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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTTACTGGAGATCTTGACAAGATGGTTGCACTACAAAGGTTATTAGAGCCATATGGCATCTGCGAGgtatgtttcttatcactccacatgaacttaactaaagtgtgaaaatgcagtttgggtcctttgggatgaatgaacagtcactcctttttatctgaccctaggtgttgttttgtgtgttctgtacacggtcctcaccattgttttgcacacatgacag

Basic information

species Zea mays
transcript GRMZM2G007647_T01
intron # 11
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G007647_T01 (Zea mays), 5'ss of exon 11
lower sequence: LOC_Os02g39570.1 (Oryza sativa), 5'ss of exon 11
CTTACTGGAGATCTTGACAAGATGGTTGCACTACAAAGGTTATTAGAGCCATATGGCATCTGCGAGgtatgtttc-ttatcactccacatgaacttaactaaagtgtgaaaatgcagtttgggtcctttgggatgaatgaacagtcactcctttttatctgaccctaggtgttgttttgtgtgttctgtacacggtcctcaccattgttttgcacacatgacag
|||||||| ||||| ||||||||||||||| |||||||| | || ||||| ||||||||||| ||||||| ||   || |   |  || |    || ||   |         |||   |  |||  | ||   ||||   |   |  |  |   |||||||  |  |  |                                                      
CTTACTGGGGATCTCGACAAGATGGTTGCATTACAAAGGCTGTTGGAGCCTTATGGCATCTGTGAGgtatattgaattctttttgtacttttctttcacctcatccgtttgttgctcatgtggttatgtgatgtgaa---atgatgtcaacagattatctg--cgcaaata-----------------------------------------------------

upper sequence: GRMZM2G007647_T01 (Zea mays), 5'ss of exon 11
lower sequence: GLYMA08G13290.1 (Glycine max), 5'ss of exon 11
CTTACTGGAGATCTTGACAAGATGGTTGCACTACAAAGGTTATTAGAGCCATATGGCATCTGCGAGgtatgtttcttatcactccacatgaacttaactaaagtgtgaaaatgcagtttgggtcctttgggatgaatgaacagtcactcctttttatctgaccctaggtgttgttttgtgtgttctgtacacggtcctcaccattgttttgcacacatgacag
|||||||||||| | ||||||||||||||| | || || || ||||| ||||||||||| || |||||||||||  ||| | |   | |  ||||| |  |   ||  | ||   | | | | |  |||   ||  | ||        | | ||      | |   ||    |  ||                                              
CTTACTGGAGATTTGGACAAGATGGTTGCATTGCAGAGATTGTTAGAACCATATGGCATTTGTGAGgtatgttt--tataagttttctttcacttaccata---gtagatattttgct-gagacagttgacttgtttaaat-----tccttattccataaatctccggaaccgaatt----------------------------------------------

upper sequence: GRMZM2G007647_T01 (Zea mays), 5'ss of exon 11
lower sequence: GLYMA05G30130.1 (Glycine max), 5'ss of exon 11
CTTACTGGAGATCTTGACAAGATGGTTGCACTACAAAGGTTATTAGAGCCATATGGCATCTGCGAGgtatgtttctta---tcactccacatgaacttaactaaagtgtgaaaatgcagtttgggtcctttgggatgaatgaacagtcactcctttttatctgaccctaggtgttgttttgtgtgttctgtacacggtcctcaccattgttttgcacacatgacag
|||||||||||| | ||||||||||||||| |||| || || ||||| ||||||||||| || |||||||||||  ||   |   ||||| |    |     | | | ||   |  ||||| |  |  |||    |   |   |  | |          ||  |                                                              
CTTACTGGAGATTTGGACAAGATGGTTGCATTACAGAGATTGTTAGAACCATATGGCATTTGTGAGgtatgttttataaattttttccacttaccatagtagatattttgctgagacagtt-gacttgtttaaattccgtattccataaacttccagagtcgaattt-----------------------------------------------------------

upper sequence: GRMZM2G007647_T01 (Zea mays), 5'ss of exon 11
lower sequence: AT2G31810.2 (Arabidopsis thaliana), 5'ss of exon 11
CTTACTGGAGATCTTGACAAGATGGTTGCACTACAAAGGTTATTAGAGCCATATGGCATCTGCGAGgtatgtttcttatcactccacatgaacttaactaaagtgtgaaaatgcagtttgggtcctttgggatgaatgaacagtcactcctttttatctgaccctaggtgttgttttgtgtgttctgtacacggtcctcaccattgttttgcacacatgacag
|||||||| ||||| ||||||||||||||||| ||||||||||| ||||| ||||| || || ||||| ||||||  |     |        ||||   || |  | |    |    ||   |  |||   || |||||     || |  ||   ||     || |                                                         
CTTACTGGGGATCTAGACAAGATGGTTGCACTGCAAAGGTTATTGGAGCCCTATGGTATATGTGAGgtttgtttcgcaatctactttcatctcttagtgaatgcataaccccgtgaattct-taatttcttat-aatgatactccaattgttcggataaagtcccaaa-------------------------------------------------------

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|32808276|gb|CD960510.1|CD960510
EST:     ACAAGATGGTTGCACTACAAAGGTTATTAGAGCCATATGGCATCTGCGAG                         GTCGCCAGAACTGGACGAGTGGCACTGGTCCGTGAATCGAAGGTCGACTCC
genomic: ACAAGATGGTTGCACTACAAAGGTTATTAGAGCCATATGGCATCTGCGAGgtatgtttct ... cacatgacagGTCGCCAGAACTGGACGAGTGGCACTGGTCCGTGAATCGAAGGTCGACTCC
EST: gi|6448417|gb|AW181183.1|AW181183
EST:     ACAAGATGGTTGCACTACAAAGGTTATTAGAGCCATATGGCATCTGCGAG                         GTCGCCAGAACTGGACGAGTGGCACTGGTCCGTGAATCGAAGGTCGACTCC
genomic: ACAAGATGGTTGCACTACAAAGGTTATTAGAGCCATATGGCATCTGCGAGgtatgtttct ... cacatgacagGTCGCCAGAACTGGACGAGTGGCACTGGTCCGTGAATCGAAGGTCGACTCC
EST: gi|32809421|gb|CD961655.1|CD961655
EST:     ACAAGATGGTTGCACTACAAAGGTTATTAGAGCCATATGGCACCTGCGAG                         GTCGCCAGAACTGGACGAGTGGCACTGGTCCGTGAATCGAAGGTCGACTCC
genomic: ACAAGATGGTTGCACTACAAAGGTTATTAGAGCCATATGGCATCTGCGAGgtatgtttct ... cacatgacagGTCGCCAGAACTGGACGAGTGGCACTGGTCCGTGAATCGAAGGTCGACTCC
EST: gi|60356357|gb|DN223330.1|DN223330
EST:     ACAAGATGGTTGCACTACAAAGGTTATTAGAGCCATATGGCATCTGCGAG                         GTCGCCAGAACTGGACGAGTGGCACTGGTCCGTGAATCGAAGGTCGACTCC
genomic: ACAAGATGGTTGCACTACAAAGGTTATTAGAGCCATATGGCATCTGCGAGgtatgtttct ... cacatgacagGTCGCCAGAACTGGACGAGTGGCACTGGTCCGTGAATCGAAGGTCGACTCC
EST: gi|22521063|gb|BU079874.1|BU079874
EST:     ACAAGATGGTTGCACTACAAAGGTTATTAGAGCCATATGGCATCTGCGAG                         GTCGCCAGAACTGGACGAGTGGCACTGGTCCGTGAATCGAAGGTCGACTCC
genomic: ACAAGATGGTTGCACTACAAAGGTTATTAGAGCCATATGGCATCTGCGAGgtatgtttct ... cacatgacagGTCGCCAGAACTGGACGAGTGGCACTGGTCCGTGAATCGAAGGTCGACTCC
EST: gi|32793465|gb|CD945701.1|CD945701
EST:     ACAAGATGGTTGCACTACAAAGGTTATTAGAGCCATATGGCATCTGCGAG                         GTCGCCAGAACTGGACGAGTGGCACTGGTCCGTGAATCGAAGGTCGACTCC
genomic: ACAAGATGGTTGCACTACAAAGGTTATTAGAGCCATATGGCATCTGCGAGgtatgtttct ... cacatgacagGTCGCCAGAACTGGACGAGTGGCACTGGTCCGTGAATCGAAGGTCGACTCC
EST: gi|44900488|gb|CK827033.1|CK827033
EST:     ACAAGATGGTTGCACTACAAAGGTTATTAGAGCCATATGGCATCTGCGAG                         GTCGCCAGAACTGGACGAGTGGCACTGGTCCGTGAATCGAAGGTCGACTCC
genomic: ACAAGATGGTTGCACTACAAAGGTTATTAGAGCCATATGGCATCTGCGAGgtatgtttct ... cacatgacagGTCGCCAGAACTGGACGAGTGGCACTGGTCCGTGAATCGAAGGTCGACTCC
EST: gi|4827621|gb|AI668313.1|AI668313
EST:     ACAAGATGGTTGCACTACAAAGGTTATTAGAGCCATATGGCATCTGCGAG                         GTCGCCAGAACTGGACGAGTGGCACTGGTCCGTGAATCGAAGGTCGACTCC
genomic: ACAAGATGGTTGCACTACAAAGGTTATTAGAGCCATATGGCATCTGCGAGgtatgtttct ... cacatgacagGTCGCCAGAACTGGACGAGTGGCACTGGTCCGTGAATCGAAGGTCGACTCC
EST: gi|50337798|gb|CO532924.1|CO532924
EST:     ACAAGATGGTTGCACTACAAAGGTTATTAGAGCCATATGGCATCTGCGAG                         GTCGCCAGAACTGGACGAGTGGCACTGGTCCGTGAATCGAAGGTCGACTCC
genomic: ACAAGATGGTTGCACTACAAAGGTTATTAGAGCCATATGGCATCTGCGAGgtatgtttct ... cacatgacagGTCGCCAGAACTGGACGAGTGGCACTGGTCCGTGAATCGAAGGTCGACTCC
EST: gi|87156533|gb|DY401322.1|DY401322
EST:     ACAAGATGGTTGCACTACAAAGGTTATTAGAGCCATATGGCATCTGCGAG                         GTCGCCAGAACTGGACGAGTGGCACTGGTCCGTGAATCGAAGGTCGACTCC
genomic: ACAAGATGGTTGCACTACAAAGGTTATTAGAGCCATATGGCATCTGCGAGgtatgtttct ... cacatgacagGTCGCCAGAACTGGACGAGTGGCACTGGTCCGTGAATCGAAGGTCGACTCC
EST: gi|32932919|gb|CF037731.1|CF037731
EST:     ACAAGATGGTTGCACTACAAAGGTTATTAGAGCCATATGGCATCTGCGAG                         GTCGCCAGAACTGGACGAGTGGCACTGGTCCGTGAATCGAAGGTCGACTCC
genomic: ACAAGATGGTTGCACTACAAAGGTTATTAGAGCCATATGGCATCTGCGAGgtatgtttct ... cacatgacagGTCGCCAGAACTGGACGAGTGGCACTGGTCCGTGAATCGAAGGTCGACTCC
EST: gi|211044763|gb|FL481858.1|FL481858
EST:     ACAAGATGGTTGCACTACAAAGGTTATTAGAGCCATATGGCATCTGCGAG                         GTCGCCAGAACTGGACGAGTGGCACTGGTCCGTGAATCGAAGGTCGACTCC
genomic: ACAAGATGGTTGCACTACAAAGGTTATTAGAGCCATATGGCATCTGCGAGgtatgtttct ... cacatgacagGTCGCCAGAACTGGACGAGTGGCACTGGTCCGTGAATCGAAGGTCGACTCC
EST: gi|37374784|gb|CF623779.1|CF623779
EST:     ACAAGATGGTTGCACTACAAAGGTTATTAGAGCCATATGGCATCTGCGAG                         GTCGCCAGAACTGGACGAGTGGCACTGGTCCGTGAATCGAAGGTCGACTCC
genomic: ACAAGATGGTTGCACTACAAAGGTTATTAGAGCCATATGGCATCTGCGAGgtatgtttct ... cacatgacagGTCGCCAGAACTGGACGAGTGGCACTGGTCCGTGAATCGAAGGTCGACTCC
EST: gi|67022242|gb|CO450991.1|CO450991
EST:     ACAAGATGGTTGCACTACANAGGTTATTAAAGCCATATGGCATCTGCGAG                         GTCGCCANAACTG
genomic: ACAAGATGGTTGCACTACAAAGGTTATTAGAGCCATATGGCATCTGCGAGgtatgtttct ... cacatgacagGTCGCCAGAACTG
EST: gi|67017113|gb|CO445862.1|CO445862
EST:     ACAAGATGGTTGCACTACAAAGGTTATTAGAGCCATATGGCATCTGCGAG                         GTCGCCAGAACTGGACGAGTGGCACTGGTCCGTGAATCGAAGGTCGACTCC
genomic: ACAAGATGGTTGCACTACAAAGGTTATTAGAGCCATATGGCATCTGCGAGgtatgtttct ... cacatgacagGTCGCCAGAACTGGACGAGTGGCACTGGTCCGTGAATCGAAGGTCGACTCC
EST: gi|89247462|gb|DY619248.1|DY619248
EST:     ACAAGATGGTTGCACTACAAAGGTTATTAGAGCCATATGGCATCTGCGAG                         GTCGCCAGAACTGGACGAGTGGCACTGGTCCGTGAATCGAAGGTCGACTCC
genomic: ACAAGATGGTTGCACTACAAAGGTTATTAGAGCCATATGGCATCTGCGAGgtatgtttct ... cacatgacagGTCGCCAGAACTGGACGAGTGGCACTGGTCCGTGAATCGAAGGTCGACTCC

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: 45 (upstream exon), 49 (downstream exon)
Score: 89

CTTACTGGAGATCTTGACAAGATGGTTGCACTACAAAGGTTATTAGAGCCATATGGCATCTGCGAGgtatgtttct ... cacatgacagGTCGCCAGAACTGGACGAGTGGCACTGGTCCGTGAATCGAAGGTCGACTCCAAGTACCTCCGCGGTTACTCTCTTCCATTGTAGCCTGGCATTTGTGATT


Block sizes: 43 (upstream exon), 46 (downstream exon)
Score: 32

CTTACTGGAGATCTTGACAAGATGGTTGCACTACAAAGGTTATTAGAGCCATATGGCATCTGCGAGgtatgtttct ... cacatgacagGTCGCCAGAACTGGACGAGTGGCACTGGTCCGTGAATCGAAGGTCGACTCCAAGTACCTCCGCGGTTACTCTCTTCCATTGTAGCCTGGCATTTGTGATT


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 51

CTTACTGGAGATCTTGACAAGATGGTTGCACTACAAAGGTTATTAGAGCCATATGGCATCTGCGAGgtatgtttct ... cacatgacagGTCGCCAGAACTGGACGAGTGGCACTGGTCCGTGAATCGAAGGTCGACTCCAAGTACCTCCGCGGTTACTCTCTTCCATTGTAGCCTGGCATTTGTGATT


Block sizes: 46 (upstream exon), 46 (downstream exon)
Score: 53

CTTACTGGAGATCTTGACAAGATGGTTGCACTACAAAGGTTATTAGAGCCATATGGCATCTGCGAGgtatgtttct ... cacatgacagGTCGCCAGAACTGGACGAGTGGCACTGGTCCGTGAATCGAAGGTCGACTCCAAGTACCTCCGCGGTTACTCTCTTCCATTGTAGCCTGGCATTTGTGATT


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTTACTGGAGATCTTGACAAGATGGTTGCACTACAAAGGTTATTAGAGCCATATGGCATCTGCGAGgtatgtttcttatcactccacatgaacttaactaaagtgtgaaaatgcagtttgggtcctttgggatgaatgaacagtcactcctttttatctgaccctaggtgttgttttgtgtgttctgtacacggtcctcaccattgttttgcacacatgacag

- - - - - - - - - AAGATG