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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTCTGACCGGAGTGGTTCCGTGGAGAGCACCGCTGCTTACATAATTCGAGGGCTGTGTCGGAGGTGCTGCCTTCCTGAAACAATTCTAAGATCTATGCAGgtgaggcgatcgagcaaatgatctgtgcaatcgtattgttgtacaaaatacatgtagtttcttggcgtgcccctcaccagtgtagacgattacattaatttttgttgcttttatttggcag

Basic information

species Zea mays
transcript GRMZM2G348675_T02
intron # 22
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G348675_T02 (Zea mays), 5'ss of exon 22
lower sequence: LOC_Os11g42420.1 (Oryza sativa), 5'ss of exon 22
TTCTGACCGGAGTGGTTCCGTGGAGAGCACCGCTGCTTACATAATTCGAGGGCTGTGTCGGAGGTGCTGCCTTCCTGAAACAATTCTAAGATCTATGCAGgtgaggcgatcgagcaaatgatctgtgcaatcgtattgttgtacaaaatacatgtagtttcttggcgtgcccctcaccagtgtagacgattacattaatttttgttgcttttatttggcag
||||||  |   |||||| || || ||||| ||||| ||||||||||| ||||| ||||| || |||||||| || ||||| |||||| ||||||||||||||| |      |||||        |  |  ||  |||||| | |  | |      | ||  |   ||||  ||      | |||   || | ||| ||   |||| ||| |||||  |||
TTCTGATGGTCATGGTTCAGTAGAAAGCACTGCTGCATACATAATTCGTGGGCTTTGTCGTAGATGCTGCCTGCCAGAAACTATTCTACGATCTATGCAGgtgatgt-----agcaa--------tatatccgatttgttgcagatgaaat-----gattgctactgtgctgcttgt--atatagctaat-atattgatacatgtttcttatatttttcag
















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|33096233|gb|CF056227.1|CF056227
EST:     GGCTGTGTCAGAGGTGCTGCCTTCCTGAAACAATTCTAAGATCTATGCAG                         GCATGTATCGCACTCTCCGCGGCTGGTGATGATCTAGATTACTCTCTAGAT
genomic: GGCTGTGTCGGAGGTGCTGCCTTCCTGAAACAATTCTAAGATCTATGCAGgtgaggcgat ... tatttggcagGCATGTATCGCACTCTCCGCGGCTGGTGATGATCTAGATTACTCTCTAGAT
EST: gi|60401356|gb|DN234163.1|DN234163
EST:     GGCTGTGTCGGAGGTGCTGCCTTCCTGAAACAATTCTAAGATCTATGCAG                         GCATGTATCGCACTCTCCGCGGCTGGTGATGATCTAGATTACTCTCTAGAT
genomic: GGCTGTGTCGGAGGTGCTGCCTTCCTGAAACAATTCTAAGATCTATGCAGgtgaggcgat ... tatttggcagGCATGTATCGCACTCTCCGCGGCTGGTGATGATCTAGATTACTCTCTAGAT
EST: gi|89106042|gb|DY576259.1|DY576259
EST:     GGCTGTGTCGGAGGTGCTGCCTTCCTGAAACAATTCTAAGATCTATGCAG                         GCATGTATCGCACTCTCCGCGGCTGGTGATGATCTAGATTACTCTCTAGAT
genomic: GGCTGTGTCGGAGGTGCTGCCTTCCTGAAACAATTCTAAGATCTATGCAGgtgaggcgat ... tatttggcagGCATGTATCGCACTCTCCGCGGCTGGTGATGATCTAGATTACTCTCTAGAT
EST: gi|33098458|gb|CF058418.1|CF058418
EST:     GGCTGTGTCGGAGGTGCTGCCTTCCTGAAACAATTCTAAGATCTATGCGG                         GCATGTATCGCACTCTCCGCGGCTGGTGATGATCTAGATTACTCTCTAGAT
genomic: GGCTGTGTCGGAGGTGCTGCCTTCCTGAAACAATTCTAAGATCTATGCAGgtgaggcgat ... tatttggcagGCATGTATCGCACTCTCCGCGGCTGGTGATGATCTAGATTACTCTCTAGAT
EST: gi|71444755|gb|DR825805.1|DR825805
EST:     GGCTGTGTCGGAGGTGCTGCCTTCCTGAAACAATTCTAAGATCTATGCAG                         GCATGTATCGCACTCTCCGCGGCTGGAGATGATCTAGATTACTCTCTAGAT
genomic: GGCTGTGTCGGAGGTGCTGCCTTCCTGAAACAATTCTAAGATCTATGCAGgtgaggcgat ... tatttggcagGCATGTATCGCACTCTCCGCGGCTGGTGATGATCTAGATTACTCTCTAGAT
EST: gi|31611836|gb|CD568458.1|CD568458
EST:     GGCTGTGTCGGAGGTGCTGCCTTCCTGAAACAATTCTAAGATCTATGCAG                         GCATGTATCGCACTCTCCGCGGCTGGTGATGATCTAGATTACTCTCTAGAT
genomic: GGCTGTGTCGGAGGTGCTGCCTTCCTGAAACAATTCTAAGATCTATGCAGgtgaggcgat ... tatttggcagGCATGTATCGCACTCTCCGCGGCTGGTGATGATCTAGATTACTCTCTAGAT
EST: gi|211241122|gb|FL071392.1|FL071392
EST:     GGCTGTGTCGGAGGTGCTGCCTTCCTGAAACAATTCTAAGATCTATGCAG                         GCATGTATCGCACTCTCCGCGGCTGGTGATGATCTAGATTACTCTCTAGAT
genomic: GGCTGTGTCGGAGGTGCTGCCTTCCTGAAACAATTCTAAGATCTATGCAGgtgaggcgat ... tatttggcagGCATGTATCGCACTCTCCGCGGCTGGTGATGATCTAGATTACTCTCTAGAT
EST: gi|71769927|gb|DR967864.1|DR967864
EST:     GGCTGTGTCGGAGGTGCTGCCTTCCTGAAACAATTCTAAGATCTATGCAG                         GCATGTATCGCACTCTCCGCGGCTGGTGATGATCTAGATTACTCTCTAGAT
genomic: GGCTGTGTCGGAGGTGCTGCCTTCCTGAAACAATTCTAAGATCTATGCAGgtgaggcgat ... tatttggcagGCATGTATCGCACTCTCCGCGGCTGGTGATGATCTAGATTACTCTCTAGAT
EST: gi|60337110|gb|DN204083.1|DN204083
EST:     GGCTGTGTCGGAGGTGCTGCCTTCCTGAAACAATTCTAAGATCTATGCAG                         GCATGTATCGCACTCTCCGCGGCTGGTGATGATCTAGATTACTCTCTAGAT
genomic: GGCTGTGTCGGAGGTGCTGCCTTCCTGAAACAATTCTAAGATCTATGCAGgtgaggcgat ... tatttggcagGCATGTATCGCACTCTCCGCGGCTGGTGATGATCTAGATTACTCTCTAGAT
EST: gi|91056201|gb|EB166619.1|EB166619
EST:     GGCTGTGTCGGAGGTGCTGCCTTCCTGAAACAATTCTAAGATCTATGCAG                         GCATGTATCGCACTCTCCGCGGCTGGTGATGATCTAGATTACTCTCTAGAT
genomic: GGCTGTGTCGGAGGTGCTGCCTTCCTGAAACAATTCTAAGATCTATGCAGgtgaggcgat ... tatttggcagGCATGTATCGCACTCTCCGCGGCTGGTGATGATCTAGATTACTCTCTAGAT
EST: gi|6021399|gb|AW066327.1|AW066327
EST:     GGCTGNGTCGGAGGTGCTGCCTTCCTGAAACAATTCTAAGATCTATGCAG                         GCATGTATCGCACTCTCCGCGGCTGGTGATGATCTAGATTACTCTCTAGAT
genomic: GGCTGTGTCGGAGGTGCTGCCTTCCTGAAACAATTCTAAGATCTATGCAGgtgaggcgat ... tatttggcagGCATGTATCGCACTCTCCGCGGCTGGTGATGATCTAGATTACTCTCTAGAT
EST: gi|37375043|gb|CF623932.1|CF623932
EST:     GGCTGTGTCGGAGGTGCTGCCTTCCTGAAACAATTCTAAGATCTATGCAG                         GCATGTATCGCACTCTCCGCGGCTGGTGATGATCTAGATTACTCTCTAGAT
genomic: GGCTGTGTCGGAGGTGCTGCCTTCCTGAAACAATTCTAAGATCTATGCAGgtgaggcgat ... tatttggcagGCATGTATCGCACTCTCCGCGGCTGGTGATGATCTAGATTACTCTCTAGAT
EST: gi|60394400|gb|DN227270.1|DN227270
EST:     GGCTGTGTCGGAGGTGCTGCCTTCCTGAAACAATTCTAAGATCTATGCAG                         GCATGTATCGCACTCTCCGCGGCTGGTGATGATCTAGATTACTCTCTAGAT
genomic: GGCTGTGTCGGAGGTGCTGCCTTCCTGAAACAATTCTAAGATCTATGCAGgtgaggcgat ... tatttggcagGCATGTATCGCACTCTCCGCGGCTGGTGATGATCTAGATTACTCTCTAGAT
EST: gi|8516300|gb|BE123026.1|BE123026
EST:     AAGATCTATGCAG                         GCATGTATCGCACTCTCCGCGGCTGGTGATGATCTAGATTACTCTCTAGAT
genomic: AAGATCTATGCAGgtgaggcgat ... tatttggcagGCATGTATCGCACTCTCCGCGGCTGGTGATGATCTAGATTACTCTCTAGAT
EST: gi|78077107|gb|DV505541.1|DV505541
EST:     GGCTGTGTCGGAGGTGCTGCCTTCCTGAAACAATTCTAAGATCTATGCAG                         GCATGTATCGCACTCTCCGCGGCTGGTGATGATCTAGATTACTCTCTAGAT
genomic: GGCTGTGTCGGAGGTGCTGCCTTCCTGAAACAATTCTAAGATCTATGCAGgtgaggcgat ... tatttggcagGCATGTATCGCACTCTCCGCGGCTGGTGATGATCTAGATTACTCTCTAGAT
EST: gi|21843367|gb|BQ703948.1|BQ703948
EST:     GGCTGTGTCGGAGGTGCTGCCTTCCTGAAACAATTCTAAGATCTATGCAG                         GCATGTATCGCCCTCTCCGCGGCTGGTGATGATCTAGATTACTCTCTAGAT
genomic: GGCTGTGTCGGAGGTGCTGCCTTCCTGAAACAATTCTAAGATCTATGCAGgtgaggcgat ... tatttggcagGCATGTATCGCACTCTCCGCGGCTGGTGATGATCTAGATTACTCTCTAGAT
EST: gi|32938062|gb|CF042881.1|CF042881
EST:     GGCTGTGTCGGAGGTGCTGCCTTCCTGAAACAATTCTAAGATCTATGCAG                         GCATGTATCGCACTCTCCGCGGCTGGTGATGATCTAGATTACTCTCTAGAT
genomic: GGCTGTGTCGGAGGTGCTGCCTTCCTGAAACAATTCTAAGATCTATGCAGgtgaggcgat ... tatttggcagGCATGTATCGCACTCTCCGCGGCTGGTGATGATCTAGATTACTCTCTAGAT
EST: gi|6526938|gb|AW216185.1|AW216185
EST:     GGCTGTGTCGGAGGTGCTGCCTTCCTGAAACAATTCTAAGATCTATGCAG                         GCATGTATCGCACTCTCCGCGGCTGGTGATGATCTAGATTACTCTCTAGAT
genomic: GGCTGTGTCGGAGGTGCTGCCTTCCTGAAACAATTCTAAGATCTATGCAGgtgaggcgat ... tatttggcagGCATGTATCGCACTCTCCGCGGCTGGTGATGATCTAGATTACTCTCTAGAT
EST: gi|211426538|gb|FL064839.1|FL064839
EST:     GGCTGTGTCGGAGGTGCTGCCTTCCTGAAACAATTCTAAGATCTATGCAG                         GCATGTATCGCACTCTCCGCGGCTGGTGATGATCTAGATTACTCTCTAGAT
genomic: GGCTGTGTCGGAGGTGCTGCCTTCCTGAAACAATTCTAAGATCTATGCAGgtgaggcgat ... tatttggcagGCATGTATCGCACTCTCCGCGGCTGGTGATGATCTAGATTACTCTCTAGAT
EST: gi|6012524|gb|AW061961.1|AW061961
EST:     GGCTGTGTCGGAGGTGCTGCCTTCCTGAAACAATTCTAAGATCTATGCAG                         GCATGTATCGCACTCTCCGCGGCTGGTGATGATCTAGATTACTCTCTAGAT
genomic: GGCTGTGTCGGAGGTGCTGCCTTCCTGAAACAATTCTAAGATCTATGCAGgtgaggcgat ... tatttggcagGCATGTATCGCACTCTCCGCGGCTGGTGATGATCTAGATTACTCTCTAGAT
EST: gi|60342258|gb|DN209231.1|DN209231
EST:     GGCTGTGTCGGAGGTGCTGCCTTCCTGAAACAATTCTAAGATCTATGCAG                         GCATGTATCGCACTCTCCGCGGCTGGTGATGATCTAGATTACTCTCTAGAT
genomic: GGCTGTGTCGGAGGTGCTGCCTTCCTGAAACAATTCTAAGATCTATGCAGgtgaggcgat ... tatttggcagGCATGTATCGCACTCTCCGCGGCTGGTGATGATCTAGATTACTCTCTAGAT
EST: gi|211436987|gb|FL183985.1|FL183985
EST:     GGCTGTGTCGAAGGTGCTGCCTTCCTGAAACAATTCTAAGATCTATGCAG                         GCATGTATCGCACTCTCCGCGGCTGGT
genomic: GGCTGTGTCGGAGGTGCTGCCTTCCTGAAACAATTCTAAGATCTATGCAGgtgaggcgat ... tatttggcagGCATGTATCGCACTCTCCGCGGCTGGT
EST: gi|31406262|gb|CD484994.1|CD484994
EST:     GGCTGTGTCGGAGGTGCTGCCTTCCTGAAACAATTCTAAGATCTATGCAG                         GCATGTATCGCACTCTCCGCGGCTGGTGATGATCTAGATTACTCTCTAGAT
genomic: GGCTGTGTCGGAGGTGCTGCCTTCCTGAAACAATTCTAAGATCTATGCAGgtgaggcgat ... tatttggcagGCATGTATCGCACTCTCCGCGGCTGGTGATGATCTAGATTACTCTCTAGAT
EST: gi|60358719|gb|DN225692.1|DN225692
EST:     GGCTGTGTCGGAGGTGCTGCCTTCCTGAAACAATTCTAAGATCTATGCAG                         GCATGTATCGCACTCTCCGCGGCTGGTGATGATCTAGATTACTCTCTAGAT
genomic: GGCTGTGTCGGAGGTGCTGCCTTCCTGAAACAATTCTAAGATCTATGCAGgtgaggcgat ... tatttggcagGCATGTATCGCACTCTCCGCGGCTGGTGATGATCTAGATTACTCTCTAGAT
EST: gi|32910038|gb|CF014850.1|CF014850
EST:     GGCTGTGTCGGAGGTGCTGCCTTCCTGAAACAATTCTAAGATCTATGCAG                         GCATGTATCGCACTCTCCGCGGCTGGTGATGATCTAGATTACTCTCTAGAT
genomic: GGCTGTGTCGGAGGTGCTGCCTTCCTGAAACAATTCTAAGATCTATGCAGgtgaggcgat ... tatttggcagGCATGTATCGCACTCTCCGCGGCTGGTGATGATCTAGATTACTCTCTAGAT
EST: gi|8516418|gb|BE123144.1|BE123144
EST:     AAGATCTATGCAG                         GCATGTATCGCACTCTCCGCGGCTGGTGATGATCTAGATTACTCTCTAGAT
genomic: AAGATCTATGCAGgtgaggcgat ... tatttggcagGCATGTATCGCACTCTCCGCGGCTGGTGATGATCTAGATTACTCTCTAGAT
EST: gi|60398909|gb|DN231725.1|DN231725
EST:     GGCTGTGTCGGAGGTGCTGCCTTCCTGAAACAATTCTAAGATCTATGCAG                         GCATGTATCGCACTCTCCGCGGCTGGTGATGATCTAGATTACTCTCTAGAT
genomic: GGCTGTGTCGGAGGTGCTGCCTTCCTGAAACAATTCTAAGATCTATGCAGgtgaggcgat ... tatttggcagGCATGTATCGCACTCTCCGCGGCTGGTGATGATCTAGATTACTCTCTAGAT
EST: gi|87157582|gb|DY402371.1|DY402371
EST:     GGCTGTGTCGGAGGTGCTGCCTTCCTGAAACAATTCTAAGATCTATGCAG                         GCATGTATCGCACTCTCCGCGGCTGGTGATGATCTAGATTACTCTCTAGAT
genomic: GGCTGTGTCGGAGGTGCTGCCTTCCTGAAACAATTCTAAGATCTATGCAGgtgaggcgat ... tatttggcagGCATGTATCGCACTCTCCGCGGCTGGTGATGATCTAGATTACTCTCTAGAT
EST: gi|33095636|gb|CF055630.1|CF055630
EST:     GGCTGTGTCGGAGGTGCTGCCTTCCTGAAACAATTCTAAGATCTATGCAG                         GCATGTATCGCACTCTCCGCGGCTGGTGATGATCTAGATTACTCTCTAGAT
genomic: GGCTGTGTCGGAGGTGCTGCCTTCCTGAAACAATTCTAAGATCTATGCAGgtgaggcgat ... tatttggcagGCATGTATCGCACTCTCCGCGGCTGGTGATGATCTAGATTACTCTCTAGAT
EST: gi|21432401|gb|BQ547891.1|BQ547891
EST:     GGCTGTGTCGGAGGTGCTGCCTTCCTGAAACAATTCTAAGATCTATGCAG                         GCATGTATCGCACTCTCCGCGGCTGGTGATGATCTAGATTACTCTCTAGAT
genomic: GGCTGTGTCGGAGGTGCTGCCTTCCTGAAACAATTCTAAGATCTATGCAGgtgaggcgat ... tatttggcagGCATGTATCGCACTCTCCGCGGCTGGTGATGATCTAGATTACTCTCTAGAT
EST: gi|33095263|gb|CF055257.1|CF055257
EST:     GGCTGTGTCGGAGGTGCTGCCTTCCTGAAACAATTCTAAGATCTATGCAG                         GCATGTATCGCACTCTCCGCGGCTGGTGATGATCTAGATTACTCTCTAGAT
genomic: GGCTGTGTCGGAGGTGCTGCCTTCCTGAAACAATTCTAAGATCTATGCAGgtgaggcgat ... tatttggcagGCATGTATCGCACTCTCCGCGGCTGGTGATGATCTAGATTACTCTCTAGAT
EST: gi|78024348|gb|DV492735.1|DV492735
EST:     GGCTGTGTCGGAGGTGCTGCCTTCCTGAAACAATTTTAAGATCTATGCAG                         GCATGTATCGCACTCTCCGCGGCTGGTGATGATCTAGATTACTCTCTAGAT
genomic: GGCTGTGTCGGAGGTGCTGCCTTCCTGAAACAATTCTAAGATCTATGCAGgtgaggcgat ... tatttggcagGCATGTATCGCACTCTCCGCGGCTGGTGATGATCTAGATTACTCTCTAGAT

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: 289

TTCTGACCGGAGTGGTTCCGTGGAGAGCACCGCTGCTTACATAATTCGAGGGCTGTGTCGGAGGTGCTGCCTTCCTGAAACAATTCTAAGATCTATGCAGgtgaggcgat ... tatttggcagGCATGTATCGCACTCTCCGCGGCTGGTGATGATCTAGATTACTCTCTAGATAAATGTGACGAACTTGTTGAGTTAGTTGGTTCAGCCGAGTCTGGAATGA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 69

TTCTGACCGGAGTGGTTCCGTGGAGAGCACCGCTGCTTACATAATTCGAGGGCTGTGTCGGAGGTGCTGCCTTCCTGAAACAATTCTAAGATCTATGCAGgtgaggcgat ... tatttggcagGCATGTATCGCACTCTCCGCGGCTGGTGATGATCTAGATTACTCTCTAGATAAATGTGACGAACTTGTTGAGTTAGTTGGTTCAGCCGAGTCTGGAATGA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 114

TTCTGACCGGAGTGGTTCCGTGGAGAGCACCGCTGCTTACATAATTCGAGGGCTGTGTCGGAGGTGCTGCCTTCCTGAAACAATTCTAAGATCTATGCAGgtgaggcgat ... tatttggcagGCATGTATCGCACTCTCCGCGGCTGGTGATGATCTAGATTACTCTCTAGATAAATGTGACGAACTTGTTGAGTTAGTTGGTTCAGCCGAGTCTGGAATGA


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 91

TTCTGACCGGAGTGGTTCCGTGGAGAGCACCGCTGCTTACATAATTCGAGGGCTGTGTCGGAGGTGCTGCCTTCCTGAAACAATTCTAAGATCTATGCAGgtgaggcgat ... tatttggcagGCATGTATCGCACTCTCCGCGGCTGGTGATGATCTAGATTACTCTCTAGATAAATGTGACGAACTTGTTGAGTTAGTTGGTTCAGCCGAGTCTGGAATGA


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTCTGACCGGAGTGGTTCCGTGGAGAGCACCGCTGCTTACATAATTCGAGGGCTGTGTCGGAGGTGCTGCCTTCCTGAAACAATTCTAAGATCTATGCAGgtgaggcgatcgagcaaatgatctgtgcaatcgtattgttgtacaaaatacatgtagtttcttggcgtgcccctcaccagtgtagacgattacattaatttttgttgcttttatttggcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC