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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacactttcaaatccattaagtgtgttgctcttgtgatctgattttttcctgataaacttccaggtaacagaactaatattattttataatcagGTGAGATCTGTTGTACTAAACACCCTGAATAGGGCAAGGTTCACTGTGGCTGTGGATTCTTTCATCAGGACTG

Basic information

species Zea mays
transcript GRMZM5G833124_T01
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G833124_T01 (Zea mays), 3'ss of exon 7
lower sequence: LOC_Os05g34650.1 (Oryza sativa), 3'ss of exon 7
gtacactttcaaatccattaagtgtgttgctcttgtgatctgattttttcctgataaacttccaggtaacagaactaatattat-tttataatcagGTGAGATCTGTTGTACTAAACACCCTGAATAGGGCAAGGTTCACTGTGGCTGTGGATTCTTTCATCAGGACTG
||   ||||  ||     |     || ||||||| | ||   ||  ||     | ||  |    | ||||  | | |||||||| | |||  |||||||||||||||||| || ||||| || || | |||||| || |||||||| || ||||| ||||| | ||  |
gtttgcttttgaactttct-----tgatgctcttataattaaatcattctgataaaagttattggttaaccaatcaaatattatatgtattctcagGTGAGATCTGTTGTGCTGAACACTCTAAACACGGCAAGATTTACTGTGGCAGTTGATTCCTTCATTAAGAGCG
















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|91874041|gb|EB403998.1|EB403998
EST:     CTTCATTTGCCTTCTTGTCGTGTGGATATCTTCTCAGTTCATATCATGAG                         GTGAGATCTGTTGTACTAAACACCCTGAATAGGGCAAGGTTCACTGTGGCT
genomic: CTTCATTTGCCTTCTTGTCGTGTGGATATCTTCTCAGTTCATATCATGAGgtacactttc ... ttataatcagGTGAGATCTGTTGTACTAAACACCCTGAATAGGGCAAGGTTCACTGTGGCT
EST: gi|60356183|gb|DN223156.1|DN223156
EST:     CTTCATTTGCCTTCTTGTCGTGTGGATATCTTCTCAGTTCATATCATGAG                         GTGAGATCTGTTGTACTAAACACCCTGAATAGGGCAAGGTTCACTGTGGCT
genomic: CTTCATTTGCCTTCTTGTCGTGTGGATATCTTCTCAGTTCATATCATGAGgtacactttc ... ttataatcagGTGAGATCTGTTGTACTAAACACCCTGAATAGGGCAAGGTTCACTGTGGCT
EST: gi|32932638|gb|CF037450.1|CF037450
EST:     CTTCATTTGCCTTCTTGTCGTGTGGATATCTTCTCAGTTCATATCATGAG                         GTGAGATCTGTTGTA
genomic: CTTCATTTGCCTTCTTGTCGTGTGGATATCTTCTCAGTTCATATCATGAGgtacactttc ... ttataatcagGTGAGATCTGTTGTA

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), 47 (downstream exon)
Score: 119

GGGAACTGGAATGAGCATACTAATCTCAAAGAGCAATCCATCACTGGTAACTTCATTTGCCTTCTTGTCGTGTGGATATCTTCTCAGTTCATATCATGAGgtacactttc ... ttataatcagGTGAGATCTGTTGTACTAAACACCCTGAATAGGGCAAGGTTCACTGTGGCTGTGGATTCTTTCATCAGGACTG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 223

GGGAACTGGAATGAGCATACTAATCTCAAAGAGCAATCCATCACTGGTAACTTCATTTGCCTTCTTGTCGTGTGGATATCTTCTCAGTTCATATCATGAGgtacactttc ... ttataatcagGTGAGATCTGTTGTACTAAACACCCTGAATAGGGCAAGGTTCACTGTGGCTGTGGATTCTTTCATCAGGACTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 196

GGGAACTGGAATGAGCATACTAATCTCAAAGAGCAATCCATCACTGGTAACTTCATTTGCCTTCTTGTCGTGTGGATATCTTCTCAGTTCATATCATGAGgtacactttc ... ttataatcagGTGAGATCTGTTGTACTAAACACCCTGAATAGGGCAAGGTTCACTGTGGCTGTGGATTCTTTCATCAGGACTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 162

GGGAACTGGAATGAGCATACTAATCTCAAAGAGCAATCCATCACTGGTAACTTCATTTGCCTTCTTGTCGTGTGGATATCTTCTCAGTTCATATCATGAGgtacactttc ... ttataatcagGTGAGATCTGTTGTACTAAACACCCTGAATAGGGCAAGGTTCACTGTGGCTGTGGATTCTTTCATCAGGACTG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgattttttcctgataaacttccaggtaacagaactaatattattttataatcagGTGAGATCTGTTGTACTAAACACCCTGAATAGGGCAAGGTTCACTGTGGCTGTGGATTCTTTCATCAGGACTG
                                aactaat  putative branch site (score: 162)
                                        ttatttt  CT-rich tract
                          taacagaactaatatt  TA-rich tract