCA
EST: gi|31354698|gb|CD439055.1|CD439055
EST:     TGGCAATTGATGGTGGCCTTATTACACCTGTCCTTCAGGATGCTGACAAG                         CTGGATATTTATTTGCTCTCGCAAAATTGGAAGGACCTAGTCAAGAAAGCA
genomic: TGGCAATTGATGGTGGCCTTATTACACCTGTCCTTCAGGATGCAGACAAGgtatatagta ... tacactgtagCTGGATATTTATTTGCTCTCGCAAAATTGGAAGGACCTAGTCAAGAAAGCA
EST: gi|5325071|gb|AI783262.1|AI783262
EST:     TGGCAATTGATGGTGGCCTTATTACACCTGTCCTTCAGGATGCAGACAAG                         CTGGATATTTATTTGCTCTCGCAAAATTGGAAGGACCTAGTCAAGAAAGCA
genomic: TGGCAATTGATGGTGGCCTTATTACACCTGTCCTTCAGGATGCAGACAAGgtatatagta ... tacactgtagCTGGATATTTATTTGCTCTCGCAAAATTGGAAGGACCTAGTCAAGAAAGCA
EST: gi|91053207|gb|EB163625.1|EB163625
EST:     TGGCAATTGATGGTGGCCTTATTACACCTGTCCTTCAGGATGCAGACAAG                         CTGGATATTTATTTGCTCTCGCAAAATTGGAAGGACCTAGTCAAGAAAGCA
genomic: TGGCAATTGATGGTGGCCTTATTACACCTGTCCTTCAGGATGCAGACAAGgtatatagta ... tacactgtagCTGGATATTTATTTGCTCTCGCAAAATTGGAAGGACCTAGTCAAGAAAGCA
EST: gi|60396288|gb|DN229157.1|DN229157
EST:     TGGCAATTGATGGTGGCCTTATTACACCTGTCCTTCAGGATGCAGACAAG                         CTGGATATTTATTTGCTCTCGCAAAATTGGAAGGACCTAGTCAAGAAAGCA
genomic: TGGCAATTGATGGTGGCCTTATTACACCTGTCCTTCAGGATGCAGACAAGgtatatagta ... tacactgtagCTGGATATTTATTTGCTCTCGCAAAATTGGAAGGACCTAGTCAAGAAAGCA
EST: gi|76013819|gb|DT940989.1|DT940989
EST:     TGGCAATTGATGGTGGCCTTATTACACCTGTCCTTCAGGATGCAGACAAG                         CTGGATATTTATTTGCTCTCGCAAAATTGGAAGGACCTAGTCAAGAAAGCA
genomic: TGGCAATTGATGGTGGCCTTATTACACCTGTCCTTCAGGATGCAGACAAGgtatatagta ... tacactgtagCTGGATATTTATTTGCTCTCGCAAAATTGGAAGGACCTAGTCAAGAAAGCA
EST: gi|91056736|gb|EB167154.1|EB167154
EST:     TGGCAATTGATGGTGGCCTTATTACACCTGTCCTTCAGGATGCAGACAAG                         CTGGATATTTATTTGCTCTCGCAAAATTGGAAGGACCTAGTCAAGAAAGCA
genomic: TGGCAATTGATGGTGGCCTTATTACACCTGTCCTTCAGGATGCAGACAAGgtatatagta ... tacactgtagCTGGATATTTATTTGCTCTCGCAAAATTGGAAGGACCTAGTCAAGAAAGCA
EST: gi|71763414|gb|DR961351.1|DR961351
EST:     TGGCAATTGATGGTGGCCTTATTACACCTGTCCTTCAGGATGCAGACAAG                         CTGGATATTTATTTGCTCTCGCAAAATTGGAAGGACCTAGTCAAGAAAGCA
genomic: TGGCAATTGATGGTGGCCTTATTACACCTGTCCTTCAGGATGCAGACAAGgtatatagta ... tacactgtagCTGGATATTTATTTGCTCTCGCAAAATTGGAAGGACCTAGTCAAGAAAGCA
EST: gi|74236495|gb|DT644409.1|DT644409
EST:     TGGCAATTGATGGTGGCCTTATTACACCTGTCCTTCAGGATGCAGACAAG                         CTGGATATTTATTTGCTCTCGCAAAATTGGAAGGACCTAGTCAAGAAAGCA
genomic: TGGCAATTGATGGTGGCCTTATTACACCTGTCCTTCAGGATGCAGACAAGgtatatagta ... tacactgtagCTGGATATTTATTTGCTCTCGCAAAATTGGAAGGACCTAGTCAAGAAAGCA
EST: gi|30088033|gb|CB886238.1|CB886238
EST:     TGGCAATTGATGGTGGCCTTATTACACCTGTCCTTCAGGATGCAGACAAG                         CTGGATATTTATTTGCTCTCGCAAAATTGGAAGGACCTAGTCAAGAAAGCA
genomic: TGGCAATTGATGGTGGCCTTATTACACCTGTCCTTCAGGATGCAGACAAGgtatatagta ... tacactgtagCTGGATATTTATTTGCTCTCGCAAAATTGGAAGGACCTAGTCAAGAAAGCA
EST: gi|148960322|gb|EE153578.2|EE153578
EST:     TGGCAATTGATGGTGGCCTTATTACACCTGTCCTTCAGGATGCAGACAAG                         CTGGATATTTATTTGCTCTCGCAAAATTGGAAGGACCTAGTCAAGAAAGCA
genomic: TGGCAATTGATGGTGGCCTTATTACACCTGTCCTTCAGGATGCAGACAAGgtatatagta ... tacactgtagCTGGATATTTATTTGCTCTCGCAAAATTGGAAGGACCTAGTCAAGAAAGCA
EST: gi|24768545|gb|CA403674.1|CA403674
EST:     CCTTCAGGATGCTGACAAG                         CTGGATATTTATTTGCTCTCGCAAAATTGGAAGGACCTAGTCAAGAAAGCA
genomic: CCTTCAGGATGCAGACAAGgtatatagta ... tacactgtagCTGGATATTTATTTGCTCTCGCAAAATTGGAAGGACCTAGTCAAGAAAGCA
EST: gi|149085129|gb|EE174634.2|EE174634
EST:     TGGCAATTGATGGTGGCCTTATTACACCTGTCCTTCAGGATGCAGACAAG                         CTGGATATTTATTTGCTCTCGCAAAATTGGAAGGACCTAGTCAAGAAAGCA
genomic: TGGCAATTGATGGTGGCCTTATTACACCTGTCCTTCAGGATGCAGACAAGgtatatagta ... tacactgtagCTGGATATTTATTTGCTCTCGCAAAATTGGAAGGACCTAGTCAAGAAAGCA
EST: gi|78021875|gb|DV490262.1|DV490262
EST:     TGGCAATTGATGGTGGCCTTATTACACCTGTCCTTCAGGATGCAGACAAG                         CTGGATATTTATTTGCTCTCGCAAAATTGGAAGGACCTAGTCAAGAAAGCA
genomic: TGGCAATTGATGGTGGCCTTATTACACCTGTCCTTCAGGATGCAGACAAGgtatatagta ... tacactgtagCTGGATATTTATTTGCTCTCGCAAAATTGGAAGGACCTAGTCAAGAAAGCA
EST: gi|76016286|gb|DT943456.1|DT943456
EST:     TGGCAATTGATGGTGGCCTTATTACACCTGTCCTTCAGGATGCAGACAAG                         CTGGATATTTATTTGCTCTCGCAAAATTGGAAGGACCTAGTCAAGAAAGCA
genomic: TGGCAATTGATGGTGGCCTTATTACACCTGTCCTTCAGGATGCAGACAAGgtatatagta ... tacactgtagCTGGATATTTATTTGCTCTCGCAAAATTGGAAGGACCTAGTCAAGAAAGCA
EST: gi|5846883|gb|AI999966.1|AI999966
EST:     TGGCAATTGATGGTGGCCTTATTACACCTGTCCTTCAGGATGCAGACAAG                         CTGGATATTTATTTGCTCTCGCAAAATTGGAAGGACCTAGTCAAGAAAGCA
genomic: TGGCAATTGATGGTGGCCTTATTACACCTGTCCTTCAGGATGCAGACAAGgtatatagta ... tacactgtagCTGGATATTTATTTGCTCTCGCAAAATTGGAAGGACCTAGTCAAGAAAGCA

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 4 RNA-Seq libraries.


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 72

GGATGGAAAGAGCTTCACATACAACAGTAATATCAACATTGCAGTGGCTGTGGCAATTGATGGTGGCCTTATTACACCTGTCCTTCAGGATGCAGACAAGgtatatagta ... tacactgtagCTGGATATTTATTTGCTCTCGCAAAATTGGAAGGACCTAGTCAAGAAAGCACGTGCAAAACAGCTCCAACCAAATGATTACAACTCTG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 110

GGATGGAAAGAGCTTCACATACAACAGTAATATCAACATTGCAGTGGCTGTGGCAATTGATGGTGGCCTTATTACACCTGTCCTTCAGGATGCAGACAAGgtatatagta ... tacactgtagCTGGATATTTATTTGCTCTCGCAAAATTGGAAGGACCTAGTCAAGAAAGCACGTGCAAAACAGCTCCAACCAAATGATTACAACTCTG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 69

GGATGGAAAGAGCTTCACATACAACAGTAATATCAACATTGCAGTGGCTGTGGCAATTGATGGTGGCCTTATTACACCTGTCCTTCAGGATGCAGACAAGgtatatagta ... tacactgtagCTGGATATTTATTTGCTCTCGCAAAATTGGAAGGACCTAGTCAAGAAAGCACGTGCAAAACAGCTCCAACCAAATGATTACAACTCTG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 169

GGATGGAAAGAGCTTCACATACAACAGTAATATCAACATTGCAGTGGCTGTGGCAATTGATGGTGGCCTTATTACACCTGTCCTTCAGGATGCAGACAAGgtatatagta ... tacactgtagCTGGATATTTATTTGCTCTCGCAAAATTGGAAGGACCTAGTCAAGAAAGCACGTGCAAAACAGCTCCAACCAAATGATTACAACTCTG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGATGGAAAGAGCTTCACATACAACAGTAATATCAACATTGCAGTGGCTGTGGCAATTGATGGTGGCCTTATTACACCTGTCCTTCAGGATGCAGACAAGgtatatagtatctttgtgataaatttggcttcactccggagttcggagttttagcaaacaagttcaccaaacagtttgttgaatgttacactgtag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG