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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gaccagttatcatcttatttcatttcagagatctgttttgtatggatctgagctgcatttgatatctgaccccatttgcaatgcacttgtttcatcacagGATGGCACTGCGAACTACTTGAAAGGACTTATGCTGATCCTATGTTATCTAATAGTTGCTGCCAGTTTCTTTGTTCACGTTGATCCACAATCAA

Basic information

species Zea mays
transcript GRMZM2G143356_T02
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G143356_T02 (Zea mays), 3'ss of exon 11
lower sequence: LOC_Os04g55940.2 (Oryza sativa), 3'ss of exon 9
gaccagttatcatcttatttcatttcagagatctgttttgtatggat-ctgagctgcatttgatatctgaccccatttgcaatgcacttgtttcatcacagGATGGCACTGCGAACTACTTGAAAGGACTTATGCTGATCCTATGTTATCTAATAGTTGCTGCCAGTTTCTTTGTTCACGTTGATCCACAATCAA
  |    |||| |  |||  |  |     ||  |   | | || | | ||||  |       ||  |            |  |     | | |   ||||||||||   ||||||||||||||||||||||||||||||| | ||||||||||||||||| ||||||||||| |||||||||||||||||||| |
ttcacactatc-tgctatagctctcttatgaattacctggcataggttctgatatctcaaccatcaccagttgatcacacgctctttctatgtttccacagGATGGTGTTGCGAACTACTTGAAAGGACTTATGCTGATCTTGTGTTATCTAATAGTTGCCGCCAGTTTCTTCGTTCACGTTGATCCACAATCCA

upper sequence: GRMZM2G143356_T02 (Zea mays), 3'ss of exon 11
lower sequence: GLYMA15G00380.1 (Glycine max), 3'ss of exon 9
-gaccagttatcatcttatttcatttcagagatctgttttgtatggatctgagctgcatttgatatctgacc-ccatttgcaatgcacttgtttcatcacagGATGGCACTGCGAACTACTTGAAAGGACTTATGCTGATCCTATGTTATCTAATAGTTGCTGCCAGTTTCTTTGTTCACGTTGATCCACAATCAA
 ||   ||          |||   |  ||||   | |||| | | |  |     |   | || | | ||||  |||| |  |||     |  ||| |  ||||| || ||  | || || || |||||  | ||||| || ||||| ||||||||||||||||||||||| || || || || || ||  ||    
tgatttgtgtgtgataggtttatatgtagagtatttttttttgttg-ccactattatttatgtt-tgtgacaaccatctttaatttgtgttattccttgcagGAAGGAACCTCAAATTATTTTAAAGGGTTGATGCTTATACTATGCTATCTAATAGTTGCTGCCAGTTTTTTCGTACATGTAGACCCTAAAAGTG

upper sequence: GRMZM2G143356_T02 (Zea mays), 3'ss of exon 11
lower sequence: GLYMA13G44960.1 (Glycine max), 3'ss of exon 9
--gaccagttatcatcttatttcatttcagagatctgttttgtatggatctgagctgcatttgatatctgacc-ccatttgcaatgcacttgtttcatcacagGATGGCACTGCGAACTACTTGAAAGGACTTATGCTGATCCTATGTTATCTAATAGTTGCTGCCAGTTTCTTTGTTCACGTTGATCCACAATCAA
  ||   ||          |||   |  |||| | | ||||   ||   ||    | | | || | | ||||  ||||||  |||   | |  |||    ||||| || ||  | || || || |||||  | ||||| || ||||| ||||||||||||||||||||||| || || || || || ||  ||    
ttgatttgtgtgtgataggtttatatatagagttttttttttgttgccact--attacttatgtt-tgtgacaaccattttaaatttgcgttattccatgcagGAAGGAACCTCAAATTATTTTAAAGGGTTGATGCTTATTCTATGCTATCTAATAGTTGCTGCCAGTTTTTTCGTACATGTAGACCCTAAAAGTG

upper sequence: GRMZM2G143356_T02 (Zea mays), 3'ss of exon 11
lower sequence: GLYMA15G00380.2 (Glycine max), 3'ss of exon 9
-gaccagttatcatcttatttcatttcagagatctgttttgtatggatctgagctgcatttgatatctgacc-ccatttgcaatgcacttgtttcatcacagGATGGCACTGCGAACTACTTGAAAGGACTTATGCTGATCCTATGTTATCTAATAGTTGCTGCCAGTTTCTTTGTTCACGTTGATCC-ACAATCAA---
 ||   ||          |||   |  ||||   | |||| | | |  |     |   | || | | ||||  |||| |  |||     |  ||| |  ||||| || ||  | || || || |||||  | ||||| || ||||| ||||||||||||||||||||||| || || || || || || | ||       
tgatttgtgtgtgataggtttatatgtagagtatttttttttgttg-ccactattatttatgtt-tgtgacaaccatctttaatttgtgttattccttgcagGAAGGAACCTCAAATTATTTTAAAGGGTTGATGCTTATACTATGCTATCTAATAGTTGCTGCCAGTTTTTTCGTACATGTAGACCCTAAAAGTGGTGA

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|211269252|gb|FK955991.1|FK955991
EST:     TAACAGTACTTGTGGTGGCATTTATGTTACAG                         GATGGCACTGCGAACTACTTGAAAGGACTTATGCTGATCCTATGTTATCTA
genomic: TAACAGTACTTGTGGTGGCATTTATGTTACAGgtaggttctt ... ttcatcacagGATGGCACTGCGAACTACTTGAAAGGACTTATGCTGATCCTATGTTATCTA
EST: gi|211145245|gb|FL448473.1|FL448473
EST:     AGACAGCAACTCTCTTCATAACAGTACTTGTGGTGGCATTTATGTTACAG                         GATGGCACTGCGAACTACTTGAAAGGACTTATGCTGATCCTATGTTATCTA
genomic: AGACAGCAACTCTCTTCATAACAGTACTTGTGGTGGCATTTATGTTACAGgtaggttctt ... ttcatcacagGATGGCACTGCGAACTACTTGAAAGGACTTATGCTGATCCTATGTTATCTA
EST: gi|60357296|gb|DN224269.1|DN224269
EST:     AGACAGCAACTCTCTTCATAACAGTACTTGTGGTGGCATTTATGTTACAG                         GATGGCACTGCGAACTACTTGAAAGGACTTATGCTGATCCTATGTTATCTA
genomic: AGACAGCAACTCTCTTCATAACAGTACTTGTGGTGGCATTTATGTTACAGgtaggttctt ... ttcatcacagGATGGCACTGCGAACTACTTGAAAGGACTTATGCTGATCCTATGTTATCTA
EST: gi|148952029|gb|EC897815.2|EC897815
EST:     AGACAGCAACTCTCTTCATAACAGTACTTGTGGTGGCATTTATGTTACAG                         GATGGCACTGCGAACTACTTGAAAGGACTTATGCTGATCCTATGTTATTTA
genomic: AGACAGCAACTCTCTTCATAACAGTACTTGTGGTGGCATTTATGTTACAGgtaggttctt ... ttcatcacagGATGGCACTGCGAACTACTTGAAAGGACTTATGCTGATCCTATGTTATCTA
EST: gi|211269251|gb|FK955990.1|FK955990
EST:     TAACAGTACTTGTGGTGGCATTTATGTTACAG                         GATGGCACTGCGAACTACTTGAAAGGACTTATGCTGATCCTATGTTATCTA
genomic: TAACAGTACTTGTGGTGGCATTTATGTTACAGgtaggttctt ... ttcatcacagGATGGCACTGCGAACTACTTGAAAGGACTTATGCTGATCCTATGTTATCTA
EST: gi|12968375|gb|BG265321.1|BG265321
EST:     AGACAGCAACTCTCTTCATAACAGTACTTGTGGTGGCATTTATGTTACAG                         GATGGCACTGCGAACTACTTGAAAGGACTTATGCTGATCCTATGTTATCTA
genomic: AGACAGCAACTCTCTTCATAACAGTACTTGTGGTGGCATTTATGTTACAGgtaggttctt ... ttcatcacagGATGGCACTGCGAACTACTTGAAAGGACTTATGCTGATCCTATGTTATCTA
EST: gi|91870161|gb|EB400733.1|EB400733
EST:     AGACAGCAACTCTCTTCATAACAGTACTTGTGGTGGCATTTATGTTACAG                         GATGGCACTGCGAACTACTTGAAAGGACTTATGCTGATCCTATGTTATCTA
genomic: AGACAGCAACTCTCTTCATAACAGTACTTGTGGTGGCATTTATGTTACAGgtaggttctt ... ttcatcacagGATGGCACTGCGAACTACTTGAAAGGACTTATGCTGATCCTATGTTATCTA
EST: gi|60351533|gb|DN218506.1|DN218506
EST:     AGACAGCAACTCTCTTCATAACAGTACTTGTGGTGGCATTTATGTTACAG                         GATGGCACTGCGAACTACTTGAAAGGACTTATGCTGATCCTATGTTATCTA
genomic: AGACAGCAACTCTCTTCATAACAGTACTTGTGGTGGCATTTATGTTACAGgtaggttctt ... ttcatcacagGATGGCACTGCGAACTACTTGAAAGGACTTATGCTGATCCTATGTTATCTA
EST: gi|110949660|gb|EE169817.1|EE169817
EST:     AGACAGCAACTCTCTTCATAACAGTACTTGTGGTGGCATTTATGTTACAG                         GATGGCACTGCGAACTACTTGAAAGGACTTATGCTGATCCTATGTTATTTA
genomic: AGACAGCAACTCTCTTCATAACAGTACTTGTGGTGGCATTTATGTTACAGgtaggttctt ... ttcatcacagGATGGCACTGCGAACTACTTGAAAGGACTTATGCTGATCCTATGTTATCTA
EST: gi|211269249|gb|FK955988.1|FK955988
EST:     TAACAGTACTTGTGGTGGCATTTATGTTACAG                         GATGGCACTGCGAACTACTTGAAAGGACTTATGCTGATCCTATGTTATCTA
genomic: TAACAGTACTTGTGGTGGCATTTATGTTACAGgtaggttctt ... ttcatcacagGATGGCACTGCGAACTACTTGAAAGGACTTATGCTGATCCTATGTTATCTA
EST: gi|211269248|gb|FK955987.1|FK955987
EST:     TAACAGTACTTGTGGTGGCATTTATGTTACAG                         GATGGCACTGCGAACTACTTGAAAGGACTTATGCTGATCCTATGTTATCTA
genomic: TAACAGTACTTGTGGTGGCATTTATGTTACAGgtaggttctt ... ttcatcacagGATGGCACTGCGAACTACTTGAAAGGACTTATGCTGATCCTATGTTATCTA
EST: gi|148951917|gb|EC897693.2|EC897693
EST:     AGACAGCAACTCTCTTCATAACAGTACTTGTGGTGGCATTTATGTTACAG                         GATGGCACTGCGAACTACTTGAAAGGACTTATGCTGATCCTATGTTATTTA
genomic: AGACAGCAACTCTCTTCATAACAGTACTTGTGGTGGCATTTATGTTACAGgtaggttctt ... ttcatcacagGATGGCACTGCGAACTACTTGAAAGGACTTATGCTGATCCTATGTTATCTA

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), 48 (downstream exon)
Score: 61

TATTGGTTGGACGATGGGACAAAAGATGGACTTGAATTTTCAGCTATTTGAGACAGCAACTCTCTTCATAACAGTACTTGTGGTGGCATTTATGTTACAGgtaggttctt ... ttcatcacagGATGGCACTGCGAACTACTTGAAAGGACTTATGCTGATCCTATGTTATCTAATAGTTGCTGCCAGTTTCTTTGTTCACGTTGATCCACAATCAA


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 98

TATTGGTTGGACGATGGGACAAAAGATGGACTTGAATTTTCAGCTATTTGAGACAGCAACTCTCTTCATAACAGTACTTGTGGTGGCATTTATGTTACAGgtaggttctt ... ttcatcacagGATGGCACTGCGAACTACTTGAAAGGACTTATGCTGATCCTATGTTATCTAATAGTTGCTGCCAGTTTCTTTGTTCACGTTGATCCACAATCAA


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 136

TATTGGTTGGACGATGGGACAAAAGATGGACTTGAATTTTCAGCTATTTGAGACAGCAACTCTCTTCATAACAGTACTTGTGGTGGCATTTATGTTACAGgtaggttctt ... ttcatcacagGATGGCACTGCGAACTACTTGAAAGGACTTATGCTGATCCTATGTTATCTAATAGTTGCTGCCAGTTTCTTTGTTCACGTTGATCCACAATCAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 126

TATTGGTTGGACGATGGGACAAAAGATGGACTTGAATTTTCAGCTATTTGAGACAGCAACTCTCTTCATAACAGTACTTGTGGTGGCATTTATGTTACAGgtaggttctt ... ttcatcacagGATGGCACTGCGAACTACTTGAAAGGACTTATGCTGATCCTATGTTATCTAATAGTTGCTGCCAGTTTCTTTGTTCACGTTGATCCACAATCAA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atctgagctgcatttgatatctgaccccatttgcaatgcacttgtttcatcacagGATGGCACTGCGAACTACTTGAAAGGACTTATGCTGATCCTATGTTATCTAATAGTTGCTGCCAGTTTCTTTGTTCACGTTGATCCACAATCAA
                  atctgac  putative branch site (score: 126)
                                        cttgtttc  putative PPT
           atttgatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gaccagttatcatcttatttcatttcagagatctgttttgtatggatctgagctgcatttgatatctgaccccatttgcaatgcacttgtttcatcacagGATGGCACTGCGAACTACTTGAAAGGACTTATGCTGATCCTATGTTATCTAATAGTTGCTGCCAGTTTCTTTGTTCACGTTGATCCACAATCAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - -tttcatt
- - - - - - - - - - - - - - - - -tgttttg
- - - - - - - - - - - - - - - - - - - - - - - - - -gctgcat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aatgcac