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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgtgctttgtggtttcgtgcttgttttcgtttgtacaccacaagttccagattcactaatattgagatgctgtttgcacagGATCAGCATGACCCAAACCGTAACCGTGGCTTCCTCTTTGTTGAGTATTACAACCATGCCTGCGCAGACTATGCCAGGCAGAAACTTTCATCTCCAAACT

Basic information

species Zea mays
transcript GRMZM2G103430_T02
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G103430_T05 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os11g14430.2 (Oryza sativa), 3'ss of exon 4
gtgtgctttgtggtttcgtgcttgttttcgtttgtacaccacaagttccagattcactaatattgagatgctgtttgc---acagGATCAGCATGACCCAAACCGTAACCGTGGCTTCCTCTTTGTTGAGTATTACAACCATGCCTGCGCAGACTATGCCAGGCAGAAACTTTCATCTCCAAACT
|||||  || || ||||    |||| ||   ||||||  || | || |||  ||  ||||||  ||  | || || |     ||||||   |||||||||| |||||||||||| |||||||||||||||||||| ||||| || || ||||||||||||||||||||| | ||| | |||||||
gtgtgtcttttgatttcacagttgtatt---ttgtacgacaaaggtcccaagtttgctaatagagatgttctcttggtcctgcagGATTTACATGACCCAAGCCGTAACCGTGGGTTCCTCTTTGTTGAGTATTATAACCACGCTTGTGCAGACTATGCCAGGCAGAAATTGTCAGCACCAAACT

upper sequence: GRMZM2G103430_T05 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os10g06130.2 (Oryza sativa), 3'ss of exon 4
gtgtgctttgtggtttcgtgcttgttttcgtttgtacaccacaagttccagattcactaatattgagatgctgtttg-----cacagGATCAGCATGACCCAAACCGTAACCGTGGCTTCCTCTTTGTTGAGTATTACAACCATGCCTGCGCAGACTATGCCAGGCAGAAACTTTCATCTCCAAACT
||||| | |||| |||| || ||||  |   ||| ||     | |  ||  |||  |||||  |||||   |||||        ||||||   ||||| |||| |||||||||||| |||||||||||||||||||| |||||||| || ||||||||||||| ||||||| | ||| | |||||||
gtgtg-tctgtgatttcatggttgtact---ttgcactaggaaggccccgaatttgctaat--tgagaccttgttttggtcctgcagGATTTACATGATCCAAGCCGTAACCGTGGGTTCCTCTTTGTTGAGTATTATAACCATGCTTGTGCAGACTATGCCAAGCAGAAATTGTCAGCACCAAACT
















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|40336436|gb|CK370506.1|CK370506
EST:     GGTGTTATCAACATTGAGATGTTTAAG                         GATCAGCATGACCCAAACCGTAACCGTGGCTTCCTCTTTGTTGAGTATTAC
genomic: GGTGTTATCAACATTGAGATGTTTAAGgtgtgctttg ... gtttgcacagGATCAGCATGACCCAAACCGTAACCGTGGCTTCCTCTTTGTTGAGTATTAC
EST: gi|211247169|gb|FL378129.1|FL378129
EST:     ACACTATCAANGGGAAGGGTCCAGGTGTTATCAACATTGAGATGTTTAAG                         GATCAGCATGACCCAAACCGTNAACCGTGGCTTTCCTCTTTGTTTGAGTAT
genomic: ACACTATCAAGGGGAAGGGTCCAGGTGTTATCAACATTGAGATGTTTAAGgtgtgctttg ... gtttgcacagGATCAGCATGACCCAAACCGT-AACCGTGGCTT-CCTCTTTGTT-GAGTAT
EST: gi|28910015|gb|CB331214.1|CB331214
EST:     ACACTATCAAGGGGAAGGGTCCAGGTGTTATCAACATTGAGATGTTTAAG                         GATCAGCATGACCCAAACCGTAACCGTGGCTTCCTCTTTGTTGAGTATTAC
genomic: ACACTATCAAGGGGAAGGGTCCAGGTGTTATCAACATTGAGATGTTTAAGgtgtgctttg ... gtttgcacagGATCAGCATGACCCAAACCGTAACCGTGGCTTCCTCTTTGTTGAGTATTAC
EST: gi|211538187|gb|FL238623.1|FL238623
EST:     ACACTATCAAGGGGAAGGGTCCAGGTGTTATCAACATTGAGATGTTTAAG                         GATCAGCATGACCCAAACCGTAACCGTGGCTTCCTCTTTGTTGAGTATTAC
genomic: ACACTATCAAGGGGAAGGGTCCAGGTGTTATCAACATTGAGATGTTTAAGgtgtgctttg ... gtttgcacagGATCAGCATGACCCAAACCGTAACCGTGGCTTCCTCTTTGTTGAGTATTAC

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: 615

GCTGTTTGTTGGGAATGTGCCCAAGGGGCTGAGCGAGGAGGAGCTTACCAACACTATCAAGGGGAAGGGTCCAGGTGTTATCAACATTGAGATGTTTAAGgtgtgctttg ... gtttgcacagGATCAGCATGACCCAAACCGTAACCGTGGCTTCCTCTTTGTTGAGTATTACAACCATGCCTGCGCAGACTATGCCAGGCAGAAACTTTCATCTCCAAACT


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 247

GCTGTTTGTTGGGAATGTGCCCAAGGGGCTGAGCGAGGAGGAGCTTACCAACACTATCAAGGGGAAGGGTCCAGGTGTTATCAACATTGAGATGTTTAAGgtgtgctttg ... gtttgcacagGATCAGCATGACCCAAACCGTAACCGTGGCTTCCTCTTTGTTGAGTATTACAACCATGCCTGCGCAGACTATGCCAGGCAGAAACTTTCATCTCCAAACT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 280

GCTGTTTGTTGGGAATGTGCCCAAGGGGCTGAGCGAGGAGGAGCTTACCAACACTATCAAGGGGAAGGGTCCAGGTGTTATCAACATTGAGATGTTTAAGgtgtgctttg ... gtttgcacagGATCAGCATGACCCAAACCGTAACCGTGGCTTCCTCTTTGTTGAGTATTACAACCATGCCTGCGCAGACTATGCCAGGCAGAAACTTTCATCTCCAAACT


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 278

GCTGTTTGTTGGGAATGTGCCCAAGGGGCTGAGCGAGGAGGAGCTTACCAACACTATCAAGGGGAAGGGTCCAGGTGTTATCAACATTGAGATGTTTAAGgtgtgctttg ... gtttgcacagGATCAGCATGACCCAAACCGTAACCGTGGCTTCCTCTTTGTTGAGTATTACAACCATGCCTGCGCAGACTATGCCAGGCAGAAACTTTCATCTCCAAACT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcgtttgtacaccacaagttccagattcactaatattgagatgctgtttgcacagGATCAGCATGACCCAAACCGTAACCGTGGCTTCCTCTTTGTTGAGTATTACAACCATGCCTGCGCAGACTATGCCAGGCAGAAACTTTCATCTCCAAACT
                           cactaat  putative branch site (score: 278)
                            actaatatt  TA-rich tract