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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtattaactacctagctctgccactcccatctgcgtacaatagttttatatgctgtgttatttgcattttttagACGATATTGGGGCATTGCCAAGGAGAGGACTACACTAGTCCTGCAAACGCTCTGTGTGCTCAGGCTCTGGACACTTTCAACAAT

Basic information

species Zea mays
transcript GRMZM2G471269_T04
intron # 7
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|14203015|gb|BG836692.1|BG836692
EST:     ATATCAGATCAATTGTATGAG                         ACGATATT-GGGAATTGCCAAGGAGAGGACTACACTAGTCCTGCAAACGCT
genomic: ATATCAGATCAATTGTATGAGgtattaacta ... cattttttagACGATATTGGGGCATTGCCAAGGAGAGGACTACACTAGTCCTGCAAACGCT
EST: gi|148966524|gb|EE017546.2|EE017546
EST:     GAGTGCCCTACGCTCATGGAGTCGGTATCATATCAGATCAATTGTATGAG                         ACGATATTGGGGCATTGCCAAGGAGAGGACTACACTAGTCCTGCAAACGCT
genomic: GAGTGCCCTACGCTCATGGAGTCGGTATCATATCAGATCAATTGTATGAGgtattaacta ... cattttttagACGATATTGGGGCATTGCCAAGGAGAGGACTACACTAGTCCTGCAAACGCT
EST: gi|67026269|gb|CO455018.1|CO455018
EST:     GAGTGCCCTACGCTCATGGAGTCGGTATCATATCAGATCAATTGTATGAG                         ACGATATTGGGGCATTGCCAAGGAGAGGACTACACTAGTCCTGCAAACGCT
genomic: GAGTGCCCTACGCTCATGGAGTCGGTATCATATCAGATCAATTGTATGAGgtattaacta ... cattttttagACGATATTGGGGCATTGCCAAGGAGAGGACTACACTAGTCCTGCAAACGCT

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), 48 (downstream exon)
Score: 40

CTATCTGGTGGGTAACCCAATCACGGGCGAAAGTATAGATTTCACTTCCAGAGTGCCCTACGCTCATGGAGTCGGTATCATATCAGATCAATTGTATGAGgtattaacta ... cattttttagACGATATTGGGGCATTGCCAAGGAGAGGACTACACTAGTCCTGCAAACGCTCTGTGTGCTCAGGCTCTGGACACTTTCAACAAT


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 189

CTATCTGGTGGGTAACCCAATCACGGGCGAAAGTATAGATTTCACTTCCAGAGTGCCCTACGCTCATGGAGTCGGTATCATATCAGATCAATTGTATGAGgtattaacta ... cattttttagACGATATTGGGGCATTGCCAAGGAGAGGACTACACTAGTCCTGCAAACGCTCTGTGTGCTCAGGCTCTGGACACTTTCAACAAT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 280

CTATCTGGTGGGTAACCCAATCACGGGCGAAAGTATAGATTTCACTTCCAGAGTGCCCTACGCTCATGGAGTCGGTATCATATCAGATCAATTGTATGAGgtattaacta ... cattttttagACGATATTGGGGCATTGCCAAGGAGAGGACTACACTAGTCCTGCAAACGCTCTGTGTGCTCAGGCTCTGGACACTTTCAACAAT


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 80

CTATCTGGTGGGTAACCCAATCACGGGCGAAAGTATAGATTTCACTTCCAGAGTGCCCTACGCTCATGGAGTCGGTATCATATCAGATCAATTGTATGAGgtattaacta ... cattttttagACGATATTGGGGCATTGCCAAGGAGAGGACTACACTAGTCCTGCAAACGCTCTGTGTGCTCAGGCTCTGGACACTTTCAACAAT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gccactcccatctgcgtacaatagttttatatgctgtgttatttgcattttttagACGATATTGGGGCATTGCCAAGGAGAGGACTACACTAGTCCTGCAAACGCTCTGTGTGCTCAGGCTCTGGACACTTTCAACAAT
                                             catttttt  CT-rich tract
                tacaatagttttatat  TA-rich tract