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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacaactttagctgtctcttttggttcttccatttccccattttcagtttctgaaggatgcaagtggaaagtgcagATAGAGGTTGAAGCAGTTGACAGAACAGGAACATTCATAGGTTCGTTGTGGGAGTCCAAGACCAACATGGGCTCTGTACTTCTGGAAGCTGGGCTGGCGA

Basic information

species Zea mays
transcript GRMZM2G136296_T01
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G136296_T01 (Zea mays), 3'ss of exon 12
lower sequence: LOC_Os02g32350.1 (Oryza sativa), 3'ss of exon 11
gtacaactttagctgtctcttttggttcttccatttccccattttcagtttctgaaggatgcaagtggaaagtgcagATAGAGGTTGAAGCAGTTGACAGAACAGGAACATTCATAGGTTCGTTGTGGGAGTCCAAGACCAACATGGGCTCTGTACTTCTGGAAGCTGGGCTGGCGA
|||  ||| | | ||  ||||| ||||  ||||  |||     |||  | ||| ||  || | |   ||   | ||||||||||||||||||||||| ||||| || |||||| ||||||| || ||||||||||| ||||||||||  ||||| |||||||| ||||| ||||| |
gtatgactcttg-tgcatcttt-ggttaatccacctccatggcttcgatgtctaaataataccatgtgattctacagATAGAGGTTGAAGCAGTTGATAGAACTGGGACATTCTTAGGTTCCTTATGGGAGTCCAAAACCAACATGGCTTCTGTTCTTCTGGAGGCTGGTCTGGCCA
















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|211385597|gb|FL201909.1|FL201909
EST:     ATGAAGCTATTGCTTTGATGAGGAGAAGGATACTACAGCGTGATGTGGAG                         ATAGAGGTTGAAGCAGTTGACAGAACAGGAACATTCATAGGTTCGTTGTGG
genomic: ATGAAGCTATTGCTTTGATGAGGAGAAGGATACTACAGCGTGATGTGGAGgtacaacttt ... gaaagtgcagATAGAGGTTGAAGCAGTTGACAGAACAGGAACATTCATAGGTTCGTTGTGG
EST: gi|211483956|gb|FL010659.1|FL010659
EST:     ATTGCTTTGATGAGGAGAAGGATACTACAGCGTGATGTGGAG                         ATAGAGGTTGAAGCAGTTGACAGAACAGGAACATTCATAGGTTCGTTGTGG
genomic: ATTGCTTTGATGAGGAGAAGGATACTACAGCGTGATGTGGAGgtacaacttt ... gaaagtgcagATAGAGGTTGAAGCAGTTGACAGAACAGGAACATTCATAGGTTCGTTGTGG
EST: gi|32841124|gb|CD980805.1|CD980805
EST:     ATGAAGCTATTGCTTTGATGAGGAGAAGGATACTACAGCGTGATGTGGAG                         ATAGAGGTTGAAGCAGTTGACAGAACAGGAACATTCATAGGTTCATTGTGG
genomic: ATGAAGCTATTGCTTTGATGAGGAGAAGGATACTACAGCGTGATGTGGAGgtacaacttt ... gaaagtgcagATAGAGGTTGAAGCAGTTGACAGAACAGGAACATTCATAGGTTCGTTGTGG
EST: gi|29946640|gb|CB816251.1|CB816251
EST:     ATGAAGCTATTGCTTTGATGAGGAGAAGGATACTACAGCGTGATGTGGAG                         ATAGAGGTTGAAGCAGTTGACAGAACAGGAACATTCATAGGTTCGTTGTGG
genomic: ATGAAGCTATTGCTTTGATGAGGAGAAGGATACTACAGCGTGATGTGGAGgtacaacttt ... gaaagtgcagATAGAGGTTGAAGCAGTTGACAGAACAGGAACATTCATAGGTTCGTTGTGG
EST: gi|32932038|gb|CF036850.1|CF036850
EST:     ATGAAGCTATTGCTTTGATGAGGAGAAGGATACTACAGCGTGATGTGGAG                         ATAGAGGTTGAAGCAGTTGACAGAACAGGAACATTCATAGGTTCATTGTGG
genomic: ATGAAGCTATTGCTTTGATGAGGAGAAGGATACTACAGCGTGATGTGGAGgtacaacttt ... gaaagtgcagATAGAGGTTGAAGCAGTTGACAGAACAGGAACATTCATAGGTTCGTTGTGG
EST: gi|67011396|gb|CO440145.1|CO440145
EST:     ATGAAGCTATTGCTTTGATGAGGAGAAGGATACTACAGCGTGATGTGGAG                         ATAGAGGTTGAAGCAGTTGACAGAACAGGAACATTCATAGGTTCGTTGTGG
genomic: ATGAAGCTATTGCTTTGATGAGGAGAAGGATACTACAGCGTGATGTGGAGgtacaacttt ... gaaagtgcagATAGAGGTTGAAGCAGTTGACAGAACAGGAACATTCATAGGTTCGTTGTGG
EST: gi|211388224|gb|FL201917.1|FL201917
EST:     ATGAAGCTATTGCTTTGATGAGGAGAAGGATACTACAGCGTGATGTGGAG                         ATAGAGGTTGAAGCAGTTGACAGAACAGGAACATTCATAGGTTCGTTGTGG
genomic: ATGAAGCTATTGCTTTGATGAGGAGAAGGATACTACAGCGTGATGTGGAGgtacaacttt ... gaaagtgcagATAGAGGTTGAAGCAGTTGACAGAACAGGAACATTCATAGGTTCGTTGTGG
EST: gi|211388220|gb|FL201913.1|FL201913
EST:     ATGAAGCTATTGCTTTGATGAGGAGAAGGATACTACAGCGTGATGTGGAG                         ATAGAGGTTGAAGCAGTTGACAGAACAGGAACATTCATAGGTTCGTTGTGG
genomic: ATGAAGCTATTGCTTTGATGAGGAGAAGGATACTACAGCGTGATGTGGAGgtacaacttt ... gaaagtgcagATAGAGGTTGAAGCAGTTGACAGAACAGGAACATTCATAGGTTCGTTGTGG
EST: gi|211388219|gb|FL201912.1|FL201912
EST:     ATGAAGCTATTGCTTTGATGAGGAGAAGGATACTACAGCGTGATGTGGAG                         ATAGAGGTTGAAGCAGTTGACAGAACAGGAACATTCATAGGTTCGTTGTGG
genomic: ATGAAGCTATTGCTTTGATGAGGAGAAGGATACTACAGCGTGATGTGGAGgtacaacttt ... gaaagtgcagATAGAGGTTGAAGCAGTTGACAGAACAGGAACATTCATAGGTTCGTTGTGG
EST: gi|67040223|gb|CO466478.1|CO466478
EST:     ATGAAGCTATTGCTTTGATGAGGAGAAGGATACTACAGCGTGATGTGGAG                         ATAGAGGTTGAAGCAGTTGACAGAACAGGAACATTCATAGGTTCGTTGTGG
genomic: ATGAAGCTATTGCTTTGATGAGGAGAAGGATACTACAGCGTGATGTGGAGgtacaacttt ... gaaagtgcagATAGAGGTTGAAGCAGTTGACAGAACAGGAACATTCATAGGTTCGTTGTGG
EST: gi|211388221|gb|FL201914.1|FL201914
EST:     ATTGCTTTGATGAGGAGAAGGATACTACAGCGTGATGTGGAG                         ATAGAGGTTGAAGCAGTTGACAGAACAGGAACATTCATAGGTTCGTTGTGG
genomic: ATTGCTTTGATGAGGAGAAGGATACTACAGCGTGATGTGGAGgtacaacttt ... gaaagtgcagATAGAGGTTGAAGCAGTTGACAGAACAGGAACATTCATAGGTTCGTTGTGG
EST: gi|211388222|gb|FL201915.1|FL201915
EST:     ATGAAGCTATTGCTTTGATGAGGAGAAGGATACTACAGCGTGATGTGGAG                         ATAGAGGTTGAAGCAGTTGACAGAACAGGAACATTCATAGGTTCG
genomic: ATGAAGCTATTGCTTTGATGAGGAGAAGGATACTACAGCGTGATGTGGAGgtacaacttt ... gaaagtgcagATAGAGGTTGAAGCAGTTGACAGAACAGGAACATTCATAGGTTCG
EST: gi|211385595|gb|FL201907.1|FL201907
EST:     ATGAAGCTATTGCTTTGATGAGGAGAAGGATACTACAGCGTGATGTGGAG                         ATAGAGGTTGAAGCAGTTGACAGAACAGGAACATTCATAGGTTCGTTGTGG
genomic: ATGAAGCTATTGCTTTGATGAGGAGAAGGATACTACAGCGTGATGTGGAGgtacaacttt ... gaaagtgcagATAGAGGTTGAAGCAGTTGACAGAACAGGAACATTCATAGGTTCGTTGTGG
EST: gi|60394760|gb|DN227630.1|DN227630
EST:     ATGAAGCTATTGCTTTGATGAGGAGAAGGATACTACAGCGTGATGTGGAG                         ATAGAGGTTGAAGCAGTTGACAGAACAGGAACATTCATAGGTTCGTTGTGG
genomic: ATGAAGCTATTGCTTTGATGAGGAGAAGGATACTACAGCGTGATGTGGAGgtacaacttt ... gaaagtgcagATAGAGGTTGAAGCAGTTGACAGAACAGGAACATTCATAGGTTCGTTGTGG
EST: gi|211483958|gb|FL010661.1|FL010661
EST:     ATTGCTTTGATGAGGAGAAGGATACTACAGCGTGATGTGGAG                         ATAGAGGTTGAAGCAGTTGACAGAACAGGAACATTCATAGGTTCGTTGTGG
genomic: ATTGCTTTGATGAGGAGAAGGATACTACAGCGTGATGTGGAGgtacaacttt ... gaaagtgcagATAGAGGTTGAAGCAGTTGACAGAACAGGAACATTCATAGGTTCGTTGTGG

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: 158

CTTCTCATTATCTGGTGTTCGGTGTCCTGGTAAAGGCGAGCCATACTCAGATGAAGCTATTGCTTTGATGAGGAGAAGGATACTACAGCGTGATGTGGAGgtacaacttt ... gaaagtgcagATAGAGGTTGAAGCAGTTGACAGAACAGGAACATTCATAGGTTCGTTGTGGGAGTCCAAGACCAACATGGGCTCTGTACTTCTGGAAGCTGGGCTGGCGA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 177

CTTCTCATTATCTGGTGTTCGGTGTCCTGGTAAAGGCGAGCCATACTCAGATGAAGCTATTGCTTTGATGAGGAGAAGGATACTACAGCGTGATGTGGAGgtacaacttt ... gaaagtgcagATAGAGGTTGAAGCAGTTGACAGAACAGGAACATTCATAGGTTCGTTGTGGGAGTCCAAGACCAACATGGGCTCTGTACTTCTGGAAGCTGGGCTGGCGA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 157

CTTCTCATTATCTGGTGTTCGGTGTCCTGGTAAAGGCGAGCCATACTCAGATGAAGCTATTGCTTTGATGAGGAGAAGGATACTACAGCGTGATGTGGAGgtacaacttt ... gaaagtgcagATAGAGGTTGAAGCAGTTGACAGAACAGGAACATTCATAGGTTCGTTGTGGGAGTCCAAGACCAACATGGGCTCTGTACTTCTGGAAGCTGGGCTGGCGA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 354

CTTCTCATTATCTGGTGTTCGGTGTCCTGGTAAAGGCGAGCCATACTCAGATGAAGCTATTGCTTTGATGAGGAGAAGGATACTACAGCGTGATGTGGAGgtacaacttt ... gaaagtgcagATAGAGGTTGAAGCAGTTGACAGAACAGGAACATTCATAGGTTCGTTGTGGGAGTCCAAGACCAACATGGGCTCTGTACTTCTGGAAGCTGGGCTGGCGA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tggttcttccatttccccattttcagtttctgaaggatgcaagtggaaagtgcagATAGAGGTTGAAGCAGTTGACAGAACAGGAACATTCATAGGTTCGTTGTGGGAGTCCAAGACCAACATGGGCTCTGTACTTCTGGAAGCTGGGCTGGCGA
                  attttca  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacaactttagctgtctcttttggttcttccatttccccattttcagtttctgaaggatgcaagtggaaagtgcagATAGAGGTTGAAGCAGTTGACAGAACAGGAACATTCATAGGTTCGTTGTGGGAGTCCAAGACCAACATGGGCTCTGTACTTCTGGAAGCTGGGCTGGCGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG