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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tcacagaaaatagttctgatagatagtgtctagtacattgaattggcatagcatttctcaaccgaggttctcttacccgatgcttgttccccttatgcagGATTGATAGCGTGTCTCTTTTGGAATGTCATAGCAACTACAACAGCATGGATTAAAGGGGAAG

Basic information

species Zea mays
transcript GRMZM2G174730_T01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G174730_T01 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os05g42330.1 (Oryza sativa), 3'ss of exon 5
-tcacagaaaatagttctgatagatagtgtctagtacattgaattggcatagcatttctcaaccga-ggttctcttacccgatgcttgttccccttatgcagGATTGATAGCGTGTCTCTTTTGGAATGTCATAGCAACTACAACAGCATGGATTAAAGGGGAAG
    ||  |||   |  || || | || | ||  | ||| || || | |||| ||| || ||  |   ||||| ||  || || | |||   | | |||||||||||  ||| || || ||||||||| |||||||||| ||||| |||||| | ||||||||||
tcttcatgaaagcatcttgttatacagaggctcattcatggattttgtatagaattgctaaattggtagttcttttgtcc-atacctgtgatc-tcatgcagGATTGGCAGCCTGCCTATTTTGGAATATCATAGCAACCACAACCGCATGGGTAAAAGGGGAAG

upper sequence: GRMZM2G174730_T01 (Zea mays), 3'ss of exon 5
lower sequence: Vv00s0301g00030.t01 (Vitis vinifera), 3'ss of exon 6
-tcacagaaaatagttctgatagatagtgtctagtacattgaattggcatagcatttctcaaccgaggttctctt-acccgatgcttgttccccttatgcagGATTGATAGCGTGTCTCTTTTGGAATGTCATAGCAACTACAACAGCATGGATTAAAGGGGAAG
     |  | |     |  |   |||      | || | ||  ||   | |  |      |   |        |  |    |||    ||    |  ||||||||||  |   || ||    |||||| | ||||||||||| ||||||||||||||||||||||
gctttaacatacctacccaaagaataaa--taaataaagtgctttaagacaaaaccatcaagatggttcaaagtagattttatgagcattggtgtgctgcagGATTGGCATGCTGCCTTACATGGAATATTATAGCAACTACTACAGCATGGATTAAAGGGGAAG
















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|149076952|gb|EE165608.2|EE165608
EST:     ACCTATCCATCTACAAAGGATGCAGTACCTTGCATTCTCATCATTCTTGG                         GATTGATAGCGTGTCTCTTTTGGAATGTCATAGCAACTACAACAGCATGGA
genomic: ACCTATCCATCTACAAAGGATGCAGTACCTTGCATTCTCATCATTCTTGGgtgagctttt ... ccttatgcagGATTGATAGCGTGTCTCTTTTGGAATGTCATAGCAACTACAACAGCATGGA
EST: gi|211455821|gb|FL370764.1|FL370764
EST:     ACCTATCCATCTACAAAGGATGCAGTACCTTGCATTCTCATCATTCTTGG                         GATTGATAGCGTGTCTCTTTTGGAATGTCATAGCAACTACAACAGCMTGGA
genomic: ACCTATCCATCTACAAAGGATGCAGTACCTTGCATTCTCATCATTCTTGGgtgagctttt ... ccttatgcagGATTGATAGCGTGTCTCTTTTGGAATGTCATAGCAACTACAACAGCATGGA
EST: gi|32828156|gb|CD967834.1|CD967834
EST:     ACCTATCCATCTACAAAGGATGCAGTACCTTGCATTCTCATCATTCTTGG                         GATTGATAGCGTGTCTCTTTTGGAATGTCATAGCAACTACAACAGCATGAA
genomic: ACCTATCCATCTACAAAGGATGCAGTACCTTGCATTCTCATCATTCTTGGgtgagctttt ... ccttatgcagGATTGATAGCGTGTCTCTTTTGGAATGTCATAGCAACTACAACAGCATGGA
EST: gi|32825089|gb|CD964811.1|CD964811
EST:     ACCTATCCATCTACAAAGGATGCAGTACCTTGCATTCTCATCATTCTTGG                         GATAGATAGCGTGTCTCTTTTGGAATGTCATAGCAACTACAACAGCATGGA
genomic: ACCTATCCATCTACAAAGGATGCAGTACCTTGCATTCTCATCATTCTTGGgtgagctttt ... ccttatgcagGATTGATAGCGTGTCTCTTTTGGAATGTCATAGCAACTACAACAGCATGGA
EST: gi|31353834|gb|CD438191.1|CD438191
EST:     ACCTATCCATCTACAAAGGATGCAGTACCTTGCATTCTCATCATTCTTGG                         GATTGATAGCGTGTCTCTTTTGGAATGTCATAGCAACTACAACAGCATGGA
genomic: ACCTATCCATCTACAAAGGATGCAGTACCTTGCATTCTCATCATTCTTGGgtgagctttt ... ccttatgcagGATTGATAGCGTGTCTCTTTTGGAATGTCATAGCAACTACAACAGCATGGA
EST: gi|211137749|gb|FL292364.1|FL292364
EST:     ACCTATCCATCTACAAAGGATGCAGTACCTTGCATTCTCATCATTCTTGG                         GATTGATAGCGTGTCTCTTTTGGAATGTCATAGCAACTACAACAGCATGGA
genomic: ACCTATCCATCTACAAAGGATGCAGTACCTTGCATTCTCATCATTCTTGGgtgagctttt ... ccttatgcagGATTGATAGCGTGTCTCTTTTGGAATGTCATAGCAACTACAACAGCATGGA
EST: gi|71322126|gb|DR797758.1|DR797758
EST:     ATTCTCATCATTCTTGG                         GATTGATAGCGTGTCTCTTTTGGAATGTCATAGCAACTACAACAGCATGGA
genomic: ATTCTCATCATTCTTGGgtgagctttt ... ccttatgcagGATTGATAGCGTGTCTCTTTTGGAATGTCATAGCAACTACAACAGCATGGA
EST: gi|211198979|gb|FL379473.1|FL379473
EST:     ACCTATCCATCTACAAAGGATGCAGTACCTTGCATTCTCATCATTCTTGG                         GATTGATAGCGTGTCTCTTTTGGAATGTCATAGCAACTACAACAGCATGGA
genomic: ACCTATCCATCTACAAAGGATGCAGTACCTTGCATTCTCATCATTCTTGGgtgagctttt ... ccttatgcagGATTGATAGCGTGTCTCTTTTGGAATGTCATAGCAACTACAACAGCATGGA
EST: gi|37400724|gb|CF637721.1|CF637721
EST:     AAGGATGCAGTACC-TGCATTCTCATCATTCTT-G                         GATTGATAGCGTGTCTCTTTT-GAATGTCATAGCAACTAC-ACAGCATGGA
genomic: AAGGATGCAGTACCTTGCATTCTCATCATTCTTGGgtgagctttt ... ccttatgcagGATTGATAGCGTGTCTCTTTTGGAATGTCATAGCAACTACAACAGCATGGA
EST: gi|211501973|gb|FL392126.1|FL392126
EST:     ACCTATCCATCTACAAAGGATGCAGTACCTTGCATTCTCATCATTCTTGG                         GATTGATAGCGTGTCTCTTTTGGAATGTCATAGCAACTACAACAGCATGGA
genomic: ACCTATCCATCTACAAAGGATGCAGTACCTTGCATTCTCATCATTCTTGGgtgagctttt ... ccttatgcagGATTGATAGCGTGTCTCTTTTGGAATGTCATAGCAACTACAACAGCATGGA
EST: gi|149069546|gb|EE157919.2|EE157919
EST:     ACCTATCCATCTACAAAGGATGCAGTACCTTGCATTCTCATCATTCTTGG                         GATTGATAGCGTGTCTCTTTTGGAATGTCATAGCAACTACCACAGCATGGA
genomic: ACCTATCCATCTACAAAGGATGCAGTACCTTGCATTCTCATCATTCTTGGgtgagctttt ... ccttatgcagGATTGATAGCGTGTCTCTTTTGGAATGTCATAGCAACTACAACAGCATGGA
EST: gi|76927277|gb|DV171213.1|DV171213
EST:     ACCTATCCATCTACAAAGGATGCAGTACCTTGCATTCTCATCATTCTTGG                         GATTGATAGCGTGTCTCTTTTGGAATGTCATAGCAACTACAACAGCATGGA
genomic: ACCTATCCATCTACAAAGGATGCAGTACCTTGCATTCTCATCATTCTTGGgtgagctttt ... ccttatgcagGATTGATAGCGTGTCTCTTTTGGAATGTCATAGCAACTACAACAGCATGGA
EST: gi|211138685|gb|FL292368.1|FL292368
EST:     ACCTATCCATCTACAAAGGATGCAGTAC-TTGCATTCTCATCATTCTTGG                         GATTGATAGCGTGTCTCTTTTGGAATGTCATAGC
genomic: ACCTATCCATCTACAAAGGATGCAGTACCTTGCATTCTCATCATTCTTGGgtgagctttt ... ccttatgcagGATTGATAGCGTGTCTCTTTTGGAATGTCATAGC
EST: gi|211138688|gb|FL292371.1|FL292371
EST:     ACCTATCCATCTACAAAGGATGCAGTACCTTGCATTCTCATCATTCTTGG                         GATTGATAGCGTGTCTCTTTTGGAATGTCATAAGCAACTACAACAGC
genomic: ACCTATCCATCTACAAAGGATGCAGTACCTTGCATTCTCATCATTCTTGGgtgagctttt ... ccttatgcagGATTGATAGCGTGTCTCTTTTGGAATGTCATA-GCAACTACAACAGC
EST: gi|4152018|gb|AI372152.1|AI372152
EST:     ACCTATCCATCTACAAAGGATGCAGTACCTTGCATTCTCATCATTCTTGG                         GATTGATAGCGTGTCTCTTTTGGAATGTCATAGCAACTACAACACCATGGA
genomic: ACCTATCCATCTACAAAGGATGCAGTACCTTGCATTCTCATCATTCTTGGgtgagctttt ... ccttatgcagGATTGATAGCGTGTCTCTTTTGGAATGTCATAGCAACTACAACAGCATGGA
EST: gi|5847119|gb|AW000198.1|AW000198
EST:     GCAGTACCTTGCATTCTCATCATTCTTGG                         GATTGATAGCGTGTCTCTTTTGGAATGTCATAGCAACTACAACAGCATGGA
genomic: GCAGTACCTTGCATTCTCATCATTCTTGGgtgagctttt ... ccttatgcagGATTGATAGCGTGTCTCTTTTGGAATGTCATAGCAACTACAACAGCATGGA
EST: gi|211122269|gb|FL373644.1|FL373644
EST:     ACCTATCCATCTACAAAGGATGCAGTACCTTGCATTCTCATCATTCTTGG                         GAATTGATAGCGTGTCTC
genomic: ACCTATCCATCTACAAAGGATGCAGTACCTTGCATTCTCATCATTCTTGGgtgagctttt ... ccttatgcagGA-TTGATAGCGTGTCTC
EST: gi|32825405|gb|CD965127.1|CD965127
EST:     ACCTATCCATCTACAAAGGATGCAGTACCTTGCATTCTCATCATTCTTGG                         GATTGATAGCGTGTCTCTTTTGGAATGTCATAGCAACTACAACAGCATGGA
genomic: ACCTATCCATCTACAAAGGATGCAGTACCTTGCATTCTCATCATTCTTGGgtgagctttt ... ccttatgcagGATTGATAGCGTGTCTCTTTTGGAATGTCATAGCAACTACAACAGCATGGA
EST: gi|211138687|gb|FL292370.1|FL292370
EST:     ACCTATCCATCTACAAAGGATGCAGTACCTTGCATTCTCATCATTCTTGG                         GATTGATAGCGTGTCTCT
genomic: ACCTATCCATCTACAAAGGATGCAGTACCTTGCATTCTCATCATTCTTGGgtgagctttt ... ccttatgcagGATTGATAGCGTGTCTCT
EST: gi|76289053|gb|DV028621.1|DV028621
EST:     ACCTATCCATCTACAAAGGATGCAGTACCTTGCATTCTCATCATTCTTGG                         GATTGATAGCGTGTCTCTTTTGGAATGTCATAGCAACTACAACAGCATGGA
genomic: ACCTATCCATCTACAAAGGATGCAGTACCTTGCATTCTCATCATTCTTGGgtgagctttt ... ccttatgcagGATTGATAGCGTGTCTCTTTTGGAATGTCATAGCAACTACAACAGCATGGA
EST: gi|71322127|gb|DR797759.1|DR797759
EST:     CCTATCCATCTACAAAGGATGCAGTACCTTTGCATTCTCATCATTCTTGG                         GATTGATAGCCGTGTCTCTTTTGGA
genomic: CCTATCCATCTACAAAGGATGCAGTACCTT-GCATTCTCATCATTCTTGGgtgagctttt ... ccttatgcagGATTGATAGC-GTGTCTCTTTTGGA
EST: gi|211228158|gb|FL414420.1|FL414420
EST:     ACCTATCCATCTACAAAGGATGCAGTACCTTGCATTCTCATCATTCTTGG                         GATTGATAGCGTGTCTCTTTTGGAATGTCATAGCA
genomic: ACCTATCCATCTACAAAGGATGCAGTACCTTGCATTCTCATCATTCTTGGgtgagctttt ... ccttatgcagGATTGATAGCGTGTCTCTTTTGGAATGTCATAGCA
EST: gi|32808007|gb|CD960241.1|CD960241
EST:     ACCTATCCATCTACAAAGGATGCAGTACCTTGCATTCTCATCATTCTTGG                         GATTGATAGCGTGTCTCTTTTGGAATGTCATAGCAACTACAACAGCATGG
genomic: ACCTATCCATCTACAAAGGATGCAGTACCTTGCATTCTCATCATTCTTGGgtgagctttt ... ccttatgcagGATTGATAGCGTGTCTCTTTTGGAATGTCATAGCAACTACAACAGCATGG
EST: gi|149079646|gb|EE168643.2|EE168643
EST:     ACCTATCCATCTACAAAGGATGCAGTACCTTGCATTCTCATCATTCTTGG                         GATTGATAGCGTGTCTCTTTTGGAATGTCATAGCAACTACAACAGCATGGA
genomic: ACCTATCCATCTACAAAGGATGCAGTACCTTGCATTCTCATCATTCTTGGgtgagctttt ... ccttatgcagGATTGATAGCGTGTCTCTTTTGGAATGTCATAGCAACTACAACAGCATGGA
EST: gi|78081465|gb|DV509877.1|DV509877
EST:     ACCTATCCATCTACAAAGGATGCAGTACCTTGCATTCTCATCATTCTTGG                         GATTGATAGCGTGTCTCTTTTGGAATGTCATAGCAACTACAACAGCATGGA
genomic: ACCTATCCATCTACAAAGGATGCAGTACCTTGCATTCTCATCATTCTTGGgtgagctttt ... ccttatgcagGATTGATAGCGTGTCTCTTTTGGAATGTCATAGCAACTACAACAGCATGGA
EST: gi|211130112|gb|FL389065.1|FL389065
EST:     ACCTATCCATCTACAAAGGATGCAGTACCTTGCATTCTCATCATTCTTGG                         GATTGATAGCGTGTCTCTTTTGGAATGTCATAGCAACTAC
genomic: ACCTATCCATCTACAAAGGATGCAGTACCTTGCATTCTCATCATTCTTGGgtgagctttt ... ccttatgcagGATTGATAGCGTGTCTCTTTTGGAATGTCATAGCAACTAC
EST: gi|32938227|gb|CF043046.1|CF043046
EST:     TACCTTGCATTCTCATCATTCTTGG                         GATTGATAGCGTGTCTCTTTTGGAATGTCATAGCAACTACAACAGCACGGA
genomic: TACCTTGCATTCTCATCATTCTTGGgtgagctttt ... ccttatgcagGATTGATAGCGTGTCTCTTTTGGAATGTCATAGCAACTACAACAGCATGGA
EST: gi|5343187|gb|AI795372.1|AI795372
EST:     GCAGTACCTTGCATTCTCATCATTCTTGG                         GATTGATAGCGTGTCTCTTTTGGAATGTCATAGCAACTACAACAGCATGGA
genomic: GCAGTACCTTGCATTCTCATCATTCTTGGgtgagctttt ... ccttatgcagGATTGATAGCGTGTCTCTTTTGGAATGTCATAGCAACTACAACAGCATGGA
EST: gi|78112246|gb|DV530640.1|DV530640
EST:     ACCTATCCATCTACAAAGGATGCAGTACCTTGCATTCTCATCATTCTTGG                         GATTGATAGCGTGTCTCTTTTGGAATGTCATAGCAACTACAACAGCATGGA
genomic: ACCTATCCATCTACAAAGGATGCAGTACCTTGCATTCTCATCATTCTTGGgtgagctttt ... ccttatgcagGATTGATAGCGTGTCTCTTTTGGAATGTCATAGCAACTACAACAGCATGGA
EST: gi|37417263|gb|CF646284.1|CF646284
EST:     ACCTATCCATCTACAAAGGATGCAGTACCTTGCATTCTCATCATTCTTGG                         GATTGATAGCGTGTCTCTTTTGGAATGTCAT
genomic: ACCTATCCATCTACAAAGGATGCAGTACCTTGCATTCTCATCATTCTTGGgtgagctttt ... ccttatgcagGATTGATAGCGTGTCTCTTTTGGAATGTCAT
EST: gi|211035296|gb|FL425638.1|FL425638
EST:     ACCTATCCATCTACAAAGGATGCAGTACCTTGCATTCTCATCATTCTTGG                         GATTGATAGCGTGTCTCTTTTGGAATGTCATAGCAACTAC
genomic: ACCTATCCATCTACAAAGGATGCAGTACCTTGCATTCTCATCATTCTTGGgtgagctttt ... ccttatgcagGATTGATAGCGTGTCTCTTTTGGAATGTCATAGCAACTAC
EST: gi|149104177|gb|EE289611.2|EE289611
EST:     ACCTATCCATCTACCAAGGATGCAGTACCTTGCATTCTCATCATTCTTGG                         GATTGATAGCGTGTCTCTTTTGGAATGTCATAGCAACTACAACAGCATGGA
genomic: ACCTATCCATCTACAAAGGATGCAGTACCTTGCATTCTCATCATTCTTGGgtgagctttt ... ccttatgcagGATTGATAGCGTGTCTCTTTTGGAATGTCATAGCAACTACAACAGCATGGA

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: 46 (upstream exon), 49 (downstream exon)
Score: 325

AACTGGCCTCCCTTTTTCCCCCTCATCCACCACGACATTTCCAATGAAATACCTATCCATCTACAAAGGATGCAGTACCTTGCATTCTCATCATTCTTGGgtgagctttt ... ccttatgcagGATTGATAGCGTGTCTCTTTTGGAATGTCATAGCAACTACAACAGCATGGATTAAAGGGGAAG


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 340

AACTGGCCTCCCTTTTTCCCCCTCATCCACCACGACATTTCCAATGAAATACCTATCCATCTACAAAGGATGCAGTACCTTGCATTCTCATCATTCTTGGgtgagctttt ... ccttatgcagGATTGATAGCGTGTCTCTTTTGGAATGTCATAGCAACTACAACAGCATGGATTAAAGGGGAAG


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 307

AACTGGCCTCCCTTTTTCCCCCTCATCCACCACGACATTTCCAATGAAATACCTATCCATCTACAAAGGATGCAGTACCTTGCATTCTCATCATTCTTGGgtgagctttt ... ccttatgcagGATTGATAGCGTGTCTCTTTTGGAATGTCATAGCAACTACAACAGCATGGATTAAAGGGGAAG


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 429

AACTGGCCTCCCTTTTTCCCCCTCATCCACCACGACATTTCCAATGAAATACCTATCCATCTACAAAGGATGCAGTACCTTGCATTCTCATCATTCTTGGgtgagctttt ... ccttatgcagGATTGATAGCGTGTCTCTTTTGGAATGTCATAGCAACTACAACAGCATGGATTAAAGGGGAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcatagcatttctcaaccgaggttctcttacccgatgcttgttccccttatgcagGATTGATAGCGTGTCTCTTTTGGAATGTCATAGCAACTACAACAGCATGGATTAAAGGGGAAG
                        ctcttac  putative branch site (score: 429)
                                   tgcttgttcccctt  putative PPT
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tcacagaaaatagttctgatagatagtgtctagtacattgaattggcatagcatttctcaaccgaggttctcttacccgatgcttgttccccttatgcagGATTGATAGCGTGTCTCTTTTGGAATGTCATAGCAACTACAACAGCATGGATTAAAGGGGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CATGGA
- acagaaa
- - - - - - -ttctgat
- - - - - - - - - - - - - - - - - - - tgaattg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgcttgt