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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatgccgcgattcgatgcagtgtggcgtaggtctagatcgcttgcgtttgagtgtctctagggttggcccattgtgatttctcttgtctggtttatgtgatacagTTGAAGGCTCCAGTTATCGTGGTGGGGTGCAAGCTGGACCTGAGGGACGAACAGCAGGTTAGCCTTGAACAGGTTATGGCGCCCATCATGCAGTCCTTCC

Basic information

species Zea mays
transcript GRMZM2G004459_T02
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G004459_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os03g59590.1 (Oryza sativa), 3'ss of exon 2
gtaatgccgcgattcgatgcagtgtggcgtagg-tctagatcgcttgcgtttgagtgtctctagggttggcccattgtgatttc-tcttgtctg--gtttatgtgatacagTTGAAGGCTCCAGTTATCGTGGTGGGGTGCAAGCTGGACCTGAGGGACGAACAGCAGGTTAGCCTTGAACAGGTTATGGCGCCCATCATGCAGTCCTTCC
                       |||||||||| | | ||||| | |   | | |||  |  | ||  || ||  |||||| || | |||  ||  ||||   |   |||||| ||||| || || || || |||||||| ||||||||||| |||||||| |||||||| |||||||| ||||| |||||||||||||||||| | ||| 
-------------------gttcgtggcgtaggatttggatcggtcgtaat-gggtggtttcatgggcggtccgatgtgatctcgtgttgcttgctgtttgcctatcacagTTAAAGGCACCTGTGATTGTCGTGGGGTGTAAGCTGGACCTTAGGGACGAGCAGCAGGTCAGCCTTGAGCAGGTGATGGCGCCCATCATGCAGACATTCA
















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|211518364|gb|FL160582.1|FL160582
EST:     CACTGGAGCGGCTCAGTTCGTTCTGGCTTCCCGAGCTCCGGCGACTTCAG                         TTGAAGGCTCCAGTTATCGTGGTGGGGTGCAAGCTGGACCTGAGGGACG
genomic: CACTGGAGCGGCTCAGTTCGTTCTGGCTTCCCGAGCTCCGGCGACTTCAGgtaatgccgc ... tgtgatacagTTGAAGGCTCCAGTTATCGTGGTGGGGTGCAAGCTGGACCTGAGGGACG
EST: gi|31361614|gb|CD445971.1|CD445971
EST:     CACTGGAGCGGCTCAGTTCGTTCTGGCTTCCCGAGCTCCGGCGACTTCAG                         TTGAAGGCTCCAGTTATCGTGGTGGGGTGCAAGCTGGACCTGAGGGACGAA
genomic: CACTGGAGCGGCTCAGTTCGTTCTGGCTTCCCGAGCTCCGGCGACTTCAGgtaatgccgc ... tgtgatacagTTGAAGGCTCCAGTTATCGTGGTGGGGTGCAAGCTGGACCTGAGGGACGAA
EST: gi|78084949|gb|DV513342.1|DV513342
EST:     CACTGGAGCGGCTCAGTTCGTTCTGGCTTCCCGAGCTCCGGCGACTTCAG                         TTGAAGGCTCCAGTTATCGTGGTGGGGTGCAAGCTGGACCTGAGGGACGAA
genomic: CACTGGAGCGGCTCAGTTCGTTCTGGCTTCCCGAGCTCCGGCGACTTCAGgtaatgccgc ... tgtgatacagTTGAAGGCTCCAGTTATCGTGGTGGGGTGCAAGCTGGACCTGAGGGACGAA
EST: gi|211289495|gb|FL459844.1|FL459844
EST:     CACTGGAGCGGCTCAGTTCGTTCTGGCTTCCCGAGCTCCGGCGACTTCAG                         TTGAAGGCTCCAGTTATCGTGGTGGGGTGCAAGCTGGACCTGAGGGACGAA
genomic: CACTGGAGCGGCTCAGTTCGTTCTGGCTTCCCGAGCTCCGGCGACTTCAGgtaatgccgc ... tgtgatacagTTGAAGGCTCCAGTTATCGTGGTGGGGTGCAAGCTGGACCTGAGGGACGAA
EST: gi|211153232|gb|FL160597.1|FL160597
EST:     CACTGGAGCGGCTCAGTTCGTTCTGGCTTCCCGAGCTCCGGCGACTTCAG                         TTGAAGGCTCCAGTTATCGTGGTGGGGTGCAAGCTGGACCTGAGGGACGAA
genomic: CACTGGAGCGGCTCAGTTCGTTCTGGCTTCCCGAGCTCCGGCGACTTCAGgtaatgccgc ... tgtgatacagTTGAAGGCTCCAGTTATCGTGGTGGGGTGCAAGCTGGACCTGAGGGACGAA
EST: gi|211289494|gb|FL459843.1|FL459843
EST:     CACTGGAGCGGCTCAGTTCGTTCTGGCTTCCCGAGCTCCGGCGACTTCAG                         TTGAAGGCTCCAGTTATCGTGGTGGGGTGCAAGCTGGACCTGAGGGACGAA
genomic: CACTGGAGCGGCTCAGTTCGTTCTGGCTTCCCGAGCTCCGGCGACTTCAGgtaatgccgc ... tgtgatacagTTGAAGGCTCCAGTTATCGTGGTGGGGTGCAAGCTGGACCTGAGGGACGAA
EST: gi|91053299|gb|EB163717.1|EB163717
EST:     CACTGGAGCGGCTCAGTTCGTTCTGGCTTCCCGAGCTCCGGCGACTTCAG                         TTGAAGGCTCCAGTTATCGTGGTGGGGTGCAAGCTGGACCTGAGGGACGAA
genomic: CACTGGAGCGGCTCAGTTCGTTCTGGCTTCCCGAGCTCCGGCGACTTCAGgtaatgccgc ... tgtgatacagTTGAAGGCTCCAGTTATCGTGGTGGGGTGCAAGCTGGACCTGAGGGACGAA
EST: gi|211153243|gb|FL160608.1|FL160608
EST:     CACTGGAGCGGCTCAGTTCGTTCTGGCTTCCCGAGCTCCGGCGACTTCAG                         TTGAAGGCTCCAGTTATCGTGGTGGGGTGCAAGCTGGACCTGAGGGACGAA
genomic: CACTGGAGCGGCTCAGTTCGTTCTGGCTTCCCGAGCTCCGGCGACTTCAGgtaatgccgc ... tgtgatacagTTGAAGGCTCCAGTTATCGTGGTGGGGTGCAAGCTGGACCTGAGGGACGAA

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: 244

CCAGGCAGCCGATGCGGTCGTGCTCACCTACGCCTGCGACCGGCCCGCCACACTGGAGCGGCTCAGTTCGTTCTGGCTTCCCGAGCTCCGGCGACTTCAGgtaatgccgc ... tgtgatacagTTGAAGGCTCCAGTTATCGTGGTGGGGTGCAAGCTGGACCTGAGGGACGAACAGCAGGTTAGCCTTGAACAGGTTATGGCGCCCATCATGCAGTCCTTCC


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 105

CCAGGCAGCCGATGCGGTCGTGCTCACCTACGCCTGCGACCGGCCCGCCACACTGGAGCGGCTCAGTTCGTTCTGGCTTCCCGAGCTCCGGCGACTTCAGgtaatgccgc ... tgtgatacagTTGAAGGCTCCAGTTATCGTGGTGGGGTGCAAGCTGGACCTGAGGGACGAACAGCAGGTTAGCCTTGAACAGGTTATGGCGCCCATCATGCAGTCCTTCC


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 150

CCAGGCAGCCGATGCGGTCGTGCTCACCTACGCCTGCGACCGGCCCGCCACACTGGAGCGGCTCAGTTCGTTCTGGCTTCCCGAGCTCCGGCGACTTCAGgtaatgccgc ... tgtgatacagTTGAAGGCTCCAGTTATCGTGGTGGGGTGCAAGCTGGACCTGAGGGACGAACAGCAGGTTAGCCTTGAACAGGTTATGGCGCCCATCATGCAGTCCTTCC


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

CCAGGCAGCCGATGCGGTCGTGCTCACCTACGCCTGCGACCGGCCCGCCACACTGGAGCGGCTCAGTTCGTTCTGGCTTCCCGAGCTCCGGCGACTTCAGgtaatgccgc ... tgtgatacagTTGAAGGCTCCAGTTATCGTGGTGGGGTGCAAGCTGGACCTGAGGGACGAACAGCAGGTTAGCCTTGAACAGGTTATGGCGCCCATCATGCAGTCCTTCC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agtgtctctagggttggcccattgtgatttctcttgtctggtttatgtgatacagTTGAAGGCTCCAGTTATCGTGGTGGGGTGCAAGCTGGACCTGAGGGACGAACAGCAGGTTAGCCTTGAACAGGTTATGGCGCCCATCATGCAGTCCTTCC
                                         tttatgt  TA-rich tract