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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgtcttgtaacacttgatgagatatttattatacacaccacaaaatagccaaccatttcgttgcagGTACCTTTCCATCTCGTAACGCGCCTGTGGGATACATACCTTGCCGAAGGCGACTATCTGCCAGATTTTCTCGTGTACATATCGGCTAGTTTTTTGCTGA

Basic information

species Zea mays
transcript GRMZM2G142806_T01
intron # 9
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|160481316|gb|EY254259.1|EY254259
EST:     AGTTTCTTCAGTTTGCCTTCCGCTGGTTCAACTGCCTTCTGATACGAGAG                         GTACCTTTCCATCTCGTAACGCGCCTGTGGGATACATACCTTGCCGAAGGC
genomic: AGTTTCTTCAGTTTGCCTTCCGCTGGTTCAACTGCCTTCTGATACGAGAGgtttgtcttg ... ttcgttgcagGTACCTTTCCATCTCGTAACGCGCCTGTGGGATACATACCTTGCCGAAGGC
EST: gi|149073693|gb|EE161998.2|EE161998
EST:     AGTTTCTTCAGTTTGCCTTCCGCTGGTTCAACTGCCTTCTGATACGAGAG                         GTACCTTTCCATCTCGTAACGCGCCTGTGGGATACATACCTTGCCGAAGGC
genomic: AGTTTCTTCAGTTTGCCTTCCGCTGGTTCAACTGCCTTCTGATACGAGAGgtttgtcttg ... ttcgttgcagGTACCTTTCCATCTCGTAACGCGCCTGTGGGATACATACCTTGCCGAAGGC
EST: gi|71426203|gb|DR807253.1|DR807253
EST:     AGTTTCTTCAGTTTGCCTTCCGCTGGTTCAACTGCCTTCTGATACGAGAG                         GTACCTTTCCATCTCGTAACGCGCCTGTGGGATACATACCTTGCCGAAGGC
genomic: AGTTTCTTCAGTTTGCCTTCCGCTGGTTCAACTGCCTTCTGATACGAGAGgtttgtcttg ... ttcgttgcagGTACCTTTCCATCTCGTAACGCGCCTGTGGGATACATACCTTGCCGAAGGC
EST: gi|211467151|gb|FL432006.1|FL432006
EST:     AGTTTCTTCAGTTTGCCTTCCGCTGGTTCAACTGCCTTCTGATACGAGAG                         GTACCTTTCCATCTCGTAACGCGCCTGTGGGATACATACCTTGCCGAAGGC
genomic: AGTTTCTTCAGTTTGCCTTCCGCTGGTTCAACTGCCTTCTGATACGAGAGgtttgtcttg ... ttcgttgcagGTACCTTTCCATCTCGTAACGCGCCTGTGGGATACATACCTTGCCGAAGGC
EST: gi|60355822|gb|DN222795.1|DN222795
EST:     AGTTTCTTCAGTTTGCCTTCCGCTGGTTCAACTGCCTTCTGATACGAGAG                         GTACCTTTCCATCTCGTAACGCGCCTGTGGGATACATACCTTGCCGAAGGC
genomic: AGTTTCTTCAGTTTGCCTTCCGCTGGTTCAACTGCCTTCTGATACGAGAGgtttgtcttg ... ttcgttgcagGTACCTTTCCATCTCGTAACGCGCCTGTGGGATACATACCTTGCCGAAGGC
EST: gi|86468229|gb|DY234599.1|DY234599
EST:     AGTTTCTTCAGTTTGCCTTCCGCTGGTTCAACTGCCTTCTGATACGAGAG                         GTACCTTTCCATCTCGTAACGCGCCTGTGGGATACATACCTTGCCGAAGGC
genomic: AGTTTCTTCAGTTTGCCTTCCGCTGGTTCAACTGCCTTCTGATACGAGAGgtttgtcttg ... ttcgttgcagGTACCTTTCCATCTCGTAACGCGCCTGTGGGATACATACCTTGCCGAAGGC
EST: gi|60394994|gb|DN227863.1|DN227863
EST:     AGTTTCTTCAGTTTGCCTTCCGCTGGTTCAACTGCCTTCTGATACGAGAG                         GTACCTTTCCATCTCGTAACGCGCCTGTGGGATACATACCTTGCCGAAGGC
genomic: AGTTTCTTCAGTTTGCCTTCCGCTGGTTCAACTGCCTTCTGATACGAGAGgtttgtcttg ... ttcgttgcagGTACCTTTCCATCTCGTAACGCGCCTGTGGGATACATACCTTGCCGAAGGC

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: 116

AACCTGTTTCCAAGCACATTGAAGAGCAAGGATTAGAGTTTCTTCAGTTTGCCTTCCGCTGGTTCAACTGCCTTCTGATACGAGAGgtttgtcttg ... ttcgttgcagGTACCTTTCCATCTCGTAACGCGCCTGTGGGATACATACCTTGCCGAAGGCGACTATCTGCCAGATTTTCTCGTGTACATATCGGCTAGTTTTTTGCTGA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 79

AACCTGTTTCCAAGCACATTGAAGAGCAAGGATTAGAGTTTCTTCAGTTTGCCTTCCGCTGGTTCAACTGCCTTCTGATACGAGAGgtttgtcttg ... ttcgttgcagGTACCTTTCCATCTCGTAACGCGCCTGTGGGATACATACCTTGCCGAAGGCGACTATCTGCCAGATTTTCTCGTGTACATATCGGCTAGTTTTTTGCTGA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 84

AACCTGTTTCCAAGCACATTGAAGAGCAAGGATTAGAGTTTCTTCAGTTTGCCTTCCGCTGGTTCAACTGCCTTCTGATACGAGAGgtttgtcttg ... ttcgttgcagGTACCTTTCCATCTCGTAACGCGCCTGTGGGATACATACCTTGCCGAAGGCGACTATCTGCCAGATTTTCTCGTGTACATATCGGCTAGTTTTTTGCTGA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 64

AACCTGTTTCCAAGCACATTGAAGAGCAAGGATTAGAGTTTCTTCAGTTTGCCTTCCGCTGGTTCAACTGCCTTCTGATACGAGAGgtttgtcttg ... ttcgttgcagGTACCTTTCCATCTCGTAACGCGCCTGTGGGATACATACCTTGCCGAAGGCGACTATCTGCCAGATTTTCTCGTGTACATATCGGCTAGTTTTTTGCTGA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acttgatgagatatttattatacacaccacaaaatagccaaccatttcgttgcagGTACCTTTCCATCTCGTAACGCGCCTGTGGGATACATACCTTGCCGAAGGCGACTATCTGCCAGATTTTCTCGTGTACATATCGGCTAGTTTTTTGCTGA
 acttgat  putative branch site (score: 64)
                                         ccatttc  putative PPT
     atgagatatttattat  TA-rich tract