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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTCACATTATTCCCAAAGAATCCTCTAAAAGGGGCCCATGAAATACAGAGCTTTTGCCTTGGGCATACAGAgtatgtttggtgtacaatgctattgttgacagttttttaattctgtttttaggttcttttaatgtatataacaatttgggtttactggttgggatctgtcataggagtttcagagcttagtctatggttgacaattggttgtgactcttcttgcag

Basic information

species Zea mays
transcript GRMZM2G131998_T04
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G131998_T02 (Zea mays), 5'ss of exon 6
lower sequence: AT1G03110.1 (Arabidopsis thaliana), 5'ss of exon 5
GTCACATTATTCCCAAAGAATCCTCTAAAAGGGGCCCATGAAATACAGAGCTTTTGCCTTGGGCATACAGAgtatgtttggtgtacaatgctattgttga-cagttttttaattctgtttttaggttctt-----ttaatgtatataacaatt-tgggtttactggttgggatctgtcataggagtttcagagcttagtctatggttgacaattggttgtgactcttcttgcag--------
|| ||  | || || ||||| |||||| ||||||| |||||||||||||| ||||| ||||| ||| ||||||| |||  | ||  || || |    | | | | |    |||  | | |||   |||||     ||  | | ||  | | || |  |  |  || ||   |  ||  | |       || |||| ||  ||| |   ||| ||   |     |  ||||  |         
GTGACTGTTTTTCCCAAGAAGCCTCTAGAAGGGGCTCATGAAATACAGAGTTTTTGTCTTGGACATTCAGAgtaagtt-agagtttaaagcaacatctaatctgatcccaaatattctgtttgcattcttaatgtttggtttctacgatatttatcagagtgttgtttacaaaatggaagattgtaaacaaagctgagagtattg--aacagttccattaacattatcttaaaccttaatag
















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|78091377|gb|DV519751.1|DV519751
EST:     CCTCTAAAAGGGGCCCATGAAATACAGAGCTTTTGCCTTGGGCATACAGA                         CTTTGTATCATGCATCACCTTCACTAGCATATCTGANAACCAGAGTTTTCT
genomic: CCTCTAAAAGGGGCCCATGAAATACAGAGCTTTTGCCTTGGGCATACAGAgtatgtttgg ... cttcttgcagCTTTGTATCATGCATCACCTTCACTAGCATATCTGAAAACCAGAGTTTTCT
EST: gi|13149651|gb|BG319973.1|BG319973
EST:     TGCCTTGGGCATACAGA                         CTTTGTATCATGCATCACCTTCACTAGCATATCTGAAAACCAGAGTTTTCT
genomic: TGCCTTGGGCATACAGAgtatgtttgg ... cttcttgcagCTTTGTATCATGCATCACCTTCACTAGCATATCTGAAAACCAGAGTTTTCT
EST: gi|87156923|gb|DY401712.1|DY401712
EST:     CCTCTAAAAGGGGCCCATGAAATACAGAGCTTTTGCCTTGGGCATACAGA                         CTTTGTATCATGCATCACCTTCACTAGCATATCTGAAAACCAGAGTTTTCT
genomic: CCTCTAAAAGGGGCCCATGAAATACAGAGCTTTTGCCTTGGGCATACAGAgtatgtttgg ... cttcttgcagCTTTGTATCATGCATCACCTTCACTAGCATATCTGAAAACCAGAGTTTTCT
EST: gi|89761079|gb|DY689237.1|DY689237
EST:     CCTCTAAAAGGGGCCCATGAAATACAGAGCTTTTGCCTTGGGCATACAGA                         CTTTGTATCATGCATCACCTTCACTAGCATATCTGAAAACCAGAGTTTTCT
genomic: CCTCTAAAAGGGGCCCATGAAATACAGAGCTTTTGCCTTGGGCATACAGAgtatgtttgg ... cttcttgcagCTTTGTATCATGCATCACCTTCACTAGCATATCTGAAAACCAGAGTTTTCT
EST: gi|89249366|gb|DY621152.1|DY621152
EST:     CCTCTAAAAGGGGCCCATGAAATACAGAACTTTTGCCTTGGGCATACAGA                         CTTTGTATCATGCTTCAC
genomic: CCTCTAAAAGGGGCCCATGAAATACAGAGCTTTTGCCTTGGGCATACAGAgtatgtttgg ... cttcttgcagCTTTGTATCATGCATCAC
EST: gi|71437750|gb|DR818800.1|DR818800
EST:     CCTCTAAAAGGGGCCCATGAAATACAGAGCTTTTGCCTTGGGCATACAGA                         CTTTGTATCATGCATCACCTTCACTAGCATATCTGAAAACCAGAGTTTTCT
genomic: CCTCTAAAAGGGGCCCATGAAATACAGAGCTTTTGCCTTGGGCATACAGAgtatgtttgg ... cttcttgcagCTTTGTATCATGCATCACCTTCACTAGCATATCTGAAAACCAGAGTTTTCT
EST: gi|148945698|gb|EC890971.2|EC890971
EST:     CCTCTAAAAGGGGCCCATGAAATACAGAGCTTTTGCCTTGGGCATACAGA                         CTTTGTATCATGCATCACCTTCACTAGCATATCTGAAAACCAGAGTTTTCT
genomic: CCTCTAAAAGGGGCCCATGAAATACAGAGCTTTTGCCTTGGGCATACAGAgtatgtttgg ... cttcttgcagCTTTGTATCATGCATCACCTTCACTAGCATATCTGAAAACCAGAGTTTTCT
EST: gi|148973467|gb|EE024565.2|EE024565
EST:     CCTCTAAAAGGGGCCCATGAAATACAGAGCTTTTGCCTTGGGCATACAGA                         CTTTGTATCATGCATCACCTTCACTAGCATATCTGAAAACCAGAGTTTTCT
genomic: CCTCTAAAAGGGGCCCATGAAATACAGAGCTTTTGCCTTGGGCATACAGAgtatgtttgg ... cttcttgcagCTTTGTATCATGCATCACCTTCACTAGCATATCTGAAAACCAGAGTTTTCT
EST: gi|78106892|gb|DV525310.1|DV525310
EST:     CCTCTAAAAGGGGCCCATGAAATACAGAGCTTTTGCCTTGGGCATACAGA                         CTTTGTATCATGCATCACCTTCACTAGCATATCTGANAACCAGAGTTTTCT
genomic: CCTCTAAAAGGGGCCCATGAAATACAGAGCTTTTGCCTTGGGCATACAGAgtatgtttgg ... cttcttgcagCTTTGTATCATGCATCACCTTCACTAGCATATCTGAAAACCAGAGTTTTCT
EST: gi|78081795|gb|DV510207.1|DV510207
EST:     CCTCTAAAAGGGGCCCATGAAATACAGAGCTTTTGCCTTGGGCATACAGA                         CTTTGTATCATGCATCACCTTCACTAGCATATCTGNAAACCAGAGTTTTCT
genomic: CCTCTAAAAGGGGCCCATGAAATACAGAGCTTTTGCCTTGGGCATACAGAgtatgtttgg ... cttcttgcagCTTTGTATCATGCATCACCTTCACTAGCATATCTGAAAACCAGAGTTTTCT
EST: gi|149111910|gb|EE191066.2|EE191066
EST:     CCTCTAAAAGGGGCCCATGAAATACAGAGCTTTTGCCTTGGGCATACAGA                         CTTTGTATCATGCATCACCTTCACTAGCATATCTGAAAACCAGAGTTTTCT
genomic: CCTCTAAAAGGGGCCCATGAAATACAGAGCTTTTGCCTTGGGCATACAGAgtatgtttgg ... cttcttgcagCTTTGTATCATGCATCACCTTCACTAGCATATCTGAAAACCAGAGTTTTCT
EST: gi|89759711|gb|DY688443.1|DY688443
EST:     CCTCTAAAAGGGGCCCATGAAATACAGAGCTTTTGCCTTGGGCATACAGA                         CTTTGTATCATGCATCACCTTCACTAGCATATCTGAAAACCAGAGTTTTCT
genomic: CCTCTAAAAGGGGCCCATGAAATACAGAGCTTTTGCCTTGGGCATACAGAgtatgtttgg ... cttcttgcagCTTTGTATCATGCATCACCTTCACTAGCATATCTGAAAACCAGAGTTTTCT
EST: gi|76017216|gb|DT944386.1|DT944386
EST:     CCTCTAAAAGGGGCCCATGAAATACAGAGCTTTTGCCTTGGGCATACAGA                         CTTTGTATCATGCATCACCTTCACTAGCATATCTGAAAACCAGAGTTTTCT
genomic: CCTCTAAAAGGGGCCCATGAAATACAGAGCTTTTGCCTTGGGCATACAGAgtatgtttgg ... cttcttgcagCTTTGTATCATGCATCACCTTCACTAGCATATCTGAAAACCAGAGTTTTCT
EST: gi|50331437|gb|CO526563.1|CO526563
EST:     CCTCTAAAAGGGGCCCATGAAATACAGAGCTTTTGCCTTGGGCATACAGA                         CTTTGTATCATGCATCACCTTCACTAGCATATCTGAAA
genomic: CCTCTAAAAGGGGCCCATGAAATACAGAGCTTTTGCCTTGGGCATACAGAgtatgtttgg ... cttcttgcagCTTTGTATCATGCATCACCTTCACTAGCATATCTGAAA
EST: gi|71771570|gb|DR969507.1|DR969507
EST:     CCTCTAAAAGGGGCCCATGAAATACAGAGCTTTTGCCTTGGGCATACAGA                         CTTTGTATCATGCATCACCTTCACTAGCATATCTGAAAACCAGAGTTTTTC
genomic: CCTCTAAAAGGGGCCCATGAAATACAGAGCTTTTGCCTTGGGCATACAGAgtatgtttgg ... cttcttgcagCTTTGTATCATGCATCACCTTCACTAGCATATCTGAAAACCAGAGTTTT-C

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: 308

GTCACATTATTCCCAAAGAATCCTCTAAAAGGGGCCCATGAAATACAGAGCTTTTGCCTTGGGCATACAGAgtatgtttgg ... cttcttgcagCTTTGTATCATGCATCACCTTCACTAGCATATCTGAAAACCAGAGTTTTCTTATATCAGGAGGAGGTGATTCAACT


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 99

GTCACATTATTCCCAAAGAATCCTCTAAAAGGGGCCCATGAAATACAGAGCTTTTGCCTTGGGCATACAGAgtatgtttgg ... cttcttgcagCTTTGTATCATGCATCACCTTCACTAGCATATCTGAAAACCAGAGTTTTCTTATATCAGGAGGAGGTGATTCAACT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 109

GTCACATTATTCCCAAAGAATCCTCTAAAAGGGGCCCATGAAATACAGAGCTTTTGCCTTGGGCATACAGAgtatgtttgg ... cttcttgcagCTTTGTATCATGCATCACCTTCACTAGCATATCTGAAAACCAGAGTTTTCTTATATCAGGAGGAGGTGATTCAACT


Block sizes: 47 (upstream exon), 46 (downstream exon)
Score: 140

GTCACATTATTCCCAAAGAATCCTCTAAAAGGGGCCCATGAAATACAGAGCTTTTGCCTTGGGCATACAGAgtatgtttgg ... cttcttgcagCTTTGTATCATGCATCACCTTCACTAGCATATCTGAAAACCAGAGTTTTCTTATATCAGGAGGAGGTGATTCAACT


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTCACATTATTCCCAAAGAATCCTCTAAAAGGGGCCCATGAAATACAGAGCTTTTGCCTTGGGCATACAGAgtatgtttggtgtacaatgctattgttgacagttttttaattctgtttttaggttcttttaatgtatataacaatttgggtttactggttgggatctgtcataggagtttcagagcttagtctatggttgacaattggttgtgactcttcttgcag

- - - - - - - - - - - - - - - - - - - - - - - AGAGCT
- - - - - - - - - - - - - - - - - - - - - - -  GAGCTT