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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacttctcatctttgttcctagcaagcatagttgtacttttgtttctgtttgtgcagttaatgaaattctttggaaaaaaactgcatgtaattgccaacctgagaacatttagtttcttacagcactattcctacttgttcttaagtttacctaatgtactgagtcttctgtcaccctagATGGGACTGCGGCATGTTTATGCTCAAATACATTGACTTCTACAGCAGAGATATGGACCTCATTTTCGGACAG

Basic information

species Zea mays
transcript GRMZM2G088653_T03
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G088653_T01 (Zea mays), 3'ss of exon 7
lower sequence: LOC_Os01g25370.1 (Oryza sativa), 3'ss of exon 7
gtacttctc---atctttgttcctagcaagcatagttgtacttttgtttctgtttgtgcagttaatgaaattctttggaaaaaaactgcatgtaattgccaacctgagaacatt---tagtttcttacag-cac----tattcctacttgttcttaagtttacctaatgtactgagtcttctgtcaccc------tagATGGGACTGCGGCATGTTTATGCTCAAATACATTGACTTCTACAGCAGAGATATGGACCTCATTTTCGGACAG
||| || ||   || ||| || |||| | |  ||   ||  |  |        || | || |    ||| || |||          |  | | |  ||| |  || ||||||||   |||||    |||| ||      ||| |||    |||  || ||| | ||||||||| | |  |  ||  ||       ||| ||||| || |||||||| |||||||||||||| || ||||||||||||||||||| ||| | ||| ||||||
gtatttttctcaatttttttttctagtatgtgtatcagtcttgctaaccaacattatacaatagtagaacttgttttttcc----tttaaaggaggtgcaattctaagaacattatatagttcaccacaggcatatcgcattactatgccttcgaaaatttgcgtaatgtactcattacttggttgccttccatttagGTGGGATTGTGGCATGTTCATGCTCAAATACATAGATTTCTACAGCAGAGATATGGGCCTTACTTTTGGACAG
















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|12971305|gb|BG267416.1|BG267416
EST:     CTTCCTTTGCAGGAGAATGG                         ATGGGACTGCGGCATGTTTATGCTCAAATCCATTGACTTCTACAGCAGAGA
genomic: CTTCCTTTGCAGGAGAATGGgtacttctca ... gtcaccctagATGGGACTGCGGCATGTTTATGCTCAAATACATTGACTTCTACAGCAGAGA
EST: gi|71305240|gb|DR788757.1|DR788757
EST:     CTCTCATGGAAGCAGGAAGGTGTCAAAAACCTTCCTTTGCAGGAGAATGG                         ATGGGACTGCGGCATGTTTATGCTCAAATACATTGACTTCTACAGCAGAGA
genomic: CTCTCATGGAAGCAGGAAGGTGTCAAAAACCTTCCTTTGCAGGAGAATGGgtacttctca ... gtcaccctagATGGGACTGCGGCATGTTTATGCTCAAATACATTGACTTCTACAGCAGAGA
EST: gi|78084564|gb|DV512957.1|DV512957
EST:     CTTTCATGGAAGCAGGAAGGTGTCAAAAACCTTCCTTTGCAGGAGAATGG                         ATGGGAGTGCGGCATGTTTATGCTCAAATACATTGACTTTTACAGCAGAGA
genomic: CTCTCATGGAAGCAGGAAGGTGTCAAAAACCTTCCTTTGCAGGAGAATGGgtacttctca ... gtcaccctagATGGGACTGCGGCATGTTTATGCTCAAATACATTGACTTCTACAGCAGAGA
EST: gi|78118658|gb|DV537042.1|DV537042
EST:     CTCTCATGGAAGCAGGAAGGTGTCAAAAACCTTCCTTTGCAGGAGAATGG                         ATGGGACTGCGGCATGTTTATGCTCAAATACATTGACTTCTACAGCAGAGA
genomic: CTCTCATGGAAGCAGGAAGGTGTCAAAAACCTTCCTTTGCAGGAGAATGGgtacttctca ... gtcaccctagATGGGACTGCGGCATGTTTATGCTCAAATACATTGACTTCTACAGCAGAGA
EST: gi|5439429|gb|AI820350.1|AI820350
EST:     CTCTCATGGAAGCAGGAAGGTGTCAAAAACCTTCCTTTGCAGGAGAATGG                         ATGGGACTGCGGCATGTTTATGCTCAAATACATTGACTTCTACAGCAGAGA
genomic: CTCTCATGGAAGCAGGAAGGTGTCAAAAACCTTCCTTTGCAGGAGAATGGgtacttctca ... gtcaccctagATGGGACTGCGGCATGTTTATGCTCAAATACATTGACTTCTACAGCAGAGA
EST: gi|78025320|gb|DV493707.1|DV493707
EST:     CTCTCATGGAAGCAGGAAGGTGTCAAAAACCTTCCTTTGCAGGAGAATGG                         ATGGGACTGCGGCATGTTTATGCTCAAATACATTGACTTCTACAGCAGAGA
genomic: CTCTCATGGAAGCAGGAAGGTGTCAAAAACCTTCCTTTGCAGGAGAATGGgtacttctca ... gtcaccctagATGGGACTGCGGCATGTTTATGCTCAAATACATTGACTTCTACAGCAGAGA

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: 73

AGTATATTGTGGATGAGGTCAAAGACAAAAGTGGCCAACAGATGGATGTGCTCTCATGGAAGCAGGAAGGTGTCAAAAACCTTCCTTTGCAGGAGAATGGgtacttctca ... gtcaccctagATGGGACTGCGGCATGTTTATGCTCAAATACATTGACTTCTACAGCAGAGATATGGACCTCATTTTCGGACAG


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 25

AGTATATTGTGGATGAGGTCAAAGACAAAAGTGGCCAACAGATGGATGTGCTCTCATGGAAGCAGGAAGGTGTCAAAAACCTTCCTTTGCAGGAGAATGGgtacttctca ... gtcaccctagATGGGACTGCGGCATGTTTATGCTCAAATACATTGACTTCTACAGCAGAGATATGGACCTCATTTTCGGACAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 34

AGTATATTGTGGATGAGGTCAAAGACAAAAGTGGCCAACAGATGGATGTGCTCTCATGGAAGCAGGAAGGTGTCAAAAACCTTCCTTTGCAGGAGAATGGgtacttctca ... gtcaccctagATGGGACTGCGGCATGTTTATGCTCAAATACATTGACTTCTACAGCAGAGATATGGACCTCATTTTCGGACAG


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 45

AGTATATTGTGGATGAGGTCAAAGACAAAAGTGGCCAACAGATGGATGTGCTCTCATGGAAGCAGGAAGGTGTCAAAAACCTTCCTTTGCAGGAGAATGGgtacttctca ... gtcaccctagATGGGACTGCGGCATGTTTATGCTCAAATACATTGACTTCTACAGCAGAGATATGGACCTCATTTTCGGACAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctattcctacttgttcttaagtttacctaatgtactgagtcttctgtcaccctagATGGGACTGCGGCATGTTTATGCTCAAATACATTGACTTCTACAGCAGAGATATGGACCTCATTTTCGGACAG
                        acctaat  putative branch site (score: 45)
                                       tcttctgtcaccct  putative PPT
                ttaagttta  TA-rich tract