Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   		8  
 5'  3'   		9  
 5'  3'   		10  
 5'  3'   		11  
 5'  3'   		12  
 5'  3'   		13  
 5'  3'   		14  
 5'  3'   		15  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgctggcaaaacctactctatatagcacttacatttccatcgattgtgcaatcgtatgcttgtgtggttaattcacacacattttttttagtgattatcatgcttttgttatctttttttacaactgtaatatgttgttagtgcagAAAGAAGAATGGAAACTACATCAGCTGGAGTGTAGAGCAATGGCAGCACTTACAGAGGATAGAAAGAAGATGCTTACTCCTACAATTCGGTTGATGGTTC

Basic information

species Zea mays
transcript GRMZM2G457881_T01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G457881_T03 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os03g49730.3 (Oryza sativa), 3'ss of exon 2
gtgctggcaaaacctactctatatagcacttac---atttcca-----tcgattgtgcaatcgtatgcttgtgtggttaat-tcacacacattttttttagtgatta-tcatgcttttgttatctttttttacaactgtaatatgttgttagtgcagAAAGAAGAATGGAAACTACATCAGCTGGAGTGTAGAGCAATGGCAGCACTTACAGAGGATAGAAAGAAGATGCTTACTCCTACAATTCGGTTGATGGTTC
|||||| |     |       | |  |||  |    || | ||     | | || ||  ||| | |||| ||| ||  | | | |||  |||| ||| ||||||||  || ||||||   |    |   ||      |  |||||||| ||  ||||| |||||||||||| || ||||| || || ||| ||||||| || || |||||||||||||||||||||||||||||||| |||||||| |||||||| |
gtgctgactctgtccttcaactgttacacgcatttgatatgcagagacttgcttttgtgatcatgtgct-gtgcggagactgttacatgcattatttatagtgattcctcttgctttcaatggtgtaacttttt-tggcgatatgttgctaccgcagAGAGAAGAATGGAAGCTTCATCAACTTGAATGTCGAGCAATCGCCGCGCTTACAGAGGATAGAAAGAAGATGCTTACTCCCACAATTCGTTTGATGGTGC
















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|211474515|gb|FK963004.1|FK963004
EST:     GGAAGTGCTCTATGTGTCGAGTTACTTGGTACTGCAGCAGCAACTGTCAG                         AAAGAAGAATGGAAACTACATCAGCTCGAGTGTAGAGCAATGGCAGCACTT
genomic: GGAAGTGCTCTATGTGTCGAGTTACTTGGTACTGCAGCAGCAACTGTCAGgtgctggcaa ... gttagtgcagAAAGAAGAATGGAAACTACATCAGCTGGAGTGTAGAGCAATGGCAGCACTT
EST: gi|211474521|gb|FK963010.1|FK963010
EST:     GGAAGTGCTCTATGTGTCGAGTTACTTGGTACTGCAGCAGCAACTGTCAG                         AAAGAAGAATGGAAACTACATCAGCTCGAGTGTAGAGCAATGGCAGCACTT
genomic: GGAAGTGCTCTATGTGTCGAGTTACTTGGTACTGCAGCAGCAACTGTCAGgtgctggcaa ... gttagtgcagAAAGAAGAATGGAAACTACATCAGCTGGAGTGTAGAGCAATGGCAGCACTT
EST: gi|211477029|gb|FK963011.1|FK963011
EST:     GGAAGTGCTCTATGTGTCGAGTTACTTGGTACTGCAGCAGCAACTGTCAG                         AAAGAAGAATGGAAACTACATCAGCTCGAGTGTAGAGCAATGGCAGCACTT
genomic: GGAAGTGCTCTATGTGTCGAGTTACTTGGTACTGCAGCAGCAACTGTCAGgtgctggcaa ... gttagtgcagAAAGAAGAATGGAAACTACATCAGCTGGAGTGTAGAGCAATGGCAGCACTT
EST: gi|211474511|gb|FK963000.1|FK963000
EST:     GGAAGTGCTCTATGTGTCGAGTTACTTGGTACTGCAGCAGCAACTGTCAG                         AAAGAAGAATGGAAACTACATCAGCTCGAGTGTAGAGCAATGGCAGCACTT
genomic: GGAAGTGCTCTATGTGTCGAGTTACTTGGTACTGCAGCAGCAACTGTCAGgtgctggcaa ... gttagtgcagAAAGAAGAATGGAAACTACATCAGCTGGAGTGTAGAGCAATGGCAGCACTT
EST: gi|149023564|gb|EE045895.2|EE045895
EST:     GGAAGTGCTCTATGTGTCGAGTTACTTGGTACTGCAGCAGCAACTGTCAG                         AAAGAAGAATGGAAACTACATCAGCTGGAGTGTAGAGCAATGGCAGCACTT
genomic: GGAAGTGCTCTATGTGTCGAGTTACTTGGTACTGCAGCAGCAACTGTCAGgtgctggcaa ... gttagtgcagAAAGAAGAATGGAAACTACATCAGCTGGAGTGTAGAGCAATGGCAGCACTT
EST: gi|211474516|gb|FK963005.1|FK963005
EST:     GGAAGTGCTCTATGTGTCGAGTTACTTGGTACTGCAGCAGCAACTGTCAG                         AAAGAAGAATGGAAACTACATCAGCTCGAGTGTAGAGCAATGGCAGCACTT
genomic: GGAAGTGCTCTATGTGTCGAGTTACTTGGTACTGCAGCAGCAACTGTCAGgtgctggcaa ... gttagtgcagAAAGAAGAATGGAAACTACATCAGCTGGAGTGTAGAGCAATGGCAGCACTT
EST: gi|211474513|gb|FK963002.1|FK963002
EST:     GGAAGTGCTCTATGTGTCGAGTTACTTGGTACTGCAGCAGCAACTGTCAG                         AAAGAAGAATGGAAACTACATCAGCTCGAGTGTAGAGCAATGGCAGCACTT
genomic: GGAAGTGCTCTATGTGTCGAGTTACTTGGTACTGCAGCAGCAACTGTCAGgtgctggcaa ... gttagtgcagAAAGAAGAATGGAAACTACATCAGCTGGAGTGTAGAGCAATGGCAGCACTT
EST: gi|211474517|gb|FK963006.1|FK963006
EST:     GGAAGTGCTCTATGTGTCGAGTTACTTGGTACTGCAGCAGCAACTGTCAG                         AAAGAAGAATGGAAACTACATCAGCTCGAGTGTAGAGCAATGGCAGCACTT
genomic: GGAAGTGCTCTATGTGTCGAGTTACTTGGTACTGCAGCAGCAACTGTCAGgtgctggcaa ... gttagtgcagAAAGAAGAATGGAAACTACATCAGCTGGAGTGTAGAGCAATGGCAGCACTT
EST: gi|211474510|gb|FK962999.1|FK962999
EST:     GGAAGTGCTCTATGTGTCGAGTTACTTGGTACTGCAGCAGCAACTGTCAG                         AAAGAAGAATGGAAACTACATCAGCTCGAGTGTAGAGCAATGGCAGCACTT
genomic: GGAAGTGCTCTATGTGTCGAGTTACTTGGTACTGCAGCAGCAACTGTCAGgtgctggcaa ... gttagtgcagAAAGAAGAATGGAAACTACATCAGCTGGAGTGTAGAGCAATGGCAGCACTT
EST: gi|211471995|gb|FK962992.1|FK962992
EST:     AGAAGTGCTCTATGTGTCGAGTTACTTGGTACTGCAGCAGCAACTGTCAG                         AAAGAAGAATGGAAACTACATCAGCTCGAGTGTAGAGCAATGGCAGCACTT
genomic: GGAAGTGCTCTATGTGTCGAGTTACTTGGTACTGCAGCAGCAACTGTCAGgtgctggcaa ... gttagtgcagAAAGAAGAATGGAAACTACATCAGCTGGAGTGTAGAGCAATGGCAGCACTT
EST: gi|211474507|gb|FK962996.1|FK962996
EST:     GGAAGTGCTCTATGTGTCGAGTTACTTGGTACTGCAGCAGCAACTGTCAG                         AAAGAAGAATGGAAACTACATCAGCTCGAGTGTAGAGCAATGGCAGCACTT
genomic: GGAAGTGCTCTATGTGTCGAGTTACTTGGTACTGCAGCAGCAACTGTCAGgtgctggcaa ... gttagtgcagAAAGAAGAATGGAAACTACATCAGCTGGAGTGTAGAGCAATGGCAGCACTT
EST: gi|211471996|gb|FK962993.1|FK962993
EST:     GGAAGTGCTCTATGTGTCGAGTTACTTGGTACTGCAGCAGCAACTGTCAG                         AAAGAAGAATGGAAACTACATCAGCTCGAGTGTAGAGCAATGGCAGCACTT
genomic: GGAAGTGCTCTATGTGTCGAGTTACTTGGTACTGCAGCAGCAACTGTCAGgtgctggcaa ... gttagtgcagAAAGAAGAATGGAAACTACATCAGCTGGAGTGTAGAGCAATGGCAGCACTT
EST: gi|211474508|gb|FK962997.1|FK962997
EST:     GGAAGTGCTCTATGTGTCGAGTTACTTGGTACTGCAGCAGCAACTGTCAG                         AAAGAAGAATGGAAACTACATCAGCTGGAGTGTAGAGCAATGGCAGCACTT
genomic: GGAAGTGCTCTATGTGTCGAGTTACTTGGTACTGCAGCAGCAACTGTCAGgtgctggcaa ... gttagtgcagAAAGAAGAATGGAAACTACATCAGCTGGAGTGTAGAGCAATGGCAGCACTT
EST: gi|211474518|gb|FK963007.1|FK963007
EST:     GGAAGTGCTCTATGTGTCGAGTTACTTGGTACTGCAGCAGCAACTGTCAG                         AAAGAAGAATGGAAACTACATCAGCTCGAGTGTAGAGCAATGGCAGCACTT
genomic: GGAAGTGCTCTATGTGTCGAGTTACTTGGTACTGCAGCAGCAACTGTCAGgtgctggcaa ... gttagtgcagAAAGAAGAATGGAAACTACATCAGCTGGAGTGTAGAGCAATGGCAGCACTT
EST: gi|71322965|gb|DR798157.1|DR798157
EST:     GGAAGTGCTCTATGTGTCGAGTTACTTGGTACTGCAGCAGCAACTGTCAG                         AAAGAAGAATGGAAACTACATCAGCTGGAGTGTAGAGCAATGGCAGCACTT
genomic: GGAAGTGCTCTATGTGTCGAGTTACTTGGTACTGCAGCAGCAACTGTCAGgtgctggcaa ... gttagtgcagAAAGAAGAATGGAAACTACATCAGCTGGAGTGTAGAGCAATGGCAGCACTT
EST: gi|211474514|gb|FK963003.1|FK963003
EST:     GGAAGTGCTCTATGTGTCGAGTTACTTGGTACTGCAGCAGCAACTGTCAG                         AAAGAAGAATGGAAACTACATCAGCTCGAGTGTAGAGCAATGGCAGCACTT
genomic: GGAAGTGCTCTATGTGTCGAGTTACTTGGTACTGCAGCAGCAACTGTCAGgtgctggcaa ... gttagtgcagAAAGAAGAATGGAAACTACATCAGCTGGAGTGTAGAGCAATGGCAGCACTT
EST: gi|211474519|gb|FK963008.1|FK963008
EST:     GGAAGTGCTCTATGTGTCGAGTTACTTGGTACTGCAGCAGCAACTGTCAG                         AAAGAAGAATGGAAACTACATCAGCTGGAGTGTAGAGCAATGGCAGCACTT
genomic: GGAAGTGCTCTATGTGTCGAGTTACTTGGTACTGCAGCAGCAACTGTCAGgtgctggcaa ... gttagtgcagAAAGAAGAATGGAAACTACATCAGCTGGAGTGTAGAGCAATGGCAGCACTT
EST: gi|211474512|gb|FK963001.1|FK963001
EST:     GGAAGTGCTCTATGTGTCGAGTTACTTGGTACTGCAGCAGCAACTGTCAG                         AAAGAAGAATGGAAACTACATCAGCTCGAGTGTAGAGCAATGGCAGCACTT
genomic: GGAAGTGCTCTATGTGTCGAGTTACTTGGTACTGCAGCAGCAACTGTCAGgtgctggcaa ... gttagtgcagAAAGAAGAATGGAAACTACATCAGCTGGAGTGTAGAGCAATGGCAGCACTT
EST: gi|211474509|gb|FK962998.1|FK962998
EST:     GGAAGTGCTCTATGTGTCGAGTTACTTGGTACTGCAGCAGCAACTGTCAG                         AAAGAAGAATGGAAACTACATCAGCTCGAGTGTAGAGCAATGGCAGCACTT
genomic: GGAAGTGCTCTATGTGTCGAGTTACTTGGTACTGCAGCAGCAACTGTCAGgtgctggcaa ... gttagtgcagAAAGAAGAATGGAAACTACATCAGCTGGAGTGTAGAGCAATGGCAGCACTT
EST: gi|211471998|gb|FK962995.1|FK962995
EST:     GGAAGTGCTCTATGTGTCGAGTTACTTGGTACTGCAGCAGCAACTGTCAG                         AAAGAAGAATGGAAACTACATCAGCTCGAGTGTAGAGCAATGGCAGCACTT
genomic: GGAAGTGCTCTATGTGTCGAGTTACTTGGTACTGCAGCAGCAACTGTCAGgtgctggcaa ... gttagtgcagAAAGAAGAATGGAAACTACATCAGCTGGAGTGTAGAGCAATGGCAGCACTT

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), 48 (downstream exon)
Score: 78

GATTTTAGTTGGATCGAGCTGTGACCATTGTTTCACCTCTGGCAACCTGAGGAAGTGCTCTATGTGTCGAGTTACTTGGTACTGCAGCAGCAACTGTCAGgtgctggcaa ... gttagtgcagAAAGAAGAATGGAAACTACATCAGCTGGAGTGTAGAGCAATGGCAGCACTTACAGAGGATAGAAAGAAGATGCTTACTCCTACAATTCGGTTGATGGTTC


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 42

GATTTTAGTTGGATCGAGCTGTGACCATTGTTTCACCTCTGGCAACCTGAGGAAGTGCTCTATGTGTCGAGTTACTTGGTACTGCAGCAGCAACTGTCAGgtgctggcaa ... gttagtgcagAAAGAAGAATGGAAACTACATCAGCTGGAGTGTAGAGCAATGGCAGCACTTACAGAGGATAGAAAGAAGATGCTTACTCCTACAATTCGGTTGATGGTTC


Block sizes: 48 (upstream exon), 47 (downstream exon)
Score: 40

GATTTTAGTTGGATCGAGCTGTGACCATTGTTTCACCTCTGGCAACCTGAGGAAGTGCTCTATGTGTCGAGTTACTTGGTACTGCAGCAGCAACTGTCAGgtgctggcaa ... gttagtgcagAAAGAAGAATGGAAACTACATCAGCTGGAGTGTAGAGCAATGGCAGCACTTACAGAGGATAGAAAGAAGATGCTTACTCCTACAATTCGGTTGATGGTTC


Block sizes: 46 (upstream exon), 48 (downstream exon)
Score: 35

GATTTTAGTTGGATCGAGCTGTGACCATTGTTTCACCTCTGGCAACCTGAGGAAGTGCTCTATGTGTCGAGTTACTTGGTACTGCAGCAGCAACTGTCAGgtgctggcaa ... gttagtgcagAAAGAAGAATGGAAACTACATCAGCTGGAGTGTAGAGCAATGGCAGCACTTACAGAGGATAGAAAGAAGATGCTTACTCCTACAATTCGGTTGATGGTTC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgattatcatgcttttgttatctttttttacaactgtaatatgttgttagtgcagAAAGAAGAATGGAAACTACATCAGCTGGAGTGTAGAGCAATGGCAGCACTTACAGAGGATAGAAAGAAGATGCTTACTCCTACAATTCGGTTGATGGTTC
            ttttgttatctttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgctggcaaaacctactctatatagcacttacatttccatcgattgtgcaatcgtatgcttgtgtggttaattcacacacattttttttagtgattatcatgcttttgttatctttttttacaactgtaatatgttgttagtgcagAAAGAAGAATGGAAACTACATCAGCTGGAGTGTAGAGCAATGGCAGCACTTACAGAGGATAGAAAGAAGATGCTTACTCCTACAATTCGGTTGATGGTTC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG