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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTACATAGAGACAGCCGATCGGCCTGGCCTACTTCTTGAGATAATCAAGATCATCGCGGACACAAATATTGATGTGGAGTCAGCTGAGATTGATACTGAAgtatgctatgttccactccccttgctttttctagtttctaagaccagtaaaacctatcagatgatatctggcactgtatacag

Basic information

species Zea mays
transcript GRMZM2G066496_T01
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G066496_T01 (Zea mays), 5'ss of exon 8
lower sequence: LOC_Os12g05650.1 (Oryza sativa), 5'ss of exon 8
TTACATAGAGACAGCCGATCGGCCTGGCCTACTTCTTGAGATAATCAAGATCATCGCGGACACAAATATTGATGTGGAGTCAGCTGAGATTGATACTGAAgtatgctatgttccactccccttgctttttctagtttctaagaccagtaaaacctatc----agatgatatctggcactgtatacag
 |||||||||||||| ||||||||||| |||||||| || ||| | ||||||||| | |||   ||  |||||||||| ||||||||||| ||||||||||||||| |||||||  |  | |||  || |  | |  |   |  | || ||  |  |     |  | |||| ||    | ||| |||
GTACATAGAGACAGCTGATCGGCCTGGTCTACTTCTGGAAATAGTGAAGATCATCACTGACGTGAACGTTGATGTGGAATCAGCTGAGATAGATACTGAAgtatgccatgttcctatttctttg--ttatgaaatccccttgttctgtcaactcccttccttacttcatatgtgatgttttattcag
















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|67011780|gb|CO440529.1|CO440529
EST:     TCATCGCGGACACAAATATTGATGTGGAGTCAGCTGAGATTGATACTGAA                         GGTTTGGTTGCGAAGGACAAGTTCCATGTGAGTTACAGAGGTGCAAAACTA
genomic: TCATCGCGGACACAAATATTGATGTGGAGTCAGCTGAGATTGATACTGAAgtatgctatg ... ctgtatacagGGTTTGGTTGCGAAGGACAAGTTCCATGTGAGTTACAGAGGTGCAAAACTA
EST: gi|67022635|gb|CO451384.1|CO451384
EST:     TCATCGCGGACACAAATATTGATGTGGAGTCAGCTGAGATTGATACTGAA                         GGTTTGGTTGCGAAGGACAAGTTCCATGTGAGTTACAGAGGTGCAAAACTA
genomic: TCATCGCGGACACAAATATTGATGTGGAGTCAGCTGAGATTGATACTGAAgtatgctatg ... ctgtatacagGGTTTGGTTGCGAAGGACAAGTTCCATGTGAGTTACAGAGGTGCAAAACTA
EST: gi|32830465|gb|CD970143.1|CD970143
EST:     TCATCGCGGACACAAATATTGATGTGGAGTCAGCTGAGATTGATACTGAA                         GGTTTGGTTGCGAAGGACAAGTTCCATGTGAGTTACAGAGGTGCAAAACTA
genomic: TCATCGCGGACACAAATATTGATGTGGAGTCAGCTGAGATTGATACTGAAgtatgctatg ... ctgtatacagGGTTTGGTTGCGAAGGACAAGTTCCATGTGAGTTACAGAGGTGCAAAACTA
EST: gi|32804124|gb|CD956360.1|CD956360
EST:     TCATCGCGGACACAAATATTGATGTGGAGTCAGCTGAGATTGATACTGAA                         GGTTTGGTTGCGAAGGACAAGTTCCATGTGAGTTACAGAGGTGCAAAACTA
genomic: TCATCGCGGACACAAATATTGATGTGGAGTCAGCTGAGATTGATACTGAAgtatgctatg ... ctgtatacagGGTTTGGTTGCGAAGGACAAGTTCCATGTGAGTTACAGAGGTGCAAAACTA
EST: gi|6993917|gb|AW453131.1|AW453131
EST:     TCATCGCGGACACAAATATTGATGTGGAGTCAGCTGAGATTGATACTGAA                         GGTTTGGTTGCGAAGGACAAGTTCCATGTGAGTTAGAGAGGGGCAAAACTA
genomic: TCATCGCGGACACAAATATTGATGTGGAGTCAGCTGAGATTGATACTGAAgtatgctatg ... ctgtatacagGGTTTGGTTGCGAAGGACAAGTTCCATGTGAGTTACAGAGGTGCAAAACTA
EST: gi|17931807|gb|BM268767.1|BM268767
EST:     TCATCGCGGACACAAATATTGATGTGGAGTCAGCTGAGATTGATACTGAA                         GGTTTGGTTGCGAAGGACAAGTTCCATGTGAGTTACAGAGGTGCAAAACTA
genomic: TCATCGCGGACACAAATATTGATGTGGAGTCAGCTGAGATTGATACTGAAgtatgctatg ... ctgtatacagGGTTTGGTTGCGAAGGACAAGTTCCATGTGAGTTACAGAGGTGCAAAACTA
EST: gi|32859901|gb|CD999582.1|CD999582
EST:     TCATCGCGGACACAAATATTGATGTGGAGTCAGCTGAGATTGATACTGAA                         GGTTTGGTTGCGAAGGACAAGTTCCATGTGAGTTACAGAGGTGCAAAACTA
genomic: TCATCGCGGACACAAATATTGATGTGGAGTCAGCTGAGATTGATACTGAAgtatgctatg ... ctgtatacagGGTTTGGTTGCGAAGGACAAGTTCCATGTGAGTTACAGAGGTGCAAAACTA
EST: gi|37385755|gb|CF630034.1|CF630034
EST:     TTATCGCGGACACAAATATTGATGTGGAGTCAGCTGAGATTGATACTGAA                         GGTTTGGTTGCGAAGGACAAGTTCCATGTGAGTTACAGAGGTGCAAAACTA
genomic: TCATCGCGGACACAAATATTGATGTGGAGTCAGCTGAGATTGATACTGAAgtatgctatg ... ctgtatacagGGTTTGGTTGCGAAGGACAAGTTCCATGTGAGTTACAGAGGTGCAAAACTA
EST: gi|6851575|gb|AW352585.1|AW352585
EST:     TCATCGCGGACACAAATATTGATGTGGAGTCAGCTGAGATTGATACTGAA                         GGTTTGGTTGCGAAGGACAAGTTCCATGTGAGTTAGAGAGGTGCAAAACTA
genomic: TCATCGCGGACACAAATATTGATGTGGAGTCAGCTGAGATTGATACTGAAgtatgctatg ... ctgtatacagGGTTTGGTTGCGAAGGACAAGTTCCATGTGAGTTACAGAGGTGCAAAACTA
EST: gi|31558031|gb|CD527243.1|CD527243
EST:     TCATCGCGGACACAAATATTGATGTGGAGTCAGCTGAGATTGATACTGAA                         GGTTTGGTTGCGAAGGACAAGTTCCATGTGAGTTACAGAGGTGCAAAACTA
genomic: TCATCGCGGACACAAATATTGATGTGGAGTCAGCTGAGATTGATACTGAAgtatgctatg ... ctgtatacagGGTTTGGTTGCGAAGGACAAGTTCCATGTGAGTTACAGAGGTGCAAAACTA
EST: gi|148954707|gb|EC900159.2|EC900159
EST:     TCATCGCGGACACAAATATTGATGTGGAGTCAGCTGAGATTGATACTGAA                         GGTTTGGTTGCGAAGGACAAGTTCCATGTGAGTTACAGAGGTGCAAAACTA
genomic: TCATCGCGGACACAAATATTGATGTGGAGTCAGCTGAGATTGATACTGAAgtatgctatg ... ctgtatacagGGTTTGGTTGCGAAGGACAAGTTCCATGTGAGTTACAGAGGTGCAAAACTA
EST: gi|32801615|gb|CD953851.1|CD953851
EST:     TCATCGCGGACACAAATATTGATGTGGAGTCAGCTGAGATTGATACTGAA                         GGTTTGGTTGCGAAGGACAAGTTCCATGTGAGTTACAGAGGTGCAGAACTA
genomic: TCATCGCGGACACAAATATTGATGTGGAGTCAGCTGAGATTGATACTGAAgtatgctatg ... ctgtatacagGGTTTGGTTGCGAAGGACAAGTTCCATGTGAGTTACAGAGGTGCAAAACTA
EST: gi|18164129|gb|BM333968.1|BM333968
EST:     TCATCGCGGACACAAATATTGATGTGGAGTCAGCTGAGATTGATACTGAA                         GGTTTGGTTGCGAAGGACAAGTTCCATGTGAGTTACAGAGGTGCAAAACTA
genomic: TCATCGCGGACACAAATATTGATGTGGAGTCAGCTGAGATTGATACTGAAgtatgctatg ... ctgtatacagGGTTTGGTTGCGAAGGACAAGTTCCATGTGAGTTACAGAGGTGCAAAACTA
EST: gi|118406764|gb|EH038212.1|EH038212
EST:     TTATCGCGGACACAAATATTGATGTGGAGTCAGCTGAGATTGATACTGAA                         GGTTTGGTTGCGAAGGACAAGTTCCATGTGAGTTACAGAGGTGCAAAACTA
genomic: TCATCGCGGACACAAATATTGATGTGGAGTCAGCTGAGATTGATACTGAAgtatgctatg ... ctgtatacagGGTTTGGTTGCGAAGGACAAGTTCCATGTGAGTTACAGAGGTGCAAAACTA
EST: gi|31997712|gb|CD661732.1|CD661732
EST:     AAATATTGATGTGGAGTCAGCTGAGATTGATACTGAA                         GGTTTGGTTGCGAAGGACAAGTTCCATGTGAGTTACAGAGGTGCAAAACTA
genomic: AAATATTGATGTGGAGTCAGCTGAGATTGATACTGAAgtatgctatg ... ctgtatacagGGTTTGGTTGCGAAGGACAAGTTCCATGTGAGTTACAGAGGTGCAAAACTA
EST: gi|28985362|gb|CB350603.1|CB350603
EST:     TCATCGCGGACACAAATATTGATGTGGAGTCAGCTGAGATTGATACTGAA                         GGTTTGGTTGCGAAGGACAAGTTCCATGTGAGTTACAGAGGTGCAAAACTA
genomic: TCATCGCGGACACAAATATTGATGTGGAGTCAGCTGAGATTGATACTGAAgtatgctatg ... ctgtatacagGGTTTGGTTGCGAAGGACAAGTTCCATGTGAGTTACAGAGGTGCAAAACTA
EST: gi|37375358|gb|CF624110.1|CF624110
EST:     TTATCGCGGACACAAATATTGATGTGGAGTCAGCTGAGATTGATACTGAA                         GGTTTGGTTGCGAAGGACAAGTTCCATGTGAGTTACAGAGGTGCAAAACTA
genomic: TCATCGCGGACACAAATATTGATGTGGAGTCAGCTGAGATTGATACTGAAgtatgctatg ... ctgtatacagGGTTTGGTTGCGAAGGACAAGTTCCATGTGAGTTACAGAGGTGCAAAACTA
EST: gi|5901282|gb|AW042382.1|AW042382
EST:     TCATCGCGGACACAAATATTGATGTGGAGTCAGCTGAGATTGATACTGAA                         GGTTTGGTTGCGAAGGACAAGTTCCATGTGAGTTACAGAGGTGCAAAACTA
genomic: TCATCGCGGACACAAATATTGATGTGGAGTCAGCTGAGATTGATACTGAAgtatgctatg ... ctgtatacagGGTTTGGTTGCGAAGGACAAGTTCCATGTGAGTTACAGAGGTGCAAAACTA
EST: gi|89759755|gb|DY688471.1|DY688471
EST:     TCATCGCGGACACAAATATTGATGTGGAGTCAGCTGAGATTGATACTGAA                         GGTTTGGTTGCGAAGGACAAGTTCCATGTGAGTTACAGAGGTGCAAAACTA
genomic: TCATCGCGGACACAAATATTGATGTGGAGTCAGCTGAGATTGATACTGAAgtatgctatg ... ctgtatacagGGTTTGGTTGCGAAGGACAAGTTCCATGTGAGTTACAGAGGTGCAAAACTA
EST: gi|4776010|gb|AI665013.1|AI665013
EST:     TCATCGCGGACACAAATATTGATGTGGAGTCAGCTGAGATTGATACTGAA                         GGTTTGGTTGCGAAGGACAAGTTCCATGTGAGTTACAGAGGTGCAAAACTA
genomic: TCATCGCGGACACAAATATTGATGTGGAGTCAGCTGAGATTGATACTGAAgtatgctatg ... ctgtatacagGGTTTGGTTGCGAAGGACAAGTTCCATGTGAGTTACAGAGGTGCAAAACTA
EST: gi|60359682|gb|DN226655.1|DN226655
EST:     TCATCGCGGACACAAATATTGATGTGGAGTCAGCTGAGATTGATACTGAA                         GGTTTGGTTGCGAAGGACAAGTTCCATGTGAGTTACAGAGGTGCAAAACTA
genomic: TCATCGCGGACACAAATATTGATGTGGAGTCAGCTGAGATTGATACTGAAgtatgctatg ... ctgtatacagGGTTTGGTTGCGAAGGACAAGTTCCATGTGAGTTACAGAGGTGCAAAACTA
EST: gi|6851488|gb|AW352498.1|AW352498
EST:     CAAATATTGATGTGGAGTCAGCTGAGATTGATACTGAA                         GGTTTGGTTGCGAAGGACAAGTTCCATGTGAGGTACAGAGGTGCAAAACTA
genomic: CAAATATTGATGTGGAGTCAGCTGAGATTGATACTGAAgtatgctatg ... ctgtatacagGGTTTGGTTGCGAAGGACAAGTTCCATGTGAGTTACAGAGGTGCAAAACTA
EST: gi|60342007|gb|DN208980.1|DN208980
EST:     TTATCGCGGACACAAATATTGATGTGGAGTCAGCTGAGATTGATACTGAA                         GGTTTGGTTGCGAAGGACAAGTTCCATGTGAGTTACAGAGGTGCAAAACTA
genomic: TCATCGCGGACACAAATATTGATGTGGAGTCAGCTGAGATTGATACTGAAgtatgctatg ... ctgtatacagGGTTTGGTTGCGAAGGACAAGTTCCATGTGAGTTACAGAGGTGCAAAACTA

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), 48 (downstream exon)
Score: 192

TTACATAGAGACAGCCGATCGGCCTGGCCTACTTCTTGAGATAATCAAGATCATCGCGGACACAAATATTGATGTGGAGTCAGCTGAGATTGATACTGAAgtatgctatg ... ctgtatacagGGTTTGGTTGCGAAGGACAAGTTCCATGTGAGTTACAGAGGTGCAAAACTAAACAGCTCCTCATCTCAG


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 348

TTACATAGAGACAGCCGATCGGCCTGGCCTACTTCTTGAGATAATCAAGATCATCGCGGACACAAATATTGATGTGGAGTCAGCTGAGATTGATACTGAAgtatgctatg ... ctgtatacagGGTTTGGTTGCGAAGGACAAGTTCCATGTGAGTTACAGAGGTGCAAAACTAAACAGCTCCTCATCTCAG


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 347

TTACATAGAGACAGCCGATCGGCCTGGCCTACTTCTTGAGATAATCAAGATCATCGCGGACACAAATATTGATGTGGAGTCAGCTGAGATTGATACTGAAgtatgctatg ... ctgtatacagGGTTTGGTTGCGAAGGACAAGTTCCATGTGAGTTACAGAGGTGCAAAACTAAACAGCTCCTCATCTCAG


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 165

TTACATAGAGACAGCCGATCGGCCTGGCCTACTTCTTGAGATAATCAAGATCATCGCGGACACAAATATTGATGTGGAGTCAGCTGAGATTGATACTGAAgtatgctatg ... ctgtatacagGGTTTGGTTGCGAAGGACAAGTTCCATGTGAGTTACAGAGGTGCAAAACTAAACAGCTCCTCATCTCAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTACATAGAGACAGCCGATCGGCCTGGCCTACTTCTTGAGATAATCAAGATCATCGCGGACACAAATATTGATGTGGAGTCAGCTGAGATTGATACTGAAgtatgctatgttccactccccttgctttttctagtttctaagaccagtaaaacctatcagatgatatctggcactgtatacag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGA