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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ACGAATACGTTGACATGGTGAAGGCTGGTATCATTGATCCGCTAAAGGTCATCAGAACTGCATTGGTGGATGCTGCTAGgtaaactgaccttttattttgaacagtaggaagttattaattagtttccacggtgaactcggggagccagcagccaacaatgatgaggttgtaacgttca...

Basic information

species Zea mays
transcript GRMZM2G416120_T01
intron # 16
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G416120_T01 (Zea mays), 5'ss of exon 16
lower sequence: LOC_Os10g32550.1 (Oryza sativa), 5'ss of exon 17
ACGAATACGTTGACATGGTGAAGGCTGGTATCATTGATCCGCTAAAGGTCATCAGAACTGCATTGGTGGATGCTGCTAGgtaaact----gaccttttattttgaacagtaggaagtt--attaattagtt--tc---cacggtgaactcggggagccagcagccaacaatgatgaggttgtaacgttca----------------------------------------------------------------------------
  ||||| || |||||||||||||||||||||||||| || ||||| || ||||||||||| |||||||||||||| |||||| ||          |  || ||  |  |||    ||  ||||| | |||  ||   || ||   |  |   ||  || |  ||        || | || |  || |                                                                              
GTGAATATGTGGACATGGTGAAGGCTGGTATCATTGACCCACTAAAAGTGATCAGAACTGCCTTGGTGGATGCTGCAAGgtaagctctcaagttcatggttctgtgctttagttctttacattaaattgttgatcaaacatgggtgatacactgaagcacccacctcatcccttgtgcttatttcggtttttgatctgaaatttttcacccatttaacgttacttttggctcttgcgggttcttacaagttgtttgccttctgcag

upper sequence: GRMZM2G416120_T01 (Zea mays), 5'ss of exon 16
lower sequence: PP1S149_289V6.1 (Physcomitrella patens), 5'ss of exon 16
ACGAATACGTTGACATGGTGAAGGCTGGTATCATTGATCCGCTAAAGGTCATCAGAACTGCATTGGTGGATGCTGCTAGgtaaactgacctttt----attttgaacagtaggaagttattaattagtttccacggtgaactcggggagccagcagccaacaatgatgaggttgtaacgttca
 ||| ||||| ||||||||||||||||| || ||||||||  ||||||| || ||||| ||  | || ||||| ||||||||   |   |||      ||| ||    |  |  |       ||    | |  |  |||   | | |     |    |   |    ||    |     |||  
CCGAGTACGTCGACATGGTGAAGGCTGGAATTATTGATCCTGTAAAGGTTATTAGAACAGCTCTTGTTGATGCCGCTAGgtacttttttcttccttggattctggcttgctg--atccgcgcatcctgtccttcattgatgcccgagttttggggatccgtatgtttgtctctagcttgtt--

upper sequence: GRMZM2G416120_T01 (Zea mays), 5'ss of exon 16
lower sequence: PP1S378_9V6.1 (Physcomitrella patens), 5'ss of exon 16
ACGAATACGTTGACATGGTGAAGGCTGGTATCATTGATCCGCTAAAGGTCATCAGAACTGCATTGGTGGATGCTGCTAGgtaaactgaccttttattttgaacagtaggaagttattaatt--agtttccacggtgaactcggggagccagcagccaacaatgatgaggttgtaacgttca
  || ||||| |||||||||||||| || || ||||||||  |||||||||||||||| ||  | || |||||||||||||  |||   ||  | ||  |  | ||       | ||  ||  | |||  |  |  |  |         ||  | |  ||  | |    ||   |  ||  
CTGAGTACGTCGACATGGTGAAGGCAGGAATAATTGATCCTGTAAAGGTCATCAGAACAGCGCTTGTTGATGCTGCTAGgt--acttttctgctcttgggttctgtcttcttctcttggttctattttttattgctatgtatttcctgtagatgtcttcacggttatacttcctagattat

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|6445583|gb|AW179546.1|AW179546
EST:     ATCATTGATCCGCTAAAGGTCATCAGANCTGCATTGGTGGATGCTGCTAG                         TGTGTCGTCCCTGATGACCACCACGGAATCCATAATTGTAGAGATCCCCAA
genomic: ATCATTGATCCGCTAAAGGTCATCAGAACTGCATTGGTGGATGCTGCTAGgtaaactgac ... cattttgcagTGTGTCGTCCCTGATGACCACCACGGAATCCATAATTGTAGAGATCCCCAA
EST: gi|149073907|gb|EE162235.2|EE162235
EST:     ATCATTGATCCGCTAAAGGTCATCAGAACTGCATTGGTGGATGCTGCTAG                         TGTGTCGTCCCTGATGACCACCACGGAATCCATAATTGTGGAGATCCCCAA
genomic: ATCATTGATCCGCTAAAGGTCATCAGAACTGCATTGGTGGATGCTGCTAGgtaaactgac ... cattttgcagTGTGTCGTCCCTGATGACCACCACGGAATCCATAATTGTAGAGATCCCCAA
EST: gi|19770412|gb|BQ035133.1|BQ035133
EST:     ATCATTGATCCGCTAAAGGTCATCAGAACTGCATTGGTGGATGCTGCTAG                         TGTGTCGTCCCTGATGACCACCACGGAATCCATAATTGTAGAGATCCCCAA
genomic: ATCATTGATCCGCTAAAGGTCATCAGAACTGCATTGGTGGATGCTGCTAGgtaaactgac ... cattttgcagTGTGTCGTCCCTGATGACCACCACGGAATCCATAATTGTAGAGATCCCCAA
EST: gi|32914117|gb|CF018929.1|CF018929
EST:     ATCATTGATCCGCTAAAGGTCATCAGAACTGCATTGGTGGATGCTGCTAG                         TGTGTCGTCCCTGATGACCACCACGGAATCCATAATTGTAGAGATCCCCAA
genomic: ATCATTGATCCGCTAAAGGTCATCAGAACTGCATTGGTGGATGCTGCTAGgtaaactgac ... cattttgcagTGTGTCGTCCCTGATGACCACCACGGAATCCATAATTGTAGAGATCCCCAA
EST: gi|91875568|gb|EB405525.1|EB405525
EST:     ATCATTGATCCGCTAAAGGTCATCAGAACTGCATTGGTGGATGCTGCTAG                         TGTGTCGTCCCTGATGACCACCACGGAATCCATAATTGTAGAGATCCCCAA
genomic: ATCATTGATCCGCTAAAGGTCATCAGAACTGCATTGGTGGATGCTGCTAGgtaaactgac ... cattttgcagTGTGTCGTCCCTGATGACCACCACGGAATCCATAATTGTAGAGATCCCCAA
EST: gi|60337000|gb|DN203973.1|DN203973
EST:     ATCATTGATCCGCTAAAGGTCATCAGAACTGCATTGGTGGATGCTGCTAG                         TGTGTCGTCCCTGATGACCACCACGGAATCCATAATTGTAGAGATCCCCAA
genomic: ATCATTGATCCGCTAAAGGTCATCAGAACTGCATTGGTGGATGCTGCTAGgtaaactgac ... cattttgcagTGTGTCGTCCCTGATGACCACCACGGAATCCATAATTGTAGAGATCCCCAA
EST: gi|60353910|gb|DN220883.1|DN220883
EST:     ATCATTGATCCGCTAAAGGTCATCAGAACTGCATTGGTGGATGCTGCTAG                         TGTGTCGTCCCTGATGACCACCACGGAATCCATAATTGTAGAGATCCCCAA
genomic: ATCATTGATCCGCTAAAGGTCATCAGAACTGCATTGGTGGATGCTGCTAGgtaaactgac ... cattttgcagTGTGTCGTCCCTGATGACCACCACGGAATCCATAATTGTAGAGATCCCCAA
EST: gi|24764192|gb|CA399359.1|CA399359
EST:     ATCATTGATCCGCTAAAGGTCATCAGAACTGCATTGGTGGATGCTGCTAG                         TGTGTCGTCCCTGATGACCACCACGGAATCCATAATTGTAGAGATCCCCAA
genomic: ATCATTGATCCGCTAAAGGTCATCAGAACTGCATTGGTGGATGCTGCTAGgtaaactgac ... cattttgcagTGTGTCGTCCCTGATGACCACCACGGAATCCATAATTGTAGAGATCCCCAA
EST: gi|14997318|gb|BI319298.1|BI319298
EST:     ATCATTGATCCGCTAAAGGTCATCAGAACTGCATTGGTGGATGCTGCTAG                         TGTGTCGTCCCTGATGACCACCACGGAATCCATAATTGTAGAGATCCCCAA
genomic: ATCATTGATCCGCTAAAGGTCATCAGAACTGCATTGGTGGATGCTGCTAGgtaaactgac ... cattttgcagTGTGTCGTCCCTGATGACCACCACGGAATCCATAATTGTAGAGATCCCCAA
EST: gi|67023389|gb|CO452138.1|CO452138
EST:     ATCATTGATCCGCTAAAGGTCATCAGAACTGCATTGGTGGATGCTGCTAG                         TGTGTCGTCCCTGATGACCACCACGGAATCCATAATTGTAGAGATCCCCAA
genomic: ATCATTGATCCGCTAAAGGTCATCAGAACTGCATTGGTGGATGCTGCTAGgtaaactgac ... cattttgcagTGTGTCGTCCCTGATGACCACCACGGAATCCATAATTGTAGAGATCCCCAA
EST: gi|60347399|gb|DN214372.1|DN214372
EST:     ATCATTGATCCGCTAAAGGTCATCAGAACTGCATTGGTGGATGCTGCTAG                         TGTGTCGTCCCTGATGACCACCACGGAATCCATAATTGTAGAGATCCCCAA
genomic: ATCATTGATCCGCTAAAGGTCATCAGAACTGCATTGGTGGATGCTGCTAGgtaaactgac ... cattttgcagTGTGTCGTCCCTGATGACCACCACGGAATCCATAATTGTAGAGATCCCCAA
EST: gi|149077208|gb|EE165874.2|EE165874
EST:     ATCATTGATCCGCTAAAGGTCATCAGAACTGCATTGGTGGATGCTGCTAG                         TGTGTCGTCCCTGATGACCACCACGGAATCCATAATTGTAGAGATCCCCAA
genomic: ATCATTGATCCGCTAAAGGTCATCAGAACTGCATTGGTGGATGCTGCTAGgtaaactgac ... cattttgcagTGTGTCGTCCCTGATGACCACCACGGAATCCATAATTGTAGAGATCCCCAA
EST: gi|32858330|gb|CD998011.1|CD998011
EST:     ATCATTGATCCGCTAAAGGTCATCAGAACTGCATTGGTGGATGCTGCTAG                         TGTGTCGTCCCTGATGACCACCACGGAATCCATAATTGTAGAGATCCCCAA
genomic: ATCATTGATCCGCTAAAGGTCATCAGAACTGCATTGGTGGATGCTGCTAGgtaaactgac ... cattttgcagTGTGTCGTCCCTGATGACCACCACGGAATCCATAATTGTAGAGATCCCCAA
EST: gi|37374359|gb|CF623530.1|CF623530
EST:     ATCATTGATCCGCTAAAGGTCATCAGAACTGCATTGGTGGATGCTGCTAG                         TGTGTCGTCCCTGATGACCACCACGGAATCCATAATTGTAGAGATCCCCAA
genomic: ATCATTGATCCGCTAAAGGTCATCAGAACTGCATTGGTGGATGCTGCTAGgtaaactgac ... cattttgcagTGTGTCGTCCCTGATGACCACCACGGAATCCATAATTGTAGAGATCCCCAA
EST: gi|60397601|gb|DN230417.1|DN230417
EST:     ATCATTGATCCGCTAAAGGTCATCAGAACTGCATTGGTGGATGCTGCTAG                         TGTGTCGTCCCTGATGACCACCACGGAATCCATAATTGTAGAGATCCCCAA
genomic: ATCATTGATCCGCTAAAGGTCATCAGAACTGCATTGGTGGATGCTGCTAGgtaaactgac ... cattttgcagTGTGTCGTCCCTGATGACCACCACGGAATCCATAATTGTAGAGATCCCCAA
EST: gi|4874396|gb|AI673916.1|AI673916
EST:     ATCATTGATCCGCTAAAGGTCATCAGAACTGCATTGGTGGATGCTGCTAG                         TGTGTCGTCCCTGATGACCACCCCGGAATCCATAATTGTAGAGATCCCCAA
genomic: ATCATTGATCCGCTAAAGGTCATCAGAACTGCATTGGTGGATGCTGCTAGgtaaactgac ... cattttgcagTGTGTCGTCCCTGATGACCACCACGGAATCCATAATTGTAGAGATCCCCAA
EST: gi|30088021|gb|CB886226.1|CB886226
EST:     ATCATTGATCCGCTAAAGGTCATCAGAACTGCATTGGTGGATGCTGCTAG                         TGTGTCGTCCCTGATGANNNNNNNGGAATCCATAATTGTAGAGATCCCCAA
genomic: ATCATTGATCCGCTAAAGGTCATCAGAACTGCATTGGTGGATGCTGCTAGgtaaactgac ... cattttgcagTGTGTCGTCCCTGATGACCACCACGGAATCCATAATTGTAGAGATCCCCAA
EST: gi|45847330|gb|CN071273.1|CN071273
EST:     ATCATTGATCCGCTAAAGGTCATCAGAACTGCATTGGTGGATGCTGCTAG                         TGTGTCGTCCCTGATGACCACCACGGAATCCATAATTGTAGAGATCCCCAA
genomic: ATCATTGATCCGCTAAAGGTCATCAGAACTGCATTGGTGGATGCTGCTAGgtaaactgac ... cattttgcagTGTGTCGTCCCTGATGACCACCACGGAATCCATAATTGTAGAGATCCCCAA
EST: gi|21432198|gb|BQ547688.1|BQ547688
EST:     ATCATTGATCCGCTAAAGGTCATCAGAACTGCATTGGTGGATGCTGCTAG                         TGTGTCGTCCCTGATGACCACCACGGAATCCATAA
genomic: ATCATTGATCCGCTAAAGGTCATCAGAACTGCATTGGTGGATGCTGCTAGgtaaactgac ... cattttgcagTGTGTCGTCCCTGATGACCACCACGGAATCCATAA
EST: gi|28982390|gb|BQ538103.2|BQ538103
EST:     ATCATTGATCCGCTAAAGGTCATCAGAACTGCATTGGTGGATGCTGCTAG                         TGTGTCGTCCCTGATGACCACCACGGAATCCATAATTGTAGAGATCCCCAA
genomic: ATCATTGATCCGCTAAAGGTCATCAGAACTGCATTGGTGGATGCTGCTAGgtaaactgac ... cattttgcagTGTGTCGTCCCTGATGACCACCACGGAATCCATAATTGTAGAGATCCCCAA
EST: gi|30088022|gb|CB886227.1|CB886227
EST:     ATCATTGATCCGCTAAAGGTCATCAGAACTGCATTGGTGGATGCTGCTAG                         TGTGTCGTCCCTGATGACCACCACGGAATCCATAATTGTAGAGATCCCCAA
genomic: ATCATTGATCCGCTAAAGGTCATCAGAACTGCATTGGTGGATGCTGCTAGgtaaactgac ... cattttgcagTGTGTCGTCCCTGATGACCACCACGGAATCCATAATTGTAGAGATCCCCAA

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: 47 (upstream exon), 49 (downstream exon)
Score: 140

ACGAATACGTTGACATGGTGAAGGCTGGTATCATTGATCCGCTAAAGGTCATCAGAACTGCATTGGTGGATGCTGCTAGgtaaactgac ... cattttgcagTGTGTCGTCCCTGATGACCACCACGGAATCCATAATTGTAGAGATCCCCAAGGAAGAGGCACCGGCTCCAGCAATGGGTGGCATGGGTGGAATGGATTAC


Block sizes: 46 (upstream exon), 48 (downstream exon)
Score: 64

ACGAATACGTTGACATGGTGAAGGCTGGTATCATTGATCCGCTAAAGGTCATCAGAACTGCATTGGTGGATGCTGCTAGgtaaactgac ... cattttgcagTGTGTCGTCCCTGATGACCACCACGGAATCCATAATTGTAGAGATCCCCAAGGAAGAGGCACCGGCTCCAGCAATGGGTGGCATGGGTGGAATGGATTAC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 56

ACGAATACGTTGACATGGTGAAGGCTGGTATCATTGATCCGCTAAAGGTCATCAGAACTGCATTGGTGGATGCTGCTAGgtaaactgac ... cattttgcagTGTGTCGTCCCTGATGACCACCACGGAATCCATAATTGTAGAGATCCCCAAGGAAGAGGCACCGGCTCCAGCAATGGGTGGCATGGGTGGAATGGATTAC


Block sizes: 46 (upstream exon), 48 (downstream exon)
Score: 86

ACGAATACGTTGACATGGTGAAGGCTGGTATCATTGATCCGCTAAAGGTCATCAGAACTGCATTGGTGGATGCTGCTAGgtaaactgac ... cattttgcagTGTGTCGTCCCTGATGACCACCACGGAATCCATAATTGTAGAGATCCCCAAGGAAGAGGCACCGGCTCCAGCAATGGGTGGCATGGGTGGAATGGATTAC


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ACGAATACGTTGACATGGTGAAGGCTGGTATCATTGATCCGCTAAAGGTCATCAGAACTGCATTGGTGGATGCTGCTAGgtaaactgaccttttattttgaacagtaggaagttattaattagtttccacggtgaactcggggagccagcagccaacaatgatgaggttgtaacgttca

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT