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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtaaatcatgttgcttctctaaatgccatgtttggtagcgatctttcttaaggctccttattttttcactgaaaatggctcttgtaaaaaagagcgtgtggatgagcatcactatctatgccacaatatcaagtcatttttttttgggttatatatttgtacagGCCAACATCTGGCGGAGTGGTTCGTAGCTGTGCTGCTGTGCCTCCTATTCGCGCCAAGAGGGTGCACCGAGAAGACGTGCTAAACCAACGGAGAGTAGAC

Basic information

species Zea mays
transcript GRMZM2G118208_T01
intron # 5
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|211414538|gb|FL447526.1|FL447526
EST:     ACAGGAGCGCAATGGGCAGCCTATGACGCGTTTAAAGTGTTTGTTGGACT                         GCCAACATCTGGCGGAGTGGTTCGTAGCTGTGCTGCTGTGCCTCCTATTCG
genomic: ACAGGAGCGCAATGGGCAGCCTATGACGCGTTTAAAGTGTTTGTTGGACTgtaagtaaat ... atttgtacagGCCAACATCTGGCGGAGTGGTTCGTAGCTGTGCTGCTGTGCCTCCTATTCG
EST: gi|60347958|gb|DN214931.1|DN214931
EST:     ACAGGAGCGCAATGGGCAGCCTATGACGCGTTTAAAGTGTTTGTTGGACT                         GCCAACATCTGGCGGAGTGGTTCGTAGCTGTGCTGCTGTGCCTCCTATTCG
genomic: ACAGGAGCGCAATGGGCAGCCTATGACGCGTTTAAAGTGTTTGTTGGACTgtaagtaaat ... atttgtacagGCCAACATCTGGCGGAGTGGTTCGTAGCTGTGCTGCTGTGCCTCCTATTCG
EST: gi|71759052|gb|DR956989.1|DR956989
EST:     ACAGGAGCGCAATGGGCAGCCTATGACGCGTTTAAAGTGTTTGTTGGACT                         GCCAACATCTGGCGGAGTGGTTCGTAGCTGTGCTGCTGTGCCTCCTATTCG
genomic: ACAGGAGCGCAATGGGCAGCCTATGACGCGTTTAAAGTGTTTGTTGGACTgtaagtaaat ... atttgtacagGCCAACATCTGGCGGAGTGGTTCGTAGCTGTGCTGCTGTGCCTCCTATTCG
EST: gi|88751268|gb|DY535409.1|DY535409
EST:     ACAGGAGCGCAATGGGCAGCCTATGACGCGTTTAAAGTGTTTGTTGGACT                         GCCAACATCTGGCGGAGTGGTTCGTAGCTGTGCTGCTGTGCCTCCTATTCG
genomic: ACAGGAGCGCAATGGGCAGCCTATGACGCGTTTAAAGTGTTTGTTGGACTgtaagtaaat ... atttgtacagGCCAACATCTGGCGGAGTGGTTCGTAGCTGTGCTGCTGTGCCTCCTATTCG
EST: gi|76281616|gb|DV021184.1|DV021184
EST:     ACAGGAGCGCAATGGGCAGCCTATGACGCGTTTAAAGTGTTTGTTGGACT                         GCCAACATCTGGCGGAGTGGTTCGTAGCTGTGCTGCTGTGCCTCCTATTCG
genomic: ACAGGAGCGCAATGGGCAGCCTATGACGCGTTTAAAGTGTTTGTTGGACTgtaagtaaat ... atttgtacagGCCAACATCTGGCGGAGTGGTTCGTAGCTGTGCTGCTGTGCCTCCTATTCG
EST: gi|110947457|gb|EE167614.1|EE167614
EST:     TTGTTGGGACT                         GCCAACATTTGGCGGAGTGGTTTGTAGCTGGGCTGCTGTGCCTCCTATTC
genomic: TTGTT-GGACTgtaagtaaat ... atttgtacagGCCAACATCTGGCGGAGTGGTTCGTAGCTGTGCTGCTGTGCCTCCTATTC
EST: gi|211372685|gb|FL440590.1|FL440590
EST:     ACAGGAGCGCAATGGGCAGCCTATGACGCGTTTAAAGTGTTTGTTGGACT                         GCCAACATCTGGCGGAGTGGTTCGTAGCTGTGCTGCTGTGCCTCCTATTCG
genomic: ACAGGAGCGCAATGGGCAGCCTATGACGCGTTTAAAGTGTTTGTTGGACTgtaagtaaat ... atttgtacagGCCAACATCTGGCGGAGTGGTTCGTAGCTGTGCTGCTGTGCCTCCTATTCG
EST: gi|74245908|gb|DT653822.1|DT653822
EST:     ACAGGAGCGCAATGGGCAGCCTATGACGCGTTTAAAGTGTTTGTTGGACT                         GCCAACATCTGGCGGAGTGGTTCGTAGCTGTGCTGCTGTGCCTCCTATTCG
genomic: ACAGGAGCGCAATGGGCAGCCTATGACGCGTTTAAAGTGTTTGTTGGACTgtaagtaaat ... atttgtacagGCCAACATCTGGCGGAGTGGTTCGTAGCTGTGCTGCTGTGCCTCCTATTCG
EST: gi|71417465|gb|DR804063.1|DR804063
EST:     ACAGGAGCGCAATGGGCAGCCTATGACGCGTTTAAAGTGTTTGTTGGACT                         GCCAACATTTGGCGGAGTGGTTTGTAGCTGTGCTGCTGTGCCTCCTATTCG
genomic: ACAGGAGCGCAATGGGCAGCCTATGACGCGTTTAAAGTGTTTGTTGGACTgtaagtaaat ... atttgtacagGCCAACATCTGGCGGAGTGGTTCGTAGCTGTGCTGCTGTGCCTCCTATTCG
EST: gi|71426615|gb|DR807665.1|DR807665
EST:     ACAGGAGCGCAATGGGCAGCCTATGACGCGTTTAAAGTGTTTGTTGGACT                         GCCAACATCTGGCGGAGTGGTTCGTAGCTGTGCTGCTGTGCCTCCTATTCG
genomic: ACAGGAGCGCAATGGGCAGCCTATGACGCGTTTAAAGTGTTTGTTGGACTgtaagtaaat ... atttgtacagGCCAACATCTGGCGGAGTGGTTCGTAGCTGTGCTGCTGTGCCTCCTATTCG
EST: gi|71767405|gb|DR965342.1|DR965342
EST:     ACAGGAGCGCAATGGGCAGCCTATGACGCGTTTAAAGTGTTTGTTGGACT                         GCCAACATCTGGCGGAGTGGTTCGTAGCTGTGCTGCTGTGCCTCCTATTCG
genomic: ACAGGAGCGCAATGGGCAGCCTATGACGCGTTTAAAGTGTTTGTTGGACTgtaagtaaat ... atttgtacagGCCAACATCTGGCGGAGTGGTTCGTAGCTGTGCTGCTGTGCCTCCTATTCG
EST: gi|211162309|gb|FL458141.1|FL458141
EST:     ACAGGAGCGCAATGGGCAGCCTATGACGCGTTTAAAGTGTTTGTTGGACT                         GCCAACATCTGGCGGAGTGGTTCGTAGCTGTGCTGCTGTGCCTCCTATTCG
genomic: ACAGGAGCGCAATGGGCAGCCTATGACGCGTTTAAAGTGTTTGTTGGACTgtaagtaaat ... atttgtacagGCCAACATCTGGCGGAGTGGTTCGTAGCTGTGCTGCTGTGCCTCCTATTCG
EST: gi|6056814|gb|AW091219.1|AW091219
EST:     CCAGGAGCGCAATGGGCAGCCTATGACGCGTTTAAAGTGTTTGTTGGACT                         GCCAACATCTGGCGGAGTGGTTCGTAGCTGTGCTGCTGTGCCTCCTATTCG
genomic: ACAGGAGCGCAATGGGCAGCCTATGACGCGTTTAAAGTGTTTGTTGGACTgtaagtaaat ... atttgtacagGCCAACATCTGGCGGAGTGGTTCGTAGCTGTGCTGCTGTGCCTCCTATTCG
EST: gi|78024338|gb|DV492725.1|DV492725
EST:     ACAGGAGCGCAATGGGCAGCCTATGACGCGTTTAAAGTGTTTGTTGGACT                         GCCAACATCTGGCGGAGTGGTTCGTAGCTGTGCTGCTGTGCCTCCTATTCG
genomic: ACAGGAGCGCAATGGGCAGCCTATGACGCGTTTAAAGTGTTTGTTGGACTgtaagtaaat ... atttgtacagGCCAACATCTGGCGGAGTGGTTCGTAGCTGTGCTGCTGTGCCTCCTATTCG
EST: gi|60354997|gb|DN221970.1|DN221970
EST:     ACAGGAGCGCAATGGGCAGCCTATGACGCGTTTAAAGTGTTTGTTGGACT                         GCCAACATCTGGCGGAGTGGTTCGTAGCTGTGCTGCTGTGCCTCCTATTCG
genomic: ACAGGAGCGCAATGGGCAGCCTATGACGCGTTTAAAGTGTTTGTTGGACTgtaagtaaat ... atttgtacagGCCAACATCTGGCGGAGTGGTTCGTAGCTGTGCTGCTGTGCCTCCTATTCG
EST: gi|37398965|gb|CF636804.1|CF636804
EST:     ACAGGAGCGCAATGGGCAGCCTATGACGCGTTTAAAGTGTTTGTTGGACT                         GCCAACATCTGGCGGAGTGGTTCGTAGCTCTGCTGCTTTGCCTCCTATTCG
genomic: ACAGGAGCGCAATGGGCAGCCTATGACGCGTTTAAAGTGTTTGTTGGACTgtaagtaaat ... atttgtacagGCCAACATCTGGCGGAGTGGTTCGTAGCTGTGCTGCTGTGCCTCCTATTCG
EST: gi|91874482|gb|EB404439.1|EB404439
EST:     ACAGGAGCGCAATGGGCAGCCTATGACGCGTTTAAAGTGTTTGTTGGACT                         GCCAACATCTGGCGGAGTGGTTGGTAGCTGTGCTGCTGTGCCTCCTATTCG
genomic: ACAGGAGCGCAATGGGCAGCCTATGACGCGTTTAAAGTGTTTGTTGGACTgtaagtaaat ... atttgtacagGCCAACATCTGGCGGAGTGGTTCGTAGCTGTGCTGCTGTGCCTCCTATTCG
EST: gi|78544938|gb|DV622436.1|DV622436
EST:     ACAGGAGCGCAATGGGCAGCCTATGACGCGTTTAAAGTGTTTGTTGGACT                         GCCAACATCTGGCGGAGTGGTTCGTAGCTGTGCTGCTGTGCCTCCTATTCG
genomic: ACAGGAGCGCAATGGGCAGCCTATGACGCGTTTAAAGTGTTTGTTGGACTgtaagtaaat ... atttgtacagGCCAACATCTGGCGGAGTGGTTCGTAGCTGTGCTGCTGTGCCTCCTATTCG
EST: gi|94477099|gb|EB706057.1|EB706057
EST:     ACAGGAGCGCAATGGGCAGCCTATGACGCGTTTAAAGTGTTTGTTGGACT                         GCCAACATCTGGCGGAGTGGTTTGTAGCTGTGCTGCTGTGCCTCCTATTCG
genomic: ACAGGAGCGCAATGGGCAGCCTATGACGCGTTTAAAGTGTTTGTTGGACTgtaagtaaat ... atttgtacagGCCAACATCTGGCGGAGTGGTTCGTAGCTGTGCTGCTGTGCCTCCTATTCG
EST: gi|60354455|gb|DN221428.1|DN221428
EST:     ACAGGAGCGCAATGGGCAGCCTATGACGCGTTTAAAGTGTTTGTTGGACT                         GCCAACATCTGGCGGAGTGGTTCGTAGCTGTGCTGCTGTGCCTCCTATTCG
genomic: ACAGGAGCGCAATGGGCAGCCTATGACGCGTTTAAAGTGTTTGTTGGACTgtaagtaaat ... atttgtacagGCCAACATCTGGCGGAGTGGTTCGTAGCTGTGCTGCTGTGCCTCCTATTCG
EST: gi|5108094|gb|AI739807.1|AI739807
EST:     ACAGGAGCGCAATGGGCAGCCTATGACGCGTTTAAAGTGTTTGTTGGACT                         GCCAACATCTGGCGGAGTGGTTCGTAGCTGTGCTGCTGTGCCTCCTATTCG
genomic: ACAGGAGCGCAATGGGCAGCCTATGACGCGTTTAAAGTGTTTGTTGGACTgtaagtaaat ... atttgtacagGCCAACATCTGGCGGAGTGGTTCGTAGCTGTGCTGCTGTGCCTCCTATTCG
EST: gi|67010579|gb|CO439328.1|CO439328
EST:     ANGAGCGCAATGGGCAGCCTATGACGCGNTTTAA-GTGTTTGT-GGNACT                         GCCCACATCTG-CNGAGTGGTTCGTANCTGTGCTGCTGTGCCTC
genomic: AGGAGCGCAATGGGCAGCCTATGACGCG-TTTAAAGTGTTTGTTGG-ACTgtaagtaaat ... atttgtacagGCCAACATCTGGCGGAGTGGTTCGTAGCTGTGCTGCTGTGCCTC
EST: gi|37381517|gb|CF627652.1|CF627652
EST:     ACAGGAGCGCAATGGGCAGCCTATGACGCGTTTAAAGTGTTTGTTGGACT                         GCCAACATCTGGCGGAGTGGTTGGTAGCTGTGCTGCTGTGCCTCCTATTCG
genomic: ACAGGAGCGCAATGGGCAGCCTATGACGCGTTTAAAGTGTTTGTTGGACTgtaagtaaat ... atttgtacagGCCAACATCTGGCGGAGTGGTTCGTAGCTGTGCTGCTGTGCCTCCTATTCG

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), 44 (downstream exon)
Score: 37

GTCTTTTCACACGCGGCCTTCCTCTTCGTATAATTATGGTTGGTACTCTCACAGGAGCGCAATGGGCAGCCTATGACGCGTTTAAAGTGTTTGTTGGACTgtaagtaaat ... atttgtacagGCCAACATCTGGCGGAGTGGTTCGTAGCTGTGCTGCTGTGCCTCCTATTCGCGCCAAGAGGGTGCACCGAGAAGACGTGCTAAACCAACGGAGAGTAGAC


Block sizes: 49 (upstream exon), 45 (downstream exon)
Score: 37

GTCTTTTCACACGCGGCCTTCCTCTTCGTATAATTATGGTTGGTACTCTCACAGGAGCGCAATGGGCAGCCTATGACGCGTTTAAAGTGTTTGTTGGACTgtaagtaaat ... atttgtacagGCCAACATCTGGCGGAGTGGTTCGTAGCTGTGCTGCTGTGCCTCCTATTCGCGCCAAGAGGGTGCACCGAGAAGACGTGCTAAACCAACGGAGAGTAGAC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 38

GTCTTTTCACACGCGGCCTTCCTCTTCGTATAATTATGGTTGGTACTCTCACAGGAGCGCAATGGGCAGCCTATGACGCGTTTAAAGTGTTTGTTGGACTgtaagtaaat ... atttgtacagGCCAACATCTGGCGGAGTGGTTCGTAGCTGTGCTGCTGTGCCTCCTATTCGCGCCAAGAGGGTGCACCGAGAAGACGTGCTAAACCAACGGAGAGTAGAC


Block sizes: 41 (upstream exon), 33 (downstream exon)
Score: 19

GTCTTTTCACACGCGGCCTTCCTCTTCGTATAATTATGGTTGGTACTCTCACAGGAGCGCAATGGGCAGCCTATGACGCGTTTAAAGTGTTTGTTGGACTgtaagtaaat ... atttgtacagGCCAACATCTGGCGGAGTGGTTCGTAGCTGTGCTGCTGTGCCTCCTATTCGCGCCAAGAGGGTGCACCGAGAAGACGTGCTAAACCAACGGAGAGTAGAC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cactatctatgccacaatatcaagtcatttttttttgggttatatatttgtacagGCCAACATCTGGCGGAGTGGTTCGTAGCTGTGCTGCTGTGCCTCCTATTCGCGCCAAGAGGGTGCACCGAGAAGACGTGCTAAACCAACGGAGAGTAGAC
                          atttttttttgggtta  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtaaatcatgttgcttctctaaatgccatgtttggtagcgatctttcttaaggctccttattttttcactgaaaatggctcttgtaaaaaagagcgtgtggatgagcatcactatctatgccacaatatcaagtcatttttttttgggttatatatttgtacagGCCAACATCTGGCGGAGTGGTTCGTAGCTGTGCTGCTGTGCCTCCTATTCGCGCCAAGAGGGTGCACCGAGAAGACGTGCTAAACCAACGGAGAGTAGAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGG