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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tcaatgctcctcttttaagatcattgcatacttttggttggagtatatcccttttattggtgcttccatttgttcatttgcttatatgaattgctggcagGTGGCCATGAAGCTCTCTCCTAATAGAGATAAATTCATGGAGGTCATTAGTGGAACTGGTGATATCAATGCAGATATTGAGAAATTTTGCACGACCTTCT

Basic information

species Zea mays
transcript GRMZM2G060870_T02
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G060870_T02 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os02g40890.2 (Oryza sativa), 3'ss of exon 5
tcaatgctcctcttttaagatcattgcatacttttggttggagtatatcccttttattgg---tgcttccatttgttcatttgcttatatgaattgctggcagGTGGCCATGAAGCTCTCTCCTAATAGAGATAAATTCATGGAGGTCATTAGTGGAACTGGTGATATCAATGCAGATATTGAGAAATTTTGCACGACCTTCT
       | |  || |  ||  | | | |   ||||||    || |    | |||||| |   | | ||| |||||     |||| ||||||     ||||||||||| ||||||||  ||||||||||||| ||||| |||||||||||||||||||| ||||| || || || ||||| |||||||| ||||||||||| |
--ggctttgcctttctgtgagaagttctttaatttggtcat-gtttgcttcctttatttgcttttcctccgtttgtatgagtgctcatatgagaaattggcagGTGGCAATGAAGCTTGCTCCTAATAGAGAGAAATTTATGGAGGTCATTAGTGGAACGGGTGACATAAAAGCTGATATCGAGAAATTCTGCACGACCTTTT
















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|32934286|gb|CF039098.1|CF039098
EST:     CCAAGACCCTCAAGAAATTTCATGGCTGGCTTGCCAGTTCTAGTTTTACG                         GTGGCCATGAAGCTCTCTCCTAATAGAGATAAATTTATGGAGGTCATTAGT
genomic: CCAAGACCTTGAAGAAATTTCATGGCTGGCTTGCCAGTTCTAGTTTTACGgtagaatctt ... ttgctggcagGTGGCCATGAAGCTCTCTCCTAATAGAGATAAATTCATGGAGGTCATTAGT
EST: gi|32932161|gb|CF036973.1|CF036973
EST:     CCAAGACCCTCAAGAAATTTCATGGCTGGCTTGCCAGTTCTAGTTTTACG                         GTGGCCATGAAGCTCTCTCCTAATAGAGATAAATTTATGGAGGTCATTAGT
genomic: CCAAGACCTTGAAGAAATTTCATGGCTGGCTTGCCAGTTCTAGTTTTACGgtagaatctt ... ttgctggcagGTGGCCATGAAGCTCTCTCCTAATAGAGATAAATTCATGGAGGTCATTAGT
EST: gi|32866744|gb|CF006426.1|CF006426
EST:     CCAAGACCCTCAAGAAATTTCATGGCTGGCTTGCCAGTTCTAGTTTTACG                         GTGGCCATGAAGCTCTCTCCTAATAGAGATAAATTTATGGAGGTCATTAGT
genomic: CCAAGACCTTGAAGAAATTTCATGGCTGGCTTGCCAGTTCTAGTTTTACGgtagaatctt ... ttgctggcagGTGGCCATGAAGCTCTCTCCTAATAGAGATAAATTCATGGAGGTCATTAGT
EST: gi|32934643|gb|CF039455.1|CF039455
EST:     CCAAGACCCTCAAGAAATTTCATGGCTGGCTTGCCAGTTCTAGTTTTACG                         GTGGCCATGAAGCTCTCTCCTAATAGAGATAAATTTATGGAGGTCATTAGT
genomic: CCAAGACCTTGAAGAAATTTCATGGCTGGCTTGCCAGTTCTAGTTTTACGgtagaatctt ... ttgctggcagGTGGCCATGAAGCTCTCTCCTAATAGAGATAAATTCATGGAGGTCATTAGT
EST: gi|32832496|gb|CD972174.1|CD972174
EST:     CCAAGACCCTCAAGAAATTTCATGGCTGGCTTGCCAGTTCTAGTTTTACG                         GTGGCCATGAAGCTCTCTCCTAATAGAGATAAATTTATGGAGGTCATTAGT
genomic: CCAAGACCTTGAAGAAATTTCATGGCTGGCTTGCCAGTTCTAGTTTTACGgtagaatctt ... ttgctggcagGTGGCCATGAAGCTCTCTCCTAATAGAGATAAATTCATGGAGGTCATTAGT
EST: gi|32930749|gb|CF035561.1|CF035561
EST:     CCAAGACCCTCAAGAAATTTCATGGCTGGCTTGCCAGTTCTAGTTTTACG                         GTGGCCATGAAGCTCTCTCCTAATAGAGATAAATTTATGGAGGTCATTAGT
genomic: CCAAGACCTTGAAGAAATTTCATGGCTGGCTTGCCAGTTCTAGTTTTACGgtagaatctt ... ttgctggcagGTGGCCATGAAGCTCTCTCCTAATAGAGATAAATTCATGGAGGTCATTAGT
EST: gi|32867862|gb|CF007544.1|CF007544
EST:     CCAAGACCCTCAAGAAATTTCATGGCTGGCTTGCCAGTTCTAGTTTTACG                         GTGGCCATGAAGCTCTCTCC
genomic: CCAAGACCTTGAAGAAATTTCATGGCTGGCTTGCCAGTTCTAGTTTTACGgtagaatctt ... ttgctggcagGTGGCCATGAAGCTCTCTCC
EST: gi|45567822|gb|CK985763.1|CK985763
EST:     CCAAGACCCTCAAGAAATTTCATGGCTGGCTTGCCAGTTCTAGTTTTACG                         GTGGCCATGAAGCTCTCTCCTAATAGAGATAAATTTATGGAGGTCATTAGT
genomic: CCAAGACCTTGAAGAAATTTCATGGCTGGCTTGCCAGTTCTAGTTTTACGgtagaatctt ... ttgctggcagGTGGCCATGAAGCTCTCTCCTAATAGAGATAAATTCATGGAGGTCATTAGT
EST: gi|60346084|gb|DN213057.1|DN213057
EST:     CCAAGACCTTGAAGAAATTTCATGGCTGGCTTGCCAGTTCTAGTTTTACG                         GTGGCCATGAAGCTCTCTCCTAATAGAGATAAATTCATGGAGGTCATTAGT
genomic: CCAAGACCTTGAAGAAATTTCATGGCTGGCTTGCCAGTTCTAGTTTTACGgtagaatctt ... ttgctggcagGTGGCCATGAAGCTCTCTCCTAATAGAGATAAATTCATGGAGGTCATTAGT
EST: gi|22542222|gb|BU092660.1|BU092660
EST:     CCAAGACCCTGAAGAAATTTCATGGCTGGCTTGCCAGTTCTAGTTTTACG                         GTGGCCATGAAGCTCTCTCCTAATAGAGATAAATTCATGGAGGTCATTAGT
genomic: CCAAGACCTTGAAGAAATTTCATGGCTGGCTTGCCAGTTCTAGTTTTACGgtagaatctt ... ttgctggcagGTGGCCATGAAGCTCTCTCCTAATAGAGATAAATTCATGGAGGTCATTAGT
EST: gi|211296158|gb|FL473352.1|FL473352
EST:     CCAAGACCCTCAAGAAATTTCATGGCTGGCTTGCCAGTTCTAGTTTTACG                         GTGGCCATGAAGCTCTCTCCTAATAGAGATAAATTTATGGAGGTCATTAGT
genomic: CCAAGACCTTGAAGAAATTTCATGGCTGGCTTGCCAGTTCTAGTTTTACGgtagaatctt ... ttgctggcagGTGGCCATGAAGCTCTCTCCTAATAGAGATAAATTCATGGAGGTCATTAGT
EST: gi|17932440|gb|BM269400.1|BM269400
EST:     CCAAGACCTTGAAGAAATTTCATGGCTGGCTTGCCAGTTCTAGTTTTACG                         GTGGCCATGAAGCTCTCTCCTAATAGAGATAAATTCATGGAGGTCATTAGT
genomic: CCAAGACCTTGAAGAAATTTCATGGCTGGCTTGCCAGTTCTAGTTTTACGgtagaatctt ... ttgctggcagGTGGCCATGAAGCTCTCTCCTAATAGAGATAAATTCATGGAGGTCATTAGT
EST: gi|6056907|gb|AW091312.1|AW091312
EST:     CCAAGACCCTGAAGAAATTTCATGGCTGGCTTGCCAGTTCTAGTTTTACG                         GTGGCCATGAAGCTCTCTCCTAATAGAGATAAATTCATGGAGGTCATTAGT
genomic: CCAAGACCTTGAAGAAATTTCATGGCTGGCTTGCCAGTTCTAGTTTTACGgtagaatctt ... ttgctggcagGTGGCCATGAAGCTCTCTCCTAATAGAGATAAATTCATGGAGGTCATTAGT
EST: gi|211377984|gb|FK983375.1|FK983375
EST:     CCAAGACCCTGAAGAAATTTCATGGCTGGCTTGCCAGTTCTAGTTTTACG                         GTGGCCATGAAGCTCTCTCCTAATAGAGATAAATTCATGGAGGTCATTAGT
genomic: CCAAGACCTTGAAGAAATTTCATGGCTGGCTTGCCAGTTCTAGTTTTACGgtagaatctt ... ttgctggcagGTGGCCATGAAGCTCTCTCCTAATAGAGATAAATTCATGGAGGTCATTAGT
EST: gi|60401114|gb|DN233921.1|DN233921
EST:     CCAAGACCTTGAAGAAATTTCATGGCTGGCTTGCCAGTTCTAGTTTTACG                         GTGGCCATGAAGCTCTCTCCTAATAGAGATAAATTCATGGAGGTCATTAGT
genomic: CCAAGACCTTGAAGAAATTTCATGGCTGGCTTGCCAGTTCTAGTTTTACGgtagaatctt ... ttgctggcagGTGGCCATGAAGCTCTCTCCTAATAGAGATAAATTCATGGAGGTCATTAGT
EST: gi|5686769|gb|AI939862.1|AI939862
EST:     CCAAGACCCTGAAGAAATTTCATGGCTGGCTTGCCAGTTCTAGTTTTACG                         GTGGCCATGAAGCTCTCTCCTAATAGAGATAAATTCATGGAGGTCATTAGT
genomic: CCAAGACCTTGAAGAAATTTCATGGCTGGCTTGCCAGTTCTAGTTTTACGgtagaatctt ... ttgctggcagGTGGCCATGAAGCTCTCTCCTAATAGAGATAAATTCATGGAGGTCATTAGT
EST: gi|84351358|gb|DW245763.1|DW245763
EST:     CCAAGACCTTGAAGAAATTTCATGGCTGGCTTGCCAGTTCTAGTTTTACG                         GTGGCCATGAAGCTCTCTCCTAATAGAGATAAATTCATGGAGGTCATTAGT
genomic: CCAAGACCTTGAAGAAATTTCATGGCTGGCTTGCCAGTTCTAGTTTTACGgtagaatctt ... ttgctggcagGTGGCCATGAAGCTCTCTCCTAATAGAGATAAATTCATGGAGGTCATTAGT
EST: gi|32866745|gb|CF006427.1|CF006427
EST:     CCAAGACCCTCAAGAAATTTCATGGCTGGCTTGCCAGTTCTAGTTTTACG                         GTGGCCATGAAGCTCTCTCCTAATAGAGATAAATT
genomic: CCAAGACCTTGAAGAAATTTCATGGCTGGCTTGCCAGTTCTAGTTTTACGgtagaatctt ... ttgctggcagGTGGCCATGAAGCTCTCTCCTAATAGAGATAAATT
EST: gi|211453293|gb|FL230455.1|FL230455
EST:     CCAAGACCCTCAAGAAATTTCATGGCTGGCTTGCCAGTTCTAGTTTTACG                         GTGGCCATGAAGCTCTCTCCTAATAGAGNATAATTT-ATGGAGGTCATTAG
genomic: CCAAGACCTTGAAGAAATTTCATGGCTGGCTTGCCAGTTCTAGTTTTACGgtagaatctt ... ttgctggcagGTGGCCATGAAGCTCTCTCCTAATAGAG-ATAAATTCATGGAGGTCATTAG
EST: gi|87157246|gb|DY402035.1|DY402035
EST:     CCAAGACCCTGAAGAAATTTCATGGCTGGCTTGCCAGTTCTAGTTTTACG                         GTGGCCATGAAGCTCTCTCCTAATAGAGATAAATTCATGGAGGTCATTAGT
genomic: CCAAGACCTTGAAGAAATTTCATGGCTGGCTTGCCAGTTCTAGTTTTACGgtagaatctt ... ttgctggcagGTGGCCATGAAGCTCTCTCCTAATAGAGATAAATTCATGGAGGTCATTAGT
EST: gi|26559123|gb|CA831358.1|CA831358
EST:     CCAAGACCCTGAAGAAATTTCATGGCTGGCTTGCCAGTTCTAGTTTTACG                         GNGGCCATGAAGCTCTCTCCTAATAGAGATAAA
genomic: CCAAGACCTTGAAGAAATTTCATGGCTGGCTTGCCAGTTCTAGTTTTACGgtagaatctt ... ttgctggcagGTGGCCATGAAGCTCTCTCCTAATAGAGATAAA
EST: gi|60401080|gb|DN233887.1|DN233887
EST:     CCAAGACCTTGAAGAAATTTCATGGCTGGCTTGCCAGTTCTAGTTTTACG                         GTGGCCATGAAGCTCTCTCCTAATAGAGATAAATTCATGGAGGTCATTAGT
genomic: CCAAGACCTTGAAGAAATTTCATGGCTGGCTTGCCAGTTCTAGTTTTACGgtagaatctt ... ttgctggcagGTGGCCATGAAGCTCTCTCCTAATAGAGATAAATTCATGGAGGTCATTAGT
EST: gi|31359252|gb|CD443609.1|CD443609
EST:     CCAAGACCCTGAAGAAATTTCATGGCTGGCTTGCCAGTTCTAGTTTTACG                         GTGGCCATGAAGCTCTCTCCTAATAGAGATAAATTCATGGAGGTCATTAGT
genomic: CCAAGACCTTGAAGAAATTTCATGGCTGGCTTGCCAGTTCTAGTTTTACGgtagaatctt ... ttgctggcagGTGGCCATGAAGCTCTCTCCTAATAGAGATAAATTCATGGAGGTCATTAGT
EST: gi|32932571|gb|CF037383.1|CF037383
EST:     CCAAGACCCTCAAGAAATTTCATGGCTGGCTTGCCAGTTCTAGTTTTACG                         GTGGCCATGAAGCTCTCTCCTAATAGAGATAAATTTATGGAGGTCATTAGT
genomic: CCAAGACCTTGAAGAAATTTCATGGCTGGCTTGCCAGTTCTAGTTTTACGgtagaatctt ... ttgctggcagGTGGCCATGAAGCTCTCTCCTAATAGAGATAAATTCATGGAGGTCATTAGT
EST: gi|71770686|gb|DR968623.1|DR968623
EST:     CCAAGACCTTGAAGAAATTTCATGGCTGGCTTGCCAGTTCTAGTTTTACG                         GTGGCCATGAAGCTCTCTCCTAATAGAGATAAATTCATGGAGGTCATTAGT
genomic: CCAAGACCTTGAAGAAATTTCATGGCTGGCTTGCCAGTTCTAGTTTTACGgtagaatctt ... ttgctggcagGTGGCCATGAAGCTCTCTCCTAATAGAGATAAATTCATGGAGGTCATTAGT
EST: gi|32840612|gb|CD980293.1|CD980293
EST:     CCAAGACCCTCAAGAAATTTCATGGCTGGCTTGCCAGTTCTAGTTTTACG                         GTGGCCATGAAGCTCTCTCCTAATAGAGATAAATTTATGGAGGTCATTAGT
genomic: CCAAGACCTTGAAGAAATTTCATGGCTGGCTTGCCAGTTCTAGTTTTACGgtagaatctt ... ttgctggcagGTGGCCATGAAGCTCTCTCCTAATAGAGATAAATTCATGGAGGTCATTAGT
EST: gi|60399775|gb|DN232585.1|DN232585
EST:     CCAAGACCTTGAAGAAATTTCATGGCTGGCTTGCCAGTTCTAGTTTTACG                         GTGGCCATGAAGCTCTCTCCTAATAGAGATAAATTCATGGAGGTCATTAGT
genomic: CCAAGACCTTGAAGAAATTTCATGGCTGGCTTGCCAGTTCTAGTTTTACGgtagaatctt ... ttgctggcagGTGGCCATGAAGCTCTCTCCTAATAGAGATAAATTCATGGAGGTCATTAGT
EST: gi|211375011|gb|FL430792.1|FL430792
EST:     CCAAGACCCTGAAGAAATTTCATGGCTGGCTTGCCAGTTCTAGTTTTACG                         GTGGCCATGAAGCTCTCTCCTAATAGAGATAAATTCATGGAGGTCATTAGT
genomic: CCAAGACCTTGAAGAAATTTCATGGCTGGCTTGCCAGTTCTAGTTTTACGgtagaatctt ... ttgctggcagGTGGCCATGAAGCTCTCTCCTAATAGAGATAAATTCATGGAGGTCATTAGT
EST: gi|211296159|gb|FL473353.1|FL473353
EST:     CCAAGACCCTCAAGAAATTTCATGGCTGGCTTGCCAGTTCTAGTTTTACG                         GTGGCCATGAAGCTCTCTCCTAATAGAGATAAATTTATGGAGGTCATTAGT
genomic: CCAAGACCTTGAAGAAATTTCATGGCTGGCTTGCCAGTTCTAGTTTTACGgtagaatctt ... ttgctggcagGTGGCCATGAAGCTCTCTCCTAATAGAGATAAATTCATGGAGGTCATTAGT
EST: gi|32932100|gb|CF036912.1|CF036912
EST:     CCAAGACCCTCAAGAAATTTCATGGCTGGCTTGCCAGTTCTAGTTTTACG                         GTGGCCATGAAGCTCTCTCCTAATAGAGATAAATTTATGGAGGTCATTAGT
genomic: CCAAGACCTTGAAGAAATTTCATGGCTGGCTTGCCAGTTCTAGTTTTACGgtagaatctt ... ttgctggcagGTGGCCATGAAGCTCTCTCCTAATAGAGATAAATTCATGGAGGTCATTAGT
EST: gi|211365280|gb|FL463922.1|FL463922
EST:     CCAAGACCCTCAAGAAATTTCATGGCTGGCTTGCCAGTTCTAGTTTTACG                         GTGGCCATGAAGCTCTCTCCTAATAGAGATAAATTTATGGAGGTCATTAGT
genomic: CCAAGACCTTGAAGAAATTTCATGGCTGGCTTGCCAGTTCTAGTTTTACGgtagaatctt ... ttgctggcagGTGGCCATGAAGCTCTCTCCTAATAGAGATAAATTCATGGAGGTCATTAGT
EST: gi|32867861|gb|CF007543.1|CF007543
EST:     CCAAGACCCTCAAGAAATTTCATGGCTGGCTTGCCAGTTCTAGTTTTACG                         GTGGCCATGAAGCTCTCTCCTAATAGAGATAAATTTATGGAGGTCATTAGT
genomic: CCAAGACCTTGAAGAAATTTCATGGCTGGCTTGCCAGTTCTAGTTTTACGgtagaatctt ... ttgctggcagGTGGCCATGAAGCTCTCTCCTAATAGAGATAAATTCATGGAGGTCATTAGT

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: 38

GCTTGAGCATCCAGACTGGACCATGACTCAAGCTTGCGCTGATTCATACACCAAGACCTTGAAGAAATTTCATGGCTGGCTTGCCAGTTCTAGTTTTACGgtagaatctt ... ttgctggcagGTGGCCATGAAGCTCTCTCCTAATAGAGATAAATTCATGGAGGTCATTAGTGGAACTGGTGATATCAATGCAGATATTGAGAAATTTTGCACGACCTTCT


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 81

GCTTGAGCATCCAGACTGGACCATGACTCAAGCTTGCGCTGATTCATACACCAAGACCTTGAAGAAATTTCATGGCTGGCTTGCCAGTTCTAGTTTTACGgtagaatctt ... ttgctggcagGTGGCCATGAAGCTCTCTCCTAATAGAGATAAATTCATGGAGGTCATTAGTGGAACTGGTGATATCAATGCAGATATTGAGAAATTTTGCACGACCTTCT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 113

GCTTGAGCATCCAGACTGGACCATGACTCAAGCTTGCGCTGATTCATACACCAAGACCTTGAAGAAATTTCATGGCTGGCTTGCCAGTTCTAGTTTTACGgtagaatctt ... ttgctggcagGTGGCCATGAAGCTCTCTCCTAATAGAGATAAATTCATGGAGGTCATTAGTGGAACTGGTGATATCAATGCAGATATTGAGAAATTTTGCACGACCTTCT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 86

GCTTGAGCATCCAGACTGGACCATGACTCAAGCTTGCGCTGATTCATACACCAAGACCTTGAAGAAATTTCATGGCTGGCTTGCCAGTTCTAGTTTTACGgtagaatctt ... ttgctggcagGTGGCCATGAAGCTCTCTCCTAATAGAGATAAATTCATGGAGGTCATTAGTGGAACTGGTGATATCAATGCAGATATTGAGAAATTTTGCACGACCTTCT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatcccttttattggtgcttccatttgttcatttgcttatatgaattgctggcagGTGGCCATGAAGCTCTCTCCTAATAGAGATAAATTCATGGAGGTCATTAGTGGAACTGGTGATATCAATGCAGATATTGAGAAATTTTGCACGACCTTCT
                                    ttatatgaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tcaatgctcctcttttaagatcattgcatacttttggttggagtatatcccttttattggtgcttccatttgttcatttgcttatatgaattgctggcagGTGGCCATGAAGCTCTCTCCTAATAGAGATAAATTCATGGAGGTCATTAGTGGAACTGGTGATATCAATGCAGATATTGAGAAATTTTGCACGACCTTCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGAT
- - tgctcct
- - - - - - - - - - - - tgcatac
- - - - - - - - - - - - - - - - -ttggttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgcttcc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tttgctt