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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttattattacatattattttgtggttctttatctattgtccaacttaagtgtaagccagtgttcatgttttgttactttgctcagGGTCACATTTTGATGGTGATCCGGGGCTTGGAGTTGGTGGAAATTCAGTAGCTTCAAGGCTGAGGCTACACCCAGAGAAAGACAAGGACTTCACTCCATT

Basic information

species Zea mays
transcript GRMZM2G163658_T01
intron # 11
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|32857873|gb|CD997554.1|CD997554
EST:     CCATACCAATGATGTTGATAATTTCAGACCCAACAAGAGGACCAGAACAG                         GGTCACATTTTGATGGTGATCCGGGGCTTGGAGTTGGTGGAAATTCAGTAG
genomic: CCATACCAATGATGTTGATAATTTCAGACCCAACAAGAGGACCAGAACAGgttattatta ... ctttgctcagGGTCACATTTTGATGGTGATCCGGGGCTTGGAGTTGGTGGAAATTCAGTAG
EST: gi|60355947|gb|DN222920.1|DN222920
EST:     CCATACCAATGATGTTGATAATTTCAGACCCAACAAGAGGACCAGAACAG                         GGTCACATTTTGATGGTGATCCGGGGCTTGGAGTTGGTGGAAATTCAGTAG
genomic: CCATACCAATGATGTTGATAATTTCAGACCCAACAAGAGGACCAGAACAGgttattatta ... ctttgctcagGGTCACATTTTGATGGTGATCCGGGGCTTGGAGTTGGTGGAAATTCAGTAG
EST: gi|32942785|gb|CF047604.1|CF047604
EST:     CCATACCAATGATGTTGATAATTTCAGACCCAACAAGAGGACCAGAACAG                         GGTCACATTTTGATGGTGATCCGGGGCTTGGAGTTGGTGGAAATTCAGTAG
genomic: CCATACCAATGATGTTGATAATTTCAGACCCAACAAGAGGACCAGAACAGgttattatta ... ctttgctcagGGTCACATTTTGATGGTGATCCGGGGCTTGGAGTTGGTGGAAATTCAGTAG
EST: gi|60339901|gb|DN206874.1|DN206874
EST:     CCATACCAATGATGTTGATAATTTCAGACCCAACAAGAGGACCAGAACAG                         GGTCACATTTTGATGGTGATCCGGGGCTTGGAGTTGGTGGAAATTCAGTAG
genomic: CCATACCAATGATGTTGATAATTTCAGACCCAACAAGAGGACCAGAACAGgttattatta ... ctttgctcagGGTCACATTTTGATGGTGATCCGGGGCTTGGAGTTGGTGGAAATTCAGTAG
EST: gi|32857853|gb|CD997534.1|CD997534
EST:     CCATACCAATGATGGTGATAATTTCAAACCCAACAAGAGGACCAGAACAG                         GGTCACATTTTGATGGTGATCCGGGGCTTGGAGTTGGTGGAAATTCAGTAG
genomic: CCATACCAATGATGTTGATAATTTCAGACCCAACAAGAGGACCAGAACAGgttattatta ... ctttgctcagGGTCACATTTTGATGGTGATCCGGGGCTTGGAGTTGGTGGAAATTCAGTAG
EST: gi|32942784|gb|CF047603.1|CF047603
EST:     CCATACCAATGATGTTGATAATTTCAGACCCAACAAGAGGACCAGAACAG                         GGTCACATTTTGATGGTGATCCGGGGCTTGGAGTTGGTGGAAATTCAGTAG
genomic: CCATACCAATGATGTTGATAATTTCAGACCCAACAAGAGGACCAGAACAGgttattatta ... ctttgctcagGGTCACATTTTGATGGTGATCCGGGGCTTGGAGTTGGTGGAAATTCAGTAG

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: 48 (upstream exon), 47 (downstream exon)
Score: 65

CTCCATACCAATGATGTTGATAATTTCAGACCCAACAAGAGGACCAGAACAGgttattatta ... ctttgctcagGGTCACATTTTGATGGTGATCCGGGGCTTGGAGTTGGTGGAAATTCAGTAGCTTCAAGGCTGAGGCTACACCCAGAGAAAGACAAGGACTTCACTCCATT


Block sizes: 45 (upstream exon), 49 (downstream exon)
Score: 24

CTCCATACCAATGATGTTGATAATTTCAGACCCAACAAGAGGACCAGAACAGgttattatta ... ctttgctcagGGTCACATTTTGATGGTGATCCGGGGCTTGGAGTTGGTGGAAATTCAGTAGCTTCAAGGCTGAGGCTACACCCAGAGAAAGACAAGGACTTCACTCCATT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 55

CTCCATACCAATGATGTTGATAATTTCAGACCCAACAAGAGGACCAGAACAGgttattatta ... ctttgctcagGGTCACATTTTGATGGTGATCCGGGGCTTGGAGTTGGTGGAAATTCAGTAGCTTCAAGGCTGAGGCTACACCCAGAGAAAGACAAGGACTTCACTCCATT


Block sizes: 46 (upstream exon), 46 (downstream exon)
Score: 11

CTCCATACCAATGATGTTGATAATTTCAGACCCAACAAGAGGACCAGAACAGgttattatta ... ctttgctcagGGTCACATTTTGATGGTGATCCGGGGCTTGGAGTTGGTGGAAATTCAGTAGCTTCAAGGCTGAGGCTACACCCAGAGAAAGACAAGGACTTCACTCCATT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atctattgtccaacttaagtgtaagccagtgttcatgttttgttactttgctcagGGTCACATTTTGATGGTGATCCGGGGCTTGGAGTTGGTGGAAATTCAGTAGCTTCAAGGCTGAGGCTACACCCAGAGAAAGACAAGGACTTCACTCCATT
                                             ctttgctc  CT-rich tract
                                     ttttgtta  TA-rich tract