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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAAAGGATACAGCTAGAGACTGCTCGGTTATACAAGCAAGCTGGTGTAAACCCTTTAGCAGgtttcttgaatttttccgtcctaaaccatactgactatttattttgtgcttcattcccgaataggaatcctttcgtgtgatatttgttttttttctgatatagtactccctgctatgcaataccgtgcttttatgacagtacaatcatgacctcatactttatctgacag

Basic information

species Zea mays
transcript GRMZM5G839422_T01
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G839422_T01 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os01g05800.1 (Oryza sativa), 5'ss of exon 4
GAAAGGATACAGCTAGAGACTGCTCGGTTATACAAGCAAGCTGGTGTAAACCCTTTAGCAGgtttcttgaatttttccgtcctaaaccatactgactatttattttgtgcttcattcccgaataggaatcctttcgtgtgatatttgttttttttctgat-atagtactccctgctatgcaataccgtgcttttatgacagtacaatcatgacctcatactttatctgacag
|||||||||||||| ||||||||||||||||||||||||||||| || |||||| | ||||||  |||  | || ||| | ||  | | || | |||  ||  |   ||  |  ||||   || | |    ||| || |||  |||||| ||| |  | | ||  || |                                                               
GAAAGGATACAGCTTGAGACTGCTCGGTTATACAAGCAAGCTGGAGTCAACCCTCTGGCAGgtcgctt--acttctccattctttagcctattaact--ttgatagttgaattgttcc---attgcatcttttttgtatga-gtttgttatttattagttgatcatatt---------------------------------------------------------------
















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|148969314|gb|EE020088.2|EE020088
EST:     GCTAGAGACTGCTCGGTTATACAAGCAAGCTGGTGTAAACCCTTTAGCAG                         GATGTTTTCCAACGTTAGCAACAATTCCTGTATGGATTGGTCTTTACCAGG
genomic: GCTAGAGACTGCTCGGTTATACAAGCAAGCTGGTGTAAACCCTTTAGCAGgtttcttgaa ... tatctgacagGATGTTTTCCAACGTTAGCAACAATTCCTGTATGGATTGGTCTTTACCAGG
EST: gi|32841389|gb|CD981070.1|CD981070
EST:     GCTAGAGACTGCTCGGTTATACAAGC-AGCTGGTGTAAA-CCTTTAGCAG                         GATGTTTTCCAACGTTAGCAACAATTCCTGTATGGATTGGTCTTTACCAGG
genomic: GCTAGAGACTGCTCGGTTATACAAGCAAGCTGGTGTAAACCCTTTAGCAGgtttcttgaa ... tatctgacagGATGTTTTCCAACGTTAGCAACAATTCCTGTATGGATTGGTCTTTACCAGG
EST: gi|71418332|gb|DR804406.1|DR804406
EST:     GCTAGAGACTGCTCGGTTATACAAGCAAGCTGGTGTAAACCCTTTAGCAG                         GATGTTTTCCAACGTTAGCAACAATTCCTGTATGGATAGGTCTTTACC
genomic: GCTAGAGACTGCTCGGTTATACAAGCAAGCTGGTGTAAACCCTTTAGCAGgtttcttgaa ... tatctgacagGATGTTTTCCAACGTTAGCAACAATTCCTGTATGGATTGGTCTTTACC
EST: gi|149096236|gb|EE181940.2|EE181940
EST:     GCTAGAGACTGCTCGGTTATACAAGCAAGCTGGTGTAAACCCTTTAGCAG                         GATGTTTTCCAACGTTAGCAACAATTCCTGTATGGATTGGTCTTTACCAGG
genomic: GCTAGAGACTGCTCGGTTATACAAGCAAGCTGGTGTAAACCCTTTAGCAGgtttcttgaa ... tatctgacagGATGTTTTCCAACGTTAGCAACAATTCCTGTATGGATTGGTCTTTACCAGG
EST: gi|149102538|gb|EE287895.2|EE287895
EST:     GCTAGAGACTGCTCGGTTATACAAGCAAGCTGGTGTAAACCCTTTAGCAG                         GATGTTTTCCAACGTTAGCAACAATTCCTGTATGGATTGGTCTTTACCAGG
genomic: GCTAGAGACTGCTCGGTTATACAAGCAAGCTGGTGTAAACCCTTTAGCAGgtttcttgaa ... tatctgacagGATGTTTTCCAACGTTAGCAACAATTCCTGTATGGATTGGTCTTTACCAGG
EST: gi|148965120|gb|EE015934.2|EE015934
EST:     GCTAGAGACTGCTCGGTTATACAAGCAAGCTGGTGTAAACCCTTTAGCAG                         GATGTTTTTCCA-CGTTAGCAACAATTCCTGTAT
genomic: GCTAGAGACTGCTCGGTTATACAAGCAAGCTGGTGTAAACCCTTTAGCAGgtttcttgaa ... tatctgacagGATGTTTT-CCAACGTTAGCAACAATTCCTGTAT
EST: gi|149073189|gb|EE161473.2|EE161473
EST:     GCTAGAGACTGCTCGGTTATACAAGCAAGCTGGTGTAAACCCTTTAGCAG                         GATGTTTTCCAACGTTAGCAACAATTCCTGTATGGATTGGTCTTTACCAGG
genomic: GCTAGAGACTGCTCGGTTATACAAGCAAGCTGGTGTAAACCCTTTAGCAGgtttcttgaa ... tatctgacagGATGTTTTCCAACGTTAGCAACAATTCCTGTATGGATTGGTCTTTACCAGG
EST: gi|32840360|gb|CD980041.1|CD980041
EST:     GCTAGAGACTGCTCGGTTATACAAGCAAGCTGGTGTAAACCCTTTAGCAG                         GATGTTTTCCAACGTTAGCAACAATTCCTGTATGGATTGGTCTTTACCAGG
genomic: GCTAGAGACTGCTCGGTTATACAAGCAAGCTGGTGTAAACCCTTTAGCAGgtttcttgaa ... tatctgacagGATGTTTTCCAACGTTAGCAACAATTCCTGTATGGATTGGTCTTTACCAGG
EST: gi|32839884|gb|CD979565.1|CD979565
EST:     GCTAGAGACTGCTCGGTTATACAAGCAAGCTGGTGTAAACCCTTTAGCAG                         GATGTTTTCCAACGTTAGCAACAATTCCTGTATGGATTGGTCTTTACCAGG
genomic: GCTAGAGACTGCTCGGTTATACAAGCAAGCTGGTGTAAACCCTTTAGCAGgtttcttgaa ... tatctgacagGATGTTTTCCAACGTTAGCAACAATTCCTGTATGGATTGGTCTTTACCAGG
EST: gi|149110452|gb|EE190424.2|EE190424
EST:     GCTAGAGACTGCTCGGTTATACAAGCAAGCTGGTGTAAACCTTTTAGCAG                         GATGTTTTCCAACGTTAGCAACAATTCCTGTATGGATTGGTCTTTACCAGG
genomic: GCTAGAGACTGCTCGGTTATACAAGCAAGCTGGTGTAAACCCTTTAGCAGgtttcttgaa ... tatctgacagGATGTTTTCCAACGTTAGCAACAATTCCTGTATGGATTGGTCTTTACCAGG
EST: gi|149098971|gb|EE184984.2|EE184984
EST:     GCTAGAGACTGCTCGGTTATACAAGCAAGCTGGTGTAAACCCTTTAGCAG                         GATGTTTTCCAACGTTAGCAACAATTCCTGTATGGATTGGTCTTTACCAGG
genomic: GCTAGAGACTGCTCGGTTATACAAGCAAGCTGGTGTAAACCCTTTAGCAGgtttcttgaa ... tatctgacagGATGTTTTCCAACGTTAGCAACAATTCCTGTATGGATTGGTCTTTACCAGG
EST: gi|32840666|gb|CD980347.1|CD980347
EST:     GCTAGAGACTGCTCGGTTATACAAGCAAGCTGGTGTAAACCCTTTAGCAG                         GATGTTTTCCAACGTTAGCAACAATTCCTGTATGGATTGGTCTTTACCAGG
genomic: GCTAGAGACTGCTCGGTTATACAAGCAAGCTGGTGTAAACCCTTTAGCAGgtttcttgaa ... tatctgacagGATGTTTTCCAACGTTAGCAACAATTCCTGTATGGATTGGTCTTTACCAGG

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: 47 (upstream exon), 44 (downstream exon)
Score: 82

GAAAGGATACAGCTAGAGACTGCTCGGTTATACAAGCAAGCTGGTGTAAACCCTTTAGCAGgtttcttgaa ... tatctgacagGATGTTTTCCAACGTTAGCAACAATTCCTGTATGGATTGGTCTTTACCAGGCCCTTTCAAATGTAGCAAATGAG


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 212

GAAAGGATACAGCTAGAGACTGCTCGGTTATACAAGCAAGCTGGTGTAAACCCTTTAGCAGgtttcttgaa ... tatctgacagGATGTTTTCCAACGTTAGCAACAATTCCTGTATGGATTGGTCTTTACCAGGCCCTTTCAAATGTAGCAAATGAG


Block sizes: 48 (upstream exon), 47 (downstream exon)
Score: 60

GAAAGGATACAGCTAGAGACTGCTCGGTTATACAAGCAAGCTGGTGTAAACCCTTTAGCAGgtttcttgaa ... tatctgacagGATGTTTTCCAACGTTAGCAACAATTCCTGTATGGATTGGTCTTTACCAGGCCCTTTCAAATGTAGCAAATGAG


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 100

GAAAGGATACAGCTAGAGACTGCTCGGTTATACAAGCAAGCTGGTGTAAACCCTTTAGCAGgtttcttgaa ... tatctgacagGATGTTTTCCAACGTTAGCAACAATTCCTGTATGGATTGGTCTTTACCAGGCCCTTTCAAATGTAGCAAATGAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAAAGGATACAGCTAGAGACTGCTCGGTTATACAAGCAAGCTGGTGTAAACCCTTTAGCAGgtttcttgaatttttccgtcctaaaccatactgactatttattttgtgcttcattcccgaataggaatcctttcgtgtgatatttgttttttttctgatatagtactccctgctatgcaataccgtgcttttatgacagtacaatcatgacctcatactttatctgacag

- - - - - - - - - - - - - - - -  AAGCAA
- - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - CAAGCT
- - - - - - - - - - - - - - - - - -  AAGCTG