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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgctgtcgttaaaagtgcattttttttgtcttgccaattgccattggcattttgtgtgcgttgccgctgcacgtgcatgtgcacgtatgcgtgggtgtatgcatggtacggagtcgtggctcgcgtgacattttcattgatcagGTGACATGGGTGGAGCACATGGAGATCGAGGACAGGGTTCCCATCCACCTGCTCTACCGCGACCTCATCCTCAGCGGCGCCGCGTTCGGGGCGCACCGGT

Basic information

species Zea mays
transcript GRMZM2G126646_T01
intron # 6
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|148936205|gb|EC880279.2|EC880279
EST:     GCCTCCCGTCGGGATGCCTCATCGCCGATATGGCCGACGGCTCCTCCAAG                         GTGACATGGGTGGAGCACATGGAGATCGAGGACAGGGTTCCCATCCACCTG
genomic: GCCTCCCGTCGGGATGCCTCATCGCCGATATGGCCGACGGCTCCTCCAAGgtgctgtcgt ... cattgatcagGTGACATGGGTGGAGCACATGGAGATCGAGGACAGGGTTCCCATCCACCTG
EST: gi|148973684|gb|EE024804.2|EE024804
EST:     GCCTCCCGTCGGGATGCCTCATCGCCGATATGGCCGACGGCTCCTCCAAG                         GTGACATGGGTGGAGCACATGGAGATCGAGGACAGGGTTCCCATCCACCTG
genomic: GCCTCCCGTCGGGATGCCTCATCGCCGATATGGCCGACGGCTCCTCCAAGgtgctgtcgt ... cattgatcagGTGACATGGGTGGAGCACATGGAGATCGAGGACAGGGTTCCCATCCACCTG
EST: gi|148973683|gb|EE024803.2|EE024803
EST:     GCCTCCCGTCGGGATGCCTCATCGCCGATATGGCCGACGGCTCCTCCAAG                         GTGACATGGGTGGAGCACATGGAGATCGAGGA
genomic: GCCTCCCGTCGGGATGCCTCATCGCCGATATGGCCGACGGCTCCTCCAAGgtgctgtcgt ... cattgatcagGTGACATGGGTGGAGCACATGGAGATCGAGGA

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: 44 (upstream exon), 48 (downstream exon)
Score: 35

CCTGCAGCAGCACGACGCGAGGTTCGGCGCGCCGCCGTCGCGCTCGTGCCGCCTCCCGTCGGGATGCCTCATCGCCGATATGGCCGACGGCTCCTCCAAGgtgctgtcgt ... cattgatcagGTGACATGGGTGGAGCACATGGAGATCGAGGACAGGGTTCCCATCCACCTGCTCTACCGCGACCTCATCCTCAGCGGCGCCGCGTTCGGGGCGCACCGGT


Block sizes: 21 (upstream exon), 48 (downstream exon)
Score: 3

CCTGCAGCAGCACGACGCGAGGTTCGGCGCGCCGCCGTCGCGCTCGTGCCGCCTCCCGTCGGGATGCCTCATCGCCGATATGGCCGACGGCTCCTCCAAGgtgctgtcgt ... cattgatcagGTGACATGGGTGGAGCACATGGAGATCGAGGACAGGGTTCCCATCCACCTGCTCTACCGCGACCTCATCCTCAGCGGCGCCGCGTTCGGGGCGCACCGGT


Block sizes: 21 (upstream exon), 29 (downstream exon)
Score: 1

CCTGCAGCAGCACGACGCGAGGTTCGGCGCGCCGCCGTCGCGCTCGTGCCGCCTCCCGTCGGGATGCCTCATCGCCGATATGGCCGACGGCTCCTCCAAGgtgctgtcgt ... cattgatcagGTGACATGGGTGGAGCACATGGAGATCGAGGACAGGGTTCCCATCCACCTGCTCTACCGCGACCTCATCCTCAGCGGCGCCGCGTTCGGGGCGCACCGGT


Block sizes: 44 (upstream exon), 44 (downstream exon)
Score: 18

CCTGCAGCAGCACGACGCGAGGTTCGGCGCGCCGCCGTCGCGCTCGTGCCGCCTCCCGTCGGGATGCCTCATCGCCGATATGGCCGACGGCTCCTCCAAGgtgctgtcgt ... cattgatcagGTGACATGGGTGGAGCACATGGAGATCGAGGACAGGGTTCCCATCCACCTGCTCTACCGCGACCTCATCCTCAGCGGCGCCGCGTTCGGGGCGCACCGGT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cgtgggtgtatgcatggtacggagtcgtggctcgcgtgacattttcattgatcagGTGACATGGGTGGAGCACATGGAGATCGAGGACAGGGTTCCCATCCACCTGCTCTACCGCGACCTCATCCTCAGCGGCGCCGCGTTCGGGGCGCACCGGT
                                         ttttcatt  CT-rich tract
                                        attttcatt  TA-rich tract