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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaattgcatattttcccgtcataatcttgctctttagtaccttctgttttgcgtgctgtgctaatttttgtttcaatcagGCCATTTCATGATGCAGCAAGTTCCGAACAGCATGCCCATGCCCGAGCAACAACCTAATAGCATGCTTGTAAC

Basic information

species Zea mays
transcript GRMZM2G043056_T01
intron # 12
splice site 3'
intron type U2

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|60358393|gb|DN225366.1|DN225366
EST:     TGTTCCTCCACAGCAGCCTCACCAGCTCTATCAATCAGCCGCACATCCAA                         GCCATTTCATGATGCAGCAAGTTCCGAACAGCATGCCCATGCCCGAGCAAC
genomic: TGTTCCTCCACAGCAGCCTCACCAGCTCTATCAATCAGCCGCACATCCAAgtaattgcat ... tttcaatcagGCCATTTCATGATGCAGCAAGTTCCGAACAGCATGCCCATGCCCGAGCAAC
EST: gi|60357017|gb|DN223990.1|DN223990
EST:     TGTTCCTTCACAGCAGCCTCACCAGCTCTATCAATCAGCCGCACATCCAA                         GCCATTTCATAATGCAGCAAGTTCCGAACAGCATGCCCATGCCCGAGCAAC
genomic: TGTTCCTCCACAGCAGCCTCACCAGCTCTATCAATCAGCCGCACATCCAAgtaattgcat ... tttcaatcagGCCATTTCATGATGCAGCAAGTTCCGAACAGCATGCCCATGCCCGAGCAAC
EST: gi|60355844|gb|DN222817.1|DN222817
EST:     TGTTCCTCCACAGCAGCCTCACCAGCTCTATCAATCAGCCGCACATCCAA                         GCCATTTCATGATGCAGCAAGTTCCGAACAGCATGCCCATGCCCGAGCAAC
genomic: TGTTCCTCCACAGCAGCCTCACCAGCTCTATCAATCAGCCGCACATCCAAgtaattgcat ... tttcaatcagGCCATTTCATGATGCAGCAAGTTCCGAACAGCATGCCCATGCCCGAGCAAC
EST: gi|60338909|gb|DN205882.1|DN205882
EST:     TGTTCCTCCACAGCAGCCTCACCAGCTCTATCAATCAGCCGCACATCCAA                         GCCATTTCATGATGCAGCAAGTTCCGAACAGCATGCCCATGCCCGAGCAAC
genomic: TGTTCCTCCACAGCAGCCTCACCAGCTCTATCAATCAGCCGCACATCCAAgtaattgcat ... tttcaatcagGCCATTTCATGATGCAGCAAGTTCCGAACAGCATGCCCATGCCCGAGCAAC
EST: gi|31355485|gb|CD439842.1|CD439842
EST:     TGTTCCTCCACAGCAGCCTCACCAGCTCTATCAATCAGCCGCACATCCAA                         GCCATTTCATGATGCAGCAAGTTCC
genomic: TGTTCCTCCACAGCAGCCTCACCAGCTCTATCAATCAGCCGCACATCCAAgtaattgcat ... tttcaatcagGCCATTTCATGATGCAGCAAGTTCC
EST: gi|78115032|gb|DV533420.1|DV533420
EST:     TGTTCCTCCACAGCAGCCTCACCAGCTCTATCAATCAGCCGCACATCCAA                         GCCATTTCATGATGCAGCAAGTTCCGAACAGCATGCCCATGCCCGAGCAAC
genomic: TGTTCCTCCACAGCAGCCTCACCAGCTCTATCAATCAGCCGCACATCCAAgtaattgcat ... tttcaatcagGCCATTTCATGATGCAGCAAGTTCCGAACAGCATGCCCATGCCCGAGCAAC
EST: gi|211019067|gb|FL469808.1|FL469808
EST:     TGTTCCTCCACAGCAGCCTCACCAGCTCTATCAATCAGCCGCACATCCAA                         GCCATTTCATGATGCAGCAAGTTCCGAACAGCATGCCCATGCCCGAGCAAC
genomic: TGTTCCTCCACAGCAGCCTCACCAGCTCTATCAATCAGCCGCACATCCAAgtaattgcat ... tttcaatcagGCCATTTCATGATGCAGCAAGTTCCGAACAGCATGCCCATGCCCGAGCAAC
EST: gi|31361667|gb|CD446024.1|CD446024
EST:     TGTTCCTCCACAGCAGCCTCACCAGCTCTATCAATCAGCCGCACATCCAA                         GCCATTTCATGATGCAGCAAGTTCCGAACAGCATGCCCATGCCCGAGCAAC
genomic: TGTTCCTCCACAGCAGCCTCACCAGCTCTATCAATCAGCCGCACATCCAAgtaattgcat ... tttcaatcagGCCATTTCATGATGCAGCAAGTTCCGAACAGCATGCCCATGCCCGAGCAAC

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: 187

GTATTAGCAGGCCCAGCTCCCCAAACCTTAATTAGCAACTCTAGTTTTGGTGTTCCTCCACAGCAGCCTCACCAGCTCTATCAATCAGCCGCACATCCAAgtaattgcat ... tttcaatcagGCCATTTCATGATGCAGCAAGTTCCGAACAGCATGCCCATGCCCGAGCAACAACCTAATAGCATGCTTGTAAC


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 89

GTATTAGCAGGCCCAGCTCCCCAAACCTTAATTAGCAACTCTAGTTTTGGTGTTCCTCCACAGCAGCCTCACCAGCTCTATCAATCAGCCGCACATCCAAgtaattgcat ... tttcaatcagGCCATTTCATGATGCAGCAAGTTCCGAACAGCATGCCCATGCCCGAGCAACAACCTAATAGCATGCTTGTAAC


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 52

GTATTAGCAGGCCCAGCTCCCCAAACCTTAATTAGCAACTCTAGTTTTGGTGTTCCTCCACAGCAGCCTCACCAGCTCTATCAATCAGCCGCACATCCAAgtaattgcat ... tttcaatcagGCCATTTCATGATGCAGCAAGTTCCGAACAGCATGCCCATGCCCGAGCAACAACCTAATAGCATGCTTGTAAC


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 78

GTATTAGCAGGCCCAGCTCCCCAAACCTTAATTAGCAACTCTAGTTTTGGTGTTCCTCCACAGCAGCCTCACCAGCTCTATCAATCAGCCGCACATCCAAgtaattgcat ... tttcaatcagGCCATTTCATGATGCAGCAAGTTCCGAACAGCATGCCCATGCCCGAGCAACAACCTAATAGCATGCTTGTAAC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttgctctttagtaccttctgttttgcgtgctgtgctaatttttgtttcaatcagGCCATTTCATGATGCAGCAAGTTCCGAACAGCATGCCCATGCCCGAGCAACAACCTAATAGCATGCTTGTAAC
                                 tgctaat  putative branch site (score: 78)
                                       tttttgtttc  CT-rich tract
                                    taatttttgtttcaat  TA-rich tract