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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttatccttacatggccgtcaagcttagctgttcaaaattattcctgcaatatttgtttcttgattttccattatatcgcagGTTGCTAGGACACGACCTCTGGCGGTGACAAACTGCAATGTGGACTTGGAGAGTTTGTTGTCAGACCAGAACAGGAGTATAGCGACCCTGGCAATTACTA

Basic information

species Zea mays
transcript GRMZM2G012501_T02
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G012501_T02 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os03g12590.1 (Oryza sativa), 3'ss of exon 8
gttatccttacatggccgtcaagcttagctgttcaaaattattcctgcaatatttgtttcttgattt-tccattatatcgcagGTTGCTAGGACACGACCTCTGGCGGTGACAAACTGCAATGTGGACTTGGAGAGTTTGTTGTCAGACCAGAACAGGAGTATAGCGACCCTGGCAATTACTA
||||||| | ||||    | || ||| |   || ||| ||  ||     || | | | |||||||||  |  |||| ||||||||||||| |||||| ||| |||| |||||||||||||||||||||||||| ||| || |||| |||||||| ||||||||||| ||||||||||| ||||
gttatccctgcatgatgtttaatctttgacatttaaattttctcagcttatgtctatatcttgatttgcctgttatctcgcagGTTGCTATGACACGCCCTTTGGCAGTGACAAACTGCAATGTGGACTTGGAAAGTCTGATGTCGGACCAGAATAGGAGTATAGCAACCCTGGCAATCACTA
















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|32942885|gb|CF047704.1|CF047704
EST:     GTTCATCCAAGCCTGTGCTTCGATTTGCTGCTGTCCGGACTCTCAATAAG                         GTTGCTAGGACACGACCTCTGGCGGTGACAAACTGCAATGTGGACTTGGAG
genomic: GTTCATCCAAGCCTGTGCTTCGATTTGCTGCTGTCCGGACTCTCAATAAGgttatcctta ... tatatcgcagGTTGCTAGGACACGACCTCTGGCGGTGACAAACTGCAATGTGGACTTGGAG
EST: gi|67030306|gb|CO459055.1|CO459055
EST:     GTTCATCCAAGCCTGTGCTTCGATTTGCTGCTGTCCGGACTCTCAATAAG                         GTTGCTAGGACACGACCTCTGGCGGTGACAAACTGCAATGTGGACTTGGAG
genomic: GTTCATCCAAGCCTGTGCTTCGATTTGCTGCTGTCCGGACTCTCAATAAGgttatcctta ... tatatcgcagGTTGCTAGGACACGACCTCTGGCGGTGACAAACTGCAATGTGGACTTGGAG
EST: gi|32945171|gb|CF049990.1|CF049990
EST:     GTTCATCCAAGCCTGTGCTTCGATTTGCTGCTGTCCGGACTCTCAATAAG                         GTTGCTAGGACACGACCTCTGGCGGTGACAAACTGCAATGTGGACTTGGAG
genomic: GTTCATCCAAGCCTGTGCTTCGATTTGCTGCTGTCCGGACTCTCAATAAGgttatcctta ... tatatcgcagGTTGCTAGGACACGACCTCTGGCGGTGACAAACTGCAATGTGGACTTGGAG

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: 47 (upstream exon), 49 (downstream exon)
Score: 210

TACAAGCCGTGAATTGGCACCAGCAATTACTTTGTTACAGTTATACTTGAGTTCATCCAAGCCTGTGCTTCGATTTGCTGCTGTCCGGACTCTCAATAAGgttatcctta ... tatatcgcagGTTGCTAGGACACGACCTCTGGCGGTGACAAACTGCAATGTGGACTTGGAGAGTTTGTTGTCAGACCAGAACAGGAGTATAGCGACCCTGGCAATTACTA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 131

TACAAGCCGTGAATTGGCACCAGCAATTACTTTGTTACAGTTATACTTGAGTTCATCCAAGCCTGTGCTTCGATTTGCTGCTGTCCGGACTCTCAATAAGgttatcctta ... tatatcgcagGTTGCTAGGACACGACCTCTGGCGGTGACAAACTGCAATGTGGACTTGGAGAGTTTGTTGTCAGACCAGAACAGGAGTATAGCGACCCTGGCAATTACTA


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 133

TACAAGCCGTGAATTGGCACCAGCAATTACTTTGTTACAGTTATACTTGAGTTCATCCAAGCCTGTGCTTCGATTTGCTGCTGTCCGGACTCTCAATAAGgttatcctta ... tatatcgcagGTTGCTAGGACACGACCTCTGGCGGTGACAAACTGCAATGTGGACTTGGAGAGTTTGTTGTCAGACCAGAACAGGAGTATAGCGACCCTGGCAATTACTA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 189

TACAAGCCGTGAATTGGCACCAGCAATTACTTTGTTACAGTTATACTTGAGTTCATCCAAGCCTGTGCTTCGATTTGCTGCTGTCCGGACTCTCAATAAGgttatcctta ... tatatcgcagGTTGCTAGGACACGACCTCTGGCGGTGACAAACTGCAATGTGGACTTGGAGAGTTTGTTGTCAGACCAGAACAGGAGTATAGCGACCCTGGCAATTACTA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gctgttcaaaattattcctgcaatatttgtttcttgattttccattatatcgcagGTTGCTAGGACACGACCTCTGGCGGTGACAAACTGCAATGTGGACTTGGAGAGTTTGTTGTCAGACCAGAACAGGAGTATAGCGACCCTGGCAATTACTA
                               tcttgat  putative branch site (score: 189)
                                     ttttccatt  CT-rich tract
                     aatatttgtttctt  TA-rich tract