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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacttcctgtggtgctgttttttttttaccttgaaattttggtttatcaaatatttgttctgattagcttatgcatgtaatgtgttttcggtttatatacagGATACATTCCGTGGAAGAGTTTGCGAGTGTCCAGTTGTGAAAGGCGTCAAATTTGTTGGCGATGGCTATACTCACTGTGAAG

Basic information

species Zea mays
transcript GRMZM2G347541_T01
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G347541_T01 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os12g02390.1 (Oryza sativa), 3'ss of exon 6
gtacttcctgtggtgctgttttttttttaccttgaaattttggtttatcaaatatttgttctgattagcttatgcatgtaatgtgttttcggtttatatacagGATACATTCCGTGGAAGAGTTTGCGAGTGTCCAGTTGTGAAAGGCGTCAAATTTGTTGGCGATGGCTATACTCACTGTGAAG
                         | |  |||    | ||   || |  |  |  | |||    | ||| |||||| | ||   ||  | || ||  |  |||| || || |||||||||||||| || ||||||||||||||||| || ||||||||||| |||||||| |||||||||||||
------------------------gtatttcttatggtgttatcttcttcagaaacttttccatctggct-atgcatatcatac-ttggctgtgtacgtgtagGACACTTTTCGTGGAAGAGTTTGTGAATGTCCAGTTGTGAAAGGTGTTAAATTTGTTGGTGATGGCTACACTCACTGTGAAG

upper sequence: GRMZM2G347541_T01 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os11g02464.1 (Oryza sativa), 3'ss of exon 6
gtacttcctgtggtgctgttttttttttaccttgaaattttggtttatcaaatatttgttctgattagcttatgcatgtaatgtgttttcggtttatatacagGATACATTCCGTGGAAGAGTTTGCGAGTGTCCAGTTGTGAAAGGCGTCAAATTTGTTGGCGATGGCTATACTCACTGTGAAG
                         | |  |||    | ||   || |  |  |  | |||    | ||| |||||| | ||   ||  | || ||  |  |||| || || |||||||||||||| || ||||||||||| ||||| || ||||||||||| |||||||| |||||||||||||
------------------------gtatttcttatggtgttatcttcttcagaaacttttccatctggct-atgcatatcatac-ttggctgtgtacgtgtagGACACTTTTCGTGGAAGAGTTTGTGAATGTCCAGTTGTAAAAGGTGTTAAATTTGTTGGTGATGGCTACACTCACTGTGAAG

upper sequence: GRMZM2G347541_T01 (Zea mays), 3'ss of exon 6
lower sequence: EFJ30872 (Selaginella moellendorffii), 3'ss of exon 6
gtacttcctgtggtgctgttttttttttaccttgaaattttggtttatcaaatatttgttctgattagcttatgcatgtaatgtgttttcggtttatatacagGATACATTCCGTGGAAGAGTTTGCGAGTGTCCAGTTGTGAAAGGCGTCAAATTTGTTGGCGATGGCTATACTCACTGTGAAG
                                        |   |||||| || ||| ||||  ||      ||||   |  |  ||||||  ||   | |||||||| |||||||||||||| |||||||||||  ||||| | |||||  | |     || ||||| || | |||||||||||
---------------------------------------gtaagttatcagat-tttattcttgtt------tgcagtca--gctttttcgtctt---tgcagGATACTTTCCGTGGAAGAGTGTGCGAGTGTCCCATTGTGCAGGGCGTGCAGTACAGCGGAGATGGATACAGTCACTGTGAAG

upper sequence: GRMZM2G347541_T01 (Zea mays), 3'ss of exon 6
lower sequence: EFJ22768 (Selaginella moellendorffii), 3'ss of exon 6
gtacttcctgtggtgctgttttttttttaccttgaaattttggtttatcaaatatttgttctgattagcttatgcatgtaatgtgttttcggtttatatacagGATACATTCCGTGGAAGAGTTTGCGAGTGTCCAGTTGTGAAAGGCGTCAAATTTGTTGGCGATGGCTATACTCACTGTGAAG
                                        |   |||||| || ||| ||||  ||      ||||   |  |  ||||||  ||   | |||||||| |||||||||||||| |||||||||||  ||||| |||||||  | |     || ||||| || | |||||||||||
---------------------------------------gtaagttatcagat-tttattcttgtt------tgcagtca--gctttttcgtctt---tgcagGATACTTTCCGTGGAAGAGTGTGCGAGTGTCCCATTGTGCAAGGCGTGCAGTACAGCGGAGATGGATACAGTCACTGTGAAG

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|71299569|gb|DR785796.1|DR785796
EST:     ACAATGGTGGCTGTTGGCAAGATAAGGCTGCCAACATCACTGCATGCAAG                         GATACATTCCGTGGAAGAGTTTGCGAGTGTCCAGTTGTGAAAGGCGTCAAA
genomic: ACAATGGTGGCTGTTGGCAAGATAAGGCTGCCAACATCACTGCATGCAAGgtacttcctg ... ttatatacagGATACATTCCGTGGAAGAGTTTGCGAGTGTCCAGTTGTGAAAGGCGTCAAA
EST: gi|67021468|gb|CO450217.1|CO450217
EST:     ACAATGGTGGCTGTTGGCAAGATAA-GTTGCCAACATCACTGCATGCAAG                         GATACATTCCGTGGAAGAGTTTGCGAGTGTCCAGTTGTGAAAGGCGTCAAA
genomic: ACAATGGTGGCTGTTGGCAAGATAAGGCTGCCAACATCACTGCATGCAAGgtacttcctg ... ttatatacagGATACATTCCGTGGAAGAGTTTGCGAGTGTCCAGTTGTGAAAGGCGTCAAA
EST: gi|67028179|gb|CO456928.1|CO456928
EST:     ACAATGGTGGCTGTTGGCAAGATAAGGCTGCCAACATCACTGCATGCAAG                         GATACATTCCGTGGAAGAGTTTGCGAGTGTCCAGTTGTGAAAGGCGTCAAA
genomic: ACAATGGTGGCTGTTGGCAAGATAAGGCTGCCAACATCACTGCATGCAAGgtacttcctg ... ttatatacagGATACATTCCGTGGAAGAGTTTGCGAGTGTCCAGTTGTGAAAGGCGTCAAA
EST: gi|211315828|gb|FK969311.1|FK969311
EST:     ACAATGGTGGCTGTTGGCAAGATAAGGCTGCCAACATCACTGCATGCAAG                         GATACATTCCG
genomic: ACAATGGTGGCTGTTGGCAAGATAAGGCTGCCAACATCACTGCATGCAAGgtacttcctg ... ttatatacagGATACATTCCG
EST: gi|211301945|gb|FL333154.1|FL333154
EST:     ACAATGGTGGCTGTTGGCAAGATAAGGCTGCCAACATCACTGCATGCAAG                         GATACATTCCGTGGAAGAGTTTGCGAGTGTCCAGTTGTGAAAGGCGTCAAA
genomic: ACAATGGTGGCTGTTGGCAAGATAAGGCTGCCAACATCACTGCATGCAAGgtacttcctg ... ttatatacagGATACATTCCGTGGAAGAGTTTGCGAGTGTCCAGTTGTGAAAGGCGTCAAA

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: 48 (upstream exon), 49 (downstream exon)
Score: 222

ATATACAAACAAACGAGTGCCTAGAGAACAATGGTGGCTGTTGGCAAGATAAGGCTGCCAACATCACTGCATGCAAGgtacttcctg ... ttatatacagGATACATTCCGTGGAAGAGTTTGCGAGTGTCCAGTTGTGAAAGGCGTCAAATTTGTTGGCGATGGCTATACTCACTGTGAAG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 117

ATATACAAACAAACGAGTGCCTAGAGAACAATGGTGGCTGTTGGCAAGATAAGGCTGCCAACATCACTGCATGCAAGgtacttcctg ... ttatatacagGATACATTCCGTGGAAGAGTTTGCGAGTGTCCAGTTGTGAAAGGCGTCAAATTTGTTGGCGATGGCTATACTCACTGTGAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 57

ATATACAAACAAACGAGTGCCTAGAGAACAATGGTGGCTGTTGGCAAGATAAGGCTGCCAACATCACTGCATGCAAGgtacttcctg ... ttatatacagGATACATTCCGTGGAAGAGTTTGCGAGTGTCCAGTTGTGAAAGGCGTCAAATTTGTTGGCGATGGCTATACTCACTGTGAAG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 148

ATATACAAACAAACGAGTGCCTAGAGAACAATGGTGGCTGTTGGCAAGATAAGGCTGCCAACATCACTGCATGCAAGgtacttcctg ... ttatatacagGATACATTCCGTGGAAGAGTTTGCGAGTGTCCAGTTGTGAAAGGCGTCAAATTTGTTGGCGATGGCTATACTCACTGTGAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

caaatatttgttctgattagcttatgcatgtaatgtgttttcggtttatatacagGATACATTCCGTGGAAGAGTTTGCGAGTGTCCAGTTGTGAAAGGCGTCAAATTTGTTGGCGATGGCTATACTCACTGTGAAG
          ttctgat  putative branch site (score: 148)
                                            tttatataca  TA-rich tract