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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacgaatggcttctgattctttttctatctcgattgtggtttgatacaatatttagaagctatgtctggtttcattcataaatttgatatacactttcatgttgcagTATTGTGCAATGGGTCTTGGCTTAGTCGGATTGGATTTTCGTGGCCTTCTTCCACCGATCTTTGAGAA

Basic information

species Zea mays
transcript GRMZM2G006781_T01
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G006781_T01 (Zea mays), 3'ss of exon 7
lower sequence: LOC_Os12g35290.1 (Oryza sativa), 3'ss of exon 7
gtacgaatggcttctgattctttttctatctcgattgtggtttgatacaatatttagaagctatgtctggtttcattcataaatttgatatacac-tttcatgttgcagTATTGTGCAATGGGTCTTGGCTTAGTCGGATTGGATTTTCGTGGCCTTCTTCCACCGATCTTTGAGAA
                        |     ||   |   |  | | |  |  |||    |  ||   | | ||||| ||||||||||    ||   |||||| |||||||||||||||||||| |||||||| || ||| ||||||| |||||| | |||||||| || ||||| ||
-----------------------gtaagcttctgctagtgagtaacagga-gtttgattgggatcatttgattcat-cataaatttgcatcacttgtttcatcttgcagTATTGTGCAATGGGCCTTGGCTTGGTTGGACTGGATTTCCGTGGCTTACTTCCACCAATTTTTGAAAA
















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|31360458|gb|CD444815.1|CD444815
EST:     CAAACATAACAGAAGGTGGTTCTCTGTCCAACATTCTTGAACAATGCATG                         TATTGTGCAATGGGTCTTGGCTTAGTCGGATTGGATTTTCGTGGCCTTCTT
genomic: CAAACATAACAGAAGGTGGTTCTCTGTCCAACATTCTTGAACAATGCATGgtacgaatgg ... catgttgcagTATTGTGCAATGGGTCTTGGCTTAGTCGGATTGGATTTTCGTGGCCTTCTT
EST: gi|211248709|gb|FL119552.1|FL119552
EST:     CAAACATAACAGAAGGTGGTTCTCTGTCCAACATTCTTGAACAATGCATG                         TATTGTGCAATGGGTCTTGGCTTAGTCGGATTGGATTTTCGTGGCCTTCTT
genomic: CAAACATAACAGAAGGTGGTTCTCTGTCCAACATTCTTGAACAATGCATGgtacgaatgg ... catgttgcagTATTGTGCAATGGGTCTTGGCTTAGTCGGATTGGATTTTCGTGGCCTTCTT

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: 61

GGCAATGCAACAAGTTAGTAATCACCTCACTACTCTTCAAGTTATGTTACCAAACATAACAGAAGGTGGTTCTCTGTCCAACATTCTTGAACAATGCATGgtacgaatgg ... catgttgcagTATTGTGCAATGGGTCTTGGCTTAGTCGGATTGGATTTTCGTGGCCTTCTTCCACCGATCTTTGAGAA


Block sizes: 48 (upstream exon), 43 (downstream exon)
Score: 39

GGCAATGCAACAAGTTAGTAATCACCTCACTACTCTTCAAGTTATGTTACCAAACATAACAGAAGGTGGTTCTCTGTCCAACATTCTTGAACAATGCATGgtacgaatgg ... catgttgcagTATTGTGCAATGGGTCTTGGCTTAGTCGGATTGGATTTTCGTGGCCTTCTTCCACCGATCTTTGAGAA


Block sizes: 45 (upstream exon), 49 (downstream exon)
Score: 52

GGCAATGCAACAAGTTAGTAATCACCTCACTACTCTTCAAGTTATGTTACCAAACATAACAGAAGGTGGTTCTCTGTCCAACATTCTTGAACAATGCATGgtacgaatgg ... catgttgcagTATTGTGCAATGGGTCTTGGCTTAGTCGGATTGGATTTTCGTGGCCTTCTTCCACCGATCTTTGAGAA


Block sizes: 46 (upstream exon), 46 (downstream exon)
Score: 33

GGCAATGCAACAAGTTAGTAATCACCTCACTACTCTTCAAGTTATGTTACCAAACATAACAGAAGGTGGTTCTCTGTCCAACATTCTTGAACAATGCATGgtacgaatgg ... catgttgcagTATTGTGCAATGGGTCTTGGCTTAGTCGGATTGGATTTTCGTGGCCTTCTTCCACCGATCTTTGAGAA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttagaagctatgtctggtttcattcataaatttgatatacactttcatgttgcagTATTGTGCAATGGGTCTTGGCTTAGTCGGATTGGATTTTCGTGGCCTTCTTCCACCGATCTTTGAGAA
                             atttgat  putative branch site (score: 33)
                                       cactttc  putative PPT
                 tttcattcataaattt  TA-rich tract