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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtgcatgccattgtacattatacatgatggaaatacccctgttgactttggttttctaagatcttcatgaatgttttgtccagATGGAGGCACTTGTTCACCCATTCTTTGATGAGCTTCGAGATCCTAATACTCGCCTTCCAAATGGTCGCTTTTTGCCACCACTATTCAATTTCAAGCCTC

Basic information

species Zea mays
transcript GRMZM2G024151_T01
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G024151_T01 (Zea mays), 3'ss of exon 10
lower sequence: LOC_Os01g14860.3 (Oryza sativa), 3'ss of exon 10
--------------------gtaagtgcatgccattgtacattat---acatgatg---gaaatacccctgttgactttggttttctaagatcttcatgaatgttttgtccagATGGAGGCACTTGTTCACCCATTCTTTGATGAGCTTCGAGATCCTAATACTCGCCTTCCAAATGGTCGCTTTTTGCCACCACTATTCAATTTCAAGCCTC
                      |||| ||    | |    |||||   || |  |    || |||    ||  ||| ||  |||  |||    ||  ||     |||| |||| |||| ||||||||||||||||||||||||||||||||||| |||||| |||||||||| ||||| ||||||||||| || || ||||| ||||||||||
gtaagtatatatttaatggttgaagtacagataaattagtattatggcacttagttcctgagataattgtgcagacattcatttcataaatattttctgttacctttgaccagGTGGAAGCACTTGTTCACCCATTCTTTGATGAGCTTCGAGACCCTAATGCTCGCCTTCCGAATGGCCGCTTTTTGCCTCCTCTCTTCAACTTCAAGCCTC

upper sequence: GRMZM2G024151_T01 (Zea mays), 3'ss of exon 10
lower sequence: EFJ10962 (Selaginella moellendorffii), 3'ss of exon 10
gtaagtgcatgccattgtacattatacatgatggaaatacccctgttgactttggttttctaagatcttcatga-atgttttgtccagATGGAGGCACTTGTTCACCCATTCTTTGATGAGCTTCGAGATCCTAATACTCGCCTTCCAAATGGTCGCTTTTTGCCACCACTATTCAATTTCAAGCCTC
                      ||    |     ||||      ||  ||||||     |   ||   |  ||  ||    |   ||| | || || ||||  |||||||||||||||||| | || |||||||| ||||| ||||||||||||||     | ||||| || | |||||||||||   
---------------------gtaagtttctcccaaat-----cgtccactttgaagggccctgacactggtggtatacacttcacagCTAGAAGCGCTTGCACACCCATTCTTTGATGAGTTGCGGGATCCTAACACTCGACTTCCAAATGGTCGTCCGCTACCACCTCTGTACAATTTCAAGCAAT

upper sequence: GRMZM2G024151_T01 (Zea mays), 3'ss of exon 10
lower sequence: EFJ04915 (Selaginella moellendorffii), 3'ss of exon 10
gtaagtgcatgccattgtacattatacatgatggaaatacccctgttgactttggttttctaagatcttcatga-atgttttgtccagATGGAGGCACTTGTTCACCCATTCTTTGATGAGCTTCGAGATCCTAATACTCGCCTTCCAAATGGTCGCTTTTTGCCACCACTATTCAATTTCAAGCCTC
                      ||    |     ||||      ||  ||||||     |   ||   |  ||  ||    |   ||| | || || ||||  |||||||||||||||||| | || |||||||| ||||| ||||||||||||||     | ||||| || | |||||||||||   
---------------------gtaagtttctcccaaat-----cgtccactttgaagagcactgacactggtggtatacacttcacagCTAGAAGCGCTTGCACACCCATTCTTTGATGAGTTGCGGGATCCTAACACTCGACTTCCAAATGGTCGTCCGCTACCACCTCTGTACAATTTCAAGCAAT

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|211161694|gb|FL418712.1|FL418712
EST:     ATCTGGTCTCTCGGCTACTCCAGTACTCCCCAAATCTGAGATGCACTGCT                         ATGGAGGCACTTGTTCACCCATTCTTTGATGAGCTTCGAGATCCTAATACT
genomic: ATCTGGTCTCTCGGCTACTCCAGTACTCCCCAAATCTGAGATGCACTGCTgtaagtgcat ... ttttgtccagATGGAGGCACTTGTTCACCCATTCTTTGATGAGCTTCGAGATCCTAATACT
EST: gi|61117965|gb|DN558926.1|DN558926
EST:     ATCTGGTCTCTCGGCTACTCCAGTACTCCCCAAATCTGAGATGCACTGCT                         ATGGAGGCACTTGTTCACCCATTCTTTGATGAGCTTCGAGATCCTAATACT
genomic: ATCTGGTCTCTCGGCTACTCCAGTACTCCCCAAATCTGAGATGCACTGCTgtaagtgcat ... ttttgtccagATGGAGGCACTTGTTCACCCATTCTTTGATGAGCTTCGAGATCCTAATACT
EST: gi|61117966|gb|DN558927.1|DN558927
EST:     ATCTGGTCTCTCGGCTACTCCAGTACTCCCCAAATCTGAGATGCACTGCT                         ATGGAGGCACTTGTTCACCCATTCTTTGATGAGCTTCGAGATCCTAATACT
genomic: ATCTGGTCTCTCGGCTACTCCAGTACTCCCCAAATCTGAGATGCACTGCTgtaagtgcat ... ttttgtccagATGGAGGCACTTGTTCACCCATTCTTTGATGAGCTTCGAGATCCTAATACT
EST: gi|33097248|gb|CF057208.1|CF057208
EST:     ATCTGGTCTCTCGGCTACTCCAGTACTCCCCAAATCTGAGATGCACTGCT                         ATGGAGGCACTTGTTCACCCATTCTTTGATGAGCTTCGAGA
genomic: ATCTGGTCTCTCGGCTACTCCAGTACTCCCCAAATCTGAGATGCACTGCTgtaagtgcat ... ttttgtccagATGGAGGCACTTGTTCACCCATTCTTTGATGAGCTTCGAGA
EST: gi|33104403|gb|CF064363.1|CF064363
EST:     ATCTGGTCTCTCGGCTACTCCAGTACTCCCCAAATCTGAGATGCACTGCT                         ATGGAGGCACTTGTTCACCCATTCTTTGATGAGCTTCGAGATC
genomic: ATCTGGTCTCTCGGCTACTCCAGTACTCCCCAAATCTGAGATGCACTGCTgtaagtgcat ... ttttgtccagATGGAGGCACTTGTTCACCCATTCTTTGATGAGCTTCGAGATC
EST: gi|32827595|gb|CD967273.1|CD967273
EST:     ATCTGGTCTCTCGGCTACTCCAGTACTCCCCAAATCTGAGATGCACTGCT                         ATGGAGGCACTTGTTCACCCATTCTTTGATGAGCT-CGAGATC
genomic: ATCTGGTCTCTCGGCTACTCCAGTACTCCCCAAATCTGAGATGCACTGCTgtaagtgcat ... ttttgtccagATGGAGGCACTTGTTCACCCATTCTTTGATGAGCTTCGAGATC

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: 1008

GTATTCCACAAAAGGATGCCGCCAGAAGCTGTTGATCTGGTCTCTCGGCTACTCCAGTACTCCCCAAATCTGAGATGCACTGCTgtaagtgcat ... ttttgtccagATGGAGGCACTTGTTCACCCATTCTTTGATGAGCTTCGAGATCCTAATACTCGCCTTCCAAATGGTCGCTTTTTGCCACCACTATTCAATTTCAAGCCTC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 204

GTATTCCACAAAAGGATGCCGCCAGAAGCTGTTGATCTGGTCTCTCGGCTACTCCAGTACTCCCCAAATCTGAGATGCACTGCTgtaagtgcat ... ttttgtccagATGGAGGCACTTGTTCACCCATTCTTTGATGAGCTTCGAGATCCTAATACTCGCCTTCCAAATGGTCGCTTTTTGCCACCACTATTCAATTTCAAGCCTC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 160

GTATTCCACAAAAGGATGCCGCCAGAAGCTGTTGATCTGGTCTCTCGGCTACTCCAGTACTCCCCAAATCTGAGATGCACTGCTgtaagtgcat ... ttttgtccagATGGAGGCACTTGTTCACCCATTCTTTGATGAGCTTCGAGATCCTAATACTCGCCTTCCAAATGGTCGCTTTTTGCCACCACTATTCAATTTCAAGCCTC


Block sizes: 49 (upstream exon), 44 (downstream exon)
Score: 253

GTATTCCACAAAAGGATGCCGCCAGAAGCTGTTGATCTGGTCTCTCGGCTACTCCAGTACTCCCCAAATCTGAGATGCACTGCTgtaagtgcat ... ttttgtccagATGGAGGCACTTGTTCACCCATTCTTTGATGAGCTTCGAGATCCTAATACTCGCCTTCCAAATGGTCGCTTTTTGCCACCACTATTCAATTTCAAGCCTC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggaaatacccctgttgactttggttttctaagatcttcatgaatgttttgtccagATGGAGGCACTTGTTCACCCATTCTTTGATGAGCTTCGAGATCCTAATACTCGCCTTCCAAATGGTCGCTTTTTGCCACCACTATTCAATTTCAAGCCTC
           tgttgac  putative branch site (score: 253)
                                             ttttgtcc  putative PPT
                       ttttctaa  TA-rich tract