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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cttatgccattttagaaccttccttaaggttgtggtatttgaagtctacatgtaagtgtaggaattcacttctgacgatgtggtttcgatgatattatagGTTTTGCATATGGACAGAAATGACTACTATGGAGGAGATTCCACCTCACTCAACCTTAATCAG

Basic information

species Zea mays
transcript GRMZM2G117507_T01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G117507_T01 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os05g34540.1 (Oryza sativa), 3'ss of exon 1
--cttatgcc-attttagaaccttccttaaggttgtggtatttgaagtctacatgtaagtgtaggaattcacttctgacgatgtggtttcgatgatattatagGTTTTGCATATGGACAGAAATGACTACTATGGAGGAGATTCCACCTCACTCAACCTTAATCAG
   ||||  | || |           |||||||| ||           |    |||  ||    | |    |       || ||| ||  |||| | ||  |||| ||||| ||||| |||||||||||||||||||| ||||||||||| ||||||||||| |||
tctttatatctatctgtatgagaattttaaggttctgcagacgacccaccgtctgtgggtt---gtacatgccctaacagacgtgcttgtgatggtttttcagGTGTTGCACATGGATAGAAATGACTACTATGGAGGGGATTCCACCTCGCTCAACCTTAACCAG

upper sequence: GRMZM2G117507_T01 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os05g23860.1 (Oryza sativa), 3'ss of exon 1
--cttatgccattttagaaccttccttaaggttgtggtatttgaag--tctacatgtaagtgtaggaattcacttctgacgatgtggtttcgatgatattatagGTTTTGCATATGGACAGAAATGACTACTATGGAGGAGATTCCACCTCACTCAACCTTAATCAG
  ||||| |||||| | |   |  |      | | | | || |  |  |  |||   |  | ||   |  ||  || || |   |  |||| ||| | ||  |||| ||||| ||||| || ||||||||||||||||||||||||||||| ||||||||||| |||
cccttatcccatttaaaagagtagc--ggcatagcgattttgggggatttcacaacaagatctaactaaacagatcggatgcact--tttcaatgtttttgcagGTCTTGCACATGGATAGGAATGACTACTATGGAGGAGATTCCACCTCGCTCAACCTTAACCAG
















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|211472425|gb|FL096495.1|FL096495
EST:     GGCTCAAGGAGTGCATCCTCAGCGGTCTCCTCTCTGTGGACGGCCTCAAG                         GTTTTGCATATGGACAGAAATGACTACTATGGAGGAGATTCCACCTCGCTC
genomic: GGCTCAAGGAGTGCATCCTCAGCGGTCTCCTCTCTGTAGACGGCCTCAAGgtaagcccgc ... gatattatagGTTTTGCATATGGACAGAAATGACTACTATGGAGGAGATTCCACCTCACTC
EST: gi|211472428|gb|FL096498.1|FL096498
EST:     GGCTCAAGGAGTGCATCCTCAGCGGTCTCCTCTCTGTGGACGGCCTCAAG                         GTTTTGCATATGGACAGAAATGACTACTATGGAGGAGATTCCACCTCGCTC
genomic: GGCTCAAGGAGTGCATCCTCAGCGGTCTCCTCTCTGTAGACGGCCTCAAGgtaagcccgc ... gatattatagGTTTTGCATATGGACAGAAATGACTACTATGGAGGAGATTCCACCTCACTC
EST: gi|33101206|gb|CF061166.1|CF061166
EST:     GGCTCAAGGAGTGCATCCTCAGCGGTCTCCTCTCTGTAGACGGCCTCAAG                         GTTTTGCATATGGACAGAAATGACTACTATGGAGGAGATTCCACCTCACTC
genomic: GGCTCAAGGAGTGCATCCTCAGCGGTCTCCTCTCTGTAGACGGCCTCAAGgtaagcccgc ... gatattatagGTTTTGCATATGGACAGAAATGACTACTATGGAGGAGATTCCACCTCACTC
EST: gi|15590140|gb|BI674756.1|BI674756
EST:     GGCTCAAGGAGTGCATCCTCAGCGGTCTCCTCTCTGTAGACGGCCTCAAG                         GTTTTGCATATGGACAGAAATGACTACTATGGAGGAGATTCCACCTCACTC
genomic: GGCTCAAGGAGTGCATCCTCAGCGGTCTCCTCTCTGTAGACGGCCTCAAGgtaagcccgc ... gatattatagGTTTTGCATATGGACAGAAATGACTACTATGGAGGAGATTCCACCTCACTC
EST: gi|211474937|gb|FL096500.1|FL096500
EST:     GGCTCAAGGAGTGCATCCTCAGCGGTCTCCTCTCTGTAGACGGCCTCAAG                         GTTTTGCATATGGACAGAAATGACTACTATGGAGGAGATTCCACCTCACTC
genomic: GGCTCAAGGAGTGCATCCTCAGCGGTCTCCTCTCTGTAGACGGCCTCAAGgtaagcccgc ... gatattatagGTTTTGCATATGGACAGAAATGACTACTATGGAGGAGATTCCACCTCACTC
EST: gi|211474947|gb|FL096510.1|FL096510
EST:     GGCTCAAGGAGTGCATCCTCAGCGGTCTCCTCTCTGTGGACGGCCTCAAG                         GTTTTGCATATGGACAGAAATGACTACTATGGAGGAGATTCCACCTCGCTC
genomic: GGCTCAAGGAGTGCATCCTCAGCGGTCTCCTCTCTGTAGACGGCCTCAAGgtaagcccgc ... gatattatagGTTTTGCATATGGACAGAAATGACTACTATGGAGGAGATTCCACCTCACTC
EST: gi|211474946|gb|FL096509.1|FL096509
EST:     GGCTCAAGGAGTGCATCCTCAGCGGTCTCCTCTCTGTGGACGGCCTCAAG                         GTTTTGCATATGGACAGAAATGACTACTATGGAGGAGATTCCACCTCGCTC
genomic: GGCTCAAGGAGTGCATCCTCAGCGGTCTCCTCTCTGTAGACGGCCTCAAGgtaagcccgc ... gatattatagGTTTTGCATATGGACAGAAATGACTACTATGGAGGAGATTCCACCTCACTC
EST: gi|60396978|gb|DN229797.1|DN229797
EST:     GGCTCAAGGAGTGCATCCTCAGCGGTCTCCTCTCTGTAGACGGCCTCAAG                         GTTTTGCATATGGACAGAAATGACTACTATGGAGGAGATTCCACCTCACTC
genomic: GGCTCAAGGAGTGCATCCTCAGCGGTCTCCTCTCTGTAGACGGCCTCAAGgtaagcccgc ... gatattatagGTTTTGCATATGGACAGAAATGACTACTATGGAGGAGATTCCACCTCACTC
EST: gi|29544525|gb|CB604905.1|CB604905
EST:     GGCTCAAGGAGTGCATCCTCAGCGGTCTCCTCTCTGTAGACGGCCTCAAG                         GTTTTGCATATGGACAGAAATGACTACTATGGAGGAGATTCCACCTCACTC
genomic: GGCTCAAGGAGTGCATCCTCAGCGGTCTCCTCTCTGTAGACGGCCTCAAGgtaagcccgc ... gatattatagGTTTTGCATATGGACAGAAATGACTACTATGGAGGAGATTCCACCTCACTC
EST: gi|211472424|gb|FL096494.1|FL096494
EST:     GGCTCAAGGAGTGCATCCTCAGCGGTCTCCTCTCTGTGGACGGCCTCAAG                         GTTTTGCATATGGACAGAAATGACTACTATGGAGGAGATTCCACCTCGCTC
genomic: GGCTCAAGGAGTGCATCCTCAGCGGTCTCCTCTCTGTAGACGGCCTCAAGgtaagcccgc ... gatattatagGTTTTGCATATGGACAGAAATGACTACTATGGAGGAGATTCCACCTCACTC
EST: gi|211472420|gb|FL096490.1|FL096490
EST:     GGCTCAAGGAGTGCATCCTCAGCGGTCTCCTCTCTGTGGACGGCCTCAAG                         GTTTTGCATATGGACAGAAATGACTACTATGGAGGAGATTCCACCTCGCTC
genomic: GGCTCAAGGAGTGCATCCTCAGCGGTCTCCTCTCTGTAGACGGCCTCAAGgtaagcccgc ... gatattatagGTTTTGCATATGGACAGAAATGACTACTATGGAGGAGATTCCACCTCACTC
EST: gi|31351669|gb|CD436026.1|CD436026
EST:     GGCTCAAGGAGTGCATCCTCAGCGGTCTCCTCTCTGTAGACGGCCTCAAG                         GTTTTGCATATGGACAGAAATGACTACTATGGAGGAGATTCCACCTCACTC
genomic: GGCTCAAGGAGTGCATCCTCAGCGGTCTCCTCTCTGTAGACGGCCTCAAGgtaagcccgc ... gatattatagGTTTTGCATATGGACAGAAATGACTACTATGGAGGAGATTCCACCTCACTC
EST: gi|33101002|gb|CF060962.1|CF060962
EST:     GGCTCAAGGAGTGCATCCTCAGCGGTCTCCTCTCTGTAGACGGCCTCAAG                         GTTTTGCATATGGACAGAAATGACTACTATGGAGGAGATTCCACCTCACTC
genomic: GGCTCAAGGAGTGCATCCTCAGCGGTCTCCTCTCTGTAGACGGCCTCAAGgtaagcccgc ... gatattatagGTTTTGCATATGGACAGAAATGACTACTATGGAGGAGATTCCACCTCACTC
EST: gi|211474939|gb|FL096502.1|FL096502
EST:     GGCTCAAGGAGTGCATCCTCAGCGGTCTCCTCTCTGTAGACGGCCTCAAG                         GTTTTGCATATGGACAGAAATGACTACTATGGAGGAGATTCCACCTCACTC
genomic: GGCTCAAGGAGTGCATCCTCAGCGGTCTCCTCTCTGTAGACGGCCTCAAGgtaagcccgc ... gatattatagGTTTTGCATATGGACAGAAATGACTACTATGGAGGAGATTCCACCTCACTC
EST: gi|211474948|gb|FL096511.1|FL096511
EST:     GGCTCAAGGAGTGCATCCTCAGCGGTCTCCTCTCTGTGGACGGCCTCAAG                         GTTTTGCATATGGACAGAAATGACTACTATGGAGGAGATTCCACCTCGCTC
genomic: GGCTCAAGGAGTGCATCCTCAGCGGTCTCCTCTCTGTAGACGGCCTCAAGgtaagcccgc ... gatattatagGTTTTGCATATGGACAGAAATGACTACTATGGAGGAGATTCCACCTCACTC
EST: gi|211474938|gb|FL096501.1|FL096501
EST:     GGCTCAAGGAGTGCATCCTCAGCGGTCTCCTCTCTGTAGACGGCCTCAAG                         GTTTTGCATATGGACAGAAATGACTACTATGGAGGAGATTCCACCTCACTC
genomic: GGCTCAAGGAGTGCATCCTCAGCGGTCTCCTCTCTGTAGACGGCCTCAAGgtaagcccgc ... gatattatagGTTTTGCATATGGACAGAAATGACTACTATGGAGGAGATTCCACCTCACTC
EST: gi|211474941|gb|FL096504.1|FL096504
EST:     GGCTCGAGGAGTGCATCCTCAGCGGTCTCCTCTCTGTAGACGGCCTCAAG                         GTTTTGCATATGGACAGAAATGACTACTATGGAGGAGATTCCACCTCACTC
genomic: GGCTCAAGGAGTGCATCCTCAGCGGTCTCCTCTCTGTAGACGGCCTCAAGgtaagcccgc ... gatattatagGTTTTGCATATGGACAGAAATGACTACTATGGAGGAGATTCCACCTCACTC
EST: gi|31360108|gb|CD444465.1|CD444465
EST:     GGCTCAAGGAGTGCATCCTCAGCGGTCTCCTCTCTGTAGACGGCCTCAAG                         GTTGGGGGTATGGACAGAAATGACTACTATGGAGGAGATTCCACCTCACTC
genomic: GGCTCAAGGAGTGCATCCTCAGCGGTCTCCTCTCTGTAGACGGCCTCAAGgtaagcccgc ... gatattatagGTTTTGCATATGGACAGAAATGACTACTATGGAGGAGATTCCACCTCACTC
EST: gi|211472423|gb|FL096493.1|FL096493
EST:     GGCTCAAGGAGTGCATCCTCAGCGGTCTCCTCTCTGTGGACGGCCTCAAG                         GTTTTGCATATGGACAGAAATGACTACTATGGAGGAGATTCCACCTCGCTC
genomic: GGCTCAAGGAGTGCATCCTCAGCGGTCTCCTCTCTGTAGACGGCCTCAAGgtaagcccgc ... gatattatagGTTTTGCATATGGACAGAAATGACTACTATGGAGGAGATTCCACCTCACTC
EST: gi|211472427|gb|FL096497.1|FL096497
EST:     GGCTCAAGGAGTGCATCCTCAGCGGTCTCCTCTCTGTAGACGGCCTCAAG                         GTTTTGCATATGGACAGAAATGACTACTATGGAGGAGATTCCACCTCACTC
genomic: GGCTCAAGGAGTGCATCCTCAGCGGTCTCCTCTCTGTAGACGGCCTCAAGgtaagcccgc ... gatattatagGTTTTGCATATGGACAGAAATGACTACTATGGAGGAGATTCCACCTCACTC
EST: gi|211472426|gb|FL096496.1|FL096496
EST:     GGCTCAAGGAGTGCATCCTCAGCGGTCTCCTCTCTGTAGACGGCCTCAAG                         GTTTTGCATATGGACAGAAATGACTACTATGGAGGAGATTCCACCTCACTC
genomic: GGCTCAAGGAGTGCATCCTCAGCGGTCTCCTCTCTGTAGACGGCCTCAAGgtaagcccgc ... gatattatagGTTTTGCATATGGACAGAAATGACTACTATGGAGGAGATTCCACCTCACTC
EST: gi|211474943|gb|FL096506.1|FL096506
EST:     GGCTCAAGGAGTGCATCCTCAGCGGTCTCCTCTCTGTAGACGGCCTCAAG                         GTTTTGCATATGGACAGAAATGACTACTATGGAGGAGATTCCACCTCACTC
genomic: GGCTCAAGGAGTGCATCCTCAGCGGTCTCCTCTCTGTAGACGGCCTCAAGgtaagcccgc ... gatattatagGTTTTGCATATGGACAGAAATGACTACTATGGAGGAGATTCCACCTCACTC
EST: gi|211472429|gb|FL096499.1|FL096499
EST:     GGCTCAAGGAGTGCATCCTCAGCGGTCTCCTCTCTGTGGACGGCCTCAAG                         GTTTTGCATATGGACAGAAATGACTACTATGGAGGAGATTCCACCTCGCTC
genomic: GGCTCAAGGAGTGCATCCTCAGCGGTCTCCTCTCTGTAGACGGCCTCAAGgtaagcccgc ... gatattatagGTTTTGCATATGGACAGAAATGACTACTATGGAGGAGATTCCACCTCACTC
EST: gi|29946002|gb|CB815929.1|CB815929
EST:     GGCTCAAGGAGTGCATCCTCAGCGGTCTCCTCTCTGTAGACGGCCTCAAG                         GTTTTGCATATGGACAGAAATGACTACTATGGAGGAGATTCCACCTCACTC
genomic: GGCTCAAGGAGTGCATCCTCAGCGGTCTCCTCTCTGTAGACGGCCTCAAGgtaagcccgc ... gatattatagGTTTTGCATATGGACAGAAATGACTACTATGGAGGAGATTCCACCTCACTC
EST: gi|26557597|gb|CA829832.1|CA829832
EST:     GCTCAAGGAGTGCATCCTCAGCGGTCTCCTCTCTGTAAGACGGCCTCAAG                         GATTTGCATATGGACAGAAATGACTACTATGGAGGAGATTCCACCTCACTC
genomic: GCTCAAGGAGTGCATCCTCAGCGGTCTCCTCTCTGT-AGACGGCCTCAAGgtaagcccgc ... gatattatagGTTTTGCATATGGACAGAAATGACTACTATGGAGGAGATTCCACCTCACTC
EST: gi|211113229|gb|FL096514.1|FL096514
EST:     GGCTCAAGGAGTGCATCCTCAGCGGTCTCCTCTCTGTGGACGGCCTCAAG                         GTTTTGCATATGGACAGAAATGACTACTATGGAGGAGATTCCACCTCGCTC
genomic: GGCTCAAGGAGTGCATCCTCAGCGGTCTCCTCTCTGTAGACGGCCTCAAGgtaagcccgc ... gatattatagGTTTTGCATATGGACAGAAATGACTACTATGGAGGAGATTCCACCTCACTC

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: 236

CCGGCAGCCAGCCATGGATGAGGAGTACGACGTGATCGTACTAGGCACGGGGCTCAAGGAGTGCATCCTCAGCGGTCTCCTCTCTGTAGACGGCCTCAAGgtaagcccgc ... gatattatagGTTTTGCATATGGACAGAAATGACTACTATGGAGGAGATTCCACCTCACTCAACCTTAATCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 326

CCGGCAGCCAGCCATGGATGAGGAGTACGACGTGATCGTACTAGGCACGGGGCTCAAGGAGTGCATCCTCAGCGGTCTCCTCTCTGTAGACGGCCTCAAGgtaagcccgc ... gatattatagGTTTTGCATATGGACAGAAATGACTACTATGGAGGAGATTCCACCTCACTCAACCTTAATCAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 470

CCGGCAGCCAGCCATGGATGAGGAGTACGACGTGATCGTACTAGGCACGGGGCTCAAGGAGTGCATCCTCAGCGGTCTCCTCTCTGTAGACGGCCTCAAGgtaagcccgc ... gatattatagGTTTTGCATATGGACAGAAATGACTACTATGGAGGAGATTCCACCTCACTCAACCTTAATCAG


Block sizes: 48 (upstream exon), 47 (downstream exon)
Score: 157

CCGGCAGCCAGCCATGGATGAGGAGTACGACGTGATCGTACTAGGCACGGGGCTCAAGGAGTGCATCCTCAGCGGTCTCCTCTCTGTAGACGGCCTCAAGgtaagcccgc ... gatattatagGTTTTGCATATGGACAGAAATGACTACTATGGAGGAGATTCCACCTCACTCAACCTTAATCAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctacatgtaagtgtaggaattcacttctgacgatgtggtttcgatgatattatagGTTTTGCATATGGACAGAAATGACTACTATGGAGGAGATTCCACCTCACTCAACCTTAATCAG
                        ttctgac  putative branch site (score: 157)
                                           atgatattata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cttatgccattttagaaccttccttaaggttgtggtatttgaagtctacatgtaagtgtaggaattcacttctgacgatgtggtttcgatgatattatagGTTTTGCATATGGACAGAAATGACTACTATGGAGGAGATTCCACCTCACTCAACCTTAATCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAT
- - tgccatt
- - - - - - - - - - - - - - - - - - - - - - -ctacatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cgatgtg