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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgcctcgactttagttaatatcaggagcactttggtattctagagagctgctagaaacgcagccaactcactgtgtcacctcttcatgctgcagTTCGTCGACGTGGGGACGATGGTGTCGCCAACAGTGTACGCGAGGCGGAGCTTGTGCCACCTCATGTGCGACCAGCCTGACGCCGCCCTCCGTGACGCCA

Basic information

species Zea mays
transcript GRMZM2G127050_T01
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G127050_T01 (Zea mays), 3'ss of exon 8
lower sequence: LOC_Os03g04050.1 (Oryza sativa), 3'ss of exon 8
gtgcctcgactttagttaatatcaggagcactttggtattctagagagctgctagaaacgcagccaactcactgtgtcacctcttcat---gctgcagTTCGTCGACGTGGGGACGATGGTGTCGCCAACAGTGTACGCGAGGCGGAGCTTGTGCCACCTCATGTGCGACCAGCCTGACGCCGCCCTCCGTGACGCCA
  |     || | |   |||||||||| |  | |||| ||  | | |  |  |   |  | ||  | ||||||   | ||||| || |   | ||||||| || || ||||| || ||||| || ||||| || ||||| || |||||||| |||||||||||||  ||||| ||||| || |||||||| || || |
--gttggaacgtca---aatatcaggaaccttctggtgttacaaaaaaatcgttagattgaagttatctcactcctttacctcctctttgggttgcagTTTGTTGATGTGGGAACAATGGTATCACCAACGGTATACGCTAGACGGAGCTTATGCCACCTCATGTCTGACCAACCTGATGCTGCCCTCCGGGATGCAA
















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|76013660|gb|DT940830.1|DT940830
EST:     TTGCTTTCCGTGACAAAGATTTCAAGGCAGCCATAGACTGCTACACGCAG                         TTCGTCGACGTGGGGACGATGGTGTCGCCAACAGTGTACGCGAGGCGGAGC
genomic: TTGCTTTCCGTGACAAAGATTTCAAGGCAGCCATAGACTGCTACACGCAGgtgcctcgac ... catgctgcagTTCGTCGACGTGGGGACGATGGTGTCGCCAACAGTGTACGCGAGGCGGAGC
EST: gi|110518366|gb|EE022953.1|EE022953
EST:     ACAAAGATTTCAAGGCAGCCATAGACTGCTACACGCAG                         TTCGTCGACGTGGGGACGATGGTGTCGCCAACAGTGTACGCGAGGCGGAGC
genomic: ACAAAGATTTCAAGGCAGCCATAGACTGCTACACGCAGgtgcctcgac ... catgctgcagTTCGTCGACGTGGGGACGATGGTGTCGCCAACAGTGTACGCGAGGCGGAGC
EST: gi|71310550|gb|DR791570.1|DR791570
EST:     TTGCTTTCCGTGACAAAGATTTCAAGGCAGCCATAGACTGCTACACGCAG                         TTCGTCGATGTGGGGACGATGGTGTCGCCAACAGTGTACGCGAGGCGGAGC
genomic: TTGCTTTCCGTGACAAAGATTTCAAGGCAGCCATAGACTGCTACACGCAGgtgcctcgac ... catgctgcagTTCGTCGACGTGGGGACGATGGTGTCGCCAACAGTGTACGCGAGGCGGAGC
EST: gi|32919403|gb|CF024215.1|CF024215
EST:     TTGCTTTCCGCGACAAAGATTTCAAGGCAGCCATAGACTGCTACACGCAG                         TTCGTCGATGTGGGGACGATGGTGTCGCCAACAGTGTACGCGAGGCGGAGC
genomic: TTGCTTTCCGTGACAAAGATTTCAAGGCAGCCATAGACTGCTACACGCAGgtgcctcgac ... catgctgcagTTCGTCGACGTGGGGACGATGGTGTCGCCAACAGTGTACGCGAGGCGGAGC
EST: gi|148931336|gb|EC874214.2|EC874214
EST:     TTGCTTTCCGTGACAAAGATTTCAAGGCAGCCATAGACTGCTACACGCAG                         TTCGTCGACGTGGGGACGATGGTGTCGCCAACAGTGTACGCGAGGCGGAGC
genomic: TTGCTTTCCGTGACAAAGATTTCAAGGCAGCCATAGACTGCTACACGCAGgtgcctcgac ... catgctgcagTTCGTCGACGTGGGGACGATGGTGTCGCCAACAGTGTACGCGAGGCGGAGC
EST: gi|149059663|gb|EE157007.2|EE157007
EST:     TTGCTTTCCGTGACAAAGATTTCAAGGCAGCCATAGACTGCTACACGCAG                         TTCGTCGACGTGGGGAGGATGGTGTCGCCAACAGTGTACGCGAGGCGGAGC
genomic: TTGCTTTCCGTGACAAAGATTTCAAGGCAGCCATAGACTGCTACACGCAGgtgcctcgac ... catgctgcagTTCGTCGACGTGGGGACGATGGTGTCGCCAACAGTGTACGCGAGGCGGAGC
EST: gi|32919355|gb|CF024167.1|CF024167
EST:     TTGCTTTCCGCGACAAAGATTTCAAGGCAGCCATAGACTGCTACACGCAG                         TTCGTCGATGTGGGGACGATGGTGTCGCCAACAGTGTACGCGAGGCGGAGC
genomic: TTGCTTTCCGTGACAAAGATTTCAAGGCAGCCATAGACTGCTACACGCAGgtgcctcgac ... catgctgcagTTCGTCGACGTGGGGACGATGGTGTCGCCAACAGTGTACGCGAGGCGGAGC
EST: gi|76015318|gb|DT942488.1|DT942488
EST:     TTGCTTTCCGTGACAAAGATTTCAAGGCAGCCATAGACTGCTACACGCAG                         TTCGTCGACGTGGGGACGATGGTGTCGCCAACAGTGTACGCGAGGCGGAGC
genomic: TTGCTTTCCGTGACAAAGATTTCAAGGCAGCCATAGACTGCTACACGCAGgtgcctcgac ... catgctgcagTTCGTCGACGTGGGGACGATGGTGTCGCCAACAGTGTACGCGAGGCGGAGC

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: 43 (upstream exon), 45 (downstream exon)
Score: 32

ATGGACGCAGCAGATGAGGGACATGCTGGAAGCTAGGAAACGTGGGGACTTTGCTTTCCGTGACAAAGATTTCAAGGCAGCCATAGACTGCTACACGCAGgtgcctcgac ... catgctgcagTTCGTCGACGTGGGGACGATGGTGTCGCCAACAGTGTACGCGAGGCGGAGCTTGTGCCACCTCATGTGCGACCAGCCTGACGCCGCCCTCCGTGACGCCA


Block sizes: 43 (upstream exon), 46 (downstream exon)
Score: 73

ATGGACGCAGCAGATGAGGGACATGCTGGAAGCTAGGAAACGTGGGGACTTTGCTTTCCGTGACAAAGATTTCAAGGCAGCCATAGACTGCTACACGCAGgtgcctcgac ... catgctgcagTTCGTCGACGTGGGGACGATGGTGTCGCCAACAGTGTACGCGAGGCGGAGCTTGTGCCACCTCATGTGCGACCAGCCTGACGCCGCCCTCCGTGACGCCA


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 81

ATGGACGCAGCAGATGAGGGACATGCTGGAAGCTAGGAAACGTGGGGACTTTGCTTTCCGTGACAAAGATTTCAAGGCAGCCATAGACTGCTACACGCAGgtgcctcgac ... catgctgcagTTCGTCGACGTGGGGACGATGGTGTCGCCAACAGTGTACGCGAGGCGGAGCTTGTGCCACCTCATGTGCGACCAGCCTGACGCCGCCCTCCGTGACGCCA


Block sizes: 46 (upstream exon), 47 (downstream exon)
Score: 40

ATGGACGCAGCAGATGAGGGACATGCTGGAAGCTAGGAAACGTGGGGACTTTGCTTTCCGTGACAAAGATTTCAAGGCAGCCATAGACTGCTACACGCAGgtgcctcgac ... catgctgcagTTCGTCGACGTGGGGACGATGGTGTCGCCAACAGTGTACGCGAGGCGGAGCTTGTGCCACCTCATGTGCGACCAGCCTGACGCCGCCCTCCGTGACGCCA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctagagagctgctagaaacgcagccaactcactgtgtcacctcttcatgctgcagTTCGTCGACGTGGGGACGATGGTGTCGCCAACAGTGTACGCGAGGCGGAGCTTGTGCCACCTCATGTGCGACCAGCCTGACGCCGCCCTCCGTGACGCCA
                         aactcac  putative branch site (score: 40)
                                    tcacctcttc  putative PPT