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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtactacatactcctaccaaactttcgtacacctcaggaaacacggagctcgagtgaagaaagacattgacactacgctaccgtcgaaattgcagGCGTTCAAGAAGGCGAGGAGCCTGGGGCTGGGAGACCAGGATTTTTCGGCGGTCTATGAGGTTGTGAAGGGCGCGGGTGGTTCTGGATCTGGCCAGCCGT

Basic information

species Zea mays
transcript GRMZM2G153984_T01
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|60397979|gb|DN230795.1|DN230795
EST:     TGGGAGATGAGAACGCCGTCGCCATGCCCGTCTCAGCAGCTGCCAATGAG                         GCGTTCAAGAAGGCGAGGAGCCTGGGGCTGGGAGACCAGGATTTTTCGGCG
genomic: TGGGAGATGAGAACGCCGTCGCCATGCCCGTCTCAGCAGCTGCCAATGAGgtactacata ... gaaattgcagGCGTTCAAGAAGGCGAGGAGCCTGGGGCTGGGAGACCAGGATTTTTCGGCG
EST: gi|13558888|gb|BG550243.1|BG550243
EST:     TGGGAGATGAGAACGCCGTCGCCATGCCCGTCTCAGCAGCTGCCAATGAG                         GCGTTCAAGAAGGCGAGGAGCCTGGGGCTGGGAGACCAGGATTTTTCGGCG
genomic: TGGGAGATGAGAACGCCGTCGCCATGCCCGTCTCAGCAGCTGCCAATGAGgtactacata ... gaaattgcagGCGTTCAAGAAGGCGAGGAGCCTGGGGCTGGGAGACCAGGATTTTTCGGCG
EST: gi|148969717|gb|EE020589.2|EE020589
EST:     TGGGAGATGAGAACGCCGTCGCCATGCCCGTCTCAGCAGCTGCCAATGAG                         GCGTTCAAGAAGGCGAGGAGCCTGGGGCTGGGAGACCAGGATTTTTCGGCG
genomic: TGGGAGATGAGAACGCCGTCGCCATGCCCGTCTCAGCAGCTGCCAATGAGgtactacata ... gaaattgcagGCGTTCAAGAAGGCGAGGAGCCTGGGGCTGGGAGACCAGGATTTTTCGGCG
EST: gi|161407569|gb|DW042386.1|DW042386
EST:     TGGGAGATGAGAACGCCGTCGCCATGCCCGTCTCAGCAGCTGCCAATGAG                         GCGTTCAAGAAGGCGAGGAGCCTGGGGCTGGGAGACCAGGATTTTTCGGCG
genomic: TGGGAGATGAGAACGCCGTCGCCATGCCCGTCTCAGCAGCTGCCAATGAGgtactacata ... gaaattgcagGCGTTCAAGAAGGCGAGGAGCCTGGGGCTGGGAGACCAGGATTTTTCGGCG
EST: gi|149112754|gb|EE295577.2|EE295577
EST:     TGGGAGATGAGAACGCCGTCGCCATGCCCGTCTCAGCAGCTGCCAATGAG                         GCGTTCAAGAAGGCGAGGAGCCTGGGGCTGGGAGACCAGGATTTTTCGGCG
genomic: TGGGAGATGAGAACGCCGTCGCCATGCCCGTCTCAGCAGCTGCCAATGAGgtactacata ... gaaattgcagGCGTTCAAGAAGGCGAGGAGCCTGGGGCTGGGAGACCAGGATTTTTCGGCG
EST: gi|110515150|gb|EE019739.1|EE019739
EST:     TGGGAGATGAGAACGCCGTCGCCATGCCCGTCTCAGCAGCTGCCAATGAG                         GCGTTCAAGAAGGCGAGGAGCCTGGGGCTGGGAGACCAGGATTTTTCGGCG
genomic: TGGGAGATGAGAACGCCGTCGCCATGCCCGTCTCAGCAGCTGCCAATGAGgtactacata ... gaaattgcagGCGTTCAAGAAGGCGAGGAGCCTGGGGCTGGGAGACCAGGATTTTTCGGCG
EST: gi|78085473|gb|DV513866.1|DV513866
EST:     TGGGAGATGAGAACGCCGTCGCCATGCCCGTCTCAGCAGCTGCCAATGAG                         GCGTTCAAGAAGGCGAGGAGCCTGGGGCTGGGAGACCAGGATTTTTCGGCG
genomic: TGGGAGATGAGAACGCCGTCGCCATGCCCGTCTCAGCAGCTGCCAATGAGgtactacata ... gaaattgcagGCGTTCAAGAAGGCGAGGAGCCTGGGGCTGGGAGACCAGGATTTTTCGGCG
EST: gi|78092309|gb|DV520683.1|DV520683
EST:     TGGGAGATGAGAACGCCGTCGCCATGCCCGTCTCAGCAGCTGCCAATGAG                         GCGTTCAAGAAGGCGAGGAGCCTGGGGCTGGGAGACCAGGATTTTTCGGCG
genomic: TGGGAGATGAGAACGCCGTCGCCATGCCCGTCTCAGCAGCTGCCAATGAGgtactacata ... gaaattgcagGCGTTCAAGAAGGCGAGGAGCCTGGGGCTGGGAGACCAGGATTTTTCGGCG
EST: gi|89754425|gb|DY685206.1|DY685206
EST:     TGGGAGATGAGAACGCCGTCGCCATGCCCGTCTCAGCAGCTGCCAATGAG                         GCGTTCAAGAAGGCGAGGAGCCTGGGGCTGGGAGACCAGGATTTTTCGGCG
genomic: TGGGAGATGAGAACGCCGTCGCCATGCCCGTCTCAGCAGCTGCCAATGAGgtactacata ... gaaattgcagGCGTTCAAGAAGGCGAGGAGCCTGGGGCTGGGAGACCAGGATTTTTCGGCG
EST: gi|60396988|gb|DN229807.1|DN229807
EST:     TGGGAGATGAGAACGCCGTCGCCATGCCCGTCTCAGCAGCTGCCAATGAG                         GCGTTCAAGAAGGCGAGGAGCCTGGGGCTGGGAGACCAGGATTTTTCGGCG
genomic: TGGGAGATGAGAACGCCGTCGCCATGCCCGTCTCAGCAGCTGCCAATGAGgtactacata ... gaaattgcagGCGTTCAAGAAGGCGAGGAGCCTGGGGCTGGGAGACCAGGATTTTTCGGCG
EST: gi|29130084|gb|CB380788.1|CB380788
EST:     TGGGAGATGAGAACGCCGTCGCCATGCCCGTCTCAGCAGCTGCCAATGAG                         GCGTTCAAGAAGGCGAGGAGCCTGGGGCTGGGAGACCAGGATTTTTCGGCG
genomic: TGGGAGATGAGAACGCCGTCGCCATGCCCGTCTCAGCAGCTGCCAATGAGgtactacata ... gaaattgcagGCGTTCAAGAAGGCGAGGAGCCTGGGGCTGGGAGACCAGGATTTTTCGGCG
EST: gi|20512918|gb|BQ280104.1|BQ280104
EST:     TGGGAGATGAGAACGCCGTCGCCATGCCCGTCTCAGCAGCTGCCAATGAG                         GCGTTCAAGAAGGCGAGGAGCCTGGGGCTGGGAGACCAGGATTTTTCGGCG
genomic: TGGGAGATGAGAACGCCGTCGCCATGCCCGTCTCAGCAGCTGCCAATGAGgtactacata ... gaaattgcagGCGTTCAAGAAGGCGAGGAGCCTGGGGCTGGGAGACCAGGATTTTTCGGCG
EST: gi|78078378|gb|DV506792.1|DV506792
EST:     TGGGAGATGAGAACGCCGTCGCCATGCCCGTCTCAGCAGCTGCCAATGAG                         GCGTTCAAGAAGGCGAGGAGCCTGGGGCTGGGAGACCAGGATTTTTCGGCG
genomic: TGGGAGATGAGAACGCCGTCGCCATGCCCGTCTCAGCAGCTGCCAATGAGgtactacata ... gaaattgcagGCGTTCAAGAAGGCGAGGAGCCTGGGGCTGGGAGACCAGGATTTTTCGGCG
EST: gi|149081804|gb|EE170962.2|EE170962
EST:     TGGGAGATGAGAACGCCGTCGCCATGCCCGTCTCAGCAGCTGCCAATGAG                         GCGTTCAAGAAGGCGAGGAGCCTGGGGCTGGGAGACCAGGATTTTTCGGCG
genomic: TGGGAGATGAGAACGCCGTCGCCATGCCCGTCTCAGCAGCTGCCAATGAGgtactacata ... gaaattgcagGCGTTCAAGAAGGCGAGGAGCCTGGGGCTGGGAGACCAGGATTTTTCGGCG
EST: gi|101388577|gb|EB816275.1|EB816275
EST:     TGGGAGATGAGAACGCCGTCGCCATGCCCGTCTCAGCAGCTGCCAATGAG                         GCGTTCAAGAAGGCGAGGAGCCTGGGGCTGGGAGACCAGGATTTTTCGGCG
genomic: TGGGAGATGAGAACGCCGTCGCCATGCCCGTCTCAGCAGCTGCCAATGAGgtactacata ... gaaattgcagGCGTTCAAGAAGGCGAGGAGCCTGGGGCTGGGAGACCAGGATTTTTCGGCG
EST: gi|60336934|gb|DN203907.1|DN203907
EST:     TGGGAGATGAGAACGCCGTCGCCATGCCCGTCTCAGCAGCTGCCAATGAG                         GCGTTCAAGAAGGCGAGGAGCCTGGGGCTGGGAGACCAGGATTTTTCGGCG
genomic: TGGGAGATGAGAACGCCGTCGCCATGCCCGTCTCAGCAGCTGCCAATGAGgtactacata ... gaaattgcagGCGTTCAAGAAGGCGAGGAGCCTGGGGCTGGGAGACCAGGATTTTTCGGCG
EST: gi|60341165|gb|DN208138.1|DN208138
EST:     TGGGAGATGAGAACGCCGTCGCCATGCCCGTCTCAGCAGCTGCCAATGAG                         GCGTTCAAGAAGGCGAGGAGCCTGGGGCTGGGAGACCAGGATTTTTCGGCG
genomic: TGGGAGATGAGAACGCCGTCGCCATGCCCGTCTCAGCAGCTGCCAATGAGgtactacata ... gaaattgcagGCGTTCAAGAAGGCGAGGAGCCTGGGGCTGGGAGACCAGGATTTTTCGGCG
EST: gi|71328007|gb|DR800650.1|DR800650
EST:     TGGGAGATGAGAACGCCGTCGCCATGCCCGTCTCAGCAGCTGCCAATGAG                         GCGTTCAAGAAGGCGAGGAGCCTGGGGCTGGGAGACCAGGATTTTTCGGCG
genomic: TGGGAGATGAGAACGCCGTCGCCATGCCCGTCTCAGCAGCTGCCAATGAGgtactacata ... gaaattgcagGCGTTCAAGAAGGCGAGGAGCCTGGGGCTGGGAGACCAGGATTTTTCGGCG
EST: gi|78092308|gb|DV520682.1|DV520682
EST:     TGGGAGATGAGAACGCCGTCGCCATGCCCGTTTCAGCAGCTGCCAATGAG                         GCGTTCAAGAAGGCGAGGAGCCTGGGGCTGGGAGACCAGGATTTTTCGGCG
genomic: TGGGAGATGAGAACGCCGTCGCCATGCCCGTCTCAGCAGCTGCCAATGAGgtactacata ... gaaattgcagGCGTTCAAGAAGGCGAGGAGCCTGGGGCTGGGAGACCAGGATTTTTCGGCG
EST: gi|76917423|gb|DV166839.1|DV166839
EST:     TGGGAGATGAGAACGCCGTCGCCATGCCCGTCTCAGCAGCTGCCAATGAG                         GCGTTCAAGAAGGCGAGGAGCCTGGGGCTGGGAGACCAGGATTTTTTGGCG
genomic: TGGGAGATGAGAACGCCGTCGCCATGCCCGTCTCAGCAGCTGCCAATGAGgtactacata ... gaaattgcagGCGTTCAAGAAGGCGAGGAGCCTGGGGCTGGGAGACCAGGATTTTTCGGCG
EST: gi|32909381|gb|CF014193.1|CF014193
EST:     TGGGAGATGAGAACGCCGTCGCCATGCCCGTCTCAGCAGCTGCCAATGAG                         GCGTTCAAGAAGGCGAGGAGCCTGGGGCTGGGAGACCAGGATTTTTCGGCG
genomic: TGGGAGATGAGAACGCCGTCGCCATGCCCGTCTCAGCAGCTGCCAATGAGgtactacata ... gaaattgcagGCGTTCAAGAAGGCGAGGAGCCTGGGGCTGGGAGACCAGGATTTTTCGGCG
EST: gi|60355928|gb|DN222901.1|DN222901
EST:     TGGGAGATGAGAACGCCGTCGCCATGCCCGTCTCAGCAGCTGCCAATGAG                         GCGTTCAAGAAGGCGAGGAGCCTGGGGCTGGGAGACCAGGATTTTTCGGCG
genomic: TGGGAGATGAGAACGCCGTCGCCATGCCCGTCTCAGCAGCTGCCAATGAGgtactacata ... gaaattgcagGCGTTCAAGAAGGCGAGGAGCCTGGGGCTGGGAGACCAGGATTTTTCGGCG
EST: gi|78113466|gb|DV531858.1|DV531858
EST:     TGGGAGATGAGAACGCCGTCGCCATGCCCGTCTCAGCAGCTGCCAATGAG                         GCGTTCAAGAAGGCGAGGAGCCTGGGGCTGGGAGACCAGGATTTTTCGGCG
genomic: TGGGAGATGAGAACGCCGTCGCCATGCCCGTCTCAGCAGCTGCCAATGAGgtactacata ... gaaattgcagGCGTTCAAGAAGGCGAGGAGCCTGGGGCTGGGAGACCAGGATTTTTCGGCG
EST: gi|37375731|gb|CF624323.1|CF624323
EST:     TGGGAGATGAGAACGCCGTCGCCATGCCCGTCTCAGCAGCTGCCAATGAG                         GCGTTCAAGAAGGCGAGGAGCCTGGGGCTGGGAGACCAGGATTTTTCGGCG
genomic: TGGGAGATGAGAACGCCGTCGCCATGCCCGTCTCAGCAGCTGCCAATGAGgtactacata ... gaaattgcagGCGTTCAAGAAGGCGAGGAGCCTGGGGCTGGGAGACCAGGATTTTTCGGCG
EST: gi|40333895|gb|CK367965.1|CK367965
EST:     TGGGAGATGAGAACGCCGTCGCCATGCCCGTCTCAGCAGCTGCCAATGAG                         GCGTTCAAGAAGGCGAGGAGCCTGGGGCTGGGAGACCAGGATTTTTCGGCG
genomic: TGGGAGATGAGAACGCCGTCGCCATGCCCGTCTCAGCAGCTGCCAATGAGgtactacata ... gaaattgcagGCGTTCAAGAAGGCGAGGAGCCTGGGGCTGGGAGACCAGGATTTTTCGGCG
EST: gi|89764407|gb|DY691229.1|DY691229
EST:     TGGGAGATGAGAACGCCGTCGCCATGCCCGTCTCAGCAGCTGCCAATGAG                         GCGTTCAAGAAGGCGAGGAGCCTGGGGCTGGGAGACCAGGATTTTTCGGCG
genomic: TGGGAGATGAGAACGCCGTCGCCATGCCCGTCTCAGCAGCTGCCAATGAGgtactacata ... gaaattgcagGCGTTCAAGAAGGCGAGGAGCCTGGGGCTGGGAGACCAGGATTTTTCGGCG
EST: gi|110944178|gb|EE164335.1|EE164335
EST:     TGGGAGATGAGAACGCCGTCGCCATGCCCGTTTCAGCAGCTGCCAATGAG                         GCGTTCAAGAAGGCGAGGAGCCTGGGGCTGGGAGACCAGGATTTTTCGGCG
genomic: TGGGAGATGAGAACGCCGTCGCCATGCCCGTCTCAGCAGCTGCCAATGAGgtactacata ... gaaattgcagGCGTTCAAGAAGGCGAGGAGCCTGGGGCTGGGAGACCAGGATTTTTCGGCG
EST: gi|78125845|gb|DV544229.1|DV544229
EST:     TGGGAGATGAGAACGCCGTCGCCATGCCCGTCTCAGCAGCTGCCAATGAG                         GCGTTCAAGAAGGCGAGGAGCCTGGGGCTGGGAGACCAGGATTTTTCGGCG
genomic: TGGGAGATGAGAACGCCGTCGCCATGCCCGTCTCAGCAGCTGCCAATGAGgtactacata ... gaaattgcagGCGTTCAAGAAGGCGAGGAGCCTGGGGCTGGGAGACCAGGATTTTTCGGCG
EST: gi|78113465|gb|DV531857.1|DV531857
EST:     TGGGAGATGAGAACGCCGTCGCCATGCCCGTCTCAGCAGCTGCCAATGAG                         GCGTTCAAGAAGGCGAGGAGCCTGGGGCTGGGAGACCAGGATTTTTCGGCG
genomic: TGGGAGATGAGAACGCCGTCGCCATGCCCGTCTCAGCAGCTGCCAATGAGgtactacata ... gaaattgcagGCGTTCAAGAAGGCGAGGAGCCTGGGGCTGGGAGACCAGGATTTTTCGGCG

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: 151

TGCGTTTCCCCTGAAGCATCAGCAGAAGGACATGAGGTTAGCGCTTGCTCTGGGAGATGAGAACGCCGTCGCCATGCCCGTCTCAGCAGCTGCCAATGAGgtactacata ... gaaattgcagGCGTTCAAGAAGGCGAGGAGCCTGGGGCTGGGAGACCAGGATTTTTCGGCGGTCTATGAGGTTGTGAAGGGCGCGGGTGGTTCTGGATCTGGCCAGCCGT


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 139

TGCGTTTCCCCTGAAGCATCAGCAGAAGGACATGAGGTTAGCGCTTGCTCTGGGAGATGAGAACGCCGTCGCCATGCCCGTCTCAGCAGCTGCCAATGAGgtactacata ... gaaattgcagGCGTTCAAGAAGGCGAGGAGCCTGGGGCTGGGAGACCAGGATTTTTCGGCGGTCTATGAGGTTGTGAAGGGCGCGGGTGGTTCTGGATCTGGCCAGCCGT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 102

TGCGTTTCCCCTGAAGCATCAGCAGAAGGACATGAGGTTAGCGCTTGCTCTGGGAGATGAGAACGCCGTCGCCATGCCCGTCTCAGCAGCTGCCAATGAGgtactacata ... gaaattgcagGCGTTCAAGAAGGCGAGGAGCCTGGGGCTGGGAGACCAGGATTTTTCGGCGGTCTATGAGGTTGTGAAGGGCGCGGGTGGTTCTGGATCTGGCCAGCCGT


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

TGCGTTTCCCCTGAAGCATCAGCAGAAGGACATGAGGTTAGCGCTTGCTCTGGGAGATGAGAACGCCGTCGCCATGCCCGTCTCAGCAGCTGCCAATGAGgtactacata ... gaaattgcagGCGTTCAAGAAGGCGAGGAGCCTGGGGCTGGGAGACCAGGATTTTTCGGCGGTCTATGAGGTTGTGAAGGGCGCGGGTGGTTCTGGATCTGGCCAGCCGT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acacggagctcgagtgaagaaagacattgacactacgctaccgtcgaaattgcagGCGTTCAAGAAGGCGAGGAGCCTGGGGCTGGGAGACCAGGATTTTTCGGCGGTCTATGAGGTTGTGAAGGGCGCGGGTGGTTCTGGATCTGGCCAGCCGT
                        cattgac  putative branch site (score: 79)
                                              aaatt  TA-rich tract