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

...agttagtggaagggacactctatttaaagcttgtactacttgattttacttctgtaatgtaggcagatatattactgtctttttttgggtatgtatgcagAGAAACATTCATTCACACATTTATGCTCCAAATTGCTGTTTTATCCAATCATCTGAATGGGAGGGATACTCATGTCCGACAGATCAAGATCTACGGGCCA

Basic information

species Zea mays
transcript GRMZM2G054247_T01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G054247_T01 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os05g50360.1 (Oryza sativa), 3'ss of exon 4
-agttagtggaagggacactctatttaaagcttgtactacttgattttacttctgtaatgtaggcagatatattactgtctttttttgggtatgtatgcagAGAAACATTCATTCACACATTTATGCTCCAAATTGCTGTTTTATCCAATCATCTGAATGGGAGGGATACTCATGTCCGACAGATCAAGATCTACGGGCCA
 | ||| |              | | |||  | ||  |   | ||| |||| || |  || || ||| | | | | | | ||| |||   ||| | |||||||||||||||||||| |||||||||||||||||| | || || ||||||||  |||||||||||||||||||| | |||||||||||||| || ||||||
aatttaatctttcatctctcacagtcaaaattggttgtttctaattgtactactctgttgaagacagttgtgtaattttttttctttca-tatttgtgcagAGAAACATTCATTCATACATTTATGCTCCAAATTTCGGTGTTGTCCAATCACTTGAATGGGAGGGATACTCATATTCGACAGATCAAGATATATGGGCCA

upper sequence: GRMZM2G054247_T01 (Zea mays), 3'ss of exon 4
lower sequence: Vv04s0023g01940.t01 (Vitis vinifera), 3'ss of exon 4
agttagtggaagggacactcta--tttaaagcttgtactacttgat-----tttacttctgtaatgtaggcagatatattactgtctttttttgggtatgtatgcagAGAAACATTCATTCACACATTTATGCTCCAAATTGCTGTTTTATCCAATCATCTGAATGGGAGGGATACTCATGTCCGACAGATCAAGATCTACGGGCCA
     | ||||  ||   ||||  |||  |  || ||| | | |       || |  |   |  ||    ||  | |  |  | | | ||  |   ||| |  |||| ||||| ||  |  |||| |||||| | ||||||||| | || || ||||| || |||||||| ||||||||||| || ||||||||  | || ||||| 
-----gaggaaatgattgtctagtttttgactttttacaagtcggcatgtgttaatattccttctgagtacaattttgat-ttatttcttcctcaatatttg-gcagGGAAACTTTTGTGAACACTTTTATGTTGCAAATTGCTATATTGTCAAATCACCTTAATGGGAGAGATACTCATGTGCGCCAGATCAAAGTTTATGGGCCT
















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|32914925|gb|CF019737.1|CF019737
EST:     GGGTCCACATATCATTATCCGGGATTGATCCACG                         AGAAACATTCATTCACACATTTATGCTCCAAATTGCTGTTTTATCCAATCA
genomic: GGGTCCACATATCATTATCCGGGATTGATCCACGgtatgcattg ... atgtatgcagAGAAACATTCATTCACACATTTATGCTCCAAATTGCTGTTTTATCCAATCA
EST: gi|32857021|gb|CD996702.1|CD996702
EST:     GGTCCACATATCATTATCCGGGATTGATCCACG                         AGAAACATTCATTCACACATTTATGCTCCAAATTGCTGTTTTATCCAATCA
genomic: GGTCCACATATCATTATCCGGGATTGATCCACGgtatgcattg ... atgtatgcagAGAAACATTCATTCACACATTTATGCTCCAAATTGCTGTTTTATCCAATCA
EST: gi|8273087|gb|BE012181.1|BE012181
EST:     GCAAAGCCAGTTGGATGGGTCCACATATCATTATCCGGGATTGATCCACG                         AGAAACATTCATTCACACATTTATGCTCCAAATTGCTGTTTTATCCAATCA
genomic: GCAAAGCCAGTTGGATGGGTCCACATATCATTATCCGGGATTGATCCACGgtatgcattg ... atgtatgcagAGAAACATTCATTCACACATTTATGCTCCAAATTGCTGTTTTATCCAATCA
EST: gi|76915292|gb|DV165923.1|DV165923
EST:     GCAAAGCCAGTTGGATGGGTCCACATATCATTATCCGGGATTGATCCACG                         AGAAACATTCATTCACACATTTATGCTCCAAATTGCTGTTTTATCCAATCA
genomic: GCAAAGCCAGTTGGATGGGTCCACATATCATTATCCGGGATTGATCCACGgtatgcattg ... atgtatgcagAGAAACATTCATTCACACATTTATGCTCCAAATTGCTGTTTTATCCAATCA
EST: gi|60400666|gb|DN233473.1|DN233473
EST:     GCAAAGCCAGTTGGATGGGTCCACATATCATTATCCGGGATTGATCCACG                         AGAAACATTCATTCACACATTTATGCTCCAAATTGCTGTTTTATTCAATCA
genomic: GCAAAGCCAGTTGGATGGGTCCACATATCATTATCCGGGATTGATCCACGgtatgcattg ... atgtatgcagAGAAACATTCATTCACACATTTATGCTCCAAATTGCTGTTTTATCCAATCA
EST: gi|78088159|gb|DV516552.1|DV516552
EST:     GCAAAGCCAGTTGGATGGGTCCACATATCATTATCCGGGATTGATCCACG                         AGAAACATTCATTCACACATTTATGCTCCAAATTGCTGTTTTATCCTATCA
genomic: GCAAAGCCAGTTGGATGGGTCCACATATCATTATCCGGGATTGATCCACGgtatgcattg ... atgtatgcagAGAAACATTCATTCACACATTTATGCTCCAAATTGCTGTTTTATCCAATCA
EST: gi|13515650|gb|BG517926.1|BG517926
EST:     GCAAAGCCAGTTGGATGGGTCCACATATCATTATCCGGGATTGATCCACG                         AGAAACATTCATTCACACATTTATGC
genomic: GCAAAGCCAGTTGGATGGGTCCACATATCATTATCCGGGATTGATCCACGgtatgcattg ... atgtatgcagAGAAACATTCATTCACACATTTATGC
EST: gi|22490544|gb|BU050467.1|BU050467
EST:     GCAAAGCCAGTTGGATGGGTCCACATATCATTATCCGGGATTGATCCGCG                         AGAAACATTCATTCACACATTTATGCTCCAAATTGCTGTTTTATCCAATCA
genomic: GCAAAGCCAGTTGGATGGGTCCACATATCATTATCCGGGATTGATCCACGgtatgcattg ... atgtatgcagAGAAACATTCATTCACACATTTATGCTCCAAATTGCTGTTTTATCCAATCA
EST: gi|71297609|gb|DR784753.1|DR784753
EST:     GCAAAGCCAGTTGGATGGGTCCACATATCATTATCCGGGATTGATCCACG                         ACAAACATTCATTCACACATTTATGCTCCAAATTGCTGTTTTATCCAATCA
genomic: GCAAAGCCAGTTGGATGGGTCCACATATCATTATCCGGGATTGATCCACGgtatgcattg ... atgtatgcagAGAAACATTCATTCACACATTTATGCTCCAAATTGCTGTTTTATCCAATCA
EST: gi|16379595|gb|BI993037.1|BI993037
EST:     GCAAAGCCAGTTGGATGGGTCCACATATCATTATCCGGGATTGATCCACG                         AGAAACATTCATTCACACATTTATGCTCCAAATATGCTGTTTTATCCAATC
genomic: GCAAAGCCAGTTGGATGGGTCCACATATCATTATCCGGGATTGATCCACGgtatgcattg ... atgtatgcagAGAAACATTCATTCACACATTTATGCTCCAAAT-TGCTGTTTTATCCAATC
EST: gi|91873253|gb|EB403210.1|EB403210
EST:     GCAAAGCCAGTTGGATGGGTCCACATATCATTATCCGGGATGGATCCACG                         AGAAACATTCATTCACACATTTATGCTCCAAATTGCTGTTTTATCCAATCA
genomic: GCAAAGCCAGTTGGATGGGTCCACATATCATTATCCGGGATTGATCCACGgtatgcattg ... atgtatgcagAGAAACATTCATTCACACATTTATGCTCCAAATTGCTGTTTTATCCAATCA
EST: gi|87153735|gb|DY398524.1|DY398524
EST:     GCAAAGCCAGTTGGATGGGTCCACATATCATTATCCGGGATTGATCCGCG                         AGAAACATTCATTCACACATTTATGCTCCAAATTGCTGTTTTATCCAATCA
genomic: GCAAAGCCAGTTGGATGGGTCCACATATCATTATCCGGGATTGATCCACGgtatgcattg ... atgtatgcagAGAAACATTCATTCACACATTTATGCTCCAAATTGCTGTTTTATCCAATCA
EST: gi|71427965|gb|DR809015.1|DR809015
EST:     GCAAAGCCAGTTGGATGGGTCCACATATCATTATCCGGGATTGATCCACG                         AGAAACATTCATTCACACATTTATGCTCCAAATTGCTGTTTTATCCAATCA
genomic: GCAAAGCCAGTTGGATGGGTCCACATATCATTATCCGGGATTGATCCACGgtatgcattg ... atgtatgcagAGAAACATTCATTCACACATTTATGCTCCAAATTGCTGTTTTATCCAATCA
EST: gi|211368075|gb|FL362342.1|FL362342
EST:     GCAAAGCCAGTTGGATG--TCCACATATCATTATCCGGGATTGATCCACG                         AGAAACATTCATTCACACATTTATGCTCCAAATTGCTGTTTTATCCAATCA
genomic: GCAAAGCCAGTTGGATGGGTCCACATATCATTATCCGGGATTGATCCACGgtatgcattg ... atgtatgcagAGAAACATTCATTCACACATTTATGCTCCAAATTGCTGTTTTATCCAATCA
EST: gi|94476642|gb|EB705600.1|EB705600
EST:     GCAAAGCCAGTTGGATGGGTCCACATATCATTATCCGGGATTGATCCACG                         AGAAACATTCATTCACACATTTATGTTCCAAATTGCTGTTTTATCCAATCA
genomic: GCAAAGCCAGTTGGATGGGTCCACATATCATTATCCGGGATTGATCCACGgtatgcattg ... atgtatgcagAGAAACATTCATTCACACATTTATGCTCCAAATTGCTGTTTTATCCAATCA
EST: gi|71449488|gb|DR830538.1|DR830538
EST:     GCAAAGCCAGTTGGATGGGTCCACATATCATTATCCGGGATTGATCCACG                         AGAAACATTCATTCACACATTTATGCTCCAAATTGCTGTTTT
genomic: GCAAAGCCAGTTGGATGGGTCCACATATCATTATCCGGGATTGATCCACGgtatgcattg ... atgtatgcagAGAAACATTCATTCACACATTTATGCTCCAAATTGCTGTTTT

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: 45 (upstream exon), 48 (downstream exon)
Score: 55

GAGATTAGAACGGTGGAGCTTGCAAAGCCAGTTGGATGGGTCCACATATCATTATCCGGGATTGATCCACGgtatgcattg ... atgtatgcagAGAAACATTCATTCACACATTTATGCTCCAAATTGCTGTTTTATCCAATCATCTGAATGGGAGGGATACTCATGTCCGACAGATCAAGATCTACGGGCCA


Block sizes: 49 (upstream exon), 40 (downstream exon)
Score: 42

GAGATTAGAACGGTGGAGCTTGCAAAGCCAGTTGGATGGGTCCACATATCATTATCCGGGATTGATCCACGgtatgcattg ... atgtatgcagAGAAACATTCATTCACACATTTATGCTCCAAATTGCTGTTTTATCCAATCATCTGAATGGGAGGGATACTCATGTCCGACAGATCAAGATCTACGGGCCA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 64

GAGATTAGAACGGTGGAGCTTGCAAAGCCAGTTGGATGGGTCCACATATCATTATCCGGGATTGATCCACGgtatgcattg ... atgtatgcagAGAAACATTCATTCACACATTTATGCTCCAAATTGCTGTTTTATCCAATCATCTGAATGGGAGGGATACTCATGTCCGACAGATCAAGATCTACGGGCCA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 36

GAGATTAGAACGGTGGAGCTTGCAAAGCCAGTTGGATGGGTCCACATATCATTATCCGGGATTGATCCACGgtatgcattg ... atgtatgcagAGAAACATTCATTCACACATTTATGCTCCAAATTGCTGTTTTATCCAATCATCTGAATGGGAGGGATACTCATGTCCGACAGATCAAGATCTACGGGCCA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttacttctgtaatgtaggcagatatattactgtctttttttgggtatgtatgcagAGAAACATTCATTCACACATTTATGCTCCAAATTGCTGTTTTATCCAATCATCTGAATGGGAGGGATACTCATGTCCGACAGATCAAGATCTACGGGCCA
                   agatatatta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
agttagtggaagggacactctatttaaagcttgtactacttgattttacttctgtaatgtaggcagatatattactgtctttttttgggtatgtatgcagAGAAACATTCATTCACACATTTATGCTCCAAATTGCTGTTTTATCCAATCATCTGAATGGGAGGGATACTCATGTCCGACAGATCAAGATCTACGGGCCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA
- - - - - - - - - - - - - - - - - -ctacttg
- - - - - - - - - - - - - - - - - - - - - - - -acttctg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgtaggc