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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgtgtttcgtgcctcacatccagctcaattgcattttgtgtttcattcgttgcttcaataggttcttactggatttccttggcagGGCATGTATATCACGCTTTAAAGACTGCCCACTATGTGGTGCTGATATAGAGGGTATTGAGCCTGATGCGGAACTTCAAGCTCTTGTTGACCGCTTCATT

Basic information

species Zea mays
transcript GRMZM2G049672_T01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G049672_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os01g01420.3 (Oryza sativa), 3'ss of exon 2
--gtgt-gtttcgtgcctcacatccagctcaattgcattt-tgtgtttcattcgttgct--tcaataggttct---tactggatttccttggcagGGCATGTATATCACGCTTTAAAGACTGCCCACTATGTGGTGCTGATATAGAGGGTATTGAGCCTGATGCGGAACTTCAAGCTCTTGTTGACCGCTTCATT
  | || || || |   |||   | ||||   |   | |  |   || | | |||   |  |  |||  ||||    |||||||||||||| ||||||||| ||||  |||||||| ||||| ||| | ||||||||||| ||  | || || ||||| ||||  || |||||||  ||||| ||||||||||||
gtgcgtagtatcatatttcaatactagctttctactagtaattccttccgtccgtcaatagtatataccttctgaacactggatttccttgtcagGGCATGCATATTGCGCTTTAAGGACTGTCCATTGTGTGGTGCTGACATCCAAGGGATCGAGCCCGATGATGAGCTTCAAGGCCTTGTCGACCGCTTCATT

upper sequence: GRMZM2G049672_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os02g55200.2 (Oryza sativa), 3'ss of exon 2
gtgtgtttcgtgcctca-----catccagctcaattg--cattttgtgt---ttcattcgttgcttcaataggttctt-------actggatttccttggcagGGCATGTATATCACGCTTTAAAGACTGCCCACTATGTGGTGCTGATATAGAGGGTATTGAGCCTGATGCGGAACTTCAAGCTCTTGTTGACCGCTTCATT
||| || || |   |||       || |  ||  |    || | | |||   |||   | |    ||  |   ||  |       |||||||||||||  ||||||||| ||||  |||||||| ||||| ||| | ||||||||||| ||  | || || ||||||||||  || |||||||  ||||| ||||||||||||
gtgcgtatcatatttcaatagctttctaattcgttctgtcaatatatgtaccttctcacttgatctccttgtctttctccaaaacactggatttccttctcagGGCATGCATATTGCGCTTTAAGGACTGTCCATTGTGTGGTGCTGACATCCAAGGGATCGAGCCTGATGATGAGCTTCAAGGCCTTGTCGACCGCTTCATT

upper sequence: GRMZM2G049672_T01 (Zea mays), 3'ss of exon 2
lower sequence: Vv13s0047g00170.t01 (Vitis vinifera), 3'ss of exon 2
------------gtgtgtttcgtgcctcacatccagctcaat-tgcattttgtgtttcattc-gttgcttcaataggttcttactggatttcc---ttgg----cagGGCATGTATATCACGCTTTAAAGACTGCCCACTATGTGGTGCTGATATAGAGGGTATTGAGCCTGATGCGGAACTTCAAGCTCTTGTTGACCGCTTCATT
              |    | |  |||   |    | |   | || ||| |   | |||||  |  | ||  |    |  |  ||  ||||      ||      ||||||||||||||||| |||||||| |||||| ||||||| ||||| || |||   |||||  |||||  | | |||||   |   ||||| ||||| |||
gtaggcagacaaaggcaacttgaacctttaagtttgttttgtgtggattattcttatcattttgcagtttttactaatattacctacatttttaatctgaaaattagGGCATGTATATCACGTTTTAAAGATTGCCCATTATGTGGAGCTGACATTGAGAAGATTGAAGCTGATATGAATCTTCAGAATACAGTTGATCGCTTTATT

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|32798632|gb|CD950868.1|CD950868
EST:     CTACTCCATGAAAGTAGCAAATGCAAGCCGTGTGCCCATAAATTTTGCAA                         GGCATGTATATCACGCTTTA
genomic: CTACTCCATGAAAGTAGCAAATGCAAGCCGTGTGCCCATAAATTTTGCAAgtgtgtttcg ... tccttggcagGGCATGTATATCACGCTTTA
EST: gi|148963602|gb|EE014642.2|EE014642
EST:     CTACTCCATGAAAGTAGCAAATGCAAGCCGTGTGCCCATAAATTTTGCAA                         GGCATGTATATCACGCTTTAAAGACTGCCCACTATGTGGTGCTGATATAGA
genomic: CTACTCCATGAAAGTAGCAAATGCAAGCCGTGTGCCCATAAATTTTGCAAgtgtgtttcg ... tccttggcagGGCATGTATATCACGCTTTAAAGACTGCCCACTATGTGGTGCTGATATAGA
EST: gi|149087899|gb|EE177162.2|EE177162
EST:     CTACTCCATGAAAGTAGCAAATGCAAGCCGTGTGCCCATAAATTTTGCAA                         GGCATGTATATCACGCTTTAAAGACTGCCCACTATGTGGTGCTGATATAGA
genomic: CTACTCCATGAAAGTAGCAAATGCAAGCCGTGTGCCCATAAATTTTGCAAgtgtgtttcg ... tccttggcagGGCATGTATATCACGCTTTAAAGACTGCCCACTATGTGGTGCTGATATAGA
EST: gi|76285103|gb|DV024671.1|DV024671
EST:     CTACTCCATGAAAGTAGCAAATGCAAGCCGTGTGCCCATAAATTTTGCAA                         GGCATGTATATCACGCTTTAAAGACTG
genomic: CTACTCCATGAAAGTAGCAAATGCAAGCCGTGTGCCCATAAATTTTGCAAgtgtgtttcg ... tccttggcagGGCATGTATATCACGCTTTAAAGACTG
EST: gi|149095771|gb|EE181414.2|EE181414
EST:     CTACTCCATGAAAGTAGCAAATGCAAGCCGTGTGCCCATAAATTTTGCAA                         GGCATGTATATCACGCTTTAAAGACTGCCCACTATGTGGTGCTGATATAGA
genomic: CTACTCCATGAAAGTAGCAAATGCAAGCCGTGTGCCCATAAATTTTGCAAgtgtgtttcg ... tccttggcagGGCATGTATATCACGCTTTAAAGACTGCCCACTATGTGGTGCTGATATAGA
EST: gi|18655054|gb|BM499859.1|BM499859
EST:     CTACTCCATGAAAGTAGCAAATGCAAGCCGTGTGCCCATAAATTCTGCAA                         GGCATGTATATCACGCTTTAAAGACTGCCCACTATGTGGTGCTGATATAGA
genomic: CTACTCCATGAAAGTAGCAAATGCAAGCCGTGTGCCCATAAATTTTGCAAgtgtgtttcg ... tccttggcagGGCATGTATATCACGCTTTAAAGACTGCCCACTATGTGGTGCTGATATAGA
EST: gi|18662073|gb|BM501731.1|BM501731
EST:     CTACTCCATGAAAGTAGCAAATGCAAGCCGTGTGCCCATAAATTCTGCAA                         GGCATGTATATCACGCTTTAAAGACTGCCCACTATGTGGGGCTGATATAGA
genomic: CTACTCCATGAAAGTAGCAAATGCAAGCCGTGTGCCCATAAATTTTGCAAgtgtgtttcg ... tccttggcagGGCATGTATATCACGCTTTAAAGACTGCCCACTATGTGGTGCTGATATAGA
EST: gi|76015372|gb|DT942542.1|DT942542
EST:     CTACTCCATGAAAGTAGCAAATGCAAGCCGTGTGCCCATAAATTTTGCAA                         GGCATGTATATCACGCTTTAAAGACTGCCCACTATGTGGTGCTGATATAGA
genomic: CTACTCCATGAAAGTAGCAAATGCAAGCCGTGTGCCCATAAATTTTGCAAgtgtgtttcg ... tccttggcagGGCATGTATATCACGCTTTAAAGACTGCCCACTATGTGGTGCTGATATAGA
EST: gi|78086285|gb|DV514678.1|DV514678
EST:     CTACTCCATGAAAGTAGCAAATGCAAGCCGTGTGCCCATAAATTTTGCAA                         GGCATGTATATCACGCTTTAAAGACTGCCCACTATGTGGTGCTGATATAGA
genomic: CTACTCCATGAAAGTAGCAAATGCAAGCCGTGTGCCCATAAATTTTGCAAgtgtgtttcg ... tccttggcagGGCATGTATATCACGCTTTAAAGACTGCCCACTATGTGGTGCTGATATAGA
EST: gi|148958313|gb|EC904535.2|EC904535
EST:     CTACTCCATGAAAGTAGCAAATGCAAGCCGTGTGCCCATAAATTTTGCAA                         GGCATGTATATCACGCTTTAAAGACTGCCCACTATGTGGTGCTGATATAGA
genomic: CTACTCCATGAAAGTAGCAAATGCAAGCCGTGTGCCCATAAATTTTGCAAgtgtgtttcg ... tccttggcagGGCATGTATATCACGCTTTAAAGACTGCCCACTATGTGGTGCTGATATAGA
EST: gi|148943141|gb|EC888200.2|EC888200
EST:     CTACTCCATGAAAGTAGCAAATGCAAGCCGTGTGCCCATAAATTTTGCAA                         GGCATGTATATCACGCTTTAAAGACTGCCCACTATGTGGTGCTGATATAGA
genomic: CTACTCCATGAAAGTAGCAAATGCAAGCCGTGTGCCCATAAATTTTGCAAgtgtgtttcg ... tccttggcagGGCATGTATATCACGCTTTAAAGACTGCCCACTATGTGGTGCTGATATAGA
EST: gi|148957544|gb|EC903637.2|EC903637
EST:     CTACTCCATGAAAGTAGCAAATGCAAGCCGTGTGCCCATAAATTTTGCAA                         GGCATGTATATCACGCTTTAAAGACTGCCCACTATGTGGTGCTGATATAGA
genomic: CTACTCCATGAAAGTAGCAAATGCAAGCCGTGTGCCCATAAATTTTGCAAgtgtgtttcg ... tccttggcagGGCATGTATATCACGCTTTAAAGACTGCCCACTATGTGGTGCTGATATAGA
EST: gi|88755689|gb|DY539830.1|DY539830
EST:     CTACTCCATGAAAGTAGCAAATGCAAGCCGTGTGCCCATAAATTTTGCAA                         GGCATGTATATCACGCTTTAAAGACTGCCCACTATGTGGTGCTGATATAGA
genomic: CTACTCCATGAAAGTAGCAAATGCAAGCCGTGTGCCCATAAATTTTGCAAgtgtgtttcg ... tccttggcagGGCATGTATATCACGCTTTAAAGACTGCCCACTATGTGGTGCTGATATAGA
EST: gi|149081888|gb|EE171050.2|EE171050
EST:     CTACTCCATGAAAGTAGCAAATGCAAGCCGTGTGCCCATAAATTTTGCAA                         GGCATGTATATCACGCTTTAAAGACTGCCCACTATGTGGTGCTGATATAGA
genomic: CTACTCCATGAAAGTAGCAAATGCAAGCCGTGTGCCCATAAATTTTGCAAgtgtgtttcg ... tccttggcagGGCATGTATATCACGCTTTAAAGACTGCCCACTATGTGGTGCTGATATAGA
EST: gi|18662075|gb|BM501732.1|BM501732
EST:     CTACTCCATGAAAGTAGCAAATGCAAGCCGTGTGCCCATAAATTCTGCAA                         GGCATGTATATCACGCTTTAAAGACTGCCCACTATGTGGTGCTGATATAGA
genomic: CTACTCCATGAAAGTAGCAAATGCAAGCCGTGTGCCCATAAATTTTGCAAgtgtgtttcg ... tccttggcagGGCATGTATATCACGCTTTAAAGACTGCCCACTATGTGGTGCTGATATAGA

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: 208

ACTCCAACACTTTCAAGCTGGGTCCGCTTAGCTGCATTGTCTGCCAGGCACTACTCCATGAAAGTAGCAAATGCAAGCCGTGTGCCCATAAATTTTGCAAgtgtgtttcg ... tccttggcagGGCATGTATATCACGCTTTAAAGACTGCCCACTATGTGGTGCTGATATAGAGGGTATTGAGCCTGATGCGGAACTTCAAGCTCTTGTTGACCGCTTCATT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 180

ACTCCAACACTTTCAAGCTGGGTCCGCTTAGCTGCATTGTCTGCCAGGCACTACTCCATGAAAGTAGCAAATGCAAGCCGTGTGCCCATAAATTTTGCAAgtgtgtttcg ... tccttggcagGGCATGTATATCACGCTTTAAAGACTGCCCACTATGTGGTGCTGATATAGAGGGTATTGAGCCTGATGCGGAACTTCAAGCTCTTGTTGACCGCTTCATT


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 243

ACTCCAACACTTTCAAGCTGGGTCCGCTTAGCTGCATTGTCTGCCAGGCACTACTCCATGAAAGTAGCAAATGCAAGCCGTGTGCCCATAAATTTTGCAAgtgtgtttcg ... tccttggcagGGCATGTATATCACGCTTTAAAGACTGCCCACTATGTGGTGCTGATATAGAGGGTATTGAGCCTGATGCGGAACTTCAAGCTCTTGTTGACCGCTTCATT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 209

ACTCCAACACTTTCAAGCTGGGTCCGCTTAGCTGCATTGTCTGCCAGGCACTACTCCATGAAAGTAGCAAATGCAAGCCGTGTGCCCATAAATTTTGCAAgtgtgtttcg ... tccttggcagGGCATGTATATCACGCTTTAAAGACTGCCCACTATGTGGTGCTGATATAGAGGGTATTGAGCCTGATGCGGAACTTCAAGCTCTTGTTGACCGCTTCATT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcattttgtgtttcattcgttgcttcaataggttcttactggatttccttggcagGGCATGTATATCACGCTTTAAAGACTGCCCACTATGTGGTGCTGATATAGAGGGTATTGAGCCTGATGCGGAACTTCAAGCTCTTGTTGACCGCTTCATT
                                ttcttac  putative branch site (score: 209)
                                           tttcctt  putative PPT
          tttcatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgtgtttcgtgcctcacatccagctcaattgcattttgtgtttcattcgttgcttcaataggttcttactggatttccttggcagGGCATGTATATCACGCTTTAAAGACTGCCCACTATGTGGTGCTGATATAGAGGGTATTGAGCCTGATGCGGAACTTCAAGCTCTTGTTGACCGCTTCATT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT