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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...catttcatgttgtttcaacttttgttacttggtatatgtcatggaatatattttttgtttccagcactctagcttttgtaacatgtgacgctgtttacagACTTGAGAGAGATGCTTACCCTCTTTTTAGAACACTTCGACAGAAGTATAAGACAAGTACAGATCGTGATGCTGTGTTTCAGGAG

Basic information

species Zea mays
transcript GRMZM2G048804_T02
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G048804_T02 (Zea mays), 3'ss of exon 9
lower sequence: LOC_Os01g07100.1 (Oryza sativa), 3'ss of exon 9
catttcatgttgtttcaacttttgttacttggtatatgtcatggaatatattttttgtttccagcactctagcttttgtaacatgtgacgc----tgtttacagACTTGAGAGAGATGCTTACCCTCTTTTTAGAACACTTCGACAGAAGTATAAGACAAGTACAGATCGTGATGCTGTGTTTCAGGAG
 ||  || |      |    |||  |||  |  | | ||  |    | |  |  ||||||||     ||  | || | | ||      |      ||||||||| || || |||||||||||||||||||| || ||||| || |||||||| ||||||||||||||||  ||  |||| ||| |||||
-ataccaagcccagacgttattttatacaagcaacaagttttt---ttttctcattgtttcctctggtcgtggttatattactgactgcatgctatgtttacagGCTCGAAAGAGATGCTTACCCTCTTTTCAGGACACTGCGGCAGAAGTACAAGACAAGTACAGATCACGACCCTGTATTTGAGGAG
















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|31558703|gb|CD527915.1|CD527915
EST:     GAATTTCCGAAAACAGATTTGATTCAGTTCATCAAGTATCTTTTACCAAC                         ACTTGAGAGAGATGCTTACCCTCTTTTTAGAACACTTCGACAGAAGTATAA
genomic: GAATTTCCGAAAACAGATTTGATTCAGTTCATCAAGTATCTTTTACCAACgtaagtttgt ... ctgtttacagACTTGAGAGAGATGCTTACCCTCTTTTTAGAACACTTCGACAGAAGTATAA
EST: gi|33771157|gb|CF272818.1|CF272818
EST:     GAATTTCCGAAAACAGATTTGATTCAGTTCATCAAGTATCTTTTACCAAC                         ACTTGAGAGAGATGCTTACCCTCTTTTTAGAACACTTCGACAGAAGTATAA
genomic: GAATTTCCGAAAACAGATTTGATTCAGTTCATCAAGTATCTTTTACCAACgtaagtttgt ... ctgtttacagACTTGAGAGAGATGCTTACCCTCTTTTTAGAACACTTCGACAGAAGTATAA
EST: gi|94472950|gb|EB701908.1|EB701908
EST:     GAATTTCCGAAAACAGATTTGATTCAGTTCATCAAGTATCTTTTACCAAC                         ACTTGAGAGAGATGCTTACCCTCTTTTTAGAACACTTCGACAGAAGTATAA
genomic: GAATTTCCGAAAACAGATTTGATTCAGTTCATCAAGTATCTTTTACCAACgtaagtttgt ... ctgtttacagACTTGAGAGAGATGCTTACCCTCTTTTTAGAACACTTCGACAGAAGTATAA
EST: gi|113704317|gb|EE681821.1|EE681821
EST:     GAATTTCCGAAAACAGATTTGATTCAGTTCATCAAGTATCTTTTACCAAC                         ACTTGAGAGAGATGCTTACCCTCTTTTTAGAACACTTCGACAGAAGTATAA
genomic: GAATTTCCGAAAACAGATTTGATTCAGTTCATCAAGTATCTTTTACCAACgtaagtttgt ... ctgtttacagACTTGAGAGAGATGCTTACCCTCTTTTTAGAACACTTCGACAGAAGTATAA
EST: gi|37379196|gb|CF626330.1|CF626330
EST:     GAATTTCCGAAAACAGATTTGATTCAGTTCATCAAGTATCTTTTACCAAC                         ACTTGAGAGAGATGCTTACCCTCTTTTTAGAACACTTCGACAGAAGTATAA
genomic: GAATTTCCGAAAACAGATTTGATTCAGTTCATCAAGTATCTTTTACCAACgtaagtttgt ... ctgtttacagACTTGAGAGAGATGCTTACCCTCTTTTTAGAACACTTCGACAGAAGTATAA
EST: gi|5791304|gb|AI978096.1|AI978096
EST:     GAATTTCCGAAAACAGATTTGATTCAGTTCATCAAGTATCTTTTACCAAC                         ACTTGAGAGAGATGCTTACCCTCTTTTTAGAACACTTCGACAGAAGTATAA
genomic: GAATTTCCGAAAACAGATTTGATTCAGTTCATCAAGTATCTTTTACCAACgtaagtttgt ... ctgtttacagACTTGAGAGAGATGCTTACCCTCTTTTTAGAACACTTCGACAGAAGTATAA
EST: gi|50339821|gb|CO534947.1|CO534947
EST:     GAATTTCCGAAAACAGATTTGATTCAGTTCATCAAGTATCTTTTACCAAC                         ACTTGAGAGAGATGCTTACCCTCTTTTTAGAACACTTCGACAGAAGTATAA
genomic: GAATTTCCGAAAACAGATTTGATTCAGTTCATCAAGTATCTTTTACCAACgtaagtttgt ... ctgtttacagACTTGAGAGAGATGCTTACCCTCTTTTTAGAACACTTCGACAGAAGTATAA
EST: gi|33467111|gb|CF244160.1|CF244160
EST:     GAATTTCCGAAAACAGATTTGATTCAGTTCATCAAGTATCTTTTACCAAC                         ACTTGAGAGAGATGCTTACCCTCTTTTTAGAACACTTCGACAGAAGTATAA
genomic: GAATTTCCGAAAACAGATTTGATTCAGTTCATCAAGTATCTTTTACCAACgtaagtttgt ... ctgtttacagACTTGAGAGAGATGCTTACCCTCTTTTTAGAACACTTCGACAGAAGTATAA
EST: gi|5005582|gb|AI711644.1|AI711644
EST:     GAATTTCCGAAAACAGATTTGATTCAGTTCATCAAGTATCTTTTACCAAC                         ACTTGAGAGAGATGCTTACCCTCTTTTTAGAACACTTCGACAGAAGTATAA
genomic: GAATTTCCGAAAACAGATTTGATTCAGTTCATCAAGTATCTTTTACCAACgtaagtttgt ... ctgtttacagACTTGAGAGAGATGCTTACCCTCTTTTTAGAACACTTCGACAGAAGTATAA
EST: gi|71773196|gb|DR971109.1|DR971109
EST:     GAATTTCCGAAAACAGATTTGATTCAGTTCATCAAGTATCTTTTACCAAC                         ACTTGAGAGAGATGCTTACCCTCTTTTTAGAACACTTCGACAGAAGTATAA
genomic: GAATTTCCGAAAACAGATTTGATTCAGTTCATCAAGTATCTTTTACCAACgtaagtttgt ... ctgtttacagACTTGAGAGAGATGCTTACCCTCTTTTTAGAACACTTCGACAGAAGTATAA
EST: gi|74236760|gb|DT644674.1|DT644674
EST:     GAATTTCCGAAAACAGATTTGATTCAGTTCATCAAGTATCTTTTACCAAC                         ACTTGAGAGAGATGCTTACCCTCTTTTTAGAACACTTCGACAGAAGTATAA
genomic: GAATTTCCGAAAACAGATTTGATTCAGTTCATCAAGTATCTTTTACCAACgtaagtttgt ... ctgtttacagACTTGAGAGAGATGCTTACCCTCTTTTTAGAACACTTCGACAGAAGTATAA
EST: gi|211155842|gb|FL114458.1|FL114458
EST:     GAATTTCCGAAAACAGATTTGATTCAGTTCATCAAGTATCTTTTACCAAC                         ACTTGAGAGAGATGCTTACCCTCTTTTTAGAACACTTCGACAGAAGTATAA
genomic: GAATTTCCGAAAACAGATTTGATTCAGTTCATCAAGTATCTTTTACCAACgtaagtttgt ... ctgtttacagACTTGAGAGAGATGCTTACCCTCTTTTTAGAACACTTCGACAGAAGTATAA
EST: gi|32911197|gb|CF016009.1|CF016009
EST:     GAATTTCCGAAAACAGATTTGATTCAGTTCATCAAGTATCTTTTACCAAC                         ACTTGAGAGAGATGCTTACCCTCTTTTTAGAACACTTCGACAGAAGTATAA
genomic: GAATTTCCGAAAACAGATTTGATTCAGTTCATCAAGTATCTTTTACCAACgtaagtttgt ... ctgtttacagACTTGAGAGAGATGCTTACCCTCTTTTTAGAACACTTCGACAGAAGTATAA
EST: gi|24764009|gb|CA399178.1|CA399178
EST:     GAATTTCCGAAAACAGATTTGATTCAGTTCATCAAGTATCTTTTACCAAC                         ACTTGAGAGAGATGCTTACCCTCTTTTTAGAACACTTCGACAGAAGTATAA
genomic: GAATTTCCGAAAACAGATTTGATTCAGTTCATCAAGTATCTTTTACCAACgtaagtttgt ... ctgtttacagACTTGAGAGAGATGCTTACCCTCTTTTTAGAACACTTCGACAGAAGTATAA
EST: gi|78021285|gb|DV489672.1|DV489672
EST:     GAATTTCCGAAAACAGATTTGATTCAGTTCATCAAGTATCTTTTACCAAC                         ACTTGAGAGAGATGCTTACCCTCTTTTTAGAACACTTCGACAGAAGTATAA
genomic: GAATTTCCGAAAACAGATTTGATTCAGTTCATCAAGTATCTTTTACCAACgtaagtttgt ... ctgtttacagACTTGAGAGAGATGCTTACCCTCTTTTTAGAACACTTCGACAGAAGTATAA
EST: gi|113702828|gb|EE680332.1|EE680332
EST:     GAATTTCCGAAAACAGATTTGATTCAGTTCATCAAGTATCTTTTACCAAC                         ACTTGAGAGAGATGCTTACCCTCTTTTTAGAACACTTCGACAGAAGTATAA
genomic: GAATTTCCGAAAACAGATTTGATTCAGTTCATCAAGTATCTTTTACCAACgtaagtttgt ... ctgtttacagACTTGAGAGAGATGCTTACCCTCTTTTTAGAACACTTCGACAGAAGTATAA

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: 45 (upstream exon), 46 (downstream exon)
Score: 69

CAAATTTACTTATGGATGAGATGAACGAACAACTAAAATCTGCTAACTCGGAATTTCCGAAAACAGATTTGATTCAGTTCATCAAGTATCTTTTACCAACgtaagtttgt ... ctgtttacagACTTGAGAGAGATGCTTACCCTCTTTTTAGAACACTTCGACAGAAGTATAAGACAAGTACAGATCGTGATGCTGTGTTTCAGGAG


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 87

CAAATTTACTTATGGATGAGATGAACGAACAACTAAAATCTGCTAACTCGGAATTTCCGAAAACAGATTTGATTCAGTTCATCAAGTATCTTTTACCAACgtaagtttgt ... ctgtttacagACTTGAGAGAGATGCTTACCCTCTTTTTAGAACACTTCGACAGAAGTATAAGACAAGTACAGATCGTGATGCTGTGTTTCAGGAG


Block sizes: 48 (upstream exon), 46 (downstream exon)
Score: 97

CAAATTTACTTATGGATGAGATGAACGAACAACTAAAATCTGCTAACTCGGAATTTCCGAAAACAGATTTGATTCAGTTCATCAAGTATCTTTTACCAACgtaagtttgt ... ctgtttacagACTTGAGAGAGATGCTTACCCTCTTTTTAGAACACTTCGACAGAAGTATAAGACAAGTACAGATCGTGATGCTGTGTTTCAGGAG


Block sizes: 48 (upstream exon), 46 (downstream exon)
Score: 164

CAAATTTACTTATGGATGAGATGAACGAACAACTAAAATCTGCTAACTCGGAATTTCCGAAAACAGATTTGATTCAGTTCATCAAGTATCTTTTACCAACgtaagtttgt ... ctgtttacagACTTGAGAGAGATGCTTACCCTCTTTTTAGAACACTTCGACAGAAGTATAAGACAAGTACAGATCGTGATGCTGTGTTTCAGGAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atatattttttgtttccagcactctagcttttgtaacatgtgacgctgtttacagACTTGAGAGAGATGCTTACCCTCTTTTTAGAACACTTCGACAGAAGTATAAGACAAGTACAGATCGTGATGCTGTGTTTCAGGAG
                              ttgtaac  putative branch site (score: 164)
     ttttttgttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
catttcatgttgtttcaacttttgttacttggtatatgtcatggaatatattttttgtttccagcactctagcttttgtaacatgtgacgctgtttacagACTTGAGAGAGATGCTTACCCTCTTTTTAGAACACTTCGACAGAAGTATAAGACAAGTACAGATCGTGATGCTGTGTTTCAGGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - -tgttgtt
- - - - - - - - - - - tgttact
- - - - - - - - - - - - - - - - - - - -catggaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gcttttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -catgtga