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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgatgtgcatggtggtctgtgggtatgcttgttttccctaactaatggtcagatgcctactggattatgtagGTTGGAACCCAAAGACACCTCTCAAGGATCTGCTGGAGACAACATTGACGTACCAGCACAAGACATACAAAGAAGCTGTGAAGAGGCAAATGTCGCAGGC

Basic information

species Zea mays
transcript GRMZM2G167872_T02
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G167872_T02 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os01g73790.1 (Oryza sativa), 3'ss of exon 8
---------------------gtatgatgtgcatggtggtctg--tgggtatgcttgttttccctaactaatggtcagatgcctactggattatg-tagGTTGGAACCCAAAGACACCTCTCAAGGATCTGCTGGAGACAACATTGACGTACCAGCACAAGACATACAAAGAAGCTGTGAAGAGGCAAATGTCGCAGGC
                      | | ||||  ||| ||  ||   ||||||  |  ||  | | |||    |   || ||    | |  | | |  |||||||||| || ||||| |||||||||||| ||||||||||||||||||| |||||||||||||| |||||||||||| | || ||||||||||| |||||
gtatttactgtcttcaataacctgttatgtctatgttgtactagttgggta-accagtggttcataa----taaccaaatattgattcaactgttctagGTTGGAATCCGAAGACCCCTCTCAAGGATTTGCTGGAGACAACATTGACCTACCAGCACAAGACTTACAAAGAAGCTATCAAAAGGCAAATGTCACAGGC
















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|78023452|gb|DV491839.1|DV491839
EST:     TGACAGTGATAAGAGAATTCCTGACATGACTATAATCAACAAGCAGCTAG                         GTTGGAACCCAAAGACGCCTCTCAAGGATCTGCTGGAGACAACATTGACGT
genomic: TGACAGTGATAAGAGAATTCCTGACATGACTATAATCAACAAGCAGCTAGgtatgatgtg ... gattatgtagGTTGGAACCCAAAGACACCTCTCAAGGATCTGCTGGAGACAACATTGACGT
EST: gi|60350531|gb|DN217504.1|DN217504
EST:     TGACAGTGATAAGAGAATTCCTGACATGACTATAATCAACAAGCAGCTAG                         GTTGGAACCCAAAGACACCTCTCAAGGATCTGCTGGAGACAACATTGACGT
genomic: TGACAGTGATAAGAGAATTCCTGACATGACTATAATCAACAAGCAGCTAGgtatgatgtg ... gattatgtagGTTGGAACCCAAAGACACCTCTCAAGGATCTGCTGGAGACAACATTGACGT
EST: gi|33097643|gb|CF057603.1|CF057603
EST:     TGACAGTGATAAGAGAATTCCTGACATGACTATAATCAACAAGCAGCTAG                         GTTGGAACCCAAAGACGCCTCTCAAGGATCTGCTGGAGACAACATTGACGT
genomic: TGACAGTGATAAGAGAATTCCTGACATGACTATAATCAACAAGCAGCTAGgtatgatgtg ... gattatgtagGTTGGAACCCAAAGACACCTCTCAAGGATCTGCTGGAGACAACATTGACGT
EST: gi|149013843|gb|EE043323.2|EE043323
EST:     TGACAGTGATAAGAGAATTCCTGACATGACTATAATCAACAAGCAGCTAG                         GTTGGAACCCAAAGACACCTCTCAAGGATCTGCTGGAGACAACATTGACGT
genomic: TGACAGTGATAAGAGAATTCCTGACATGACTATAATCAACAAGCAGCTAGgtatgatgtg ... gattatgtagGTTGGAACCCAAAGACACCTCTCAAGGATCTGCTGGAGACAACATTGACGT
EST: gi|211201981|gb|FL057813.1|FL057813
EST:     TGACAGTGATAAGAGAATTCCTGACATGACTATAATCAACAAGCAGCTAG                         GTTGGAACCCAAAGACACCTCTCAAGGATCTGCTGGAGACAACATTGACGT
genomic: TGACAGTGATAAGAGAATTCCTGACATGACTATAATCAACAAGCAGCTAGgtatgatgtg ... gattatgtagGTTGGAACCCAAAGACACCTCTCAAGGATCTGCTGGAGACAACATTGACGT
EST: gi|5922187|gb|AW055457.1|AW055457
EST:     TGACAGTGATAAGAGAATTCCTGACATGACTATAATCAACAAGCAGCTAG                         GTTGGAACCCAAAGACGCCTCTCAAGGATCTGCTGGAGACAACATTGACGT
genomic: TGACAGTGATAAGAGAATTCCTGACATGACTATAATCAACAAGCAGCTAGgtatgatgtg ... gattatgtagGTTGGAACCCAAAGACACCTCTCAAGGATCTGCTGGAGACAACATTGACGT
EST: gi|211031095|gb|FL449268.1|FL449268
EST:     GACAGTGAT-AGAGAAATTCCTGACATGACTATAATCAACAAGCAGCTAG                         GTTGGAACCCAAAGACACCTCTCAAGGATCTGCTGGAGACAACATTGACGT
genomic: GACAGTGATAAGAG-AATTCCTGACATGACTATAATCAACAAGCAGCTAGgtatgatgtg ... gattatgtagGTTGGAACCCAAAGACACCTCTCAAGGATCTGCTGGAGACAACATTGACGT
EST: gi|113689228|gb|DW846517.1|DW846517
EST:     TGACAGTGATAAGAGAATTCCTGACATGACTATAATCAACAAGCAGCTAG                         GTTGGAACCCAAAGACACCTCTCAAGGATCTGC
genomic: TGACAGTGATAAGAGAATTCCTGACATGACTATAATCAACAAGCAGCTAGgtatgatgtg ... gattatgtagGTTGGAACCCAAAGACACCTCTCAAGGATCTGC
EST: gi|5936878|gb|AW060146.1|AW060146
EST:     TGACAGTGATAAGAGAATTCCTGACATGACTATAATCAACAAGCAGCTAG                         GTTGGAACCCAAAGACNCCTCTCAAGGATCTGCTGGAGACAACATTGACGT
genomic: TGACAGTGATAAGAGAATTCCTGACATGACTATAATCAACAAGCAGCTAGgtatgatgtg ... gattatgtagGTTGGAACCCAAAGACACCTCTCAAGGATCTGCTGGAGACAACATTGACGT
EST: gi|6095362|gb|AW120029.1|AW120029
EST:     TGACAGTGATAAGAGAATTCCTGACATGACTATAATCAACAAGCAGCTAG                         GTTGGAACCCAAAGAC
genomic: TGACAGTGATAAGAGAATTCCTGACATGACTATAATCAACAAGCAGCTAGgtatgatgtg ... gattatgtagGTTGGAACCCAAAGAC
EST: gi|149048836|gb|EE048336.2|EE048336
EST:     TGACAGTGATAAGAGAATTCCTGACATGACTATAATCAACAAGCAGCTAG                         GTTGGAACCCAAAGACACCTCTCAAGGATTTGCTGGAGACAACATTGACGT
genomic: TGACAGTGATAAGAGAATTCCTGACATGACTATAATCAACAAGCAGCTAGgtatgatgtg ... gattatgtagGTTGGAACCCAAAGACACCTCTCAAGGATCTGCTGGAGACAACATTGACGT
EST: gi|78088131|gb|DV516524.1|DV516524
EST:     TGACAGTGATAAGAGAATTCCTGACATGACTATAATCAACAAGCAGCTAG                         GTTGGAACCCAAAGACACCTCTCAAGGATCTGCTGGAGACAACATTGACGT
genomic: TGACAGTGATAAGAGAATTCCTGACATGACTATAATCAACAAGCAGCTAGgtatgatgtg ... gattatgtagGTTGGAACCCAAAGACACCTCTCAAGGATCTGCTGGAGACAACATTGACGT
EST: gi|5468619|gb|AI834410.1|AI834410
EST:     TGACAGTGATAAGAGAATTCCTGACATGACTATAATCAACAAGCAGCTAG                         GTTGGAACCCAAAGACGCCTCTCAAGGATCTGCTGGAGACAACATTGACGT
genomic: TGACAGTGATAAGAGAATTCCTGACATGACTATAATCAACAAGCAGCTAGgtatgatgtg ... gattatgtagGTTGGAACCCAAAGACACCTCTCAAGGATCTGCTGGAGACAACATTGACGT
EST: gi|20507862|gb|BQ279797.1|BQ279797
EST:     TGACAGTGATAAGAGAATTCCTGACATGACTATAATCAACAAGCAGCTAG                         GTTGGAACCCAAAGACGCCTCTCAAGGATCTGCTGGAGACAACATTGACGT
genomic: TGACAGTGATAAGAGAATTCCTGACATGACTATAATCAACAAGCAGCTAGgtatgatgtg ... gattatgtagGTTGGAACCCAAAGACACCTCTCAAGGATCTGCTGGAGACAACATTGACGT
EST: gi|32859492|gb|CD999173.1|CD999173
EST:     TGACAGTGATAAGAGAATTCCTGACATGACTATAATCAACAAGCAGCTAG                         GTTGGAACCCAAAGACGCCTCTCAAGGATCTGCTGGAGACAACATTGACGT
genomic: TGACAGTGATAAGAGAATTCCTGACATGACTATAATCAACAAGCAGCTAGgtatgatgtg ... gattatgtagGTTGGAACCCAAAGACACCTCTCAAGGATCTGCTGGAGACAACATTGACGT
EST: gi|29130958|gb|CB381662.1|CB381662
EST:     TGACAGTGATAAGAGAATTCCTGACATGACTATAATCAACAAGCAGCTAG                         GTTGGAACCCAAAGACCCCTCTCAAGGATCTGCTGGAGACAACATTGACGT
genomic: TGACAGTGATAAGAGAATTCCTGACATGACTATAATCAACAAGCAGCTAGgtatgatgtg ... gattatgtagGTTGGAACCCAAAGACACCTCTCAAGGATCTGCTGGAGACAACATTGACGT
EST: gi|89755200|gb|DY685717.1|DY685717
EST:     TGACAGTGATAAGAGAATTCCTGACATGACTATAATCAACAAGCAGCTAG                         GTTGGAACCCAAAGACACCTCTCAAGGATCTGCTGGAGACAACATTGACGT
genomic: TGACAGTGATAAGAGAATTCCTGACATGACTATAATCAACAAGCAGCTAGgtatgatgtg ... gattatgtagGTTGGAACCCAAAGACACCTCTCAAGGATCTGCTGGAGACAACATTGACGT
EST: gi|29545164|gb|CB605342.1|CB605342
EST:     TGACAGTGATAAGAGAATTCCTGACATGACTATAATCAACAAGCAGCTAG                         GTTGGAACCCAAAGACACCTCTCAAGGATCTGCTGGAGACAACATTGACGT
genomic: TGACAGTGATAAGAGAATTCCTGACATGACTATAATCAACAAGCAGCTAGgtatgatgtg ... gattatgtagGTTGGAACCCAAAGACACCTCTCAAGGATCTGCTGGAGACAACATTGACGT
EST: gi|148943582|gb|EC888645.2|EC888645
EST:     TGACAGTGATAAGAGAATTCCTGACATGACTATAATCAACAAGCAGCTAG                         GTTGGAACCCAAAGACACCTCTCAAGGATCTGCTGGAGACAACATTGACGT
genomic: TGACAGTGATAAGAGAATTCCTGACATGACTATAATCAACAAGCAGCTAGgtatgatgtg ... gattatgtagGTTGGAACCCAAAGACACCTCTCAAGGATCTGCTGGAGACAACATTGACGT
EST: gi|19770313|gb|BQ035034.1|BQ035034
EST:     TGACAGTGATAAGAGAATTCCTGACATGACTATAATCAACAAGCAGCTAG                         GTTGGAACCCAAAGACGCCTCTCAAGGATCTGCTGGAGACAACATTGACGT
genomic: TGACAGTGATAAGAGAATTCCTGACATGACTATAATCAACAAGCAGCTAGgtatgatgtg ... gattatgtagGTTGGAACCCAAAGACACCTCTCAAGGATCTGCTGGAGACAACATTGACGT
EST: gi|60342920|gb|DN209893.1|DN209893
EST:     TGACAGTGATAAGAGAATTCCTGACATGACTATAATCAACAAGCAGCTAG                         GTTGGAACCCAAAGACACCTCTCAAGGATCTGCTGGAGACAACATTGACGT
genomic: TGACAGTGATAAGAGAATTCCTGACATGACTATAATCAACAAGCAGCTAGgtatgatgtg ... gattatgtagGTTGGAACCCAAAGACACCTCTCAAGGATCTGCTGGAGACAACATTGACGT
EST: gi|88754947|gb|DY539088.1|DY539088
EST:     TGACAGTGATAAGAGAATTCCTGACATGACTATAATCAACAAGCAGCTAG                         GTTGGAACCCAAAGACACCTCTCAAGGATCTGCTGGAGACAACATTGACGT
genomic: TGACAGTGATAAGAGAATTCCTGACATGACTATAATCAACAAGCAGCTAGgtatgatgtg ... gattatgtagGTTGGAACCCAAAGACACCTCTCAAGGATCTGCTGGAGACAACATTGACGT
EST: gi|32943135|gb|CF047954.1|CF047954
EST:     TGACAGTGATAAGAGAATTCCTGACATGACTACAATCAACAAGCAGCTAG                         GTTGGAACCCAAAGACGCCTCTCAAGGATCTGCTGGAGACAACATTGACGT
genomic: TGACAGTGATAAGAGAATTCCTGACATGACTATAATCAACAAGCAGCTAGgtatgatgtg ... gattatgtagGTTGGAACCCAAAGACACCTCTCAAGGATCTGCTGGAGACAACATTGACGT

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: 266

GAGCCTATGATCGACGTGAGTTCGAGTCAGTTCTACGGTGAAGGATACGATGACAGTGATAAGAGAATTCCTGACATGACTATAATCAACAAGCAGCTAGgtatgatgtg ... gattatgtagGTTGGAACCCAAAGACACCTCTCAAGGATCTGCTGGAGACAACATTGACGTACCAGCACAAGACATACAAAGAAGCTGTGAAGAGGCAAATGTCGCAGGC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 95

GAGCCTATGATCGACGTGAGTTCGAGTCAGTTCTACGGTGAAGGATACGATGACAGTGATAAGAGAATTCCTGACATGACTATAATCAACAAGCAGCTAGgtatgatgtg ... gattatgtagGTTGGAACCCAAAGACACCTCTCAAGGATCTGCTGGAGACAACATTGACGTACCAGCACAAGACATACAAAGAAGCTGTGAAGAGGCAAATGTCGCAGGC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 105

GAGCCTATGATCGACGTGAGTTCGAGTCAGTTCTACGGTGAAGGATACGATGACAGTGATAAGAGAATTCCTGACATGACTATAATCAACAAGCAGCTAGgtatgatgtg ... gattatgtagGTTGGAACCCAAAGACACCTCTCAAGGATCTGCTGGAGACAACATTGACGTACCAGCACAAGACATACAAAGAAGCTGTGAAGAGGCAAATGTCGCAGGC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 208

GAGCCTATGATCGACGTGAGTTCGAGTCAGTTCTACGGTGAAGGATACGATGACAGTGATAAGAGAATTCCTGACATGACTATAATCAACAAGCAGCTAGgtatgatgtg ... gattatgtagGTTGGAACCCAAAGACACCTCTCAAGGATCTGCTGGAGACAACATTGACGTACCAGCACAAGACATACAAAGAAGCTGTGAAGAGGCAAATGTCGCAGGC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtgggtatgcttgttttccctaactaatggtcagatgcctactggattatgtagGTTGGAACCCAAAGACACCTCTCAAGGATCTGCTGGAGACAACATTGACGTACCAGCACAAGACATACAAAGAAGCTGTGAAGAGGCAAATGTCGCAGGC
                      aactaat  putative branch site (score: 208)
                     taactaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgatgtgcatggtggtctgtgggtatgcttgttttccctaactaatggtcagatgcctactggattatgtagGTTGGAACCCAAAGACACCTCTCAAGGATCTGCTGGAGACAACATTGACGTACCAGCACAAGACATACAAAGAAGCTGTGAAGAGGCAAATGTCGCAGGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGG