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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttgctgattgagtgctgttttctttatgcttcctacatgccgtgcaaatattttctgaactcaaaaagttctcattccttttaatccttcttacatgcagTACAAAACTGAAGAGCCAGTTAAGCTTTGGGTGAATAAAGTTGGCCCTTACAATAATCCTCAAGAAACCTACAACTATTACAGCCTTCCATTTTGTCAAC

Basic information

species Zea mays
transcript GRMZM2G026231_T01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G026231_T01 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os12g07670.1 (Oryza sativa), 3'ss of exon 1
ttgctgattgagtgctgttttctttatgcttcctaca-tgccgtgcaaatattttctgaactcaaaaagttctcat-tccttttaatccttcttacatgcagTACAAAACTGAAGAGCCAGTTAAGCTTTGGGTGAATAAAGTTGGCCCTTACAATAATCCTCAAGAAACCTACAACTATTACAGCCTTCCATTTTGTCAAC
    |  |  | |    |  |  ||||| || | | | | || ||  |  | ||| ||| ||||| | |||||||| | | ||| || ||||||| ||||||||||||  |||||| ||||||||||| |||||||| ||||| ||||||||||||||||| |||||||| ||||||||| |||||||||||||||||||||
-ctttcctaaaataaattcattattatgtttaccataattccatggtagaactttgtgagctcaaca-gttctcatctgccttttatgcttcttatatgcagTACAAAGTTGAAGAACCAGTTAAGCTCTGGGTGAACAAAGTCGGCCCTTACAATAATCCACAAGAAACTTACAACTATCACAGCCTTCCATTTTGTCAAC

upper sequence: GRMZM2G026231_T01 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA05G30210.1 (Glycine max), 3'ss of exon 1
ttgctgattgagtg---ctgttttctttatgcttcctacatgccgtgcaaatattttctgaactcaaaaagttctcattccttttaatccttcttacatgcagTACAAAACTGAAGAGCCAGTTAAGCTTTGGGTGAATAAAGTTGGCCCTTACAATAATCCTCAAGAAACCTACAACTATTACAGCCTTCCATTTTGTCAAC
   ||||    |||   | | ||    ||||  |  | ||| | ||   |  |  |  |||||       ||| | |  |   |  ||  |  ||   |||||||  ||  ||| || | |||||| ||||||||||| |||||||| ||||| || ||||| |||||||| ||||||||||||||||| ||||||||||| |
--actgagctggtgaaacagattaaaatatgtgtatttcat-ctgtagtatcaagtggtgaacagcttctgtttttaaacggatgtattttattttgttgcagTATCAACATGATGAACAAGTTAACCTTTGGGTGAACAAAGTTGGTCCTTATAACAATCCACAAGAAACATACAACTATTACAGCCTCCCATTTTGTCATC

upper sequence: GRMZM2G026231_T01 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA08G13370.1 (Glycine max), 3'ss of exon 1
ttgctgattgagtgctgtt--ttctttatgcttcctacatgccgtgcaaatattttctgaactcaaaaagttctcattccttttaatccttcttacatgcagTACAAAACTGAAGAGCCAGTTAAGCTTTGGGTGAATAAAGTTGGCCCTTACAATAATCCTCAAGAAACCTACAACTATTACAGCCTTCCATTTTGTCAAC
   |||| | ||||       ||   ||||  |  | |||   ||      |  |  |||||       ||| | |      |  ||  |  ||   | |||||  ||   || || |||||||| ||||||||||| |||||||| ||||| || ||||| |||||||| ||||||||||||||||| ||||||||||| |
-cactgaattagtgaaacagattaaatatgtatatttcat-ttgtagtgccaagtggtgaacaacttctgtttttaaaagaatgtattttattttgtttcagTATCAACACGATGAACCAGTTAACCTTTGGGTGAACAAAGTTGGTCCTTATAACAATCCACAAGAAACATACAACTATTACAGCCTCCCATTTTGTCATC

upper sequence: GRMZM2G026231_T01 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA08G20100.1 (Glycine max), 3'ss of exon 1
ttgctgattgagtgctgttttctttatgcttcctacatgccgtgcaaatattttctgaactcaaaaagttctcattc-----cttttaatccttcttacatgcagTACAAAACTGAAGAGCCAGTTAAGCTTTGGGTGAATAAAGTTGGCCCTTACAATAATCCTCAAGAAACCTACAACTATTACAGCCTTCCATTTTGTCAAC
        |  | |      | | |||| |||||  || |   | || ||  | |    |   ||  | | ||  |      | | || | | | |||  || ||||  ||   || || |||||||  ||||||||||| |||||||| ||||| || ||||| |||||||| ||||| ||||||||||| |||||||| |   
-cttgagctaggagtaaagatatatatgtttcctttattc---gtaagtagctcccagtcaacaatggctatctgtttaaaacatgtattgcattttat-tgtagTATCAACAAGATGACCCAGTTATCCTTTGGGTGAACAAAGTTGGTCCTTATAACAATCCACAAGAAACGTACAATTATTACAGCCTACCATTTTGCCGTT

upper sequence: GRMZM2G026231_T01 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA12G29120.1 (Glycine max), 3'ss of exon 1
-ttgctgattgagtgctgttttctttatgcttcctacatgc-cgtgcaaatattttctgaactcaaaaagttctcattccttttaatccttcttacatgcagTACAAAACTGAAGAGCCAGTTAAGCTTTGGGTGAATAAAGTTGGCCCTTACAATAATCCTCAAGAAACCTACAACTATTACAGCCTTCCATTTTGTCAAC
 |   |||   ||   |      |   ||||||||  ||      | |  |   |    || |    |  |  | |   | | || |   | |||  |||||||  ||   || || |||||||  ||||||||||| |||||||| ||||| || ||||| |||||||| ||||| ||||||||||| |||||||| |  |
ttccttgagctaggagtaaaga-tacgtgcttcctttatttgtaagtagcttcatctcaaaatggctatctgtttaaaacatgtattggattttat-tgcagTATCAACAAGATGACCCAGTTACCCTTTGGGTGAACAAAGTTGGTCCTTATAACAATCCACAAGAAACGTACAATTATTACAGCCTACCATTTTGCCGTC

upper sequence: GRMZM2G026231_T01 (Zea mays), 3'ss of exon 1
lower sequence: AT1G10950.1 (Arabidopsis thaliana), 3'ss of exon 1
---ttgctgattgagtgctgttttctttatgcttcctacatgccgtgcaaatattttctgaactcaaaaagttctcattccttttaatccttcttacatgcagTACAAAACTGAAGAGCCAGTTAAGCTTTGGGTGAATAAAGTTGGCCCTTACAATAATCCTCAAGAAACCTACAACTATTACAGCCTTCCATTTTGTCAAC
   ||   | |      || | ||  |  |   ||| | |  |  |   | |  | |           |||   ||| |  ||||   | |       | |||||  || | || ||||  || |  || ||||| || ||||||||||| || || ||||| |||||||| |||||||||||||| ||||||||||| |  |
gaattttggttcttactctctcttactagttaatcccataaacttttacatttctgtgcttttctgtcaag---tcaattttttttgccttcacctttttcagTATCAAGCCGAGGAGCAGGTCACCCTATGGGTAAACAAAGTTGGCCCATATAACAATCCACAAGAAACATACAACTATTACAGTCTTCCATTTTGCCGCC

upper sequence: GRMZM2G026231_T01 (Zea mays), 3'ss of exon 1
lower sequence: Vv18s0041g00680.t01 (Vitis vinifera), 3'ss of exon 1
--ttgctgattgagtgctgttttctttatgcttcctacatgccgtgcaaatattttctgaactcaaaaagttctcattccttttaatccttcttacatgcagTACAAAACTGAAGAGCCAGTTAAGCTTTGGGTGAATAAAGTTGGCCCTTACAATAATCCTCAAGAAACCTACAACTATTACAGCCTTCCATTTTGTCAAC
     |||  |   || |    | || |||   |    |    |   | || |    | |||  || |   | | |     |    |   | |  | |||||||  | || || ||||  || |  || ||||| || |||||||| |||||||||||||| ||||||||||||||||| | |||||||||||||||||| |
agacactggctc--tgttacagtattcatgaaacacttaactgggaaatatgtgacttaaacataatattgtataaggaaatcatttttgtttctcctgcagTATCAGACAGATGAGCAGGTGACTCTGTGGGTAAACAAAGTTGGTCCTTACAATAATCCACAAGAAACCTACAACTACTTCAGCCTTCCATTTTGTCACC

upper sequence: GRMZM2G026231_T01 (Zea mays), 3'ss of exon 1
lower sequence: Vv12s0035g00280.t01 (Vitis vinifera), 3'ss of exon 1
ttgctgattgagtgct-gttttctttatgcttcctacat-gccgtgcaaatattt--tctgaactcaaaaagttctcattccttttaatccttcttacatgcagTACAAAACTGAAGAGCCAGTTAAGCTTTGGGTGAATAAAGTTGGCCCTTACAATAATCCTCAAGAAACCTACAACTATTACAGCCTTCCATTTTGTCAAC
 ||||  ||  || ||   ||||| || |   |  | ||  | |  |     |||  ||   |  ||    |||  || |  ||| | |   ||||    ||||||  |     | || || ||||  |||||||| ||||| ||||| |||||||||||||| |||||||| ||||| ||||| || |||||||||||||  |
atgctacttctgtacttactttctgtaagtagctcaaattacagctcttgcttttgttccagatgcactttgttaacagttttttaattttgtctt----gcagTATCAGCAGAATGAACCGGTTACCCTTTGGGTAAATAAGGTTGGACCTTACAATAATCCACAAGAAACGTACAATTATTATAGTCTTCCATTTTGTCGTC

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|31354711|gb|CD439068.1|CD439068
EST:     CTCTCGCTGCACTGCTCGCGCTCGCCTCCGCCTCCGAGTCCGACCACAAG                         TACAAAACTGAAGAGCCAGTTAAGCTTTGGGTGAATAAAGTTGGCCCTTAC
genomic: CTCTCGCTGCACTGCTCGCGCTCGCCTCCGCCTCCGAGTCCGACCACAAGgtgcgtgccc ... ttacatgcagTACAAAACTGAAGAGCCAGTTAAGCTTTGGGTGAATAAAGTTGGCCCTTAC
EST: gi|31355875|gb|CD440232.1|CD440232
EST:     CTCTCGCTGCACTGCTCGCGCTCGCCTCCGCCTCCGAGTCCGACCACAAG                         TACAAAACTGAAGAGCCAGTTAAGCTTTGGGTGAATAAAGTTGGCCCTTAC
genomic: CTCTCGCTGCACTGCTCGCGCTCGCCTCCGCCTCCGAGTCCGACCACAAGgtgcgtgccc ... ttacatgcagTACAAAACTGAAGAGCCAGTTAAGCTTTGGGTGAATAAAGTTGGCCCTTAC
EST: gi|211369512|gb|FL195175.1|FL195175
EST:     CTCTCGCTGCACTGCTCGCGCTCGCCTCCGCCTCCGAGTCCGACCACAAG                         TACAAAACTGAAGAGCCAGTTAAGCTTTGGGTGAATAAAGTTGGCCCTTAC
genomic: CTCTCGCTGCACTGCTCGCGCTCGCCTCCGCCTCCGAGTCCGACCACAAGgtgcgtgccc ... ttacatgcagTACAAAACTGAAGAGCCAGTTAAGCTTTGGGTGAATAAAGTTGGCCCTTAC
EST: gi|211369510|gb|FL195173.1|FL195173
EST:     CTCTCGCTGCACTGCTCGCGCTCGCCTCCGCCTCCGAGTCCGACCACAAG                         TACAAAACTGAAGAGCCAGTTAAGCTTTGGGTGAATAAAGTTGGCCCTTAC
genomic: CTCTCGCTGCACTGCTCGCGCTCGCCTCCGCCTCCGAGTCCGACCACAAGgtgcgtgccc ... ttacatgcagTACAAAACTGAAGAGCCAGTTAAGCTTTGGGTGAATAAAGTTGGCCCTTAC
EST: gi|211012618|gb|FL213598.1|FL213598
EST:     CTCTCGCTGCACTGCTCGCGCTCGCCTCCGCCTCCGAGTCCGACCACAAG                         TACAAAACTGAAGAGCCAGTTAAGCTTTGGGTGAATAAAGTTGGCCCTTAC
genomic: CTCTCGCTGCACTGCTCGCGCTCGCCTCCGCCTCCGAGTCCGACCACAAGgtgcgtgccc ... ttacatgcagTACAAAACTGAAGAGCCAGTTAAGCTTTGGGTGAATAAAGTTGGCCCTTAC
EST: gi|211366863|gb|FL195171.1|FL195171
EST:     CTCTCGCTGCACTGCTCGCGCTCGCCTCCGCCTCCGAGTCCGACCACAAG                         TACAAAACTGAAGAGCCAGTTAAGCTTTGGGTGAATAAAGTTGGCCCTTAC
genomic: CTCTCGCTGCACTGCTCGCGCTCGCCTCCGCCTCCGAGTCCGACCACAAGgtgcgtgccc ... ttacatgcagTACAAAACTGAAGAGCCAGTTAAGCTTTGGGTGAATAAAGTTGGCCCTTAC
EST: gi|31357584|gb|CD441941.1|CD441941
EST:     CTCTCGCTGCACTGCTCGCGCTCGCCTCCGCCTCCGAGTCCGACCACAAG                         TACAAAACTGAAGAGCCAGTTAAGCTTTGGGTGAATAAAGTTGGCCCTTAC
genomic: CTCTCGCTGCACTGCTCGCGCTCGCCTCCGCCTCCGAGTCCGACCACAAGgtgcgtgccc ... ttacatgcagTACAAAACTGAAGAGCCAGTTAAGCTTTGGGTGAATAAAGTTGGCCCTTAC
EST: gi|211012620|gb|FL213600.1|FL213600
EST:     CTCTCGCTGCACTGCTCGCGCTCGCCTCCGCCTCCGAGTCCGACCACAAG                         TACAAAACTGAAGAGCCAGTTAAGCTTTGGGTGAATAAAGTTGGCCCTTAC
genomic: CTCTCGCTGCACTGCTCGCGCTCGCCTCCGCCTCCGAGTCCGACCACAAGgtgcgtgccc ... ttacatgcagTACAAAACTGAAGAGCCAGTTAAGCTTTGGGTGAATAAAGTTGGCCCTTAC

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: 148

CGGCTGGGGCCGCGGCCGCGGCCGCCACCTATTGCTCAGCAGGGCCCTAGCTCTCGCTGCACTGCTCGCGCTCGCCTCCGCCTCCGAGTCCGACCACAAGgtgcgtgccc ... ttacatgcagTACAAAACTGAAGAGCCAGTTAAGCTTTGGGTGAATAAAGTTGGCCCTTACAATAATCCTCAAGAAACCTACAACTATTACAGCCTTCCATTTTGTCAAC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 123

CGGCTGGGGCCGCGGCCGCGGCCGCCACCTATTGCTCAGCAGGGCCCTAGCTCTCGCTGCACTGCTCGCGCTCGCCTCCGCCTCCGAGTCCGACCACAAGgtgcgtgccc ... ttacatgcagTACAAAACTGAAGAGCCAGTTAAGCTTTGGGTGAATAAAGTTGGCCCTTACAATAATCCTCAAGAAACCTACAACTATTACAGCCTTCCATTTTGTCAAC


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 166

CGGCTGGGGCCGCGGCCGCGGCCGCCACCTATTGCTCAGCAGGGCCCTAGCTCTCGCTGCACTGCTCGCGCTCGCCTCCGCCTCCGAGTCCGACCACAAGgtgcgtgccc ... ttacatgcagTACAAAACTGAAGAGCCAGTTAAGCTTTGGGTGAATAAAGTTGGCCCTTACAATAATCCTCAAGAAACCTACAACTATTACAGCCTTCCATTTTGTCAAC


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 158

CGGCTGGGGCCGCGGCCGCGGCCGCCACCTATTGCTCAGCAGGGCCCTAGCTCTCGCTGCACTGCTCGCGCTCGCCTCCGCCTCCGAGTCCGACCACAAGgtgcgtgccc ... ttacatgcagTACAAAACTGAAGAGCCAGTTAAGCTTTGGGTGAATAAAGTTGGCCCTTACAATAATCCTCAAGAAACCTACAACTATTACAGCCTTCCATTTTGTCAAC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaatattttctgaactcaaaaagttctcattccttttaatccttcttacatgcagTACAAAACTGAAGAGCCAGTTAAGCTTTGGGTGAATAAAGTTGGCCCTTACAATAATCCTCAAGAAACCTACAACTATTACAGCCTTCCATTTTGTCAAC
                                          ttcttac  putative branch site (score: 158)
                       ttctcattccttttaa  CT-rich tract
                                 ttttaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttgctgattgagtgctgttttctttatgcttcctacatgccgtgcaaatattttctgaactcaaaaagttctcattccttttaatccttcttacatgcagTACAAAACTGAAGAGCCAGTTAAGCTTTGGGTGAATAAAGTTGGCCCTTACAATAATCCTCAAGAAACCTACAACTATTACAGCCTTCCATTTTGTCAAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA
-tgctgat
- - - - - - tgctgtt
- - - - - - - - - - - - - tgcttcc
- - - - - - - - - - - - - - - - -tacatgc
- - - - - - - - - - - - - - - - - - - - cgtgcaa
- - - - - - - - - - - - - - - - - - - - - - - - - ttttctg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -aactcaa