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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgtatactgttctatcttttgaaatttgataagtacatttgctaattccctcaatctctgcagTCCTCTGAACCCATGGAGCTGACAGAGGCAGAAACTGAATATGCTGTTAGTGTGGTTAAACACATTTATGACGGCTACATTGTATTGCAGTACAATTGTG

Basic information

species Zea mays
transcript GRMZM2G012501_T02
intron # 12
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 12
lower sequence: LOC_Os03g12590.1 (Oryza sativa), 3'ss of exon 14
gtttgtatactgttctatcttttgaaatttga--taagtacatttgctaattccctcaatctctgc--agTCCTCTGAACCCATGGAGCTGACAGAGGCAGAAACTGAATATGCTGTTAGTGTGGTTAAACACATTTATGACGGCTACATTGTATTGCAGTACAATTGTG
|| ||||  ||  | || | ||    ||||    | ||||||  ||||||  |||||  | | | |  ||||||| |||||  |||||||||||||||| || |||||||||||  ||| ||||||||| ||||| ||     || |  |||| ||||||||||| ||| 
gtctgta-gcttctataccattaatgattttgattgagtacacatgctaaacccctctctttttccccagTCCTCAGAACCTGTGGAGCTGACAGAGGCGGAGACTGAATATGCGATTAATGTGGTTAAGCACATATACAGTAGCCATGTTGTGTTGCAGTACAACTGTA

upper sequence: GRMZM2G012501_T02 (Zea mays), 3'ss of exon 12
lower sequence: Vv03s0063g02450.t01 (Vitis vinifera), 3'ss of exon 14
------------------------gtttgtatac-tgttctatcttttgaaatttgataagtacatttgctaattccctcaatctctg-----cagTCCTCTGAACCCATGGAGCTGACAGAGGCAGAAACTGAATATGCTGTTAGTGTGGTTAAACACATTTATGACGGCTACATTGTATTGCAGTACAATTGTG
                         ||  |  || ||  |||   |||||||| | |  | | ||   | || |    |     | |      |||||||| | |||  | ||||||||||| |||||||| ||||||||||||| ||| || || ||||||| |||  |  |  |||| || |||||||| ||  
gtcccctgctttttttcacatacgcttcatgcacatggactaa--tttgaaatgttactaattcagaagttattcttttttcgttttatttatcagTCCTCAGCACCTGTAGAGCTGACAGAAGCAGAAACAGAATATGCTGTTAATGTTGTCAAGCACATTTTTGATAGGCATGTTGTGTTCCAGTACAACTGCA
















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|31350725|gb|CD435082.1|CD435082
EST:     AAATGCTTTCGTTCATTCCCGAGTTCTCTGGGTTTGGAAGGCTCTTCAAG                         TCCTCTGAACCCATGGAGCTGACAGAGGCAGAAACTGAATATGCTGTTAGT
genomic: AAATGCTTTCGTTCATTCCCGAGTTCTCTGGGTTTGGAAGGCTCTTCAAGgtttgtatac ... atctctgcagTCCTCTGAACCCATGGAGCTGACAGAGGCAGAAACTGAATATGCTGTTAGT
EST: gi|211320234|gb|FL338449.1|FL338449
EST:     AAATGCTTTCGTTCATTCCCGAGTTCTCTGGGTTTGGAAGGCTCTTCAAG                         TCCTCTGAACCCATGGAGCTGACAGAGGCAGAAACTGAATATGCTGTTAGT
genomic: AAATGCTTTCGTTCATTCCCGAGTTCTCTGGGTTTGGAAGGCTCTTCAAGgtttgtatac ... atctctgcagTCCTCTGAACCCATGGAGCTGACAGAGGCAGAAACTGAATATGCTGTTAGT
EST: gi|32839407|gb|CD979088.1|CD979088
EST:     AAATGCTTTCGTTCATTCCCGAGTTCTCTGGGTTTGGAAGGCTCTTCAAG                         TCCTCTGAACCCATGGAGCTGACAGAGGCAGAAACTGAATATGCTGTTAGT
genomic: AAATGCTTTCGTTCATTCCCGAGTTCTCTGGGTTTGGAAGGCTCTTCAAGgtttgtatac ... atctctgcagTCCTCTGAACCCATGGAGCTGACAGAGGCAGAAACTGAATATGCTGTTAGT
EST: gi|67012331|gb|CO441080.1|CO441080
EST:     AAATGCTTTCGTTCATTCCCGAGTTCTCTGGGTTTGGAAAGCTCTT-AAG                         TCCTCTGAACCCATGCAGCTGACAGAGGCAGAAACTGAATATGCTGTTACT
genomic: AAATGCTTTCGTTCATTCCCGAGTTCTCTGGGTTTGGAAGGCTCTTCAAGgtttgtatac ... atctctgcagTCCTCTGAACCCATGGAGCTGACAGAGGCAGAAACTGAATATGCTGTTAGT
EST: gi|74243906|gb|DT651820.1|DT651820
EST:     GAATGCTTTCGTTCATTCCCGAGTTCTCTGGGTTTGGAAGGCTCTTCAAG                         TCCTCTGAACCCATGCAGCTGACAGAGGCAGATACTGAATATGCTGTTAGT
genomic: AAATGCTTTCGTTCATTCCCGAGTTCTCTGGGTTTGGAAGGCTCTTCAAGgtttgtatac ... atctctgcagTCCTCTGAACCCATGGAGCTGACAGAGGCAGAAACTGAATATGCTGTTAGT
EST: gi|211280128|gb|FL354649.1|FL354649
EST:     AAATGCTTTCGTTCATTCCCGAGTTCTCTGGGTTTGGAAGGCTCTTCAAG                         TCCTCTGAACCCATGGAGCTGACAGAGGCAGAAACTGAATATGCTGTTAGT
genomic: AAATGCTTTCGTTCATTCCCGAGTTCTCTGGGTTTGGAAGGCTCTTCAAGgtttgtatac ... atctctgcagTCCTCTGAACCCATGGAGCTGACAGAGGCAGAAACTGAATATGCTGTTAGT
EST: gi|211537215|gb|FL317072.1|FL317072
EST:     AAATGCTTTCGTTCATTCCCGAGTTCTCTGGGTTTGGAAGGCTCTTCAAG                         TCCTCTGAACCCATGGAGCTGACAGAGGCAGAAACTGAATATGCTGTTAGT
genomic: AAATGCTTTCGTTCATTCCCGAGTTCTCTGGGTTTGGAAGGCTCTTCAAGgtttgtatac ... atctctgcagTCCTCTGAACCCATGGAGCTGACAGAGGCAGAAACTGAATATGCTGTTAGT
EST: gi|32823326|gb|CD963048.1|CD963048
EST:     AAATGCTTTCGTTCATTCCCGAGTTCTCTGGGTTTGGAAGGCTCTTCAAG                         TCCTCTGAACCCATGGAGCTGACAGAGGCAGAAACTGAATATGCTGTTAGT
genomic: AAATGCTTTCGTTCATTCCCGAGTTCTCTGGGTTTGGAAGGCTCTTCAAGgtttgtatac ... atctctgcagTCCTCTGAACCCATGGAGCTGACAGAGGCAGAAACTGAATATGCTGTTAGT
EST: gi|32837289|gb|CD976967.1|CD976967
EST:     AAATGCTTTCGTTCATTCCCGAGTTCTCTGGGTTTGGAAGGCTCTTCAAG                         TCCTCTGAACCCATGGAGCTGACAGAGGCAGAAACTGAATATGCTGTTAGT
genomic: AAATGCTTTCGTTCATTCCCGAGTTCTCTGGGTTTGGAAGGCTCTTCAAGgtttgtatac ... atctctgcagTCCTCTGAACCCATGGAGCTGACAGAGGCAGAAACTGAATATGCTGTTAGT
EST: gi|67021265|gb|CO450014.1|CO450014
EST:     AAATGCTTTCGTTCATTCCCGAGTTCTCTGGGTTTGGAAGGCTCTTCAAG                         TCCTCTGAACCCATGGAGCTGACAGAGGCAGAAACTGAATATGCTGTTAGT
genomic: AAATGCTTTCGTTCATTCCCGAGTTCTCTGGGTTTGGAAGGCTCTTCAAGgtttgtatac ... atctctgcagTCCTCTGAACCCATGGAGCTGACAGAGGCAGAAACTGAATATGCTGTTAGT

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), 49 (downstream exon)
Score: 236

TGGTGCTGCCGCCGCCGCCGCCCCTGTTTCAACTGTTGATGCTTATCAGAAAATGCTTTCGTTCATTCCCGAGTTCTCTGGGTTTGGAAGGCTCTTCAAGgtttgtatac ... atctctgcagTCCTCTGAACCCATGGAGCTGACAGAGGCAGAAACTGAATATGCTGTTAGTGTGGTTAAACACATTTATGACGGCTACATTGTATTGCAGTACAATTGTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 222

TGGTGCTGCCGCCGCCGCCGCCCCTGTTTCAACTGTTGATGCTTATCAGAAAATGCTTTCGTTCATTCCCGAGTTCTCTGGGTTTGGAAGGCTCTTCAAGgtttgtatac ... atctctgcagTCCTCTGAACCCATGGAGCTGACAGAGGCAGAAACTGAATATGCTGTTAGTGTGGTTAAACACATTTATGACGGCTACATTGTATTGCAGTACAATTGTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 173

TGGTGCTGCCGCCGCCGCCGCCCCTGTTTCAACTGTTGATGCTTATCAGAAAATGCTTTCGTTCATTCCCGAGTTCTCTGGGTTTGGAAGGCTCTTCAAGgtttgtatac ... atctctgcagTCCTCTGAACCCATGGAGCTGACAGAGGCAGAAACTGAATATGCTGTTAGTGTGGTTAAACACATTTATGACGGCTACATTGTATTGCAGTACAATTGTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 225

TGGTGCTGCCGCCGCCGCCGCCCCTGTTTCAACTGTTGATGCTTATCAGAAAATGCTTTCGTTCATTCCCGAGTTCTCTGGGTTTGGAAGGCTCTTCAAGgtttgtatac ... atctctgcagTCCTCTGAACCCATGGAGCTGACAGAGGCAGAAACTGAATATGCTGTTAGTGTGGTTAAACACATTTATGACGGCTACATTGTATTGCAGTACAATTGTG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttctatcttttgaaatttgataagtacatttgctaattccctcaatctctgcagTCCTCTGAACCCATGGAGCTGACAGAGGCAGAAACTGAATATGCTGTTAGTGTGGTTAAACACATTTATGACGGCTACATTGTATTGCAGTACAATTGTG
                               tgctaat  putative branch site (score: 225)
                                     ttccctcaatctct  CT-rich tract
        ttttgaaatttgataa  TA-rich tract