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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagttggaatgtctagcttgctacttttcagtttccacagccaattgatggggtgtcacatggacattttcatgcttttagGTTGATGCTTTCCCCGGGGATGCCATAATATTTATGAGGGTCTTGAATCTCCTCAGAG

Basic information

species Zea mays
transcript GRMZM2G140917_T01
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G140917_T01 (Zea mays), 3'ss of exon 12
lower sequence: LOC_Os06g48770.1 (Oryza sativa), 3'ss of exon 11
gtgagttggaatgtcta--gcttgctacttttcagtttccacagccaattgatggggtgtcacatggacattttcatgcttttagGTTGATGCTTTCCCCGGGGATGCCATAATATTTATGAGGGTCTTGAATCTCCTCAGAG
|||||| || ||| ||    |||  ||  | |    ||   || ||||   || || ||| ||||| ||||||||  || ||||||||||||||||||| || ||||| || ||||| |||||||| |||||||| || ||||
gtgagtaggcatgccttttacttcatatgtgtttagtttgtcaaccaagaaatagg-tgttacatgaacattttctcgcctttagGTTGATGCTTTCCCTGGTGATGCAATTATATTCATGAGGGTTTTGAATCTTCTTAGAG
















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|211142855|gb|FL032416.1|FL032416
EST:     TTCAAGAAAAGATGAAATTGAACAAGAAGGAGGTTCAACGCTTTAATCCT                         GTTGATGCTTTCCCCGGGGATGCCATAATATTTATGAGGGTCTTGAATCTC
genomic: TTCAAGAAAAGATGAAATTGAACAAGAAGGAGGTTCAACGCTTTAATCCTgtgagttgga ... atgcttttagGTTGATGCTTTCCCCGGGGATGCCATAATATTTATGAGGGTCTTGAATCTC
EST: gi|211402616|gb|FL252144.1|FL252144
EST:     TTCAAGAAAAGATGAAATTGAACAAGAAGGAGGTTCAACGCTTTAATCCT                         GTTGATGCTTTCCCCGGGGATGCCATAATATTTA--AGGGTCTTGAATCTC
genomic: TTCAAGAAAAGATGAAATTGAACAAGAAGGAGGTTCAACGCTTTAATCCTgtgagttgga ... atgcttttagGTTGATGCTTTCCCCGGGGATGCCATAATATTTATGAGGGTCTTGAATCTC
EST: gi|211145716|gb|FL032440.1|FL032440
EST:     TTCAAGAAAAGATGAAATTGAACAAGAAGGAGGTTCAACGCTTTAATCCT                         GTTGATGCTTTCCCCGGGGATGCCATAATATTTATGAGGGTCTTGAATCTC
genomic: TTCAAGAAAAGATGAAATTGAACAAGAAGGAGGTTCAACGCTTTAATCCTgtgagttgga ... atgcttttagGTTGATGCTTTCCCCGGGGATGCCATAATATTTATGAGGGTCTTGAATCTC
EST: gi|211144286|gb|FL032428.1|FL032428
EST:     TTCAAGAAAAGATGAAATTGAACAAGAAGGAGGTTCAACGCTTTAATCCT                         GTTGATGCTTTCCCCGGGGATGCCATAATATTTATGAGGGTCTTGAATCTC
genomic: TTCAAGAAAAGATGAAATTGAACAAGAAGGAGGTTCAACGCTTTAATCCTgtgagttgga ... atgcttttagGTTGATGCTTTCCCCGGGGATGCCATAATATTTATGAGGGTCTTGAATCTC
EST: gi|211144291|gb|FL032433.1|FL032433
EST:     TCAAGAAAAGATGAAATTGAACAAAGAAGGAGGTTCAACGCTTTAATCCT                         GTTGATGCTTTCCCCGGGGATGCCATAATGATTTGATGAGGGTCTTGAATC
genomic: TCAAGAAAAGATGAAATTGAACAA-GAAGGAGGTTCAACGCTTTAATCCTgtgagttgga ... atgcttttagGTTGATGCTTTCCCCGGGGATGCCATAAT-ATTT-ATGAGGGTCTTGAATC
EST: gi|89763775|gb|DY690831.1|DY690831
EST:     CAACGCTTTAATCCT                         GTTGATGCTTTCCCCGGGGATGCCATAATATTTATGAGGGTCTTGAATCTC
genomic: CAACGCTTTAATCCTgtgagttgga ... atgcttttagGTTGATGCTTTCCCCGGGGATGCCATAATATTTATGAGGGTCTTGAATCTC
EST: gi|211145718|gb|FL032442.1|FL032442
EST:     TTCAAGAAAAGATGAAATTGAACAAGAAGGAGGTTCAACGCTTTAATCCT                         GTTGATGCTTTCCCCGGGGATGCCATAATATTTATGAGGGTCTTGAATCTC
genomic: TTCAAGAAAAGATGAAATTGAACAAGAAGGAGGTTCAACGCTTTAATCCTgtgagttgga ... atgcttttagGTTGATGCTTTCCCCGGGGATGCCATAATATTTATGAGGGTCTTGAATCTC
EST: gi|148966697|gb|EE017760.2|EE017760
EST:     TTCAAGAAAAGATGAAATTGAACAAGAAGGAGGTTCAACGCTTTAATCCT                         GTTGATGCTTTCCCCGGGGATGCCATAATATTTATGAGGGTCTTGAATCTC
genomic: TTCAAGAAAAGATGAAATTGAACAAGAAGGAGGTTCAACGCTTTAATCCTgtgagttgga ... atgcttttagGTTGATGCTTTCCCCGGGGATGCCATAATATTTATGAGGGTCTTGAATCTC
EST: gi|211144288|gb|FL032430.1|FL032430
EST:     TTCAAGAAAAGATGAAATTGAACAAGAAGGAGGTTCAACGCTTTAATCCT                         GTTGATGCTTTCCCCGGGGATGCCATAATATTTATGAGGGTCTTGAATCTC
genomic: TTCAAGAAAAGATGAAATTGAACAAGAAGGAGGTTCAACGCTTTAATCCTgtgagttgga ... atgcttttagGTTGATGCTTTCCCCGGGGATGCCATAATATTTATGAGGGTCTTGAATCTC
EST: gi|211145719|gb|FL032443.1|FL032443
EST:     TTCAAGAAAAGATGAAATTGAACAAGAAGGAGGTTCAACGCTTTAATCCT                         GTTGATGCTTTCCCCGGGGATGCCATAATATTTATGAGGGTCTTGAATCTC
genomic: TTCAAGAAAAGATGAAATTGAACAAGAAGGAGGTTCAACGCTTTAATCCTgtgagttgga ... atgcttttagGTTGATGCTTTCCCCGGGGATGCCATAATATTTATGAGGGTCTTGAATCTC
EST: gi|211144285|gb|FL032427.1|FL032427
EST:     TTCAAGAAAAGATGAAATTGAACAAGAAGGAGGTTCAACGCTTTAATCCT                         GTTGATGCTTTCCCCGGGGATGCCATAATATTTATGAGGGTCTTGAATCTC
genomic: TTCAAGAAAAGATGAAATTGAACAAGAAGGAGGTTCAACGCTTTAATCCTgtgagttgga ... atgcttttagGTTGATGCTTTCCCCGGGGATGCCATAATATTTATGAGGGTCTTGAATCTC
EST: gi|211142858|gb|FL032419.1|FL032419
EST:     TTCAAGAAAAGATGAAATTGAACAAGAAGGAGGTTCAACGCTTTAATCCT                         GTTGATGCTTTCCCCGGGGATGCCATAATATTTATGAGGGTCTTGAATCTC
genomic: TTCAAGAAAAGATGAAATTGAACAAGAAGGAGGTTCAACGCTTTAATCCTgtgagttgga ... atgcttttagGTTGATGCTTTCCCCGGGGATGCCATAATATTTATGAGGGTCTTGAATCTC
EST: gi|211145714|gb|FL032438.1|FL032438
EST:     TTCAAGAAAAGATGAAATTGAACAAGAAGGAGGTTCAACGCTTTAATCCT                         GTTGATGCTTTCCCCGGGGATGCCATAATATTTATGAGGGTCTTGAATCTC
genomic: TTCAAGAAAAGATGAAATTGAACAAGAAGGAGGTTCAACGCTTTAATCCTgtgagttgga ... atgcttttagGTTGATGCTTTCCCCGGGGATGCCATAATATTTATGAGGGTCTTGAATCTC
EST: gi|211145713|gb|FL032437.1|FL032437
EST:     TTCAAGAAAAGATGAAATTGAACAAGAAGGAGGTTCAACGCTTTAATCCT                         GTTGATGCTTTCCCCGGGGATGCCATAATATTTATGAGGGTCTTGAATCTC
genomic: TTCAAGAAAAGATGAAATTGAACAAGAAGGAGGTTCAACGCTTTAATCCTgtgagttgga ... atgcttttagGTTGATGCTTTCCCCGGGGATGCCATAATATTTATGAGGGTCTTGAATCTC
EST: gi|211145715|gb|FL032439.1|FL032439
EST:     TTCAAGAAAAGATGAAATTGAACAAGAAGGAGGTTCAACGCTTTAATCCT                         GTTGATGCTTTCCCCGGGGATGCCATAATATTTATGAGGGTCTTGAATCTC
genomic: TTCAAGAAAAGATGAAATTGAACAAGAAGGAGGTTCAACGCTTTAATCCTgtgagttgga ... atgcttttagGTTGATGCTTTCCCCGGGGATGCCATAATATTTATGAGGGTCTTGAATCTC
EST: gi|211144284|gb|FL032426.1|FL032426
EST:     TTCAAGAAAAGATGAAATTGAACAAGAAGGAGGTTCAACGCTTTAATCCT                         GTTGATGCTTTCCCCGGGGATGCCATAATATTTATGAGGGTCTTGAATCTC
genomic: TTCAAGAAAAGATGAAATTGAACAAGAAGGAGGTTCAACGCTTTAATCCTgtgagttgga ... atgcttttagGTTGATGCTTTCCCCGGGGATGCCATAATATTTATGAGGGTCTTGAATCTC
EST: gi|211144294|gb|FL032436.1|FL032436
EST:     TTCAAGAAAAGATGAAATTGAACAAGAAGGAGGTTCAACGCTTTAATCCT                         GTTGATGCTTTCCCCGGGGATGCCATAATATTTATGAGGGTCTTGAATCTC
genomic: TTCAAGAAAAGATGAAATTGAACAAGAAGGAGGTTCAACGCTTTAATCCTgtgagttgga ... atgcttttagGTTGATGCTTTCCCCGGGGATGCCATAATATTTATGAGGGTCTTGAATCTC
EST: gi|211144287|gb|FL032429.1|FL032429
EST:     TTCAAGAAAAGATGAAATTGAACAAGAAGGAGGTTCAACGCTTTAATCCT                         GTTGATGCTTTCCCCGGGGATGCCATAATATTTATGAGGGTCTTGAATCTC
genomic: TTCAAGAAAAGATGAAATTGAACAAGAAGGAGGTTCAACGCTTTAATCCTgtgagttgga ... atgcttttagGTTGATGCTTTCCCCGGGGATGCCATAATATTTATGAGGGTCTTGAATCTC
EST: gi|211145717|gb|FL032441.1|FL032441
EST:     TTCAAGAAAAGATGAAATTGAACAAGAAGGAGGTTCAACGCTTTAATCCT                         GTTGATGCTTTCCCCGGGGATGCCATAATATTTATGAGGGTCTTGAATCTC
genomic: TTCAAGAAAAGATGAAATTGAACAAGAAGGAGGTTCAACGCTTTAATCCTgtgagttgga ... atgcttttagGTTGATGCTTTCCCCGGGGATGCCATAATATTTATGAGGGTCTTGAATCTC
EST: gi|211144283|gb|FL032425.1|FL032425
EST:     TTCAAGAAAAGATGAAATTGAACAAGAAGGAGGTTCAACGCTTTAATCCT                         GTTGATGCTTTCCCCGGGGATGCCATAATATTTATGAGGGTCTTGAATCTC
genomic: TTCAAGAAAAGATGAAATTGAACAAGAAGGAGGTTCAACGCTTTAATCCTgtgagttgga ... atgcttttagGTTGATGCTTTCCCCGGGGATGCCATAATATTTATGAGGGTCTTGAATCTC
EST: gi|211142856|gb|FL032417.1|FL032417
EST:     TTCAAGAAAAGATGAAATTGAACAAGAAGGAGGTTCAACGCTTTAATCCT                         GTTGATGCTTTCCCCGGGGATGCCATAATATTTATGAGGGTCTTGAATCTC
genomic: TTCAAGAAAAGATGAAATTGAACAAGAAGGAGGTTCAACGCTTTAATCCTgtgagttgga ... atgcttttagGTTGATGCTTTCCCCGGGGATGCCATAATATTTATGAGGGTCTTGAATCTC
EST: gi|211144292|gb|FL032434.1|FL032434
EST:     TTCAAGAAAAGATGAAATTGAACAAGAAGGAGGTTCAACGCTTTAATCCT                         GTTGATGCTTTCCCCGGGGATGCCATAATATTTATGAGGGTCTTGAATCTC
genomic: TTCAAGAAAAGATGAAATTGAACAAGAAGGAGGTTCAACGCTTTAATCCTgtgagttgga ... atgcttttagGTTGATGCTTTCCCCGGGGATGCCATAATATTTATGAGGGTCTTGAATCTC
EST: gi|211144280|gb|FL032422.1|FL032422
EST:     TTCAAGAAAAGATGAAATTGAACAAGAAGGAGGTTCAACGCTTTAATCCT                         GTTGATGCTTTCCCCGGGGATGCCATAATATTTATGAGGGTCTTGAATCTC
genomic: TTCAAGAAAAGATGAAATTGAACAAGAAGGAGGTTCAACGCTTTAATCCTgtgagttgga ... atgcttttagGTTGATGCTTTCCCCGGGGATGCCATAATATTTATGAGGGTCTTGAATCTC
EST: gi|211145720|gb|FL032444.1|FL032444
EST:     TTCAAGAAAAGATGAAATTGAACAAGAAGGAGGTTCAACGCTTTAATCCT                         GTTGATGCTTTCCCCGGGGATGCCATAATATTTATGAGGGTCTTGAATCTC
genomic: TTCAAGAAAAGATGAAATTGAACAAGAAGGAGGTTCAACGCTTTAATCCTgtgagttgga ... atgcttttagGTTGATGCTTTCCCCGGGGATGCCATAATATTTATGAGGGTCTTGAATCTC
EST: gi|211142860|gb|FL032421.1|FL032421
EST:     TTCAAGAAAAGATGAAATTGAACAAGAAGGAGGTTCAACGCTTTAATCCT                         GTTGATGCTTTCCCCGGNGATGCCATAATATTTATGAGGGTCTTGAATCTC
genomic: TTCAAGAAAAGATGAAATTGAACAAGAAGGAGGTTCAACGCTTTAATCCTgtgagttgga ... atgcttttagGTTGATGCTTTCCCCGGGGATGCCATAATATTTATGAGGGTCTTGAATCTC
EST: gi|211144290|gb|FL032432.1|FL032432
EST:     TTCAAGAAAAGATGAAATTGAACAAGAAGGAGGTTCAACGCTTTAATCCT                         GTTGATGCTTTCCCCGGGGATGCCATAATATTTATGAGGGTCTTGAATCTC
genomic: TTCAAGAAAAGATGAAATTGAACAAGAAGGAGGTTCAACGCTTTAATCCTgtgagttgga ... atgcttttagGTTGATGCTTTCCCCGGGGATGCCATAATATTTATGAGGGTCTTGAATCTC
EST: gi|67017334|gb|CO446083.1|CO446083
EST:     GAGGTTCAACGCTTTAATCCT                         GTTGATGCTCTCCCCGGGGATGCCATAATATTTATGAGGGTCTTGAATCTC
genomic: GAGGTTCAACGCTTTAATCCTgtgagttgga ... atgcttttagGTTGATGCTTTCCCCGGGGATGCCATAATATTTATGAGGGTCTTGAATCTC
EST: gi|211142857|gb|FL032418.1|FL032418
EST:     TTCAAGAAAAGATGAAATTGAACAAGAAGGAGGTTCAACGCTTTAATCCT                         GTTGATGCTTTCCCCGGGGATGCCATAATATTTATGAGGGTCTAGAATCTC
genomic: TTCAAGAAAAGATGAAATTGAACAAGAAGGAGGTTCAACGCTTTAATCCTgtgagttgga ... atgcttttagGTTGATGCTTTCCCCGGGGATGCCATAATATTTATGAGGGTCTTGAATCTC
EST: gi|211142859|gb|FL032420.1|FL032420
EST:     TTCAAGAAAAGATGAAATTGAACAAGAAGGAGGTTCAACGCTTTAATCCT                         GTTGATGCTTTCCCCGGGGATGCCATAATATTTATGAGGGTCTTGAATCTC
genomic: TTCAAGAAAAGATGAAATTGAACAAGAAGGAGGTTCAACGCTTTAATCCTgtgagttgga ... atgcttttagGTTGATGCTTTCCCCGGGGATGCCATAATATTTATGAGGGTCTTGAATCTC
EST: gi|211144282|gb|FL032424.1|FL032424
EST:     TTCAAGAAAAGATGAAATTGAACAAGAAGGAGGTTCAACGCTTTAATCCT                         GTTGATGCTTTCCCCGGGGATGCCATAATATTTATGAGGGTCTTGAATCTC
genomic: TTCAAGAAAAGATGAAATTGAACAAGAAGGAGGTTCAACGCTTTAATCCTgtgagttgga ... atgcttttagGTTGATGCTTTCCCCGGGGATGCCATAATATTTATGAGGGTCTTGAATCTC

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), 48 (downstream exon)
Score: 87

GAGAACATAAAAACACTTAATGACCAAAGAGAGAGAAATGTCAAAGCTCTTCAAGAAAAGATGAAATTGAACAAGAAGGAGGTTCAACGCTTTAATCCTgtgagttgga ... atgcttttagGTTGATGCTTTCCCCGGGGATGCCATAATATTTATGAGGGTCTTGAATCTCCTCAGAG


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

GAGAACATAAAAACACTTAATGACCAAAGAGAGAGAAATGTCAAAGCTCTTCAAGAAAAGATGAAATTGAACAAGAAGGAGGTTCAACGCTTTAATCCTgtgagttgga ... atgcttttagGTTGATGCTTTCCCCGGGGATGCCATAATATTTATGAGGGTCTTGAATCTCCTCAGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 476

GAGAACATAAAAACACTTAATGACCAAAGAGAGAGAAATGTCAAAGCTCTTCAAGAAAAGATGAAATTGAACAAGAAGGAGGTTCAACGCTTTAATCCTgtgagttgga ... atgcttttagGTTGATGCTTTCCCCGGGGATGCCATAATATTTATGAGGGTCTTGAATCTCCTCAGAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 306

GAGAACATAAAAACACTTAATGACCAAAGAGAGAGAAATGTCAAAGCTCTTCAAGAAAAGATGAAATTGAACAAGAAGGAGGTTCAACGCTTTAATCCTgtgagttgga ... atgcttttagGTTGATGCTTTCCCCGGGGATGCCATAATATTTATGAGGGTCTTGAATCTCCTCAGAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcagtttccacagccaattgatggggtgtcacatggacattttcatgcttttagGTTGATGCTTTCCCCGGGGATGCCATAATATTTATGAGGGTCTTGAATCTCCTCAGAG
                aattgat  putative branch site (score: 306)
                                        ttttcat  putative PPT
                                       attttcat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagttggaatgtctagcttgctacttttcagtttccacagccaattgatggggtgtcacatggacattttcatgcttttagGTTGATGCTTTCCCCGGGGATGCCATAATATTTATGAGGGTCTTGAATCTCCTCAGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTCCTC