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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aaaacactattctttgttttttttacttcattacttgtgatgcttccaagcttgcaatcgtgatttgtattatcctaaagcacgattcatttccctgtagAACCATAACTACGCAGTTGACCCAGAATCACTCCCAGAAGGAGCAAAAGTAACTCACGTCAATCTCAACGATAATAGTTGCGCTGGCCTCCAGTACTCCA

Basic information

species Zea mays
transcript GRMZM2G029573_T02
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G029573_T01 (Zea mays), 3'ss of exon 9
lower sequence: LOC_Os02g47850.1 (Oryza sativa), 3'ss of exon 10
aaaacactattctttgttttttttacttcattacttgtgatgctt-ccaagcttgcaatcgtgatt-tgtattatcctaaagc---acgattcatttccctgtagAACCATAACTACGCAGTTGACCCAGAATCACTCCCAGAAGGAGCAAAAGTAACTCACGTCAATCTCAACGATAATAGTTGCGCTGGCCTCCAGTACTCCA
     |   ||||  || ||   || ||      ||||  | |||  ||  |||||| |    | | || | | | | |  |    ||  |   |||| ||| |||||||||| || || ||||||||||| ||||| |||||||| |  |||||||| ||  ||||||||||||||||||| || || ||||| |||||| | |
-----atatttctgagtcttagctattttcccctttgttttacttgtcatacttgcatttactactgtgcaatctgcaattgtcttaccgtatttttctctgcagAACCATAATTATGCTGTTGACCCAGAGTCACTTCCAGAAGGGGTGAAAGTAACACATATCAATCTCAACGATAATAGCTGTGCCGGCCTTCAGTACCCTA
















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|31362536|gb|CD446893.1|CD446893
EST:     ATCACCCTGTCTGTGATCTCCGTAGTGGACGTGTAGACATAAGTGCACAG                         ACCCATATCTACGCAGTTGACCCAGAATCACTCCCAGAAGGAGCAAAAGTA
genomic: ATCACCCTGTCTGTGATCTCCGTAGTGGACGTGTAGACATAAGTGCACAGgtttgttcct ... ttccctgtagAACCATAACTACGCAGTTGACCCAGAATCACTCCCAGAAGGAGCAAAAGTA
EST: gi|71760287|gb|DR958224.1|DR958224
EST:     ATCACCCTGTCTGTGATCTCCGTAGTGGACGTGTAGACATAAGTGCACAG                         AACCATAACTACGCAGTTGACCCAGAATCACTCCCAGAAGGAGCAAAAGTA
genomic: ATCACCCTGTCTGTGATCTCCGTAGTGGACGTGTAGACATAAGTGCACAGgtttgttcct ... ttccctgtagAACCATAACTACGCAGTTGACCCAGAATCACTCCCAGAAGGAGCAAAAGTA
EST: gi|32845426|gb|CD985107.1|CD985107
EST:     ATCACCCTGTCTGTGATCTCCGTAGTGGACGTGTAGACATAAGTGCACAG                         AACCATAACTACGCAGTTGACCCAGAATCACTCCCAGAAGGAGCAAAAGTA
genomic: ATCACCCTGTCTGTGATCTCCGTAGTGGACGTGTAGACATAAGTGCACAGgtttgttcct ... ttccctgtagAACCATAACTACGCAGTTGACCCAGAATCACTCCCAGAAGGAGCAAAAGTA
EST: gi|211106984|gb|FL115271.1|FL115271
EST:     ATCACCCTGTCTGTGATCTCCGTAGTGGACGTGTAGACATAAGTGCACAG                         AACCATAACTACGCAGTTGACCCAGAATCACTCCCAGAAGGAGCAAAAGTA
genomic: ATCACCCTGTCTGTGATCTCCGTAGTGGACGTGTAGACATAAGTGCACAGgtttgttcct ... ttccctgtagAACCATAACTACGCAGTTGACCCAGAATCACTCCCAGAAGGAGCAAAAGTA
EST: gi|37401297|gb|CF638011.1|CF638011
EST:     ATCACCCTGTCTGTGATCTCCGTAGTGGACGTGTAGACATAAGTGCACAG                         AACCATAACTACGCAGTTGACCCAGAATCACTCCCAGAAGGAGCAAAAGTA
genomic: ATCACCCTGTCTGTGATCTCCGTAGTGGACGTGTAGACATAAGTGCACAGgtttgttcct ... ttccctgtagAACCATAACTACGCAGTTGACCCAGAATCACTCCCAGAAGGAGCAAAAGTA
EST: gi|211518595|gb|FL052563.1|FL052563
EST:     ATCACCCTGTCTGTGATCTCCGTAGTGGACGTGTAGACATAAGTGCACAG                         AACCATAACTACGCAGTTGACCCAGAATCACTCCCAGAAGGAGCAAAAGTW
genomic: ATCACCCTGTCTGTGATCTCCGTAGTGGACGTGTAGACATAAGTGCACAGgtttgttcct ... ttccctgtagAACCATAACTACGCAGTTGACCCAGAATCACTCCCAGAAGGAGCAAAAGTA
EST: gi|33101065|gb|CF061025.1|CF061025
EST:     ATCACCCTGTCTGTGATCTCCGTAGTGGACGTGTAGACATAAGTGCACAG                         AACCATAACTACGCAGTTGACCCAGAATCACTCCCAGAAGGAGCAAAAGTA
genomic: ATCACCCTGTCTGTGATCTCCGTAGTGGACGTGTAGACATAAGTGCACAGgtttgttcct ... ttccctgtagAACCATAACTACGCAGTTGACCCAGAATCACTCCCAGAAGGAGCAAAAGTA
EST: gi|6342748|gb|AW165572.1|AW165572
EST:     ATCACCCTGTCTGTGATCTCCGTAGTGGACGTGTAGACATAAGTGCACAG                         AACCATAACTACGCAGTTGACCCAGAATCACTCCCAGAAGGAGCAAAAGTA
genomic: ATCACCCTGTCTGTGATCTCCGTAGTGGACGTGTAGACATAAGTGCACAGgtttgttcct ... ttccctgtagAACCATAACTACGCAGTTGACCCAGAATCACTCCCAGAAGGAGCAAAAGTA
EST: gi|67018136|gb|CO446885.1|CO446885
EST:     ATCACCCTGTCTGTGATCTCCGTAGTGGACGTGTAGACATAAGTGCACAG                         AACCATAACTACGCAGTTGACCCAGAATCACTCCCAGAAGGAGCAAAAGTA
genomic: ATCACCCTGTCTGTGATCTCCGTAGTGGACGTGTAGACATAAGTGCACAGgtttgttcct ... ttccctgtagAACCATAACTACGCAGTTGACCCAGAATCACTCCCAGAAGGAGCAAAAGTA
EST: gi|211038354|gb|FL445366.1|FL445366
EST:     ATCACCCTGTCTGTGATCTCCGTAGTGGACGTGTAGACATAAGTGCACAG                         AACCATAACTACGCAGTTGACCCAGAATCACTCCCAGAAGGAGCAAAAGTA
genomic: ATCACCCTGTCTGTGATCTCCGTAGTGGACGTGTAGACATAAGTGCACAGgtttgttcct ... ttccctgtagAACCATAACTACGCAGTTGACCCAGAATCACTCCCAGAAGGAGCAAAAGTA
EST: gi|32844104|gb|CD983785.1|CD983785
EST:     ATCACCCTGTCTGTGATCTCCGTAGTGGACGTGTAGACATAAGTGCACAG                         AACCATAACTACGCAGTTGACCCAGAATCACTCCCAGAAGGAGCAAAAGTA
genomic: ATCACCCTGTCTGTGATCTCCGTAGTGGACGTGTAGACATAAGTGCACAGgtttgttcct ... ttccctgtagAACCATAACTACGCAGTTGACCCAGAATCACTCCCAGAAGGAGCAAAAGTA
EST: gi|60343079|gb|DN210052.1|DN210052
EST:     ATCACCCTGTCTGTGATCTCCGTAGTGGACGTGTAGACATAAGTGCACAG                         AACCATAACTACGCAGTTGACCCAGAATCACTCCCAGAAGGAGCAAAAGTA
genomic: ATCACCCTGTCTGTGATCTCCGTAGTGGACGTGTAGACATAAGTGCACAGgtttgttcct ... ttccctgtagAACCATAACTACGCAGTTGACCCAGAATCACTCCCAGAAGGAGCAAAAGTA
EST: gi|31356811|gb|CD441168.1|CD441168
EST:     ATCACCCTGTCTGTGATCTCCGTAGTGGACGTGTAGACATAAGTGCACAG                         AACCATAACTACGCAGTTGACCCAGAATCACTCCCAGAAGGAGCAAAAGTA
genomic: ATCACCCTGTCTGTGATCTCCGTAGTGGACGTGTAGACATAAGTGCACAGgtttgttcct ... ttccctgtagAACCATAACTACGCAGTTGACCCAGAATCACTCCCAGAAGGAGCAAAAGTA
EST: gi|6012497|gb|AW061934.1|AW061934
EST:     ATCACCCTGTCTGTGATCTCCGTAGTGGACGTGTAGACATAAGTGCACAG                         AACCATAACTACGCAGTTGACCCAGAATCACTCCCAGAAGGAGCAAAAGTA
genomic: ATCACCCTGTCTGTGATCTCCGTAGTGGACGTGTAGACATAAGTGCACAGgtttgttcct ... ttccctgtagAACCATAACTACGCAGTTGACCCAGAATCACTCCCAGAAGGAGCAAAAGTA
EST: gi|88751312|gb|DY535453.1|DY535453
EST:     ATCACCCTGTCTGTGATCTCCGTAGTGGACGTGTAGACATAAGTGCACAG                         AACCATAACTACGCAGTTGACCCAGAATCACTCCCAGAAGGAGCAAAAGTA
genomic: ATCACCCTGTCTGTGATCTCCGTAGTGGACGTGTAGACATAAGTGCACAGgtttgttcct ... ttccctgtagAACCATAACTACGCAGTTGACCCAGAATCACTCCCAGAAGGAGCAAAAGTA
EST: gi|71764309|gb|DR962246.1|DR962246
EST:     CATAAGTGCACAG                         AACCATAACTACGCAGTTGACCCAGAATCACTCCCAGAAGGAGCAAAAGTA
genomic: CATAAGTGCACAGgtttgttcct ... ttccctgtagAACCATAACTACGCAGTTGACCCAGAATCACTCCCAGAAGGAGCAAAAGTA
EST: gi|6445511|gb|AW179429.1|AW179429
EST:     ATCACCCTGTCTGTGATCTCCGTAGTGGACGTGTAGACATAAGTGCACAG                         AACCATAACTACGCAGTTGACCCAGAATCACTCCCAGAAG
genomic: ATCACCCTGTCTGTGATCTCCGTAGTGGACGTGTAGACATAAGTGCACAGgtttgttcct ... ttccctgtagAACCATAACTACGCAGTTGACCCAGAATCACTCCCAGAAG
EST: gi|32844356|gb|CD984037.1|CD984037
EST:     ATCACCCTGTCTGTGATCTCCGTAGTGGACGTGTAGACATAAGTGCACAG                         AACCATAACTACGCAGTTGACCCAGAATCACTCCCAGAAGGAGCAAAAGTA
genomic: ATCACCCTGTCTGTGATCTCCGTAGTGGACGTGTAGACATAAGTGCACAGgtttgttcct ... ttccctgtagAACCATAACTACGCAGTTGACCCAGAATCACTCCCAGAAGGAGCAAAAGTA
EST: gi|37379091|gb|CF626275.1|CF626275
EST:     ATCACCCTGTCTGTGATCTCCGTAGTGGACGTGTAGACTTAAGTGCACAG                         AACCATAACTACGCAGTTGACCCAGAATCACTCCCAGAAGGAGCAATAGTA
genomic: ATCACCCTGTCTGTGATCTCCGTAGTGGACGTGTAGACATAAGTGCACAGgtttgttcct ... ttccctgtagAACCATAACTACGCAGTTGACCCAGAATCACTCCCAGAAGGAGCAAAAGTA
EST: gi|211287671|gb|FL254549.1|FL254549
EST:     ATCACCCTGTCTGTGATCTCCGTAGTGGACGTGTAGACATAAGTGCACAG                         AACCATAACTACGCAGTTGACCCAGAATCACTCCCAGAATGAGCAAAAGTA
genomic: ATCACCCTGTCTGTGATCTCCGTAGTGGACGTGTAGACATAAGTGCACAGgtttgttcct ... ttccctgtagAACCATAACTACGCAGTTGACCCAGAATCACTCCCAGAAGGAGCAAAAGTA

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: 201

GGCTCTTGGTGGGAAGACATTTAAAATGAAATTTGGACATCATGGCGGGAATCACCCTGTCTGTGATCTCCGTAGTGGACGTGTAGACATAAGTGCACAGgtttgttcct ... ttccctgtagAACCATAACTACGCAGTTGACCCAGAATCACTCCCAGAAGGAGCAAAAGTAACTCACGTCAATCTCAACGATAATAGTTGCGCTGGCCTCCAGTACTCCA


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

GGCTCTTGGTGGGAAGACATTTAAAATGAAATTTGGACATCATGGCGGGAATCACCCTGTCTGTGATCTCCGTAGTGGACGTGTAGACATAAGTGCACAGgtttgttcct ... ttccctgtagAACCATAACTACGCAGTTGACCCAGAATCACTCCCAGAAGGAGCAAAAGTAACTCACGTCAATCTCAACGATAATAGTTGCGCTGGCCTCCAGTACTCCA


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 158

GGCTCTTGGTGGGAAGACATTTAAAATGAAATTTGGACATCATGGCGGGAATCACCCTGTCTGTGATCTCCGTAGTGGACGTGTAGACATAAGTGCACAGgtttgttcct ... ttccctgtagAACCATAACTACGCAGTTGACCCAGAATCACTCCCAGAAGGAGCAAAAGTAACTCACGTCAATCTCAACGATAATAGTTGCGCTGGCCTCCAGTACTCCA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 127

GGCTCTTGGTGGGAAGACATTTAAAATGAAATTTGGACATCATGGCGGGAATCACCCTGTCTGTGATCTCCGTAGTGGACGTGTAGACATAAGTGCACAGgtttgttcct ... ttccctgtagAACCATAACTACGCAGTTGACCCAGAATCACTCCCAGAAGGAGCAAAAGTAACTCACGTCAATCTCAACGATAATAGTTGCGCTGGCCTCCAGTACTCCA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccaagcttgcaatcgtgatttgtattatcctaaagcacgattcatttccctgtagAACCATAACTACGCAGTTGACCCAGAATCACTCCCAGAAGGAGCAAAAGTAACTCACGTCAATCTCAACGATAATAGTTGCGCTGGCCTCCAGTACTCCA
                           tcctaaa  putative branch site (score: 127)
                                        ttcatttccct  putative PPT
                 atttgtattat  TA-rich tract