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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...acagtgcatttttttactaatgaaatattgcacttcatttgcttgataatagattattctgatggtactttctaattggctatcggtatcgtttctgcagGATGTGAAAAACAGAATGTTCATTCTGTTCTACTTCAGGAAAAAG

Basic information

species Zea mays
transcript GRMZM5G876003_T03
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G876003_T03 (Zea mays), 3'ss of exon 7
lower sequence: LOC_Os02g38060.2 (Oryza sativa), 3'ss of exon 6
---acagtgcatttttttactaatgaaatattgcacttcatttgcttgataatagattattctgatggtactttctaa-ttggctatcggtatcgtttctgcagGATGTGAAAAACAGAATGTTCATTCTGTTCTACTTCAGGAAAAAG
   | |    | || ||   || ||| | |   |  |||   ||   || || |||  | | | ||  |  || |||| ||||| || ||| || |||||| |||||| |||||||| |||||||||||||||| | ||| ||||||||
gtgatatgaaaattgttctgtattgacacaagactgttc---tgtgcgaaaagagaacagtgtcatcatgtttcctaaattggcaattggt-tcctttctgtagGATGCGAAAAACAAAATGTTCATTCTGTTCCATTTCCGGAAAAAG
















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|60395258|gb|DN228127.1|DN228127
EST:     AAAAGTTTTCTAAAGCCATTATCCAGCTTGGCTTTTCGCTTGTTTCAAAG                         GATGTGAAAAACAGAATGTTCATTCTGTTCTACTTCAGGNNNNNN
genomic: AAAAGTTTTCTAAAGCCATTATCCAGCTTGGCTTTTCGCTTGTTTCAAAGgtttgtatgt ... gtttctgcagGATGTGAAAAACAGAATGTTCATTCTGTTCTACTTCAGGAAAAAG
EST: gi|78093364|gb|DV521738.1|DV521738
EST:     AAAAGTTTTCTAAAGCCATTATCCAGCTTGGCTTTTCGCTTGTTTCAAAG                         GATGTGAAAAACAGAATGTTCATTCTGTTCTACTTCAGGNNNNNN
genomic: AAAAGTTTTCTAAAGCCATTATCCAGCTTGGCTTTTCGCTTGTTTCAAAGgtttgtatgt ... gtttctgcagGATGTGAAAAACAGAATGTTCATTCTGTTCTACTTCAGGAAAAAG
EST: gi|78074349|gb|DV502783.1|DV502783
EST:     AAAAGTTTTCTAAAGCCATTATCCAGCTTGGCTTTTCGCTTGTTTCAAAG                         GATGTGAAAAACAGAATGTTCATTCTGTTCTACTTCAGGNNNNNN
genomic: AAAAGTTTTCTAAAGCCATTATCCAGCTTGGCTTTTCGCTTGTTTCAAAGgtttgtatgt ... gtttctgcagGATGTGAAAAACAGAATGTTCATTCTGTTCTACTTCAGGAAAAAG
EST: gi|148948105|gb|EC893614.2|EC893614
EST:     AAAAGTTTTCTAAAGCCATTATCCAGCTTGGCTTTTCGCTTGTTTCAAAG                         GATGTGAAAAACAGAATGTTCATTCTGTTCTACTTCAGGNNNNNN
genomic: AAAAGTTTTCTAAAGCCATTATCCAGCTTGGCTTTTCGCTTGTTTCAAAGgtttgtatgt ... gtttctgcagGATGTGAAAAACAGAATGTTCATTCTGTTCTACTTCAGGAAAAAG
EST: gi|74240434|gb|DT648348.1|DT648348
EST:     AAAAGTTTTCTAAAGCCATTATCCAGCTTGGCTTTTCGCTTGTTTCAAAG                         GATGTGAAAAACAGAATGTTCATTCTGTTCTACTTCAGGNNNNNN
genomic: AAAAGTTTTCTAAAGCCATTATCCAGCTTGGCTTTTCGCTTGTTTCAAAGgtttgtatgt ... gtttctgcagGATGTGAAAAACAGAATGTTCATTCTGTTCTACTTCAGGAAAAAG
EST: gi|74235314|gb|DT643228.1|DT643228
EST:     AAAAGTTTTCTAAAGCCATTATCCAGCTTGGCTTTTCGCTTGTTTCAAAG                         GATGTGAAAAACAGAATGTTCATTCTGTTTTACTTCAGGNNNNNN
genomic: AAAAGTTTTCTAAAGCCATTATCCAGCTTGGCTTTTCGCTTGTTTCAAAGgtttgtatgt ... gtttctgcagGATGTGAAAAACAGAATGTTCATTCTGTTCTACTTCAGGAAAAAG
EST: gi|78093365|gb|DV521739.1|DV521739
EST:     AAAAGTTTTCTAAAGCCATTATCCAGCTTGGCTTTTCGCTTGTTTCAAAG                         GATGTGAAAAACAGAATGTTCATTCTGTTCTACTTCAGGNNNNNN
genomic: AAAAGTTTTCTAAAGCCATTATCCAGCTTGGCTTTTCGCTTGTTTCAAAGgtttgtatgt ... gtttctgcagGATGTGAAAAACAGAATGTTCATTCTGTTCTACTTCAGGAAAAAG
EST: gi|76923219|gb|DV169381.1|DV169381
EST:     AAAAGTTTTCTAAAGCCATTATCCAGCTTGGCTTTTCGCTTGTTTCAAAG                         GATGTGAAAAACAGAATGTTCATTCTGTTTTACTTCAGGNNNNNN
genomic: AAAAGTTTTCTAAAGCCATTATCCAGCTTGGCTTTTCGCTTGTTTCAAAGgtttgtatgt ... gtttctgcagGATGTGAAAAACAGAATGTTCATTCTGTTCTACTTCAGGAAAAAG

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: 46 (upstream exon), 46 (downstream exon)
Score: 44

TGCTGAAGTGCGAAGTAGGCTAGACCCGAGCAACGGAGGTGCTGATCCTGAAAAGTTTTCTAAAGCCATTATCCAGCTTGGCTTTTCGCTTGTTTCAAAGgtttgtatgt ... gtttctgcagGATGTGAAAAACAGAATGTTCATTCTGTTCTACTTCAGGAAAAAG


Block sizes: 47 (upstream exon), 46 (downstream exon)
Score: 31

TGCTGAAGTGCGAAGTAGGCTAGACCCGAGCAACGGAGGTGCTGATCCTGAAAAGTTTTCTAAAGCCATTATCCAGCTTGGCTTTTCGCTTGTTTCAAAGgtttgtatgt ... gtttctgcagGATGTGAAAAACAGAATGTTCATTCTGTTCTACTTCAGGAAAAAG


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 52

TGCTGAAGTGCGAAGTAGGCTAGACCCGAGCAACGGAGGTGCTGATCCTGAAAAGTTTTCTAAAGCCATTATCCAGCTTGGCTTTTCGCTTGTTTCAAAGgtttgtatgt ... gtttctgcagGATGTGAAAAACAGAATGTTCATTCTGTTCTACTTCAGGAAAAAG


Block sizes: 47 (upstream exon), 46 (downstream exon)
Score: 69

TGCTGAAGTGCGAAGTAGGCTAGACCCGAGCAACGGAGGTGCTGATCCTGAAAAGTTTTCTAAAGCCATTATCCAGCTTGGCTTTTCGCTTGTTTCAAAGgtttgtatgt ... gtttctgcagGATGTGAAAAACAGAATGTTCATTCTGTTCTACTTCAGGAAAAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ataatagattattctgatggtactttctaattggctatcggtatcgtttctgcagGATGTGAAAAACAGAATGTTCATTCTGTTCTACTTCAGGAAAAAG
                        ttctaat  putative branch site (score: 69)
                                           tcgtttct  putative PPT
                       tttctaatt  TA-rich tract