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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgcattttttaacaatgtagtatgctatcttttttttgaaactacaacatgcaatgtttatgatgaaaagttgtacatggctgcactgacagtttcatgtgaaacattgtagattggacattggtgtgcactatttctttgagttcactggtgcatacaatgtgttgacagaattctgtgtgttttcagGAGTGAATGCTGATGACGTTCGAGTAACGGTAGCTGCCCTTGCTGCTCGAGGGGAAGCTAACAGTGAGTTGCTAGAATTTATGGGCAAG

Basic information

species Zea mays
transcript GRMZM2G099547_T01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G099547_T04 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os07g19470.1 (Oryza sativa), 3'ss of exon 4
gtatgcattttttaacaatgtagtatgctatcttttttttgaaactacaacatgcaatgtttatgatgaaaagttgtacatggctgcactgacagtttcatgtgaaacattgta-gattggacattggtgtgcactatttctttgagttcactggtgca-tacaatgtgttgacagaattctgtgtgttttcagGAGTGAATGCTGATGACGTTCGAGTAACGGTAGCTGCCCTTGCTGCTCGAGGGGAAGCTAACAGTGAGTTGCTAGAATTTATGGGCAAG
|||||   | || | | |  | | | |   || |  ||   ||| ||| || ||| | ||||||||| || | |  || ||    ||  ||| |||||      | ||| || |  |||  |  ||    |||    |||||||   |||||| |  ||  ||| | || ||||| || | | | |  ||| |||||||||||||||||| ||||||||||| || ||||| | |||||||||||||||||| ||||  ||  | ||||| || |||||||||
gtatgttgtgttgatctaactggaaggaagtcatactt---aaaatactacttgctaagtttatgataaataatgctagataa--gccttgaaagtttt---caacacactggacaattcaatgttaaattgct---tttcttt---ttcacttgcccaacacattctggtgacaaaactgtatttactttaagGAGTGAATGCTGATGATGTTCGAGTAACAGTTGCTGCTCCTGCTGCTCGAGGGGAAGCAAACAACGAACTACTAGAGTTCATGGGCAAG

upper sequence: GRMZM2G099547_T04 (Zea mays), 3'ss of exon 4
lower sequence: Vv17s0000g01530.t01 (Vitis vinifera), 3'ss of exon 4
gtatgcattttttaacaatgtagtatgctatcttttttttgaaactacaacatgcaatgtttatgatgaaaagttgtacatggctgcactgacagtttcatgtgaaacattgtagattggacattggtgtgcactatttctttgagttcactggtgcatacaatgtgttgacagaattctgtgtgttttcagGAGTGAATGCTGATGACGTTCGAGTAACGGTAGCTGCCCTTGCTGCTCGAGGGGAAGCTAACAGTGAGTTGCTAGAATTTATGGGCAAG
                                                                                |   |   |   || | |  ||| | | ||| ||   |   |         || || |||||       |||  ||   || |||  ||  |   ||| | |    |  |||| |||||||| ||||| |||||||| || |||||||| | ||| || || ||||||||||||| |||  |  | ||||| |||||||| 
--------------------------------------------------------------------------------tatttctccgatcattcttctgtaatagattttaagattttc-ccaaaaaacattagttctt------gacttatga--accatgcctttgc---attttatcatataccagGGGTGAATGCAGATGATGTTCGAGTGACTGTAGCTGCGCCTGCAGCCCGTGGGGAAGCTAACAATGAACTTTTGGAATTCATGGGCAAA
















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|16926773|gb|BM079841.1|BM079841
EST:     CCAAGTAGCCATTGAAGTGGAAGACCGGGCACAACGTTCAGCAATAACAA                         GAGTGAATGCTGATGACGTTCGAGTAACGGTAGCTGCCCTTGCTGCTCGAG
genomic: CCAAGTAGCCATTGAAGTGGAAGACCGGGCACAACGTTCAGCAATAACAAgtatgcattt ... gtgttttcagGAGTGAATGCTGATGACGTTCGAGTAACGGTAGCTGCCCTTGCTGCTCGAG
EST: gi|60394679|gb|DN227549.1|DN227549
EST:     CCAAGTAGCCATTGAAGTGGAAGACCGGGCACAACGTTCAGCAATAACAA                         GAGTGAATGCTGATGACGTTCGAGTAACGGTAGCTGCCCTTGCTGCTCGAG
genomic: CCAAGTAGCCATTGAAGTGGAAGACCGGGCACAACGTTCAGCAATAACAAgtatgcattt ... gtgttttcagGAGTGAATGCTGATGACGTTCGAGTAACGGTAGCTGCCCTTGCTGCTCGAG
EST: gi|101392937|gb|EB818399.1|EB818399
EST:     CCAAGTAGCCATTGAAGTGGAAGACCGGGCACAACGTTCAGCAATAACAA                         GAGTGAATGCTGATGACGTTCGAGTAACGGTAGCTGCCCTTGCTGCTCGAG
genomic: CCAAGTAGCCATTGAAGTGGAAGACCGGGCACAACGTTCAGCAATAACAAgtatgcattt ... gtgttttcagGAGTGAATGCTGATGACGTTCGAGTAACGGTAGCTGCCCTTGCTGCTCGAG
EST: gi|149104413|gb|EE289858.2|EE289858
EST:     CCAAGTAGCCATTGAAGTGGAAGACCGGGCACAACGTTCAGCAATAACAA                         GAGTGAATGCTGATGACGTTCGAGTAACGGTAGCTGCCCTTGCTGCTCGAG
genomic: CCAAGTAGCCATTGAAGTGGAAGACCGGGCACAACGTTCAGCAATAACAAgtatgcattt ... gtgttttcagGAGTGAATGCTGATGACGTTCGAGTAACGGTAGCTGCCCTTGCTGCTCGAG
EST: gi|211360252|gb|FL253401.1|FL253401
EST:     CCAAGTAGCCATTGAAGTGGAAGACCGGGCACAACGTTCAGCAGTAACAA                         GAGTGAATGCTGATGACGTTCGAGTAACGGTAGCTGCCCTTGCTGCTCGAG
genomic: CCAAGTAGCCATTGAAGTGGAAGACCGGGCACAACGTTCAGCAATAACAAgtatgcattt ... gtgttttcagGAGTGAATGCTGATGACGTTCGAGTAACGGTAGCTGCCCTTGCTGCTCGAG
EST: gi|60348216|gb|DN215189.1|DN215189
EST:     CCAAGTAGCCATTGAAGTGGAAGACCGGGCACAACGTTCAGCAATAACAA                         GAGTGAATGCTGATGACGTTCGAGTAACGGTAGCTGCCCTTGCTGCTCGAG
genomic: CCAAGTAGCCATTGAAGTGGAAGACCGGGCACAACGTTCAGCAATAACAAgtatgcattt ... gtgttttcagGAGTGAATGCTGATGACGTTCGAGTAACGGTAGCTGCCCTTGCTGCTCGAG
EST: gi|12045916|gb|BF728146.1|BF728146
EST:     CCAAGTAGCCATTGAAGTGGAAGACCGGGCACAACGTTCAGCAGTAACAA                         GAGTGAATGCTGATGACGTTCGAGTAACGGTAGCTGCCCTTGCTGCTCGAG
genomic: CCAAGTAGCCATTGAAGTGGAAGACCGGGCACAACGTTCAGCAATAACAAgtatgcattt ... gtgttttcagGAGTGAATGCTGATGACGTTCGAGTAACGGTAGCTGCCCTTGCTGCTCGAG
EST: gi|148980593|gb|EE027217.2|EE027217
EST:     CCAAGTAGCCATTGAAGTGGAAGACCGGGCACAACGTTCAGCAATAACAA                         GAGTGAATGCTGATGACGTTCGAGTAACGGTAGCTGCCCTTGCTGCTCGAG
genomic: CCAAGTAGCCATTGAAGTGGAAGACCGGGCACAACGTTCAGCAATAACAAgtatgcattt ... gtgttttcagGAGTGAATGCTGATGACGTTCGAGTAACGGTAGCTGCCCTTGCTGCTCGAG
EST: gi|32846204|gb|CD985885.1|CD985885
EST:     CCAAGTAGCCATTGAAGTGGAAGACAGGGCACAACGTTCAGCAATAACAA                         GAGTGAATGCTGATGACATTCGAGTAACGGTAGCTGCCCTTGCTGCTCGAG
genomic: CCAAGTAGCCATTGAAGTGGAAGACCGGGCACAACGTTCAGCAATAACAAgtatgcattt ... gtgttttcagGAGTGAATGCTGATGACGTTCGAGTAACGGTAGCTGCCCTTGCTGCTCGAG
EST: gi|86471527|gb|DY237897.1|DY237897
EST:     CCAAGTAGCCATTGAAGTGGAAGACCGGGCACAACGTTCAGCAATAACAA                         GAGTGAATGCTGATGACGTTCGAGTAACGGTAGCTGCCCTTGCTGCTCGAG
genomic: CCAAGTAGCCATTGAAGTGGAAGACCGGGCACAACGTTCAGCAATAACAAgtatgcattt ... gtgttttcagGAGTGAATGCTGATGACGTTCGAGTAACGGTAGCTGCCCTTGCTGCTCGAG
EST: gi|71433975|gb|DR815025.1|DR815025
EST:     CCAAGTAGCCATTGAAGTGGAAGACCGGGCACAACGTTCAGCAATAACAA                         GAGTGAATGCTGATGACGTTCGAGTAACGGTAGCTGCCCTTGCTGCTCGAG
genomic: CCAAGTAGCCATTGAAGTGGAAGACCGGGCACAACGTTCAGCAATAACAAgtatgcattt ... gtgttttcagGAGTGAATGCTGATGACGTTCGAGTAACGGTAGCTGCCCTTGCTGCTCGAG
EST: gi|60337078|gb|DN204051.1|DN204051
EST:     CCAAGTAGCCATTGAAGTGGAAGACAGGGCACAACGTTCAGCAATAACAA                         GAGTGAATGCTGATGACGTTCGAGTAACGGTAGCTGCCCTTGCTGCTCGAG
genomic: CCAAGTAGCCATTGAAGTGGAAGACCGGGCACAACGTTCAGCAATAACAAgtatgcattt ... gtgttttcagGAGTGAATGCTGATGACGTTCGAGTAACGGTAGCTGCCCTTGCTGCTCGAG
EST: gi|60337543|gb|DN204516.1|DN204516
EST:     CCAAGTAGCCATTGAAGTGGAAGACCGGGCACAACGTTCAGCAATAACAA                         GAGTGAATGCTGATGACGTTCGAGTAACGGTAGCTGCCCTTGCTGCTCGAG
genomic: CCAAGTAGCCATTGAAGTGGAAGACCGGGCACAACGTTCAGCAATAACAAgtatgcattt ... gtgttttcagGAGTGAATGCTGATGACGTTCGAGTAACGGTAGCTGCCCTTGCTGCTCGAG
EST: gi|71433974|gb|DR815024.1|DR815024
EST:     CCAAGTAGCCATTGAAGTGGAAGACCGGGCACAACGTTCAGCAATAACAA                         GAGTGAATGCTGATGACGTTCGAGTAACGGTAGCTGCCCTTGCTGCTCGAG
genomic: CCAAGTAGCCATTGAAGTGGAAGACCGGGCACAACGTTCAGCAATAACAAgtatgcattt ... gtgttttcagGAGTGAATGCTGATGACGTTCGAGTAACGGTAGCTGCCCTTGCTGCTCGAG
EST: gi|71450211|gb|DR831261.1|DR831261
EST:     CCAAGTAGCCATTGAAGTGGAAGACCGGGCACAACGTTCAGCAATAACAA                         GAGTGAATGCTGATGACGTTCGAGTAACGGTAGCTGCCCTTGCTGCTCGAG
genomic: CCAAGTAGCCATTGAAGTGGAAGACCGGGCACAACGTTCAGCAATAACAAgtatgcattt ... gtgttttcagGAGTGAATGCTGATGACGTTCGAGTAACGGTAGCTGCCCTTGCTGCTCGAG
EST: gi|60351167|gb|DN218140.1|DN218140
EST:     CCAAGTAGCCATTGAAGTGGAAGACCGGGCACAACGTTCAGCAGTAACAA                         GAGTGAATGCTGATGACGTTCGAGTAACGGTAGCTGCCCTTGCTGCTCGAG
genomic: CCAAGTAGCCATTGAAGTGGAAGACCGGGCACAACGTTCAGCAATAACAAgtatgcattt ... gtgttttcagGAGTGAATGCTGATGACGTTCGAGTAACGGTAGCTGCCCTTGCTGCTCGAG
EST: gi|32928940|gb|CF033752.1|CF033752
EST:     CCAAGTAGCCATTGAAGTGGAAGACAGGGCACAACGTTCAGCAATAACAA                         GAGTGAATGCTGATGACGTTCGAGTAACGGTAGCTGCCCTTGCTGCTCGAG
genomic: CCAAGTAGCCATTGAAGTGGAAGACCGGGCACAACGTTCAGCAATAACAAgtatgcattt ... gtgttttcagGAGTGAATGCTGATGACGTTCGAGTAACGGTAGCTGCCCTTGCTGCTCGAG
EST: gi|16920282|gb|BM074585.1|BM074585
EST:     CCAAGTAGCCATTGAAGTGGAAGACCGGGCACAACGTTCAGCAATAACAA                         GAGTGAATGCTGATGACGTTCGAGTAACGGTAGCTGCCCTTGCTGCTCGAG
genomic: CCAAGTAGCCATTGAAGTGGAAGACCGGGCACAACGTTCAGCAATAACAAgtatgcattt ... gtgttttcagGAGTGAATGCTGATGACGTTCGAGTAACGGTAGCTGCCCTTGCTGCTCGAG
EST: gi|71303362|gb|DR787781.1|DR787781
EST:     CCAAGTAGCCATTGAAG-GGAAGACCGGGCACAACGTTCAGCAATAACAA                         GAGTGAATGCTGATGACGTCCGAGTAACGGTAGCTGCCCTTGCTGCTCGAG
genomic: CCAAGTAGCCATTGAAGTGGAAGACCGGGCACAACGTTCAGCAATAACAAgtatgcattt ... gtgttttcagGAGTGAATGCTGATGACGTTCGAGTAACGGTAGCTGCCCTTGCTGCTCGAG
EST: gi|6563795|gb|AW231327.1|AW231327
EST:     CCAAGTAGCCATTGAAGTGGAAGACCGGGCACAACGTTCAGCAGTAACAA                         GAGTGAATGCTGATGACGTTCGAGTAACGGTAGCTGCCCTTGCTGCTCGAG
genomic: CCAAGTAGCCATTGAAGTGGAAGACCGGGCACAACGTTCAGCAATAACAAgtatgcattt ... gtgttttcagGAGTGAATGCTGATGACGTTCGAGTAACGGTAGCTGCCCTTGCTGCTCGAG
EST: gi|71757029|gb|DR954966.1|DR954966
EST:     CCAAGTAGCCATTGAAGTGGAAGACCGGGCACAACGTTCAGCAATAACAA                         GAGTGAATGCTGATGACGTTCGAGTAACGGTAGCTGCCCTTGCTGCTCGAG
genomic: CCAAGTAGCCATTGAAGTGGAAGACCGGGCACAACGTTCAGCAATAACAAgtatgcattt ... gtgttttcagGAGTGAATGCTGATGACGTTCGAGTAACGGTAGCTGCCCTTGCTGCTCGAG
EST: gi|16925502|gb|BM078570.1|BM078570
EST:     CCAAGTAGCCATTGAAGTGGAAGACCGGGCACAACGTTCAGCAATAACAA                         GAGTGAATGCTGATGACGTTCGAGTAACGGTAGCTGCCCTTGCTGCTCGAG
genomic: CCAAGTAGCCATTGAAGTGGAAGACCGGGCACAACGTTCAGCAATAACAAgtatgcattt ... gtgttttcagGAGTGAATGCTGATGACGTTCGAGTAACGGTAGCTGCCCTTGCTGCTCGAG
EST: gi|78180203|gb|DV550576.1|DV550576
EST:     CCAAGTAGCCATTGAAGTGGAAGACCGGGCACAACGTTCAGCAGTAACAA                         GAGTGAATGCTGATGACGTTCGAGTAACGGTAGCTGCCCTTGCTGCTCGAG
genomic: CCAAGTAGCCATTGAAGTGGAAGACCGGGCACAACGTTCAGCAATAACAAgtatgcattt ... gtgttttcagGAGTGAATGCTGATGACGTTCGAGTAACGGTAGCTGCCCTTGCTGCTCGAG
EST: gi|6827273|gb|AW330916.1|AW330916
EST:     CCAAGTAGCCATTGAAGTGGAAGACCGGGCACAACGTTCAGCAGTAACAA                         GAGTGAATGCTGATGACGTTCGAGTAACGGTAGCTGCCCTTGCTGCTCGAG
genomic: CCAAGTAGCCATTGAAGTGGAAGACCGGGCACAACGTTCAGCAATAACAAgtatgcattt ... gtgttttcagGAGTGAATGCTGATGACGTTCGAGTAACGGTAGCTGCCCTTGCTGCTCGAG
EST: gi|19822251|gb|BQ048275.1|BQ048275
EST:     CCAAGTAGCCATTGAAGTGGAAGACCGGGCACAACGTTCAGCAGTAACAA                         GAGTGAATGCTGATGACGTTCGA
genomic: CCAAGTAGCCATTGAAGTGGAAGACCGGGCACAACGTTCAGCAATAACAAgtatgcattt ... gtgttttcagGAGTGAATGCTGATGACGTTCGA
EST: gi|78117103|gb|DV535490.1|DV535490
EST:     CCAAGTAGCCATTGAAGTGGAAGACCGGGCACAACGTTCAGCAATAACAA                         GAGTGAATGCTGATGACGTTCGAGTAACGGTAGCTGCCCTTGCTGCTCGAG
genomic: CCAAGTAGCCATTGAAGTGGAAGACCGGGCACAACGTTCAGCAATAACAAgtatgcattt ... gtgttttcagGAGTGAATGCTGATGACGTTCGAGTAACGGTAGCTGCCCTTGCTGCTCGAG
EST: gi|78075508|gb|DV503942.1|DV503942
EST:     CCAAGTAGCCATTGAAGTGGAAGACCGGGCACAACGTTCAGCAATAACAA                         GAGTGAATGCTGATGACGTTCGAGTAACGGTAGCTGCCCTTGCTGCTCGAG
genomic: CCAAGTAGCCATTGAAGTGGAAGACCGGGCACAACGTTCAGCAATAACAAgtatgcattt ... gtgttttcagGAGTGAATGCTGATGACGTTCGAGTAACGGTAGCTGCCCTTGCTGCTCGAG
EST: gi|50325142|gb|CO520268.1|CO520268
EST:     CCAAGTAGCCATTGAAGTGGAAGACCGGGCACAACGTTCAGCAATAACAA                         GAGTGAATGCTGATGACGTTCGAGTAACGGTAGCTGCCCTTGCTGCTCGAG
genomic: CCAAGTAGCCATTGAAGTGGAAGACCGGGCACAACGTTCAGCAATAACAAgtatgcattt ... gtgttttcagGAGTGAATGCTGATGACGTTCGAGTAACGGTAGCTGCCCTTGCTGCTCGAG

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: 156

GATGCTCCTGTACCTCCTTGCATCACACAACTGGAAGGTGGACTTGTCCAAGTAGCCATTGAAGTGGAAGACCGGGCACAACGTTCAGCAATAACAAgtatgcattt ... gtgttttcagGAGTGAATGCTGATGACGTTCGAGTAACGGTAGCTGCCCTTGCTGCTCGAGGGGAAGCTAACAGTGAGTTGCTAGAATTTATGGGCAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 248

GATGCTCCTGTACCTCCTTGCATCACACAACTGGAAGGTGGACTTGTCCAAGTAGCCATTGAAGTGGAAGACCGGGCACAACGTTCAGCAATAACAAgtatgcattt ... gtgttttcagGAGTGAATGCTGATGACGTTCGAGTAACGGTAGCTGCCCTTGCTGCTCGAGGGGAAGCTAACAGTGAGTTGCTAGAATTTATGGGCAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 242

GATGCTCCTGTACCTCCTTGCATCACACAACTGGAAGGTGGACTTGTCCAAGTAGCCATTGAAGTGGAAGACCGGGCACAACGTTCAGCAATAACAAgtatgcattt ... gtgttttcagGAGTGAATGCTGATGACGTTCGAGTAACGGTAGCTGCCCTTGCTGCTCGAGGGGAAGCTAACAGTGAGTTGCTAGAATTTATGGGCAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 130

GATGCTCCTGTACCTCCTTGCATCACACAACTGGAAGGTGGACTTGTCCAAGTAGCCATTGAAGTGGAAGACCGGGCACAACGTTCAGCAATAACAAgtatgcattt ... gtgttttcagGAGTGAATGCTGATGACGTTCGAGTAACGGTAGCTGCCCTTGCTGCTCGAGGGGAAGCTAACAGTGAGTTGCTAGAATTTATGGGCAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttctttgagttcactggtgcatacaatgtgttgacagaattctgtgtgttttcagGAGTGAATGCTGATGACGTTCGAGTAACGGTAGCTGCCCTTGCTGCTCGAGGGGAAGCTAACAGTGAGTTGCTAGAATTTATGGGCAAG
                            tgttgac  putative branch site (score: 130)
                                              tgttttc  putative PPT
                    atacaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgcattttttaacaatgtagtatgctatcttttttttgaaactacaacatgcaatgtttatgatgaaaagttgtacatggctgcactgacagtttcatgtgaaacattgtagattggacattggtgtgcactatttctttgagttcactggtgcatacaatgtgttgacagaattctgtgtgttttcagGAGTGAATGCTGATGACGTTCGAGTAACGGTAGCTGCCCTTGCTGCTCGAGGGGAAGCTAACAGTGAGTTGCTAGAATTTATGGGCAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT