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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgacttatgttgcatcattttttaaatactggagcttatttttatccttgatgttcttacatgtctgcatggatttatttctgttcttcagGAGAGGGTTATGAAAGTTCTACAAGTTTGGGCAGACTGGTTCCTGTTTTCTGATGCATTTCTTAATGGGCTGAGGGCTACTTTTCTTAGATCAGGCAACT

Basic information

species Zea mays
transcript GRMZM2G174785_T02
intron # 15
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G174785_T02 (Zea mays), 3'ss of exon 15
lower sequence: LOC_Os02g08360.1 (Oryza sativa), 3'ss of exon 16
gtgacttatgttgcatcattttttaaatactggagcttatttttatccttgatgttcttacatgtctgcatggatttatttctgttcttcagGAGAGGGTTATGAAAGTTCTACAAGTTTGGGCAGACTGGTTCCTGTTTTCTGATGCATTTCTTAATGGGCTGAGGGCTACTTTTCTTAGATCAGGCAACT
|| | || | |||     |||||| | | ||  |  |||||  | | |||||||||     | |   ||||   ||| ||  |  ||| |||||||| ||| |||||||||||||||| ||||| ||||||||| | ||||| ||||||| ||| ||||| || || ||||| |||||||||||| || |||
gtaagttgtattgttctgttttttgagtcctttattttattcct-ttcttgatgttaccttacgatagcattattttgttgtttctctgcagGAGAGAGTTTTGAAAGTTCTACAAGTATGGGCGGACTGGTTCTTATTTTCCGATGCATATCTGAATGGACTAAGAGCTACCTTTCTTAGATCAAGCCACT

upper sequence: GRMZM2G174785_T02 (Zea mays), 3'ss of exon 15
lower sequence: GLYMA16G15820.1 (Glycine max), 3'ss of exon 11
gtgacttatgttgcatcattttttaaatactggagcttatttttatccttgatgttcttacatgtctgcatggatttatttctgttcttcagGAGAGGGTTATGAAAGTTCTACAAGTTTGGGCAGACTGGTTCCTGTTTTCTGATGCATTTCTTAATGGGCTGAGGGCTACTTTTCTTAGATCAGGCAACT
||    |          |  |||    |  |  |  || || | || |||  | |  ||     ||||  || |  |||| |        ||||  | ||  |||||||| ||||||||||||| |||||||| || ||||| ||||| | | | |||||  | || || ||||| ||| || | || ||||
gtaggctgaacaatcatagatttcct-tgatataatttcttataattcttattctgtttggtgatctgtctgaaaatattcc--------agGAACGAGTGCTGAAAGTTTTACAAGTTTGGGCCGACTGGTTTCTCTTTTCAGATGCTTATGTGAATGGATTAAGAGCCACTTTCCTTCGACCTGGGAACT

upper sequence: GRMZM2G174785_T02 (Zea mays), 3'ss of exon 15
lower sequence: GLYMA08G34030.1 (Glycine max), 3'ss of exon 15
gtgacttatgttgcatcattttttaaatactggagcttatttttatccttgatgttcttacatgtctgcatggatttatttctg---ttcttcagGAGAGGGTTATGAAAGTTCTACAAGTTTGGGCAGACTGGTTCCTGTTTTCTGATGCATTTCTTAATGGGCTGAGGGCTACTTTTCTTAGATCAGGCAACT
      || | || |  ||  |  |  |  | ||  | ||||     |||  ||||||||  | | |     ||| | | ||||   |  | |||||  | ||  |||||||| ||||||||||||| |||||||| || ||||| ||||| | | |||||||  | ||||| ||||| ||| || | || ||||
-----gtaggctgaacaatcatagacttctttgatataattt-----cttattgttcttat-tctgtttggtgatctttgtctgaaatgttccagGAACGAGTGCTGAAAGTTTTACAAGTTTGGGCCGACTGGTTTCTCTTTTCAGATGCTTATGTTAATGGATTAAGGGCCACTTTCCTTCGACCTGGGAACT

upper sequence: GRMZM2G174785_T02 (Zea mays), 3'ss of exon 15
lower sequence: Vv04s0008g06810.t01 (Vitis vinifera), 3'ss of exon 14
--gtgacttatgttgcatcattttttaaatactgga--gcttatttttatccttgatgttcttacatgtctgcatggatttattt-ctg---ttcttcagGAGAGGGTTATGAAAGTTCTACAAGTTTGGGCAGACTGGTTCCTGTTTTCTGATGCATTTCTTAATGGGCTGAGGGCTACTTTTCTTAGATCAGGCAACT
  | | | ||  |   ||  || ||||| |    |   || | || || || |  || |  || |   |||| |||   |  ||  |||   |||| |||||  | |||||||| ||||| ||||| ||||||||||||||||| ||||| ||||||| | | |||||  || |||||||||||||| |||| || ||||
gtgagccatacataaaattcttgtttaactttcagcccgcctcttcttttcttatatttagtttctattctgaatgcgctccttaactggaattctccagGAACGAGTTATGAAGGTTCTTCAAGTCTGGGCAGACTGGTTCCTATTTTCAGATGCATATGTCAATGGATTGCGGGCTACTTTTCTTCGATCTGGGAACT

upper sequence: GRMZM2G174785_T02 (Zea mays), 3'ss of exon 15
lower sequence: PP1S196_109V6.1 (Physcomitrella patens), 3'ss of exon 14
------gtgacttatgttgcatcattt-tttaaatactggagcttatttttatccttgatgttcttacat-gtctgcatggatttatttctgttcttcagGAGAGGGTTATGAAAGTTCTACAAGTTTGGGCAGACTGGTTCCTGTTTTCTGATGCATTTCTTAATGGGCTGAGGGCTACTTTTCTTAGATCAGGCAACT
       | |   |||   ||  |||   |||  |  |  | ||  |||  || |||| |  |  || || |   | || |  | | ||   |||  |||||| | ||  | |||||||| ||||||||||||||||||||| ||||||| ||| | ||| ||| |||  || | || || || ||  |  |||| ||||
cttcaacttatccatgaaacacgattcacttaggtggtcaacctcgtttcgattcttggttcttctaaattgagcgtatcgtatgacttggattcggcagGAGCGAGTGTTAAAAGTTCTTCAAGTTTGGGCAGACTGGTTCTTGTTTTCAGATTCTTTTGTTACTGGCTTGCGTGCAACATTCCTACGGCCAGGAAACT

upper sequence: GRMZM2G174785_T02 (Zea mays), 3'ss of exon 15
lower sequence: PP1S137_118V6.1 (Physcomitrella patens), 3'ss of exon 14
---------------------------------------------------------------gtgacttatgttgcatcattttttaaatactggagcttatttttatccttgatgttcttacatg---tctgcatg-gatttatttctgttctt-cagGAGAGGGTTATGAAAGTTCTACAAGTTTGGGCAGACTGGTTCCTGTTTTCTGATGCATTTCTTAATGGGCTGAGGGCTACTTTTCTTAGATCAGGCAACT
                                                                |||  ||  | ||||  | | ||   |||  ||    ||     || |  || ||      ||   |  || || | |||   |  ||| |  |||||| ||||  |||||||||| ||||||||||||||||||||| ||||||| ||| | ||| ||| |||  || | || || ||  |  || |||| ||||
gtaaaaaccggagatgatgaaacgaagttactgtgggaggaaccctccagttattgaattagcttgatgta-atcgcattgtctgtttgctacctgactcaatgcacttcttcaatatttgcttctgaactgagcgtgtggtttgccttggttttggcagGAGCGGGTATTGAAAGTTCTTCAAGTTTGGGCAGACTGGTTCTTGTTTTCAGATTCCTTTGTTACTGGCTTGCGTGCAACATTCTTGCGACCAGGAAACT

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|160481587|gb|EY254419.1|EY254419
EST:     ATGACTTGTATCGCAGTATCACTGGAAGGATTACTGCTGAAGCTCTGAAG                         GAGAGGGTTATGAAAGTTCTACAAGTTTGGGCAGACTGGTCCCTGGTTTTC
genomic: ATGACTTGTATCGCAGTATCACTGGAAGGATTACTGCTGAAGCTCTGAAGgtgacttatg ... tgttcttcagGAGAGGGTTATGAAAGTTCTACAAGTTTGGGCAGACTGGTTCCTG-TTTTC
EST: gi|22489341|gb|BU049264.1|BU049264
EST:     ATGACTTGTATCGCAGTATCACTGGAAGGATTACTGCTGAAGCTCTGAAG                         GAGAGGGTTATGAAAGTTCTACAAGTTTGGGCAGACTGGTTCCTGTTTTCT
genomic: ATGACTTGTATCGCAGTATCACTGGAAGGATTACTGCTGAAGCTCTGAAGgtgacttatg ... tgttcttcagGAGAGGGTTATGAAAGTTCTACAAGTTTGGGCAGACTGGTTCCTGTTTTCT
EST: gi|87298721|gb|DY470724.1|DY470724
EST:     ATGACTTGTATCGCAGTATCACTGGAAGGATTACTGCTGAAGCTCTGAAG                         GAGAGGGTTATGAAAGTTCTACAAGTTTGGGCAGACTGGTTCCTGTTTTCT
genomic: ATGACTTGTATCGCAGTATCACTGGAAGGATTACTGCTGAAGCTCTGAAGgtgacttatg ... tgttcttcagGAGAGGGTTATGAAAGTTCTACAAGTTTGGGCAGACTGGTTCCTGTTTTCT
EST: gi|22715204|gb|BU197636.1|BU197636
EST:     ATGACTTGTATCGCAGTATCACTGGAAGGATTACTGCTGAAGCCCTGAAG                         GAGAGGGTTATGAAAGTTCTACAAGTTTGGGCAGACTGGTTCCTGTTTTCT
genomic: ATGACTTGTATCGCAGTATCACTGGAAGGATTACTGCTGAAGCTCTGAAGgtgacttatg ... tgttcttcagGAGAGGGTTATGAAAGTTCTACAAGTTTGGGCAGACTGGTTCCTGTTTTCT
EST: gi|18384954|gb|BM418153.1|BM418153
EST:     ATGACTTGTATCGCAGTATCACTGGAAGGATTACTGCTGAAGCTCTGAAG                         GAGAGGGTTATGAAAGTTCTACAAGTTTGGGCAGACTGGNTCCTGTTTTCT
genomic: ATGACTTGTATCGCAGTATCACTGGAAGGATTACTGCTGAAGCTCTGAAGgtgacttatg ... tgttcttcagGAGAGGGTTATGAAAGTTCTACAAGTTTGGGCAGACTGGTTCCTGTTTTCT
EST: gi|18383988|gb|BM417188.1|BM417188
EST:     ATGACTTGTATCGCAGTATCACTGGAAGGATTACTGCTGAAGCTCTGAAG                         GAGAGGGTTATGAAAGTTCTACAAGTTTGGGCAGACTGGTTCCTGTTTTCT
genomic: ATGACTTGTATCGCAGTATCACTGGAAGGATTACTGCTGAAGCTCTGAAGgtgacttatg ... tgttcttcagGAGAGGGTTATGAAAGTTCTACAAGTTTGGGCAGACTGGTTCCTGTTTTCT
EST: gi|20299993|gb|BQ162936.1|BQ162936
EST:     ATGACTTGTATCGCAGTATCACTGGAAGGATTACTGCTGAAGCTCTGAAG                         GAGAGGGTTATGAAAGTTCTACAAGTTTGGGCAGACTGGTTCCTGTTTTCT
genomic: ATGACTTGTATCGCAGTATCACTGGAAGGATTACTGCTGAAGCTCTGAAGgtgacttatg ... tgttcttcagGAGAGGGTTATGAAAGTTCTACAAGTTTGGGCAGACTGGTTCCTGTTTTCT

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: 133

ATTCCGAACGAAGTTTGAAGCTTCTTTGCCAGATGTTATGGAGAGCTTTAATGACTTGTATCGCAGTATCACTGGAAGGATTACTGCTGAAGCTCTGAAGgtgacttatg ... tgttcttcagGAGAGGGTTATGAAAGTTCTACAAGTTTGGGCAGACTGGTTCCTGTTTTCTGATGCATTTCTTAATGGGCTGAGGGCTACTTTTCTTAGATCAGGCAACT


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 77

ATTCCGAACGAAGTTTGAAGCTTCTTTGCCAGATGTTATGGAGAGCTTTAATGACTTGTATCGCAGTATCACTGGAAGGATTACTGCTGAAGCTCTGAAGgtgacttatg ... tgttcttcagGAGAGGGTTATGAAAGTTCTACAAGTTTGGGCAGACTGGTTCCTGTTTTCTGATGCATTTCTTAATGGGCTGAGGGCTACTTTTCTTAGATCAGGCAACT


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 107

ATTCCGAACGAAGTTTGAAGCTTCTTTGCCAGATGTTATGGAGAGCTTTAATGACTTGTATCGCAGTATCACTGGAAGGATTACTGCTGAAGCTCTGAAGgtgacttatg ... tgttcttcagGAGAGGGTTATGAAAGTTCTACAAGTTTGGGCAGACTGGTTCCTGTTTTCTGATGCATTTCTTAATGGGCTGAGGGCTACTTTTCTTAGATCAGGCAACT


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 82

ATTCCGAACGAAGTTTGAAGCTTCTTTGCCAGATGTTATGGAGAGCTTTAATGACTTGTATCGCAGTATCACTGGAAGGATTACTGCTGAAGCTCTGAAGgtgacttatg ... tgttcttcagGAGAGGGTTATGAAAGTTCTACAAGTTTGGGCAGACTGGTTCCTGTTTTCTGATGCATTTCTTAATGGGCTGAGGGCTACTTTTCTTAGATCAGGCAACT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatttttatccttgatgttcttacatgtctgcatggatttatttctgttcttcagGAGAGGGTTATGAAAGTTCTACAAGTTTGGGCAGACTGGTTCCTGTTTTCTGATGCATTTCTTAATGGGCTGAGGGCTACTTTTCTTAGATCAGGCAACT
                 ttcttac  putative branch site (score: 82)
                                     tttatttctgttcttc  putative PPT
                                    atttatttct  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgacttatgttgcatcattttttaaatactggagcttatttttatccttgatgttcttacatgtctgcatggatttatttctgttcttcagGAGAGGGTTATGAAAGTTCTACAAGTTTGGGCAGACTGGTTCCTGTTTTCTGATGCATTTCTTAATGGGCTGAGGGCTACTTTTCTTAGATCAGGCAACT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGATCA