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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgttttccagagagtatggatttacattaactatagttctttcattgttctcttctgtcaatagtccttttctcatccattatttcctgaccatatctaagaaatcatttctcattattgtgcagCTAGTCCACAGATATTGCTTCTTGCTTCTTTCCTCTTGCTACTGTCATTCTG

Basic information

species Zea mays
transcript GRMZM2G042099_T01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G042099_T01 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os01g54784.1 (Oryza sativa), 3'ss of exon 4
gtatgttttccagagagtatggatttacattaactatagttctttcattgttctcttctgtcaata-gtccttttctcatccattatttc-ctgaccatatctaagaa--atcatttctcattattgtgcagCTAGTCCACAGATATTGCTTCTTGCTTCTTTCCTCTTGCTACTGTCATTCTG
|||| |||| | |    ||| | ||| |  |   | |  || | |  || | |     | || | | | |||||| |  |    |||||  ||||||| | |||| |    |   |||||| |||| |||||||||||||||||||||||||||||||||||| || |||||  ||||||||||
gtatattttactggatatatagctttgctgt---tgtccttttgtttttttccctgcttatctacatgaccttttattgtatgctatttttctgaccagacctaatagttgtgcattctcaatattttgcagCTAGTCCACAGATATTGCTTCTTGCTTCTTTTCTGTTGCTGTTGTCATTCTG
















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|6952350|gb|AW424418.1|AW424418
EST:     TTGTCAGAGATGGATTTGCTGGGTACATGGATGTGGATTTGTTCTCATGG                         CTAGTCCACAGATATTGCTTCTTGCTTCTTTCCTCTTGCTACTGTCATTCT
genomic: TTGTCAGAGATGGATTTGCTGGGTACATGGATGTGGATTTGTTCTCATGGgtatgttttc ... tattgtgcagCTAGTCCACAGATATTGCTTCTTGCTTCTTTCCTCTTGCTACTGTCATTCT
EST: gi|211469288|gb|FL298421.1|FL298421
EST:     ATGGATGTGGATTTGTTCTCATGG                         CTAGTCCACAGATATTGCTTCTTGCTTCTTTCCTCTTGCTACTGTCATTCT
genomic: ATGGATGTGGATTTGTTCTCATGGgtatgttttc ... tattgtgcagCTAGTCCACAGATATTGCTTCTTGCTTCTTTCCTCTTGCTACTGTCATTCT
EST: gi|78122118|gb|DV540502.1|DV540502
EST:     TTGTCAGAGATGGATTTGCTGGGTACATGGATGTGGATTTGTTCTCATGG                         CTAGTCCACAGATATTGCTTCTTGCTTCTTTCCTCTTGCTACTGTCATTCT
genomic: TTGTCAGAGATGGATTTGCTGGGTACATGGATGTGGATTTGTTCTCATGGgtatgttttc ... tattgtgcagCTAGTCCACAGATATTGCTTCTTGCTTCTTTCCTCTTGCTACTGTCATTCT

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), 48 (downstream exon)
Score: 46

TATTCCTAGTATATTTCGTGTCTACCATCATTGCTACTTGTCAGAGATGGATTTGCTGGGTACATGGATGTGGATTTGTTCTCATGGgtatgttttc ... tattgtgcagCTAGTCCACAGATATTGCTTCTTGCTTCTTTCCTCTTGCTACTGTCATTCTG


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 9

TATTCCTAGTATATTTCGTGTCTACCATCATTGCTACTTGTCAGAGATGGATTTGCTGGGTACATGGATGTGGATTTGTTCTCATGGgtatgttttc ... tattgtgcagCTAGTCCACAGATATTGCTTCTTGCTTCTTTCCTCTTGCTACTGTCATTCTG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 16

TATTCCTAGTATATTTCGTGTCTACCATCATTGCTACTTGTCAGAGATGGATTTGCTGGGTACATGGATGTGGATTTGTTCTCATGGgtatgttttc ... tattgtgcagCTAGTCCACAGATATTGCTTCTTGCTTCTTTCCTCTTGCTACTGTCATTCTG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 33

TATTCCTAGTATATTTCGTGTCTACCATCATTGCTACTTGTCAGAGATGGATTTGCTGGGTACATGGATGTGGATTTGTTCTCATGGgtatgttttc ... tattgtgcagCTAGTCCACAGATATTGCTTCTTGCTTCTTTCCTCTTGCTACTGTCATTCTG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctcatccattatttcctgaccatatctaagaaatcatttctcattattgtgcagCTAGTCCACAGATATTGCTTCTTGCTTCTTTCCTCTTGCTACTGTCATTCTG
              tcctgac  putative branch site (score: 33)
                                     tttctcatt  putative PPT
                               aaatcattt  TA-rich tract