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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgtgcatcccaaaatacttgttaaaacgagtcttaactgttgtttcaagcttgaaacctttattttgtgtgctgcctgttgctcttttgtttaattatttctctatttttagGGGACAAGGACATCCAACAGGAAACTCCGCTCCTTATTTTGGTCCCTCGCAGAAGCTTGATTTTGAGCTTGAGATG

Basic information

species Zea mays
transcript GRMZM2G029566_T01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G029566_T01 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os02g10310.3 (Oryza sativa), 3'ss of exon 4
gtgtgcatcccaaaatacttgttaaaacgagtcttaactgttgtttcaagcttgaaacctttattttgtgtgctgcctgttgctcttttgtttaattatttctctat-ttttagGGGACAAGGACATCCAACAGGAAACTCCGCTCCTTATTTTGGTCCCTCGCAGAAGCTTGATTTTGAGCTTGAGATG
              ||   |  || |  ||  | ||  ||| || |    | |   |  ||| |  |     |    || |       |  |    | |||||||   |||||| || ||||| |||||||||||| | ||    |||||||||||||| ||  |||||||||||||||| |||||||||
--------------atgtattgtagatggatacatatgtgtagtatattacattttatttttgtcataatatccaattgatatgtcaataatgtcctctttctctgccttttagAGGGCAAGGCCATCCAACAGGAGATTCTCGACCTTATTTTGGTCCTTCTAAGAAGCTTGATTTTGAACTTGAGATG

upper sequence: GRMZM2G029566_T01 (Zea mays), 3'ss of exon 5
lower sequence: AT1G12050.1 (Arabidopsis thaliana), 3'ss of exon 5
gtgtgcatcccaaaatacttgttaaaacgagtcttaactgttgtttcaagcttg---aaacctttattttgtgtgctgcctgttgctcttttgt--ttaattatttctctattttt-agGGGACAAGGACATCCAACAGGAAACTCCGCTCCTTATTTTGGTCCCTCGCAGAAGCTTGATTTTGAGCTTGAGATG
                     || |||| | | ||  | | || |  ||  |     | ||   |   |  ||   |||   || |  |||| |  ||  || |||  || | ||  || || || || ||||||  ||||||||| |  || |||||||| || ||| |||| |||||||||||||||||||||
-------------------cattgaaaccaatattggcggatggtaaaatttcatgcagacaaattaataatgaaatgctaattccagttttatctttgcttgttttgctttcttccagAGGTCAGGGCCATCCACAAGGAAACTCTGAACCATATTTTGGACCTTCGAAGAAACTTGATTTTGAGCTTGAGATG
















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|211126134|gb|FL125776.1|FL125776
EST:     GGGCGAGCATCATCTATAGTTGTGTCTGGAACCAATGTCATTAGGCCCAG                         GGGACAAGGACATCCAACAGGAAACTCCGCTCCTTATTTTGGTCCCTCGCA
genomic: GGGCGAGCATCATCTATAGTTGTGTCTGGAACCAATGTCATTAGGCCCAGgtgtgcatcc ... ctatttttagGGGACAAGGACATCCAACAGGAAACTCCGCTCCTTATTTTGGTCCCTCGCA
EST: gi|71328229|gb|DR800748.1|DR800748
EST:     GGGCGAGCATCATCTATAGTTGTGTCTGGAACCAATGTCATTAGGCCCAG                         GGGACAAGGACATCCAACAGGAAACTCCGCTCCTTATTTTGGTCCCTCGCA
genomic: GGGCGAGCATCATCTATAGTTGTGTCTGGAACCAATGTCATTAGGCCCAGgtgtgcatcc ... ctatttttagGGGACAAGGACATCCAACAGGAAACTCCGCTCCTTATTTTGGTCCCTCGCA
EST: gi|149044247|gb|EE047493.2|EE047493
EST:     GGGCGAGCATCATCTATAGTTGTGTCTGGAACCAATGTCATTAGGCCCAG                         GGGACAAGGACATCCAACAGGAAACTCCGCTCCTTATTTTGGTCCCTCGCA
genomic: GGGCGAGCATCATCTATAGTTGTGTCTGGAACCAATGTCATTAGGCCCAGgtgtgcatcc ... ctatttttagGGGACAAGGACATCCAACAGGAAACTCCGCTCCTTATTTTGGTCCCTCGCA
EST: gi|149101399|gb|EE187518.2|EE187518
EST:     GGGCGAGCATCATCTATAGTTGTGTCTGGAACCAATGTCATTAGGCCCAG                         GGGACAAGGACATCCAACAGGAAACTCCGCTCCTTATTTTGGTCCCTCGCA
genomic: GGGCGAGCATCATCTATAGTTGTGTCTGGAACCAATGTCATTAGGCCCAGgtgtgcatcc ... ctatttttagGGGACAAGGACATCCAACAGGAAACTCCGCTCCTTATTTTGGTCCCTCGCA
EST: gi|148969714|gb|EE020586.2|EE020586
EST:     GGGCGAGCATCATCTATAGTTGTGTCTGGAACCAATGTCATTAGGCCCAG                         GGGACAAGGACATCCAACAGGAAACTCCGCTCCTTATTTTGGTCCCTCGCA
genomic: GGGCGAGCATCATCTATAGTTGTGTCTGGAACCAATGTCATTAGGCCCAGgtgtgcatcc ... ctatttttagGGGACAAGGACATCCAACAGGAAACTCCGCTCCTTATTTTGGTCCCTCGCA
EST: gi|32851376|gb|CD991057.1|CD991057
EST:     GGGCGAGCATCATCTATAGTTGTGTCTGGAACCAATGTCATTAGGCCCAG                         GGGACAAGGACATCCAACAGGAAACTCCGCTCCTTATTTTGGTCCCTCGCA
genomic: GGGCGAGCATCATCTATAGTTGTGTCTGGAACCAATGTCATTAGGCCCAGgtgtgcatcc ... ctatttttagGGGACAAGGACATCCAACAGGAAACTCCGCTCCTTATTTTGGTCCCTCGCA
EST: gi|60348819|gb|DN215792.1|DN215792
EST:     GGGCGAGCATCATCTATAGTTGTGTCTGGAACCAATGTCATTAGGCCCAG                         GGGACAAGGACATCCAACAGGAAACTCCGCTCCTTATTTTGGTCCCTCGCA
genomic: GGGCGAGCATCATCTATAGTTGTGTCTGGAACCAATGTCATTAGGCCCAGgtgtgcatcc ... ctatttttagGGGACAAGGACATCCAACAGGAAACTCCGCTCCTTATTTTGGTCCCTCGCA
EST: gi|148990772|gb|EE032185.2|EE032185
EST:     GGGCGAGCATCATCTATAGTTGTGTCTGGAACCAATGTCATTAGGCCCAG                         GGGACAAGGACATCCCACAGGAAACTCCGCTCCTTATTTTGTTCCCTCCCA
genomic: GGGCGAGCATCATCTATAGTTGTGTCTGGAACCAATGTCATTAGGCCCAGgtgtgcatcc ... ctatttttagGGGACAAGGACATCCAACAGGAAACTCCGCTCCTTATTTTGGTCCCTCGCA
EST: gi|148932701|gb|EC876670.2|EC876670
EST:     GGGCGAGCATCATCTATAGTTGTGTCTGGAACCAATGTCATTAGGCCCAG                         GGGACAAGGACATCCAACAGGAAACTCCGCTCCTTATTTTGGTCCCTCGCA
genomic: GGGCGAGCATCATCTATAGTTGTGTCTGGAACCAATGTCATTAGGCCCAGgtgtgcatcc ... ctatttttagGGGACAAGGACATCCAACAGGAAACTCCGCTCCTTATTTTGGTCCCTCGCA
EST: gi|148940815|gb|EC885642.2|EC885642
EST:     GGGCGAGCATCATCTATAGTTGTGTCTGGAACCAATGTCATTAGGCCCAG                         GGGACAAGGACATCCAACAGGAAACTCCGCTCCTTATTTTGGTCCCTCGCA
genomic: GGGCGAGCATCATCTATAGTTGTGTCTGGAACCAATGTCATTAGGCCCAGgtgtgcatcc ... ctatttttagGGGACAAGGACATCCAACAGGAAACTCCGCTCCTTATTTTGGTCCCTCGCA
EST: gi|148964333|gb|EC905725.2|EC905725
EST:     GGGCGAGCATCATCTATAGTTGTGTCTGGAACCAATGTCATTAGGCCCAG                         GGGACAAGGACATCCAACAGGAAACTCCGCTCCTTATTTTGGTCCCTCGCA
genomic: GGGCGAGCATCATCTATAGTTGTGTCTGGAACCAATGTCATTAGGCCCAGgtgtgcatcc ... ctatttttagGGGACAAGGACATCCAACAGGAAACTCCGCTCCTTATTTTGGTCCCTCGCA
EST: gi|78124353|gb|DV542737.1|DV542737
EST:     GGGCGAGCATCATCTATAGTTGTGTCTGGAACCAATGTCATTAGGCCCAG                         GGGACAAGGACATCCAACAGGAAACTCCGCTCCTTATTTTGGTCCCTCGCA
genomic: GGGCGAGCATCATCTATAGTTGTGTCTGGAACCAATGTCATTAGGCCCAGgtgtgcatcc ... ctatttttagGGGACAAGGACATCCAACAGGAAACTCCGCTCCTTATTTTGGTCCCTCGCA
EST: gi|148956082|gb|EC901838.2|EC901838
EST:     GGGCGAGCATCATCTATAGTTGTGTCTGGAACCAATGTCATTAGGCCCAG                         GGGACAAGGACATCCAACAGGAAACTCCGCTCCTTATTTTGGTCCCTCGCA
genomic: GGGCGAGCATCATCTATAGTTGTGTCTGGAACCAATGTCATTAGGCCCAGgtgtgcatcc ... ctatttttagGGGACAAGGACATCCAACAGGAAACTCCGCTCCTTATTTTGGTCCCTCGCA
EST: gi|148955041|gb|EC900548.2|EC900548
EST:     GGCGAGCATCATCTTTTAGTTGTGTCTGGAACCAATGTCATTAGGCCCAG                         GGGACAAGGACATCCAACAGGAAACTCCGCTCCTTATTTTGGTCCCTCGCA
genomic: GGCGAGCATCATCTAT-AGTTGTGTCTGGAACCAATGTCATTAGGCCCAGgtgtgcatcc ... ctatttttagGGGACAAGGACATCCAACAGGAAACTCCGCTCCTTATTTTGGTCCCTCGCA
EST: gi|148983240|gb|EE029206.2|EE029206
EST:     GGGCGAGCATCATCTATAGTTGTGTCTGGAACCAATGTCATTAGGCCCCG                         GGGACAAGGACATCCAACAGGAAACTCCGCTCCTTATTTTGGTCCCTCGCA
genomic: GGGCGAGCATCATCTATAGTTGTGTCTGGAACCAATGTCATTAGGCCCAGgtgtgcatcc ... ctatttttagGGGACAAGGACATCCAACAGGAAACTCCGCTCCTTATTTTGGTCCCTCGCA
EST: gi|149042087|gb|EE047065.2|EE047065
EST:     GGGCGAGCATCATCTATAGTTGTGTCTGGAACCAATGTCATTAGGCCCAG                         GGGACAAGGACATCCAACAGGAAACTCCGCTCCTTATTTTGGTCCCTCGCA
genomic: GGGCGAGCATCATCTATAGTTGTGTCTGGAACCAATGTCATTAGGCCCAGgtgtgcatcc ... ctatttttagGGGACAAGGACATCCAACAGGAAACTCCGCTCCTTATTTTGGTCCCTCGCA
EST: gi|148949167|gb|EC894603.2|EC894603
EST:     GGGCGAGCATCATCTATAGTTGTGTCTGGAACCAATGTCATTAGGCCCAG                         GGGACAAGGACATCCAACAGGAAACTCCGCTCCTTATTTTGGTCCCTCGCA
genomic: GGGCGAGCATCATCTATAGTTGTGTCTGGAACCAATGTCATTAGGCCCAGgtgtgcatcc ... ctatttttagGGGACAAGGACATCCAACAGGAAACTCCGCTCCTTATTTTGGTCCCTCGCA
EST: gi|71421618|gb|DR805518.1|DR805518
EST:     GGGCGAGCATCATCTATAGTTGTGTCTGGAACCAATGTCATTAGGCCCAG                         GGGACAAGGACATCCAACAGGAAACTCCGCTCCTTATTTTGGTCCCTCGCA
genomic: GGGCGAGCATCATCTATAGTTGTGTCTGGAACCAATGTCATTAGGCCCAGgtgtgcatcc ... ctatttttagGGGACAAGGACATCCAACAGGAAACTCCGCTCCTTATTTTGGTCCCTCGCA
EST: gi|148941367|gb|EC886277.2|EC886277
EST:     GGGCGAGCATCATCTATAGTTGTGTCTGGAACCAATGTCATTAGGCCCAG                         GGGACAAGGACATCCAACAGGAAACTCCGCTCCTTATTTTGGTCCCTCGCA
genomic: GGGCGAGCATCATCTATAGTTGTGTCTGGAACCAATGTCATTAGGCCCAGgtgtgcatcc ... ctatttttagGGGACAAGGACATCCAACAGGAAACTCCGCTCCTTATTTTGGTCCCTCGCA
EST: gi|148959990|gb|EE153229.2|EE153229
EST:     GGGCGAGCATCATCTATAGTTGTGTCTGGAACCAATGTCATTAGGCCCAG                         GGGAACA-GGACATCCAACAGGAAACTCCGCTCCTTATTTTGGTCCCT
genomic: GGGCGAGCATCATCTATAGTTGTGTCTGGAACCAATGTCATTAGGCCCAGgtgtgcatcc ... ctatttttagGGGA-CAAGGACATCCAACAGGAAACTCCGCTCCTTATTTTGGTCCCT
EST: gi|76920587|gb|DV168250.1|DV168250
EST:     GGGCTAGCATCATCTATAGTTGTGTCTGGAACCAATGTCATTAGGCCCAG                         GGGACAAGGACATCCAACAGGAAACTCCGCTCCTTATTTTGGTCCCCTCGC
genomic: GGGCGAGCATCATCTATAGTTGTGTCTGGAACCAATGTCATTAGGCCCAGgtgtgcatcc ... ctatttttagGGGACAAGGACATCCAACAGGAAACTCCGCTCCTTATTTTGGTCCC-TCGC
EST: gi|149009361|gb|EE041411.2|EE041411
EST:     GGGCGAGCATCATCTATAGTTGTGTCTGGAACCAATGTCATTAGGCCCAG                         GGGACAAGGACATCCAACAGGAAACTCCGCTCCTTATTTTGGTCCCTCGCA
genomic: GGGCGAGCATCATCTATAGTTGTGTCTGGAACCAATGTCATTAGGCCCAGgtgtgcatcc ... ctatttttagGGGACAAGGACATCCAACAGGAAACTCCGCTCCTTATTTTGGTCCCTCGCA
EST: gi|148946154|gb|EC891448.2|EC891448
EST:     GGGCGAGCATCATCTATAGTTGTGTCTGGAACCAATGTCATTAGGCCCAG                         GGGACAAGGACATCCAACAGGAAACTCCGCTCCTTATTTTGGTCCCTCGCA
genomic: GGGCGAGCATCATCTATAGTTGTGTCTGGAACCAATGTCATTAGGCCCAGgtgtgcatcc ... ctatttttagGGGACAAGGACATCCAACAGGAAACTCCGCTCCTTATTTTGGTCCCTCGCA
EST: gi|89764162|gb|DY691069.1|DY691069
EST:     GGGCGAGCATCATCTATAGTTGTGTCTGGAACCAATGTCATTAGGCCCAG                         GGGACAAGGACATCCAACAGGAAACTCCGCCTC-TTATTTTGGTCCCTCGC
genomic: GGGCGAGCATCATCTATAGTTGTGTCTGGAACCAATGTCATTAGGCCCAGgtgtgcatcc ... ctatttttagGGGACAAGGACATCCAACAGGAAACTCCGC-TCCTTATTTTGGTCCCTCGC

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: 237

GTTTTATCTTCCAGTAGGATACAATGGGCGAGCATCATCTATAGTTGTGTCTGGAACCAATGTCATTAGGCCCAGgtgtgcatcc ... ctatttttagGGGACAAGGACATCCAACAGGAAACTCCGCTCCTTATTTTGGTCCCTCGCAGAAGCTTGATTTTGAGCTTGAGATG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 231

GTTTTATCTTCCAGTAGGATACAATGGGCGAGCATCATCTATAGTTGTGTCTGGAACCAATGTCATTAGGCCCAGgtgtgcatcc ... ctatttttagGGGACAAGGACATCCAACAGGAAACTCCGCTCCTTATTTTGGTCCCTCGCAGAAGCTTGATTTTGAGCTTGAGATG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 173

GTTTTATCTTCCAGTAGGATACAATGGGCGAGCATCATCTATAGTTGTGTCTGGAACCAATGTCATTAGGCCCAGgtgtgcatcc ... ctatttttagGGGACAAGGACATCCAACAGGAAACTCCGCTCCTTATTTTGGTCCCTCGCAGAAGCTTGATTTTGAGCTTGAGATG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 1664

GTTTTATCTTCCAGTAGGATACAATGGGCGAGCATCATCTATAGTTGTGTCTGGAACCAATGTCATTAGGCCCAGgtgtgcatcc ... ctatttttagGGGACAAGGACATCCAACAGGAAACTCCGCTCCTTATTTTGGTCCCTCGCAGAAGCTTGATTTTGAGCTTGAGATG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctttattttgtgtgctgcctgttgctcttttgtttaattatttctctatttttagGGGACAAGGACATCCAACAGGAAACTCCGCTCCTTATTTTGGTCCCTCGCAGAAGCTTGATTTTGAGCTTGAGATG
                               gtttaat  putative branch site (score: 1664)
                                     ttatttctctattttt  CT-rich tract
                         tcttttgtttaattat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgtgcatcccaaaatacttgttaaaacgagtcttaactgttgtttcaagcttgaaacctttattttgtgtgctgcctgttgctcttttgtttaattatttctctatttttagGGGACAAGGACATCCAACAGGAAACTCCGCTCCTTATTTTGGTCCCTCGCAGAAGCTTGATTTTGAGCTTGAGATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATG