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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttgtaattttctgttggtttagactgtagaaacagtcttgttacagaagtaatatcaggatccatacttctaatatctcctcaacttatcttatttgtagGAATGTGTGAGTAATATCATGAGGCACGCACGACAGGCTAATATTCCAACTGTTGTGGATGGG

Basic information

species Zea mays
transcript GRMZM5G840928_T03
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G840928_T01 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os11g17610.1 (Oryza sativa), 3'ss of exon 4
ttgtaattttctgttggtttagactgtagaaacagtcttgttacaga-agtaatatcaggatccatacttctaatatctcctcaacttatcttatttgtagGAATGTGTGAGTAATATCATGAGGCACGCACGACAGGCTAATATTCCAACTGTTGTGGATGGG
| |||| | || | | | || || ||| | || ||| || | || | | || ||||||| |||||||| ||||| |||||||||||||| || ||||| ||||| ||||||||||| || || || |||
-tctaatctcctatatggagatcatgccatcttgccctaagtacttacgatagtattcaaatttgtcagcttatgtttgttttgacatatcttacttgtagGACTGTGTAAGTAATATCATGAGACATGCACGGCAGGCAAATATTCCAACAGTCGTTGACGGG
















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|78120737|gb|DV539121.1|DV539121
EST:     TTGATTGCATTGTTGTTGGTCCTGGCCTTGGAAGGGACCCCTTTCTTCTG                         GAATGTGTGAGTAATATCATGAGGCACGCACGACAGGCTAATATTCCAACT
genomic: TTGATTGCATTGTTGTTGGTCCTGGCCTTGGAAGGGACCCCTTTCTTCTGgttagtttgc ... ttatttgtagGAATGTGTGAGTAATATCATGAGGCACGCACGACAGGCTAATATTCCAACT
EST: gi|76282803|gb|DV022371.1|DV022371
EST:     TTGATTGCATTGTTGTTGGTCCTGGCCTTGGAAGGGACCCCTTTCTTCTG                         GAATGTGTGAGTAATATCATGAGGCACGCACGACAGGCTAATATTCCAACT
genomic: TTGATTGCATTGTTGTTGGTCCTGGCCTTGGAAGGGACCCCTTTCTTCTGgttagtttgc ... ttatttgtagGAATGTGTGAGTAATATCATGAGGCACGCACGACAGGCTAATATTCCAACT
EST: gi|60400995|gb|DN233802.1|DN233802
EST:     TTGATTGCATTGTTGTTGGTCCTGGCCTTGGAAGGGACCCCTTTCTTCTG                         GAATGTGTGAGTAATATCATGAGGCACGCACGACAGGCTAATATTCCAACT
genomic: TTGATTGCATTGTTGTTGGTCCTGGCCTTGGAAGGGACCCCTTTCTTCTGgttagtttgc ... ttatttgtagGAATGTGTGAGTAATATCATGAGGCACGCACGACAGGCTAATATTCCAACT
EST: gi|71766336|gb|DR964273.1|DR964273
EST:     TGATTGCATTGTTGTTGGTTCTGGCCCTTGGAAGGGACCCCTTTCTTCTG                         GAATGTGTGAGTAATATCATGAGGCACGCACGACAGGCTAATATTCCAACT
genomic: TGATTGCATTGTTGTTGGTCCTGG-CCTTGGAAGGGACCCCTTTCTTCTGgttagtttgc ... ttatttgtagGAATGTGTGAGTAATATCATGAGGCACGCACGACAGGCTAATATTCCAACT
EST: gi|76011914|gb|DT939084.1|DT939084
EST:     TGGCCTTGGAAGGGACCCCTCTCTTCTG                         GAATGTGTGAGTAATATCATGAGGCACGCACGACAGGCTAATATTCCAACT
genomic: TGGCCTTGGAAGGGACCCCTTTCTTCTGgttagtttgc ... ttatttgtagGAATGTGTGAGTAATATCATGAGGCACGCACGACAGGCTAATATTCCAACT
EST: gi|76020591|gb|DT947761.1|DT947761
EST:     GCCTGGGAAGGGGACCCCTTTTTTCTG                         GAATGGGGGAGTAATATCATGAGGCACGCACGGCAGGCTAATATTCCAACT
genomic: GCCTTGGAA-GGGACCCCTTTCTTCTGgttagtttgc ... ttatttgtagGAATGTGTGAGTAATATCATGAGGCACGCACGACAGGCTAATATTCCAACT
EST: gi|78122651|gb|DV541035.1|DV541035
EST:     TGATTGCATTGTTGTTGGCCCTGGCCTT-GAAGGGGACCCCTTTCTTCTG                         GAGTGTGTGAGTAATATCATGAGGCACGCACGACGGGCTAATATTCCAACT
genomic: TGATTGCATTGTTGTTGGTCCTGGCCTTGGAA-GGGACCCCTTTCTTCTGgttagtttgc ... ttatttgtagGAATGTGTGAGTAATATCATGAGGCACGCACGACAGGCTAATATTCCAACT
EST: gi|60400210|gb|DN233017.1|DN233017
EST:     TTGATTGCATTGTTGTTGGTCCTGGCCTTGGAAGGGACCCCTTTCTTCTG                         GAATGTGTGAGTAATATCATGAGGCACGCACGACAGGCTAATATTCCAACT
genomic: TTGATTGCATTGTTGTTGGTCCTGGCCTTGGAAGGGACCCCTTTCTTCTGgttagtttgc ... ttatttgtagGAATGTGTGAGTAATATCATGAGGCACGCACGACAGGCTAATATTCCAACT
EST: gi|78122650|gb|DV541034.1|DV541034
EST:     TTGATTGCATTGTTGTTGGTCCTGGCCTTGGAAGGGACCCCTTTCTTCTG                         GAATGTGTGAGTAATATCATGAGGCACGCACGACAGGCTAATATTCCAACT
genomic: TTGATTGCATTGTTGTTGGTCCTGGCCTTGGAAGGGACCCCTTTCTTCTGgttagtttgc ... ttatttgtagGAATGTGTGAGTAATATCATGAGGCACGCACGACAGGCTAATATTCCAACT

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), 48 (downstream exon)
Score: 287

ATCTGTTTCTTCTAAGATTCTTACGGAAGTTGCAAAGTGGATGGAGCGCTTTGATTGCATTGTTGTTGGTCCTGGCCTTGGAAGGGACCCCTTTCTTCTGgttagtttgc ... ttatttgtagGAATGTGTGAGTAATATCATGAGGCACGCACGACAGGCTAATATTCCAACTGTTGTGGATGGG


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 88

ATCTGTTTCTTCTAAGATTCTTACGGAAGTTGCAAAGTGGATGGAGCGCTTTGATTGCATTGTTGTTGGTCCTGGCCTTGGAAGGGACCCCTTTCTTCTGgttagtttgc ... ttatttgtagGAATGTGTGAGTAATATCATGAGGCACGCACGACAGGCTAATATTCCAACTGTTGTGGATGGG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 116

ATCTGTTTCTTCTAAGATTCTTACGGAAGTTGCAAAGTGGATGGAGCGCTTTGATTGCATTGTTGTTGGTCCTGGCCTTGGAAGGGACCCCTTTCTTCTGgttagtttgc ... ttatttgtagGAATGTGTGAGTAATATCATGAGGCACGCACGACAGGCTAATATTCCAACTGTTGTGGATGGG


Block sizes: 46 (upstream exon), 46 (downstream exon)
Score: 98

ATCTGTTTCTTCTAAGATTCTTACGGAAGTTGCAAAGTGGATGGAGCGCTTTGATTGCATTGTTGTTGGTCCTGGCCTTGGAAGGGACCCCTTTCTTCTGgttagtttgc ... ttatttgtagGAATGTGTGAGTAATATCATGAGGCACGCACGACAGGCTAATATTCCAACTGTTGTGGATGGG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gaagtaatatcaggatccatacttctaatatctcctcaacttatcttatttgtagGAATGTGTGAGTAATATCATGAGGCACGCACGACAGGCTAATATTCCAACTGTTGTGGATGGG
                      ttctaat  putative branch site (score: 98)
 cttatctt  putative PPT
 aacttatcttattt  TA-rich tract