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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agcttgccaaatttataattttccatgtcatctcacctgctgcgatttttgcaatcttttgtcttttatgattctaatgccacctatttttcatctacagACCGGAGACACTATCATTCAGCTCTACAACAATTTCATTGTCGACTTTGAGACCAAGATTAATCTGCTCAAACTTGCCCATTTTGCGGTGATAACTTCTC

Basic information

species Zea mays
transcript GRMZM5G868757_T04
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G868757_T07 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os01g32800.1 (Oryza sativa), 3'ss of exon 1
agcttgccaaat-ttataattttccatgtcatc-----tcacctgctgcgatttttgcaatcttttgtcttttatgattctaatgccacctatttttcatctacagACCGGAGACACTATCATTCAGCTCTACAACAATTTCATTGTCGACTTTGAGACCAAGATTAATCTGCTCAAACTTGCCCATTTTGCGGTGATAACTTCTC
   | ||  ||| ||  ||| ||  ||  | ||      ||  ||||  |  ||||      |      |  |   ||||||| | ||   ||| | |    |||||| || ||||| ||||| ||||||||||||||||||||    ||||| ||||| ||||| ||||| |||||||||||||| || ||||| ||  |||| |
---tagctgaatgtttcaatcttggattacttcaacaaccatatgcttagggttttaactgatgggcaatcctgcaattctaacggcattcattctcc---cacagACTGGCGACACCATCATACAGCTCTACAACAATTTCATCTCTGACTTCGAGACGAAGATCAATCTTCTCAAACTTGCCCACTTCGCGGTCATCGCTTCAC

upper sequence: GRMZM5G868757_T07 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os03g11570.1 (Oryza sativa), 3'ss of exon 1
-agcttgccaaatttat---aattttccatgtcatctcacctgctgcgatttttgcaatcttttgtcttttatgattctaatgccacctatttttcatctacagACCGGAGACACTATCATTCAGCTCTACAACAATTTCATTGTCGACTTTGAGACCAAGATTAATCTGCTCAAACTTGCCCATTTTGCGGTGATAACTTCTC
 |  || |     || |   ||  || | |    |   | |||||| |    |||     | |    ||||   |||||||   |  |     |||  |||||||| || |||||  |||| ||||||||||||||||||||    || || ||||| ||||| ||||| ||||||||||| ||||| ||||| ||  |||| |
aaatttactcttgttgtttgaaccttgcttaggtttgtaactgctgtg----ttgtgccttctgcgtttttgcaattctaacagcggcatccattctcctacagACGGGTGACACCCTCATACAGCTCTACAACAATTTCATCACTGATTTCGAGACGAAGATCAATCTTCTCAAACTTGCGCATTTCGCGGTCATCGCTTCGC
















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|211277769|gb|FL330867.1|FL330867
EST:     ACCAGCTCACCCTCAAGCTCGACCAATTCTTACAGCTCCAGGTCGCACAG                         ACCGGAGACACTATCATTCAGCTCTACAACAATTTCATTGTCGACTTTGAG
genomic: ACCAGCTCACCCTCAAGCTCGACCAATTCTTACAGCTCCAGGTCGCACAGgttcgcttcc ... tcatctacagACCGGAGACACTATCATTCAGCTCTACAACAATTTCATTGTCGACTTTGAG
EST: gi|211099199|gb|FL356879.1|FL356879
EST:     ACCAGCTCACCCTCAAGCTCGACCAATTCTTACAGCTCCAGGTCGCACAG                         ACCGGAGACACTATCATTCAGCTCTACAACAATTTCATTGTCGACTTTGAG
genomic: ACCAGCTCACCCTCAAGCTCGACCAATTCTTACAGCTCCAGGTCGCACAGgttcgcttcc ... tcatctacagACCGGAGACACTATCATTCAGCTCTACAACAATTTCATTGTCGACTTTGAG
EST: gi|148930110|gb|EC872431.2|EC872431
EST:     ACCAGCTCACCCTCAAGCTCGACCAATTCTTACAGCTCCAGGTCGCACAG                         ACCGGAGACACTATCATTCAGCTCTACAACAATTTCATTGTCGACTTTGAG
genomic: ACCAGCTCACCCTCAAGCTCGACCAATTCTTACAGCTCCAGGTCGCACAGgttcgcttcc ... tcatctacagACCGGAGACACTATCATTCAGCTCTACAACAATTTCATTGTCGACTTTGAG
EST: gi|148948407|gb|EC893924.2|EC893924
EST:     ACCAGCTCACCCTCAAGCTCGACCAATTCTTACAGCTCCAGGTCGCACAG                         ACCGGAGACACTATCATTCAGCTCTACAACAATTTCATTGTCGACTTTGAG
genomic: ACCAGCTCACCCTCAAGCTCGACCAATTCTTACAGCTCCAGGTCGCACAGgttcgcttcc ... tcatctacagACCGGAGACACTATCATTCAGCTCTACAACAATTTCATTGTCGACTTTGAG
EST: gi|148986083|gb|EE029890.2|EE029890
EST:     ACCAGCTCACCCTCAAGCTCGACCAATTCTTACAGCTCCAGGTCGCACAG                         ACCGGAGACACTATCATTCAGCTCTACAACAATTTCATTGTCGACTTTGAG
genomic: ACCAGCTCACCCTCAAGCTCGACCAATTCTTACAGCTCCAGGTCGCACAGgttcgcttcc ... tcatctacagACCGGAGACACTATCATTCAGCTCTACAACAATTTCATTGTCGACTTTGAG
EST: gi|211319213|gb|FL155861.1|FL155861
EST:     ACCAGCTCACCCTCAAGCTCGACCAATTCTTACAGCTCCAGGTCGCACAG                         ACCGGAGACACTATCATTCAGCTCTACAACAATTTCATTGTCGACTTTGAG
genomic: ACCAGCTCACCCTCAAGCTCGACCAATTCTTACAGCTCCAGGTCGCACAGgttcgcttcc ... tcatctacagACCGGAGACACTATCATTCAGCTCTACAACAATTTCATTGTCGACTTTGAG
EST: gi|211319211|gb|FL155859.1|FL155859
EST:     ACCAGCTCACCCTCAAGCTCGACCAATTCTTACAGCTCCAGGTCGCACAG                         ACCGGAGACACTATCATTCAGCTCTACAACAATTTCATTGTCGACTTTGAG
genomic: ACCAGCTCACCCTCAAGCTCGACCAATTCTTACAGCTCCAGGTCGCACAGgttcgcttcc ... tcatctacagACCGGAGACACTATCATTCAGCTCTACAACAATTTCATTGTCGACTTTGAG
EST: gi|211319208|gb|FL155856.1|FL155856
EST:     ACCAGCTCACCCTCAAGCT-GACCAATTCTTACAGCTCCAGGTCGCACAG                         ACCGGAGACACTATCATTCAGCTCTACAACAATTTCATTGTCGACTTTGAG
genomic: ACCAGCTCACCCTCAAGCTCGACCAATTCTTACAGCTCCAGGTCGCACAGgttcgcttcc ... tcatctacagACCGGAGACACTATCATTCAGCTCTACAACAATTTCATTGTCGACTTTGAG
EST: gi|14529417|gb|BI096550.1|BI096550
EST:     ACCAGCTCACCCTCAAGCTCGACCAATTCTTACAGCTCCAGGTCACACAG                         ACCGGAGACACTATCATTCAGCTCTACAACAATTTCATTGTCGACTTTGAG
genomic: ACCAGCTCACCCTCAAGCTCGACCAATTCTTACAGCTCCAGGTCGCACAGgttcgcttcc ... tcatctacagACCGGAGACACTATCATTCAGCTCTACAACAATTTCATTGTCGACTTTGAG
EST: gi|211540331|gb|FL320589.1|FL320589
EST:     ACCAGCTCACCCTCAAGCTCGACCAATTCTTACAGCTCCAGGTCGCACAG                         ACCGGAGACACTATCATTCAGCTCTACAACAATTTCATTGTCGACTTTGAG
genomic: ACCAGCTCACCCTCAAGCTCGACCAATTCTTACAGCTCCAGGTCGCACAGgttcgcttcc ... tcatctacagACCGGAGACACTATCATTCAGCTCTACAACAATTTCATTGTCGACTTTGAG
EST: gi|211319212|gb|FL155860.1|FL155860
EST:     ACCAGCTCACCCTCAASCTCGACCAATTCTTACAGCTCCAGGTCGCACAG                         ACCGGAGACACTATCATTCAGCTCTACAACAATTTCATTGTCGACTTTGAG
genomic: ACCAGCTCACCCTCAAGCTCGACCAATTCTTACAGCTCCAGGTCGCACAGgttcgcttcc ... tcatctacagACCGGAGACACTATCATTCAGCTCTACAACAATTTCATTGTCGACTTTGAG
EST: gi|148965470|gb|EE016279.2|EE016279
EST:     ACCAGCTCACCCTCAAGCTCGACCAATTCTTACAGCTCCAGGTCGCACAG                         ACCGGAGACACTATCATTCAGCTCTACAACAATTTCATTGTCGACTTTGAG
genomic: ACCAGCTCACCCTCAAGCTCGACCAATTCTTACAGCTCCAGGTCGCACAGgttcgcttcc ... tcatctacagACCGGAGACACTATCATTCAGCTCTACAACAATTTCATTGTCGACTTTGAG
EST: gi|149069680|gb|EE158063.2|EE158063
EST:     ACCAGCTCACCCTCAAGCTCGACCAATTCTTACAGCTCCAGGTCGCACAG                         ACCGGAGACACTATCATTCAGCTCTACAACAATTTCATTGTCGACTTTGAG
genomic: ACCAGCTCACCCTCAAGCTCGACCAATTCTTACAGCTCCAGGTCGCACAGgttcgcttcc ... tcatctacagACCGGAGACACTATCATTCAGCTCTACAACAATTTCATTGTCGACTTTGAG
EST: gi|9731352|gb|BE510104.1|BE510104
EST:     ACCAGCTCACCCTCAAGCTCGACCAATTCTTACAGCTCCAGGTCGCACAG                         ACCGGAGACACTATCATTCAGCTCTACAACAATTTCATTGTCGACTTTGAG
genomic: ACCAGCTCACCCTCAAGCTCGACCAATTCTTACAGCTCCAGGTCGCACAGgttcgcttcc ... tcatctacagACCGGAGACACTATCATTCAGCTCTACAACAATTTCATTGTCGACTTTGAG
EST: gi|211319209|gb|FL155857.1|FL155857
EST:     ACCAGCTCACCCTCAAGCTCGACCAATTCTTACAGCTCCAGGTCGCACAG                         ACCGGAGACACTATCATTCAGCTCTACAACAATTTCATTGTCGACTTTGAG
genomic: ACCAGCTCACCCTCAAGCTCGACCAATTCTTACAGCTCCAGGTCGCACAGgttcgcttcc ... tcatctacagACCGGAGACACTATCATTCAGCTCTACAACAATTTCATTGTCGACTTTGAG
EST: gi|149081820|gb|EE170979.2|EE170979
EST:     ACCAGCTCACCCTCAAGCTCGACCAATTCTTACAGCTCCAGGTCGCACAG                         ACCGGAGACACTATCATTCAGCTCTACAACAATTTCATTGTCGACTTTGAG
genomic: ACCAGCTCACCCTCAAGCTCGACCAATTCTTACAGCTCCAGGTCGCACAGgttcgcttcc ... tcatctacagACCGGAGACACTATCATTCAGCTCTACAACAATTTCATTGTCGACTTTGAG
EST: gi|149078129|gb|EE166878.2|EE166878
EST:     ACCAGCTCACCCTCAAGCTCGACCAATTCTTACAGCTCCAGGTCGCACAG                         ACCGGAGACACTATCATTCAGCTCTACAACAATTTCATTGTCGACTTTGAG
genomic: ACCAGCTCACCCTCAAGCTCGACCAATTCTTACAGCTCCAGGTCGCACAGgttcgcttcc ... tcatctacagACCGGAGACACTATCATTCAGCTCTACAACAATTTCATTGTCGACTTTGAG
EST: gi|22521302|gb|BU080113.1|BU080113
EST:     ACCAGCTCACCCTCAAGCTCGACCAATTCTTACAGCTCCAGGTCGCACAG                         ACCGGAGACACTATCATTCAGCTCTACAACAATTTCATTGTCGACTTTGAG
genomic: ACCAGCTCACCCTCAAGCTCGACCAATTCTTACAGCTCCAGGTCGCACAGgttcgcttcc ... tcatctacagACCGGAGACACTATCATTCAGCTCTACAACAATTTCATTGTCGACTTTGAG

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: 360

CTCCGACTGGTACGCCTCCCTCGCCGACCTCTACCAGCGGAAGCTATGGCACCAGCTCACCCTCAAGCTCGACCAATTCTTACAGCTCCAGGTCGCACAGgttcgcttcc ... tcatctacagACCGGAGACACTATCATTCAGCTCTACAACAATTTCATTGTCGACTTTGAGACCAAGATTAATCTGCTCAAACTTGCCCATTTTGCGGTGATAACTTCTC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 352

CTCCGACTGGTACGCCTCCCTCGCCGACCTCTACCAGCGGAAGCTATGGCACCAGCTCACCCTCAAGCTCGACCAATTCTTACAGCTCCAGGTCGCACAGgttcgcttcc ... tcatctacagACCGGAGACACTATCATTCAGCTCTACAACAATTTCATTGTCGACTTTGAGACCAAGATTAATCTGCTCAAACTTGCCCATTTTGCGGTGATAACTTCTC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 456

CTCCGACTGGTACGCCTCCCTCGCCGACCTCTACCAGCGGAAGCTATGGCACCAGCTCACCCTCAAGCTCGACCAATTCTTACAGCTCCAGGTCGCACAGgttcgcttcc ... tcatctacagACCGGAGACACTATCATTCAGCTCTACAACAATTTCATTGTCGACTTTGAGACCAAGATTAATCTGCTCAAACTTGCCCATTTTGCGGTGATAACTTCTC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 217

CTCCGACTGGTACGCCTCCCTCGCCGACCTCTACCAGCGGAAGCTATGGCACCAGCTCACCCTCAAGCTCGACCAATTCTTACAGCTCCAGGTCGCACAGgttcgcttcc ... tcatctacagACCGGAGACACTATCATTCAGCTCTACAACAATTTCATTGTCGACTTTGAGACCAAGATTAATCTGCTCAAACTTGCCCATTTTGCGGTGATAACTTCTC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttttgcaatcttttgtcttttatgattctaatgccacctatttttcatctacagACCGGAGACACTATCATTCAGCTCTACAACAATTTCATTGTCGACTTTGAGACCAAGATTAATCTGCTCAAACTTGCCCATTTTGCGGTGATAACTTCTC
                          ttctaat  putative branch site (score: 217)
                                     cctatttttcatct  putative PPT
                  ttttatgattctaat  TA-rich tract