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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtataaactagtggtttatgtggccatttgttgtgtgggtcatggatggattttctaacactgtctggtgtctgctctagTCTCACTGGATCGGGAGAAACTACTACAGAAGGGGTCCGGAGGGCAATGACATCCACCAGACAAATGTTCCTCACATCAGGGTTGAATTTCGACACACT

Basic information

species Zea mays
transcript GRMZM2G134396_T03
intron # 17
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G134396_T03 (Zea mays), 3'ss of exon 17
lower sequence: LOC_Os07g49270.1 (Oryza sativa), 3'ss of exon 18
gtataaacta--gtggtttatgtggccatttg----ttgtgtgggt---------catggatggattttctaacactgtct-ggtg------tctgctct-----agTCTCACTGGATCGGGAGAAACTACTACAGAAGGGGTCCGGAGGGCAATGACATCCACCAGACAAATGTTCCTCACATCAGGGTTGAATTTCGACACACT
||||| | |    | ||| || | || ||||     |||| |   |           ||  |   |||| |  |  ||| | | |       | ||||||     |||| |||||||| |||||||||||||||| ||| ||||  || ||||||||||| ||||||||||||||||||||||||||| ||||||| |||||||||
gtatagattgctattgttcatttagcaattttgattttgttttcatatttttctctctgcctattttttttctccttgttttgataagacattttgctcttgtatagTCACACTGGATTGGGAGAAACTACTACAAAAGAGGTCATGATGGCAATGACATTCACCAGACAAATGTTCCTCACATCAGGATTGAATTCCGACACACT

upper sequence: GRMZM2G134396_T03 (Zea mays), 3'ss of exon 17
lower sequence: PP1S168_82V6.1 (Physcomitrella patens), 3'ss of exon 17
------------------------------gtataaactagtggtttatgtggccatttgttgtgtgggtcatgg---atggattttctaaca---ctgtctggtgt----------ctgctctagTCTCACTGGATCGGGAGAAACTACTACAGAAGGGGTCCGGAGGGCAATGACATCCACCAGACAAATGTTCCTCACATCAGGGTTGAATTTCGACACACT
                               |   || |  | |    ||||  | | |||||| |   |||  |   ||| | | |  |||    |||     |||          ||| |  |||| |||||| | || |  || || |||| ||||||||| ||||||||||| |||||  |||||||||| ||||||||  | || || || || ||    
gtgtagccttaactttttctcagtttgtgaattcgaattcatcgcccttgtgttc-tatgttgtttcaatcacagtcgatgcaatgttcaacttatctgatcaatgtggccgtgtcactgatgcagTCGCACTGGCTTGGAAAGAATTATTACAAAAGGGGTCCTGAGGGCAATGATATCCATAAGACAAATGTCCCTCACATGCGCGTGGAGTTCCGTCATCAG
















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|14203330|gb|BG837007.1|BG837007
EST:     AAATCGCTAGAAATTCTGTCTACCAGTCCGGATTCTCTCACAGGCTCAAG                         TCTCACTGGATCGGGAGAAACTACTACAGAAGGGGTCCGGAGGGCAATGAC
genomic: AAATCGCTAGAAATTCTGTCTACCAGTCCGGATTCTCTCACAGGCTCAAGgtataaacta ... tctgctctagTCTCACTGGATCGGGAGAAACTACTACAGAAGGGGTCCGGAGGGCAATGAC
EST: gi|67028452|gb|CO457201.1|CO457201
EST:     AAATCGCTAGAAATTCTGTCTACCAGTCCGGATTCTCTCACAGGCTCAAG                         TCTCACTGGATCGGGAGAAACTACTACAGAAGGNGTCCTGAGGGCAATGAC
genomic: AAATCGCTAGAAATTCTGTCTACCAGTCCGGATTCTCTCACAGGCTCAAGgtataaacta ... tctgctctagTCTCACTGGATCGGGAGAAACTACTACAGAAGGGGTCCGGAGGGCAATGAC
EST: gi|16925558|gb|BM078626.1|BM078626
EST:     AAATCGCTAGAAATTCTGTCTACCAGTCCGGATTCTCTCACAGGCTCAAG                         TCTCACTGGATCGGGAGAAACTACTACAGAAGGGGTCCGGAGGGCAATGAC
genomic: AAATCGCTAGAAATTCTGTCTACCAGTCCGGATTCTCTCACAGGCTCAAGgtataaacta ... tctgctctagTCTCACTGGATCGGGAGAAACTACTACAGAAGGGGTCCGGAGGGCAATGAC
EST: gi|78026552|gb|DV494939.1|DV494939
EST:     AAATCGCTAGAAATTCTGTCTACCAGTCCGGATTCTCTCACAGGCTCAAG                         TCTCACTGGATCGGGAGAAACTACTACAGAAGGGGTCCGGAGGGCAATGAC
genomic: AAATCGCTAGAAATTCTGTCTACCAGTCCGGATTCTCTCACAGGCTCAAGgtataaacta ... tctgctctagTCTCACTGGATCGGGAGAAACTACTACAGAAGGGGTCCGGAGGGCAATGAC
EST: gi|50336749|gb|CO531875.1|CO531875
EST:     AAATCGCTAGAAATTCTGTTTACCAGTCCGGATTCTCTCACAGGCTCAAG                         TCTCACTGGATCGGGAGAAACTACTACAGAAGGGGTCCGGAGGGCAATGAC
genomic: AAATCGCTAGAAATTCTGTCTACCAGTCCGGATTCTCTCACAGGCTCAAGgtataaacta ... tctgctctagTCTCACTGGATCGGGAGAAACTACTACAGAAGGGGTCCGGAGGGCAATGAC
EST: gi|71299097|gb|DR785545.1|DR785545
EST:     AAATCGCTAGAAATTCTGTCTACCAGTCCGGATTCTCTCACAGGCTCAAG                         TCTCACTGGATCGGGAGAAACTACTACAGAAGGGGTCCGGAGGGCAATGAC
genomic: AAATCGCTAGAAATTCTGTCTACCAGTCCGGATTCTCTCACAGGCTCAAGgtataaacta ... tctgctctagTCTCACTGGATCGGGAGAAACTACTACAGAAGGGGTCCGGAGGGCAATGAC
EST: gi|149090162|gb|EE179462.2|EE179462
EST:     AAATCGCTAGAAATTCTGTCTACCAGTCCGGATTCTCTCACAGGCTCAAG                         TCTCACTGGATCGGGAGAAACTACTACAGAAGGGGTCCGGAGGGCAATGAC
genomic: AAATCGCTAGAAATTCTGTCTACCAGTCCGGATTCTCTCACAGGCTCAAGgtataaacta ... tctgctctagTCTCACTGGATCGGGAGAAACTACTACAGAAGGGGTCCGGAGGGCAATGAC
EST: gi|211424036|gb|FL301688.1|FL301688
EST:     AAATCGCTAGAAATTCTGTCTACCAGTCCGGATTCTCTCACAGGCTCAAG                         TCTCACTGGATCGGGAGAAACTACTACAGAAGGGGTCCGGAGG
genomic: AAATCGCTAGAAATTCTGTCTACCAGTCCGGATTCTCTCACAGGCTCAAGgtataaacta ... tctgctctagTCTCACTGGATCGGGAGAAACTACTACAGAAGGGGTCCGGAGG
EST: gi|33090962|gb|CF050956.1|CF050956
EST:     AAATCGCTAGAAATTCTGTCTACCAGTCCGGATTCTCTCACAGGCTCAAG                         TCTCACTGGATCGGGAGAAACTACTACAGAAGGGGTCCGGAGGGCAATGAC
genomic: AAATCGCTAGAAATTCTGTCTACCAGTCCGGATTCTCTCACAGGCTCAAGgtataaacta ... tctgctctagTCTCACTGGATCGGGAGAAACTACTACAGAAGGGGTCCGGAGGGCAATGAC
EST: gi|32931798|gb|CF036610.1|CF036610
EST:     AAATCGCTAGAAATTCTGTCTACCAGTCCGGATTCTCTCACAGGCTCAAG                         TCTCACTGGATCGGGAGAAACTACTACAGAAGGGGTCCGGAGGGCAATGAC
genomic: AAATCGCTAGAAATTCTGTCTACCAGTCCGGATTCTCTCACAGGCTCAAGgtataaacta ... tctgctctagTCTCACTGGATCGGGAGAAACTACTACAGAAGGGGTCCGGAGGGCAATGAC
EST: gi|78121620|gb|DV540004.1|DV540004
EST:     AAATCGCTAGAAATTCTGTCTACCAGTCCGGATTCTCTCACAGGCTCAAG                         TCTCACTGGATCGGGAGAAACTACTACAGAAGGGGTCCGGAGGGCAATGAC
genomic: AAATCGCTAGAAATTCTGTCTACCAGTCCGGATTCTCTCACAGGCTCAAGgtataaacta ... tctgctctagTCTCACTGGATCGGGAGAAACTACTACAGAAGGGGTCCGGAGGGCAATGAC
EST: gi|211281929|gb|FL464725.1|FL464725
EST:     AAATCGCTAGAAATTCTGTCTACCAGTCCGGATTCTCTCACAGGCTCAAG                         TCTCACTGGATCGGGAGAAACTACTACAGAAGGGGTCCGGAGGGCAATGAC
genomic: AAATCGCTAGAAATTCTGTCTACCAGTCCGGATTCTCTCACAGGCTCAAGgtataaacta ... tctgctctagTCTCACTGGATCGGGAGAAACTACTACAGAAGGGGTCCGGAGGGCAATGAC
EST: gi|4885898|gb|AI677018.1|AI677018
EST:     AAATCGCTAGAAATTCTGTCTACCAGTCCGGATTCTCTCACAGGCTCAAG                         TCTCACTGGATCGGGAGAAACTACTACAGAAGGGGTCCGGAGGGCAATGAC
genomic: AAATCGCTAGAAATTCTGTCTACCAGTCCGGATTCTCTCACAGGCTCAAGgtataaacta ... tctgctctagTCTCACTGGATCGGGAGAAACTACTACAGAAGGGGTCCGGAGGGCAATGAC
EST: gi|211424040|gb|FL301692.1|FL301692
EST:     AAATCGCTAGAAATTCTGTCTACCAGTCCGGATTCTCTCACAGGCTCAAG                         TCTCACTGGATCGGGAGAAACTACTACAGAAGGGGTCCGGAGGGCAATGAC
genomic: AAATCGCTAGAAATTCTGTCTACCAGTCCGGATTCTCTCACAGGCTCAAGgtataaacta ... tctgctctagTCTCACTGGATCGGGAGAAACTACTACAGAAGGGGTCCGGAGGGCAATGAC
EST: gi|71772852|gb|DR970775.1|DR970775
EST:     AAATCGCTAGAAATTCTGTCTACCAGTCCGGATTCTCTCACAGGCTCAAG                         TCTCACTGGATCGGGAGAAACTACTACAGAAGGGGTCCGGAGGGCAATGAC
genomic: AAATCGCTAGAAATTCTGTCTACCAGTCCGGATTCTCTCACAGGCTCAAGgtataaacta ... tctgctctagTCTCACTGGATCGGGAGAAACTACTACAGAAGGGGTCCGGAGGGCAATGAC

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: 249

CTTTGGAAGCTGAGCTCATGTGACTTGTGTGAAATCGCTAGAAATTCTGTCTACCAGTCCGGATTCTCTCACAGGCTCAAGgtataaacta ... tctgctctagTCTCACTGGATCGGGAGAAACTACTACAGAAGGGGTCCGGAGGGCAATGACATCCACCAGACAAATGTTCCTCACATCAGGGTTGAATTTCGACACACT


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 184

CTTTGGAAGCTGAGCTCATGTGACTTGTGTGAAATCGCTAGAAATTCTGTCTACCAGTCCGGATTCTCTCACAGGCTCAAGgtataaacta ... tctgctctagTCTCACTGGATCGGGAGAAACTACTACAGAAGGGGTCCGGAGGGCAATGACATCCACCAGACAAATGTTCCTCACATCAGGGTTGAATTTCGACACACT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 430

CTTTGGAAGCTGAGCTCATGTGACTTGTGTGAAATCGCTAGAAATTCTGTCTACCAGTCCGGATTCTCTCACAGGCTCAAGgtataaacta ... tctgctctagTCTCACTGGATCGGGAGAAACTACTACAGAAGGGGTCCGGAGGGCAATGACATCCACCAGACAAATGTTCCTCACATCAGGGTTGAATTTCGACACACT


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 124

CTTTGGAAGCTGAGCTCATGTGACTTGTGTGAAATCGCTAGAAATTCTGTCTACCAGTCCGGATTCTCTCACAGGCTCAAGgtataaacta ... tctgctctagTCTCACTGGATCGGGAGAAACTACTACAGAAGGGGTCCGGAGGGCAATGACATCCACCAGACAAATGTTCCTCACATCAGGGTTGAATTTCGACACACT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atttgttgtgtgggtcatggatggattttctaacactgtctggtgtctgctctagTCTCACTGGATCGGGAGAAACTACTACAGAAGGGGTCCGGAGGGCAATGACATCCACCAGACAAATGTTCCTCACATCAGGGTTGAATTTCGACACACT
                           ttctaac  putative branch site (score: 124)
                                             tctgctct  putative PPT
                        attttctaa  TA-rich tract