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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatggagtaagagattgttttttttaccaagttcttagtgccctgcattgtacttctgatagccgaagctttcatgtttgctttagtcattactatatcttctgtatcgtgatcttgctattcggaacccttgtagGAATTCGCGGAAGCGGATTCATTCTTTTGCTTCGTCGAGTTGCTTAGTGGGTTCAGAGACAACTTCTGCCAGAAACTGGACAACAGTGCTGTTGGCATTC

Basic information

species Zea mays
transcript GRMZM2G068392_T01
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G068392_T01 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os01g68010.3 (Oryza sativa), 3'ss of exon 6
gtatggagtaagagattgttttttttaccaagttcttagtgccctgcat--tgtacttctga---tagccgaa-gct-ttcatgtttgctttagtcattactatatcttctg----tatcgtgatcttgctattcggaacccttgtagGAATTCGCGGAAGCGGATTCATTCTTTTGCTTCGTCGAGTTGCTTAGTGGGTTCAGAGACAACTTCTGCCAGAAACTGGACAACAGTGCTGTTGGCATTC
       |||||  ||||||||       |  | |||| ||||||| ||  | ||   | ||   ||| |    ||| ||| |  | ||  ||||   |     |   |||     |    | || ||||||| ||||| || |  || | || || ||||| ||||| ||||| |||||| | ||||| ||||||||||| ||||||||||||||||||||||| ||||||||||||||||||||||
-------gtaagcaattgttttaccatatatatgcttaatgccctgtatgatttagagcagactgtagtcagttgctgttcgttatagcaatagtttctgtgggactatctaaccatgattttattttgctatccggaatccctacagAACTTTGCAGAAGCTGATTCTTTCTTCTGCTTCATGGAGTTACTTAGTGGGTTTAGAGACAACTTCTGCCAGAAACTAGACAACAGTGCTGTTGGCATTC

upper sequence: GRMZM2G068392_T01 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os01g68010.1 (Oryza sativa), 3'ss of exon 6
gtatggagtaagagattgttttttttaccaagttcttagtgccctgcat--tgtacttctga---tagccgaa-gct-ttcatgtttgctttagtcattactatatcttctg----tatcgtgatcttgctattcggaacccttgtagGAATTCGCGGAAGCGGATTCATTCTTTTGCTTCGTCGAGTTGCTTAGTGGGTTCAGAGACAACTTCTGCCAGAAACTGGACAACAGTGCTGTTGGCATTC
||||||||||||  ||||||||       |  | |||| ||||||| ||  | ||   | ||   ||| |    ||| ||| |  | ||  ||||   |     |   |||     |    | || ||||||| ||||| || |  || | || || ||||| ||||| ||||| |||||| | ||||| ||||||||||| ||||||||||||||||||||||| ||||||||||||||||||||||
gtatggagtaagcaattgttttaccatatatatgcttaatgccctgtatgatttagagcagactgtagtcagttgctgttcgttatagcaatagtttctgtgggactatctaaccatgattttattttgctatccggaatccctacagAACTTTGCAGAAGCTGATTCTTTCTTCTGCTTCATGGAGTTACTTAGTGGGTTTAGAGACAACTTCTGCCAGAAACTAGACAACAGTGCTGTTGGCATTC
















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|211178282|gb|FL421437.1|FL421437
EST:     TGATCCGGATGATAAAAATGCT                         GAATTCGCGTAAGCGGATTCATTCTTTTGCTTCGTCGAGTTGCTTAGTGGG
genomic: TGATCCGGATGATAAAAATGCTgtatggagta ... acccttgtagGAATTCGCGGAAGCGGATTCATTCTTTTGCTTCGTCGAGTTGCTTAGTGGG
EST: gi|78076513|gb|DV504947.1|DV504947
EST:     AGTGATCCGGATGATAAAAATGCT                         GAATTCGCGGAAGCGGATTCATTCTTTTGCTTCGTCGAGTTGCTTAGTGGG
genomic: AGTGATCCGGATGATAAAAATGCTgtatggagta ... acccttgtagGAATTCGCGGAAGCGGATTCATTCTTTTGCTTCGTCGAGTTGCTTAGTGGG
EST: gi|60342736|gb|DN209709.1|DN209709
EST:     TGGCACCCCTCTTCTTTGTATTTCGGAGTGATCCGGATGATAAAAATGCTGTAT                      
genomic: TGGCACCCCTCTTCTTTGTATTTCGGAGTGATCCGGATGATAAAAATGC----Tgtatggagta ... acccttg
EST: gi|60342736|gb|DN209709.1|DN209709
EST:     TGGCACCCCTCTTCTTTGTATTTCGGAGTGATCCGGATGATAAAAATGCTGTAT                      
genomic: TGGCACCCCTCTTCTTTGTATTTCGGAGTGATCCGGATGATAAAAATGC----Tgtatggagta ... acccttg
EST: gi|60342736|gb|DN209709.1|DN209709
EST:     TGGCACCCCTCTTCTTTGTATTTCGGAGTGATCCGGATGATAAAAATGCTGTAT                      
genomic: TGGCACCCCTCTTCTTTGTATTTCGGAGTGATCCGGATGATAAAAATGC----Tgtatggagta ... acccttg
EST: gi|60342736|gb|DN209709.1|DN209709
EST:     TGGCACCCCTCTTCTTTGTATTTCGGAGTGATCCGGATGATAAAAATGCTGTAT                      
genomic: TGGCACCCCTCTTCTTTGTATTTCGGAGTGATCCGGATGATAAAAATGC----Tgtatggagta ... acccttg
EST: gi|71433967|gb|DR815017.1|DR815017
EST:     TGGCACCCCTCTTCTTTGTATTTCGGAGTGATCCGGATGATAAAAATGCT                         GAATTCGCGGAAGCGGATTCATTCTTTTGCTTCGTCGAGTTGCTTAGTGGG
genomic: TGGCACCCCTCTTCTTTGTATTTCGGAGTGATCCGGATGATAAAAATGCTgtatggagta ... acccttgtagGAATTCGCGGAAGCGGATTCATTCTTTTGCTTCGTCGAGTTGCTTAGTGGG
EST: gi|50324142|gb|CO519268.1|CO519268
EST:     TGGCACCCCTCTTCTTTGTATTTCGGAGTGATCCGGATGATAAAAATGCT                         GAATTCGCGGAA
genomic: TGGCACCCCTCTTCTTTGTATTTCGGAGTGATCCGGATGATAAAAATGCTgtatggagta ... acccttgtagGAATTCGCGGAA
EST: gi|38502614|gb|CF972474.1|CF972474
EST:     TGGCACCCCTCTTCTTTGTATTTCGGAGTGATCCGGATGATAAAAATGCT                         GAATTCCCGGAAGCGGATTCATTCTTTTGCTTCGCCGAGTTGCTTA
genomic: TGGCACCCCTCTTCTTTGTATTTCGGAGTGATCCGGATGATAAAAATGCTgtatggagta ... acccttgtagGAATTCGCGGAAGCGGATTCATTCTTTTGCTTCGTCGAGTTGCTTA
EST: gi|50331308|gb|CO526434.1|CO526434
EST:     TGGCACCCCTCTTCTTTGTATTTCGGAGTGATCCGGATGATAAAAATGCT                         GTATGGAGAATTCGCGGAAGCGGATTCATTCTTTTGCTTCGTCGAGTTGCT
genomic: TGGCACCCCTCTTCTTTGTATTTCGGAGTGATCCGGATGATAAAAATGCTgtatggagta ... acccttgtagG-A---A---TTCGCGGAAGCGGATTCATTCTTTTGCTTCGTCGAGTTGCT

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: 127

TGCCAAGCTGAATGCTGGAATAAGATATGTACAAGGGATGAATGAAGTTTTGGCACCCCTCTTCTTTGTATTTCGGAGTGATCCGGATGATAAAAATGCTgtatggagta ... acccttgtagGAATTCGCGGAAGCGGATTCATTCTTTTGCTTCGTCGAGTTGCTTAGTGGGTTCAGAGACAACTTCTGCCAGAAACTGGACAACAGTGCTGTTGGCATTC


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 109

TGCCAAGCTGAATGCTGGAATAAGATATGTACAAGGGATGAATGAAGTTTTGGCACCCCTCTTCTTTGTATTTCGGAGTGATCCGGATGATAAAAATGCTgtatggagta ... acccttgtagGAATTCGCGGAAGCGGATTCATTCTTTTGCTTCGTCGAGTTGCTTAGTGGGTTCAGAGACAACTTCTGCCAGAAACTGGACAACAGTGCTGTTGGCATTC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 71

TGCCAAGCTGAATGCTGGAATAAGATATGTACAAGGGATGAATGAAGTTTTGGCACCCCTCTTCTTTGTATTTCGGAGTGATCCGGATGATAAAAATGCTgtatggagta ... acccttgtagGAATTCGCGGAAGCGGATTCATTCTTTTGCTTCGTCGAGTTGCTTAGTGGGTTCAGAGACAACTTCTGCCAGAAACTGGACAACAGTGCTGTTGGCATTC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 68

TGCCAAGCTGAATGCTGGAATAAGATATGTACAAGGGATGAATGAAGTTTTGGCACCCCTCTTCTTTGTATTTCGGAGTGATCCGGATGATAAAAATGCTgtatggagta ... acccttgtagGAATTCGCGGAAGCGGATTCATTCTTTTGCTTCGTCGAGTTGCTTAGTGGGTTCAGAGACAACTTCTGCCAGAAACTGGACAACAGTGCTGTTGGCATTC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttagtcattactatatcttctgtatcgtgatcttgctattcggaacccttgtagGAATTCGCGGAAGCGGATTCATTCTTTTGCTTCGTCGAGTTGCTTAGTGGGTTCAGAGACAACTTCTGCCAGAAACTGGACAACAGTGCTGTTGGCATTC
                                              cccttgt  CT-rich tract
       attactatat  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatggagtaagagattgttttttttaccaagttcttagtgccctgcattgtacttctgatagccgaagctttcatgtttgctttagtcattactatatcttctgtatcgtgatcttgctattcggaacccttgtagGAATTCGCGGAAGCGGATTCATTCTTTTGCTTCGTCGAGTTGCTTAGTGGGTTCAGAGACAACTTCTGCCAGAAACTGGACAACAGTGCTGTTGGCATTC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT