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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatatctaccgaccgagctttcatcgtgagctggtccttgttctctcgcaagcttattatgacctctggtcttattatacatatatacatggtctctatcagGCTGACCTCGAGGAAGTCAGCGGGCTCTATTTGGATGCCAAATCCTCGGCTCGCCTGCTCCAGGAGCAACAAGAAAGATACATCACCTAGACTTGCATCT

Basic information

species Zea mays
transcript GRMZM2G032267_T02
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G032267_T01 (Zea mays), 3'ss of exon 11
lower sequence: LOC_Os01g62040.2 (Oryza sativa), 3'ss of exon 10
------------------------------gta-tatctaccgaccgagctttcatcgtgagctggtccttgttctctcgcaagcttattatgacctctggtcttattatacatatatacatggtctctatcagGCTGACCTCGAGGAAGTCAGCGGGCTCTATTTGGATGCCAAATCCTCGGCTCGCCTGCTCCAGGAGCAACAAGAAAGATACATCACCTAGACTTGCATCT
                              |||  |||  |    |    |  |  |  |||||| | | ||  ||          ||||||     ||  |||||       |  |  ||||  || || ||||| || || ||||||||||| || || || |||||||| ||||| ||||| || || || |||||||| || |||||||||||||||||   |  | |  
gtatgtattgacatttcatcaggatatattgtaacatcctcttcgcctcttcgctcctagagctgctacctgcacttatattgtgatattattcttacta-tcttacacacggtgaactcatgacctttaccagGCCGATCTTGAGGAAGTCAGTGGTCTGTACTTGGATGCTAAATCGTCGGCGCGTCTCCTTCAGGAGCAGCAGGAAAGATACATCACCTAAGATCTCTTGC

upper sequence: GRMZM2G032267_T01 (Zea mays), 3'ss of exon 11
lower sequence: LOC_Os07g08170.1 (Oryza sativa), 3'ss of exon 11
---------------------------------------------gtatatctaccgaccgagctttcatcgtgagctggtc---cttgttc-tctcgcaagcttattatgacctctggtcttattatacatatatacatggtctctatcagGCTGACCTCGAGGAAGTCAGCGGGCTCTATTTGGATGCCAAATCCTCGGCTCGCCTGCTCCAGGAGCAACAAGAAAGATACATCACCTAGACTTGCATCT
                                                | | | |||   | ||| |    |   |||       ||||||   ||   |   || ||   |  | |     |  |  ||  ||   | || | |  ||||||| || || ||||||||||| |  || |||||||| || ||||| |||||||| || || |||||||| |||| ||||||||| || || | ||   |  
gtatgtgttgaaattccagcaggatattgtaacgtcctcttgttgtcttttttgccgtatgggctatggctggctgctacattcacttgttagcctgatattgttcttgcaagttttatgtatgctgaacccatgaccttgtttttaatcagGCCGATCTTGAGGAAGTCAGTGCTCTGTATTTGGACGCTAAATCATCGGCTCGTCTCCTTCAGGAGCAGCAAGGAAGATACATTACTTAAATTTCTCTTG
















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|32932061|gb|CF036873.1|CF036873
EST:     CACCTGCCAGCGTGGTCGCAAAGACCAACGGGAGAGAAAAGATGTGCAAG                         GCTGACCTCGAGGAAGTCAGCGGGCTCTATTTGGATGCCAAATCCTCGGCT
genomic: CACCTGCCAGCGTGGTCGCAAAGACCAACGGGAGAGAAAAGATGTGCAAGgtatatctac ... tctctatcagGCTGACCTCGAGGAAGTCAGCGGGCTCTATTTGGATGCCAAATCCTCGGCT
EST: gi|4314889|gb|AI444686.2|AI444686
EST:     CACCTGCCAGCGTGGTCGCAAAGACCAACGGGAGAGAAAAGATGTGCAAG                         GCTGACCTCGAGGAAGTCAGCGGGCTCTATTTGGATGCCAAATCCTCGGCT
genomic: CACCTGCCAGCGTGGTCGCAAAGACCAACGGGAGAGAAAAGATGTGCAAGgtatatctac ... tctctatcagGCTGACCTCGAGGAAGTCAGCGGGCTCTATTTGGATGCCAAATCCTCGGCT
EST: gi|60351813|gb|DN218786.1|DN218786
EST:     CACCTGCCAGCGTGGTCGCAAAGACCAACGGGAGAGAAAAGATGTGCAAG                         GCTGACCTCGAGGAAGTCAGCGGGCTCTATTTGGATGCCAAATCCTCGGCT
genomic: CACCTGCCAGCGTGGTCGCAAAGACCAACGGGAGAGAAAAGATGTGCAAGgtatatctac ... tctctatcagGCTGACCTCGAGGAAGTCAGCGGGCTCTATTTGGATGCCAAATCCTCGGCT
EST: gi|4826086|gb|AI667714.1|AI667714
EST:     CACCTGCCAGCGTGGTCGCAAAGACCAACGGGAGAGAAAAGATGTGCAAG                         GCTGACCTCGAGGAAGTCAGCGGGCTCTATTTGGATGCCAAATCCTCGGCT
genomic: CACCTGCCAGCGTGGTCGCAAAGACCAACGGGAGAGAAAAGATGTGCAAGgtatatctac ... tctctatcagGCTGACCTCGAGGAAGTCAGCGGGCTCTATTTGGATGCCAAATCCTCGGCT
EST: gi|21331671|gb|BQ487052.1|BQ487052
EST:     CACCTGCCAGCGTGGTCGCAAAGACCAACGGGAGAGAAAAGATGTGCAAG                         GCTGACCTCGAGGAAGTCAGCGGGCTCTATTTGGATGCCAAATCCTCGGCT
genomic: CACCTGCCAGCGTGGTCGCAAAGACCAACGGGAGAGAAAAGATGTGCAAGgtatatctac ... tctctatcagGCTGACCTCGAGGAAGTCAGCGGGCTCTATTTGGATGCCAAATCCTCGGCT
EST: gi|211496869|gb|FL295227.1|FL295227
EST:     CACCTGCCAGCGTGGTCGCAAAGACCAACGGGAGAGAAAAGATGTGCAAG                         GCTGACCTCGAGGAAGTCAGCGGGCTCTATTTGGATGCCAAATCCTCGGCT
genomic: CACCTGCCAGCGTGGTCGCAAAGACCAACGGGAGAGAAAAGATGTGCAAGgtatatctac ... tctctatcagGCTGACCTCGAGGAAGTCAGCGGGCTCTATTTGGATGCCAAATCCTCGGCT
EST: gi|60358619|gb|DN225592.1|DN225592
EST:     CACCTGCCAGCGTGGTCGCAAAGACCAACGGGAGAGAAAAGATGTGCAAG                         GCTGACCTCGAGGAAGTCAGCGGGCTCTATTTGGATGCCAAATCCTCGGCT
genomic: CACCTGCCAGCGTGGTCGCAAAGACCAACGGGAGAGAAAAGATGTGCAAGgtatatctac ... tctctatcagGCTGACCTCGAGGAAGTCAGCGGGCTCTATTTGGATGCCAAATCCTCGGCT
EST: gi|60347035|gb|DN214008.1|DN214008
EST:     CACCTGCCAGCGTGGTCGCAAAGACCAACGGGAGAGAAAAGATGTGCAAG                         GCTGACCTCGAGGAAGTCAGCGGGCTCTATTTGGATGCCAAATCCTCGGCT
genomic: CACCTGCCAGCGTGGTCGCAAAGACCAACGGGAGAGAAAAGATGTGCAAGgtatatctac ... tctctatcagGCTGACCTCGAGGAAGTCAGCGGGCTCTATTTGGATGCCAAATCCTCGGCT
EST: gi|22819003|gb|BU499093.1|BU499093
EST:     CACCTGCCAGCGTGGTCGCAAAGACCAACGGGAGAGAAAAGATGTGCAAG                         GCTGACCTCGAGGAAGTCAGCGGGCTCTATTTGGATGCCAAATCCTCGGCT
genomic: CACCTGCCAGCGTGGTCGCAAAGACCAACGGGAGAGAAAAGATGTGCAAGgtatatctac ... tctctatcagGCTGACCTCGAGGAAGTCAGCGGGCTCTATTTGGATGCCAAATCCTCGGCT
EST: gi|87157723|gb|DY402512.1|DY402512
EST:     CACCTGCCAGCGTGGTCGCAAAGACCAACGGGAGAGAAAAGATGTGCAAG                         GCTGACCTCGAGGAAGTCAGCGGGCTCTATTTGGATGCCAAATCCTCGGCT
genomic: CACCTGCCAGCGTGGTCGCAAAGACCAACGGGAGAGAAAAGATGTGCAAGgtatatctac ... tctctatcagGCTGACCTCGAGGAAGTCAGCGGGCTCTATTTGGATGCCAAATCCTCGGCT
EST: gi|26559755|gb|CA831990.1|CA831990
EST:     CACCTGCCAGCGTGGTCGCAAAGACCAACGGGAGAGAAAAGATGTGCAAG                         GCTGACCTCGAGGAAGTCAGCGGGCTCTATTTGGATGCCAAATCCTCGGCT
genomic: CACCTGCCAGCGTGGTCGCAAAGACCAACGGGAGAGAAAAGATGTGCAAGgtatatctac ... tctctatcagGCTGACCTCGAGGAAGTCAGCGGGCTCTATTTGGATGCCAAATCCTCGGCT
EST: gi|33096873|gb|CF056833.1|CF056833
EST:     CACCTGCCAGCGTGGTCGCAAAGACCAACGGGAGAGAAAAGATGTGCAAG                         GCTGACCTCGAGGAAGTCAGCGGGCTCTATTTGGATGCCAAATCCTCGGCT
genomic: CACCTGCCAGCGTGGTCGCAAAGACCAACGGGAGAGAAAAGATGTGCAAGgtatatctac ... tctctatcagGCTGACCTCGAGGAAGTCAGCGGGCTCTATTTGGATGCCAAATCCTCGGCT
EST: gi|5670860|gb|AI932123.1|AI932123
EST:     CACCTGCCAGCGTGGTCGCAAAGACCAACGGGAGAGAAAAGATGTGCAAG                         GCTGACCTCGAGGAAGTCAGCGGGCTCTATTTGGATGCCAAATCCTCGGCT
genomic: CACCTGCCAGCGTGGTCGCAAAGACCAACGGGAGAGAAAAGATGTGCAAGgtatatctac ... tctctatcagGCTGACCTCGAGGAAGTCAGCGGGCTCTATTTGGATGCCAAATCCTCGGCT
EST: gi|28983722|gb|BQ538786.2|BQ538786
EST:     CACCTGCCAGCGTGGTCGCAAAGACCAACGGGAGAGAAAAGATGTGCAAG                         GCTGACCTCGAGGAAGTCAGCGGGCTCTATTTGGATGCCAAATCCTCGGCT
genomic: CACCTGCCAGCGTGGTCGCAAAGACCAACGGGAGAGAAAAGATGTGCAAGgtatatctac ... tctctatcagGCTGACCTCGAGGAAGTCAGCGGGCTCTATTTGGATGCCAAATCCTCGGCT
EST: gi|4321073|gb|AI467736.1|AI467736
EST:     CACCTGCCAGCGTGGTCGCAAAGACCAACGGGAGAGAAAAGATGTGCAAG                         GCTGACCTCGAGGAAGTCAGCGGGCTCTATTTGGATGCCAAATCCTCGGCT
genomic: CACCTGCCAGCGTGGTCGCAAAGACCAACGGGAGAGAAAAGATGTGCAAGgtatatctac ... tctctatcagGCTGACCTCGAGGAAGTCAGCGGGCTCTATTTGGATGCCAAATCCTCGGCT
EST: gi|67016264|gb|CO445013.1|CO445013
EST:     CACCTGCCAGCGTGGTCGCAAAGACCAACGGGAGAGAAAAGATGTGCAAG                         GCTGACCTCGAGGAAGTCAGCGGGCTCTATTTGGATGCCAAATCCTCGGCT
genomic: CACCTGCCAGCGTGGTCGCAAAGACCAACGGGAGAGAAAAGATGTGCAAGgtatatctac ... tctctatcagGCTGACCTCGAGGAAGTCAGCGGGCTCTATTTGGATGCCAAATCCTCGGCT
EST: gi|148952636|gb|EC898467.2|EC898467
EST:     CACCTGCCAGCGTGGTCGCAAAGACCAACGGGAGAGAAAAGATGTGCAAG                         GCTGACCTCGAGGAAGTCAGCGGGCTCTATTTGGATGCCAAATCCTCGGCT
genomic: CACCTGCCAGCGTGGTCGCAAAGACCAACGGGAGAGAAAAGATGTGCAAGgtatatctac ... tctctatcagGCTGACCTCGAGGAAGTCAGCGGGCTCTATTTGGATGCCAAATCCTCGGCT
EST: gi|88757068|gb|DY541209.1|DY541209
EST:     CACCTCCCAGCGTGGTGGCAAAGACCAACGGGAGAGAAAAGATGTGCAAG                         GCTGACCTCGAGGAAGTCAGCGGGCTTTATTTGGATGCCAAATCCTCGGTT
genomic: CACCTGCCAGCGTGGTCGCAAAGACCAACGGGAGAGAAAAGATGTGCAAGgtatatctac ... tctctatcagGCTGACCTCGAGGAAGTCAGCGGGCTCTATTTGGATGCCAAATCCTCGGCT
EST: gi|7162558|gb|AW520180.1|AW520180
EST:     CACCTGCCAGCGTGGTCGCAAAGACCAACGGGAGAGAAAAGATGTGCAAG                         GCTGACCTCGAGGAAGTCAGCGGGCTCTATTTGGATGCCAAATCCTCGGCT
genomic: CACCTGCCAGCGTGGTCGCAAAGACCAACGGGAGAGAAAAGATGTGCAAGgtatatctac ... tctctatcagGCTGACCTCGAGGAAGTCAGCGGGCTCTATTTGGATGCCAAATCCTCGGCT
EST: gi|7227451|gb|AW566092.1|AW566092
EST:     CACCTGCCAGCGTGGTCGCAAAGACCAACGGGAGAGAAAAGATGTGCAAG                         GCTGACCTCGAGGAAGTCAGCGGGCTCTATTTGGATGCCAAATCCTCGGCT
genomic: CACCTGCCAGCGTGGTCGCAAAGACCAACGGGAGAGAAAAGATGTGCAAGgtatatctac ... tctctatcagGCTGACCTCGAGGAAGTCAGCGGGCTCTATTTGGATGCCAAATCCTCGGCT
EST: gi|71420713|gb|DR805175.1|DR805175
EST:     CACCTGCCAGCGTGGTCGCAAAGACCAACGGGAGAGAAAAGATGTGCAAG                         GCTGACCTCGAGGAAGTCAGCGGGCTCTATTTGGATGCCAAATCCTCGGCT
genomic: CACCTGCCAGCGTGGTCGCAAAGACCAACGGGAGAGAAAAGATGTGCAAGgtatatctac ... tctctatcagGCTGACCTCGAGGAAGTCAGCGGGCTCTATTTGGATGCCAAATCCTCGGCT

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: 48 (upstream exon), 42 (downstream exon)
Score: 46

ACATGCTATTCAGTTGCTATCACCTGCCAGCGTGGTCGCAAAGACCAACGGGAGAGAAAAGATGTGCAAGgtatatctac ... tctctatcagGCTGACCTCGAGGAAGTCAGCGGGCTCTATTTGGATGCCAAATCCTCGGCTCGCCTGCTCCAGGAGCAACAAGAAAGATACATCACCTAGACTTGCATCT


Block sizes: 45 (upstream exon), 32 (downstream exon)
Score: 3

ACATGCTATTCAGTTGCTATCACCTGCCAGCGTGGTCGCAAAGACCAACGGGAGAGAAAAGATGTGCAAGgtatatctac ... tctctatcagGCTGACCTCGAGGAAGTCAGCGGGCTCTATTTGGATGCCAAATCCTCGGCTCGCCTGCTCCAGGAGCAACAAGAAAGATACATCACCTAGACTTGCATCT


Block sizes: 48 (upstream exon), 44 (downstream exon)
Score: 5

ACATGCTATTCAGTTGCTATCACCTGCCAGCGTGGTCGCAAAGACCAACGGGAGAGAAAAGATGTGCAAGgtatatctac ... tctctatcagGCTGACCTCGAGGAAGTCAGCGGGCTCTATTTGGATGCCAAATCCTCGGCTCGCCTGCTCCAGGAGCAACAAGAAAGATACATCACCTAGACTTGCATCT


Block sizes: 48 (upstream exon), 30 (downstream exon)
Score: 25

ACATGCTATTCAGTTGCTATCACCTGCCAGCGTGGTCGCAAAGACCAACGGGAGAGAAAAGATGTGCAAGgtatatctac ... tctctatcagGCTGACCTCGAGGAAGTCAGCGGGCTCTATTTGGATGCCAAATCCTCGGCTCGCCTGCTCCAGGAGCAACAAGAAAGATACATCACCTAGACTTGCATCT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcaagcttattatgacctctggtcttattatacatatatacatggtctctatcagGCTGACCTCGAGGAAGTCAGCGGGCTCTATTTGGATGCCAAATCCTCGGCTCGCCTGCTCCAGGAGCAACAAGAAAGATACATCACCTAGACTTGCATCT
                                             tctctatc  CT-rich tract
                      tcttattatacatata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatatctaccgaccgagctttcatcgtgagctggtccttgttctctcgcaagcttattatgacctctggtcttattatacatatatacatggtctctatcagGCTGACCTCGAGGAAGTCAGCGGGCTCTATTTGGATGCCAAATCCTCGGCTCGCCTGCTCCAGGAGCAACAAGAAAGATACATCACCTAGACTTGCATCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA