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

gttcaaccggatctgtccacgcctgctctgctatttctttccatctttccctgtttccttcggtcgatgcgtttcttgattcaacgtttctgggggttgcagATGAGGCGTACTACAGAGGCGGCGTGATTAAATGCAGGGACGGATCAGGCAGGTTCTCCCGGGAGCAGCTCAACGACGACTTCTGCGACTGCCCCGACGG

Basic information

species Zea mays
transcript GRMZM2G052875_T02
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G052875_T01 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os01g16970.2 (Oryza sativa), 3'ss of exon 1
gttcaaccggatctgtccacgcctgctctgctatttctttccatctttccctgtttccttcggtcgatgcgtttcttgattcaacgtttctgggggt-----------------------tgcagATGAGGCGTACTACAGAGGCGGCGTGATTAAATGCAGGGACGGATCAGGCAGGTTCTCCCGGGAGCAGCTCAACGACGACTTCTGCGACTGCCCCGACGG
|||| | |   |   |   | ||  | | |  || |   |  |||| ||  | ||      | | |||||| |||||||||    |  | ||||||                        |||||| |||||||||| ||| ||||||||||| |  |||||||||||||| || |||||| || ||||  ||||||||||||||||||||||||||||||||||
gttccatcttgttctttttctccccccccgg-atctgcctgtatctctctttcttggt---gcttgatgcggttcttgatttggtgcctgtgggggcgggggtggctggctgcactgcactgcagACGAGGCGTACTTCAGGGGCGGCGTGATCAGGTGCAGGGACGGATCGGGGAGGTTCGCCAGGGACAAGCTCAACGACGACTTCTGCGACTGCCCCGACGG
















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|87153726|gb|DY398515.1|DY398515
EST:     GGCGGTGGAGTCCAAGCCGCCCCTCGACACCCTGGGCATACCCCCGCAAG                         ATGAGGCGTACTACAGAGGCGGCGTGATTAAATGCAGGGACGGATCAGGCA
genomic: GGCGGTGGAGTCCAAGCCGCCCCTCGACACCCTGGGCATACCCCCGCAAGgttcaaccgg ... ggggttgcagATGAGGCGTACTACAGAGGCGGCGTGATTAAATGCAGGGACGGATCAGGCA
EST: gi|22490637|gb|BU050560.1|BU050560
EST:     GGCGGTGGAGTCCAAGCCGCCCCTCGACACCCTGGGCATACCCCCGCAAG                         ATGAGGCGTACTACAGAGGCGGCGTGATTAAATGCAGGGACGGATCAGGCA
genomic: GGCGGTGGAGTCCAAGCCGCCCCTCGACACCCTGGGCATACCCCCGCAAGgttcaaccgg ... ggggttgcagATGAGGCGTACTACAGAGGCGGCGTGATTAAATGCAGGGACGGATCAGGCA
EST: gi|211322390|gb|FL223767.1|FL223767
EST:     GGCGGTGGAGTCCAAGCCGCCCCTCGACACCCTGGGCATACCCCCGCAAG                         ATGAGGCGTACTACAGAGGCGGCGTGATTAAATGCAGGGACGGATCAGGCA
genomic: GGCGGTGGAGTCCAAGCCGCCCCTCGACACCCTGGGCATACCCCCGCAAGgttcaaccgg ... ggggttgcagATGAGGCGTACTACAGAGGCGGCGTGATTAAATGCAGGGACGGATCAGGCA
EST: gi|19057817|gb|BM736484.1|BM736484
EST:     GGCGG-GGAGTCCAAGCCGCCCCTCGACACCCTGGGCATACCCCCGCAAG                         ATGAGGCGTACTACAGAGGCGGCGTGATTAAATGCAGGGACGGATCAGGCA
genomic: GGCGGTGGAGTCCAAGCCGCCCCTCGACACCCTGGGCATACCCCCGCAAGgttcaaccgg ... ggggttgcagATGAGGCGTACTACAGAGGCGGCGTGATTAAATGCAGGGACGGATCAGGCA
EST: gi|31612130|gb|CD568752.1|CD568752
EST:     GGCGGTGGAGTCCAAGCCGCCCCTCGACACCCTGGGCATACCCCCGCAAG                         ATGAGGCGTACTACAGAGGCGGCGTGATTAAATGCAGGGACGGATCAGGCA
genomic: GGCGGTGGAGTCCAAGCCGCCCCTCGACACCCTGGGCATACCCCCGCAAGgttcaaccgg ... ggggttgcagATGAGGCGTACTACAGAGGCGGCGTGATTAAATGCAGGGACGGATCAGGCA
EST: gi|19058293|gb|BM736960.1|BM736960
EST:     TGGGCATACCCCCGCAAG                         ATGAGGCGTACTACAGAGGCGGCGTGATTAAATGCAGGGCCGGATCAGGCA
genomic: TGGGCATACCCCCGCAAGgttcaaccgg ... ggggttgcagATGAGGCGTACTACAGAGGCGGCGTGATTAAATGCAGGGACGGATCAGGCA
EST: gi|211320224|gb|FL223759.1|FL223759
EST:     CGCCCCTCGACACCCTGGGCATACCCCCGCAAG                         ATGAGGNGTACTACAGAGGCGGNGTGATTAAATGNAGGGACGGATCAGGCA
genomic: CGCCCCTCGACACCCTGGGCATACCCCCGCAAGgttcaaccgg ... ggggttgcagATGAGGCGTACTACAGAGGCGGCGTGATTAAATGCAGGGACGGATCAGGCA
EST: gi|211322386|gb|FL223763.1|FL223763
EST:     GGCGGTGGAGTCCAAGCCGCCCCTCGACACCCTGGGCATACCCCCGCAAG                         ATGAGGCGTACTACAGAGGCGGCGTGATTAAATGCAGGGACGGATCAGGCA
genomic: GGCGGTGGAGTCCAAGCCGCCCCTCGACACCCTGGGCATACCCCCGCAAGgttcaaccgg ... ggggttgcagATGAGGCGTACTACAGAGGCGGCGTGATTAAATGCAGGGACGGATCAGGCA
EST: gi|211322388|gb|FL223765.1|FL223765
EST:     GGCGGTGGAGTCCAAGCCGCCCCTCGACACCCTGGGCATACCCCCGCAAG                         ATGAGGCGTACTACAGAGGCGGCGTGATTAAATGCAGGGACGGATCAGGCA
genomic: GGCGGTGGAGTCCAAGCCGCCCCTCGACACCCTGGGCATACCCCCGCAAGgttcaaccgg ... ggggttgcagATGAGGCGTACTACAGAGGCGGCGTGATTAAATGCAGGGACGGATCAGGCA
EST: gi|211322389|gb|FL223766.1|FL223766
EST:     GGCGGTGGAGTCCAAGCCGCCCCTCGACACCCTGGGCATACCCCCGCAAG                         ATGAGGCGTACTACAGAGGCGGCGTGATTAAATGCAGGGACGGATCAGGCA
genomic: GGCGGTGGAGTCCAAGCCGCCCCTCGACACCCTGGGCATACCCCCGCAAGgttcaaccgg ... ggggttgcagATGAGGCGTACTACAGAGGCGGCGTGATTAAATGCAGGGACGGATCAGGCA
EST: gi|211320227|gb|FL223762.1|FL223762
EST:     GGCGGTGGAGTCCAAGCCGCCCCTCGACACCCTGGGCATACCCCCGCAAG                         ATGAGGCGTACTACAGAGGCGGCGTGATTAAATGCAGGGACGGATCAGGCA
genomic: GGCGGTGGAGTCCAAGCCGCCCCTCGACACCCTGGGCATACCCCCGCAAGgttcaaccgg ... ggggttgcagATGAGGCGTACTACAGAGGCGGCGTGATTAAATGCAGGGACGGATCAGGCA
EST: gi|211320225|gb|FL223760.1|FL223760
EST:     GGCGGTGGAGTCCAAGCCGCCCCTCGACACCCTGGGCATACCCCCGCAAG                         ATGAGGCGTACTACAGAGGCGGCGTGATTAAATGCAGGGACGGATCAGGCA
genomic: GGCGGTGGAGTCCAAGCCGCCCCTCGACACCCTGGGCATACCCCCGCAAGgttcaaccgg ... ggggttgcagATGAGGCGTACTACAGAGGCGGCGTGATTAAATGCAGGGACGGATCAGGCA
EST: gi|211320223|gb|FL223758.1|FL223758
EST:     GGCGGTGGAGTCCAAGCCGCCCCTCGACACCCTGGGCATACCCCCGCAAG                         ATGAGGCGTACTACAGAGGCGGCGTGATTAAATGCAGGGACGGATCAGGCA
genomic: GGCGGTGGAGTCCAAGCCGCCCCTCGACACCCTGGGCATACCCCCGCAAGgttcaaccgg ... ggggttgcagATGAGGCGTACTACAGAGGCGGCGTGATTAAATGCAGGGACGGATCAGGCA

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: 48 (upstream exon), 49 (downstream exon)
Score: 194

GCAGGCATGAGGCTCCTCCTCGTCGGCGCCCTACTCCTATGTGCCACCGCGGCGGTGGAGTCCAAGCCGCCCCTCGACACCCTGGGCATACCCCCGCAAGgttcaaccgg ... ggggttgcagATGAGGCGTACTACAGAGGCGGCGTGATTAAATGCAGGGACGGATCAGGCAGGTTCTCCCGGGAGCAGCTCAACGACGACTTCTGCGACTGCCCCGACGG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 210

GCAGGCATGAGGCTCCTCCTCGTCGGCGCCCTACTCCTATGTGCCACCGCGGCGGTGGAGTCCAAGCCGCCCCTCGACACCCTGGGCATACCCCCGCAAGgttcaaccgg ... ggggttgcagATGAGGCGTACTACAGAGGCGGCGTGATTAAATGCAGGGACGGATCAGGCAGGTTCTCCCGGGAGCAGCTCAACGACGACTTCTGCGACTGCCCCGACGG


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 91

GCAGGCATGAGGCTCCTCCTCGTCGGCGCCCTACTCCTATGTGCCACCGCGGCGGTGGAGTCCAAGCCGCCCCTCGACACCCTGGGCATACCCCCGCAAGgttcaaccgg ... ggggttgcagATGAGGCGTACTACAGAGGCGGCGTGATTAAATGCAGGGACGGATCAGGCAGGTTCTCCCGGGAGCAGCTCAACGACGACTTCTGCGACTGCCCCGACGG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 251

GCAGGCATGAGGCTCCTCCTCGTCGGCGCCCTACTCCTATGTGCCACCGCGGCGGTGGAGTCCAAGCCGCCCCTCGACACCCTGGGCATACCCCCGCAAGgttcaaccgg ... ggggttgcagATGAGGCGTACTACAGAGGCGGCGTGATTAAATGCAGGGACGGATCAGGCAGGTTCTCCCGGGAGCAGCTCAACGACGACTTCTGCGACTGCCCCGACGG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tccctgtttccttcggtcgatgcgtttcttgattcaacgtttctgggggttgcagATGAGGCGTACTACAGAGGCGGCGTGATTAAATGCAGGGACGGATCAGGCAGGTTCTCCCGGGAGCAGCTCAACGACGACTTCTGCGACTGCCCCGACGG
                          tcttgat  putative branch site (score: 251)
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttcaaccggatctgtccacgcctgctctgctatttctttccatctttccctgtttccttcggtcgatgcgtttcttgattcaacgtttctgggggttgcagATGAGGCGTACTACAGAGGCGGCGTGATTAAATGCAGGGACGGATCAGGCAGGTTCTCCCGGGAGCAGCTCAACGACGACTTCTGCGACTGCCCCGACGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA