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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gattgtgctcgtacaggcatgccttctatttgttccttccatactgagtatccgcttaagatggagatattgattctaacttttgaactctgaatcacagGCTGAGGGTGCCATCATGGCTCTGAATTGCAGCGGGATGATTTTGGGAACACTGCCTGTCAG

Basic information

species Zea mays
transcript GRMZM2G051043_T01
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G051043_T01 (Zea mays), 3'ss of exon 8
lower sequence: LOC_Os01g11120.1 (Oryza sativa), 3'ss of exon 8
-----------------------------------------gattgtgctcgta-caggcatgccttctatttg---ttccttccatactgagtatccgcttaagatggagat---------attgattctaacttt---tgaactctg--aatcacagGCTGAGGGTGCCATCATGGCTCTGAATTGCAGCGGGATGATTTTGGGAACACTGCCTGTCAG
                                          |||   || ||| |      ||  | ||  ||   || ||  ||  |    |  | |   ||  |    ||         |||||||| |  |||   | | |||||  || | ||||| ||| ||||||||||||||||||||||||| |||||||||||||| ||||||||||||||
gtaagaactaagggcctttgcattgcttatatttcaatataaatttacctagtagcttatcagctatttacctggagttactggcacgcgactttgctgaccaaagtcatcatgaacaaataattgattccatttttaactaagctctgtcaaccgcagGCCGAGTGTGCCATCATGGCTCTGAATTGCAGTGGGATGATTTTGGGTACACTGCCTGTCAG
















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|5058613|gb|AI737089.1|AI737089
EST:     TAGGGGATAATGTACATTCCACAAGGATTGCTTTTGTTGAATTTGTCCAT                         GCTGAGGGTGCCATCATGGCTCTGAATTGCAGCGGGATGATTTTGGGAACA
genomic: TAGGGGATAATGTACATTCCACAAGGATTGCTTTTGTTGAATTTGTCCATgtaagaacaa ... tgaatcacagGCTGAGGGTGCCATCATGGCTCTGAATTGCAGCGGGATGATTTTGGGAACA
EST: gi|4609957|gb|AI600796.1|AI600796
EST:     AGGATTGCTTTTGTTGAATTTGTCCAT                         GCTGAGGGTGCCATCATGGCTCTGAATTGCAGCGGGATGATTTTGGGAACA
genomic: AGGATTGCTTTTGTTGAATTTGTCCATgtaagaacaa ... tgaatcacagGCTGAGGGTGCCATCATGGCTCTGAATTGCAGCGGGATGATTTTGGGAACA
EST: gi|78180075|gb|DV550448.1|DV550448
EST:     TAGGGGATAATGTACATTCCACAAGGATTGCTTTTGTTGAATTTGTCCAT                         GCTGAGGGTGCCATCATG
genomic: TAGGGGATAATGTACATTCCACAAGGATTGCTTTTGTTGAATTTGTCCATgtaagaacaa ... tgaatcacagGCTGAGGGTGCCATCATG
EST: gi|37392334|gb|CF633416.1|CF633416
EST:     TAGGGGATAATGTACATTCCACAAGGATTGCTTTTGTTGAATTTGTCCAT                         GCTGAGGGTGCCATCATGGCTCTGAATTGCAGCGGGATGATATTGGGAACA
genomic: TAGGGGATAATGTACATTCCACAAGGATTGCTTTTGTTGAATTTGTCCATgtaagaacaa ... tgaatcacagGCTGAGGGTGCCATCATGGCTCTGAATTGCAGCGGGATGATTTTGGGAACA
EST: gi|32836018|gb|CD975696.1|CD975696
EST:     ACATTCCACAAGGATTGCTTTTGTTGAATTTGTCCAT                         GCTGAGGGTGCCATCATGGCTCTGAATTGCAGCGGGATGATTTTGGGAACA
genomic: ACATTCCACAAGGATTGCTTTTGTTGAATTTGTCCATgtaagaacaa ... tgaatcacagGCTGAGGGTGCCATCATGGCTCTGAATTGCAGCGGGATGATTTTGGGAACA
EST: gi|78106612|gb|DV525030.1|DV525030
EST:     TAGGGGATAATGTACATTCCACAAGGATTGCTTTTGTTGAATTTGTCCAT                         GCTGAGGGTGCCATCATGGCTCTGAATTGCAGCGGGATGATTTTGGGAACA
genomic: TAGGGGATAATGTACATTCCACAAGGATTGCTTTTGTTGAATTTGTCCATgtaagaacaa ... tgaatcacagGCTGAGGGTGCCATCATGGCTCTGAATTGCAGCGGGATGATTTTGGGAACA
EST: gi|61236519|gb|DN586269.1|DN586269
EST:     TAGGGGATAATGTACATTCCACAAGGATTGCTTTTGTTGAATTTGTCCAT                         GCTGAGGGTGCCATCATGGCTCTGAATTGCAGCGGGATGATTTTGGGAACA
genomic: TAGGGGATAATGTACATTCCACAAGGATTGCTTTTGTTGAATTTGTCCATgtaagaacaa ... tgaatcacagGCTGAGGGTGCCATCATGGCTCTGAATTGCAGCGGGATGATTTTGGGAACA
EST: gi|12046008|gb|BF728043.1|BF728043
EST:     TAGGGGATAATGTACATTCCACAAGGATTGCTTTTGTTGAATTTGTCCAT                         GCTGAGGGTGCCATCATGGCTCTGAATTGCAGCGGGATGATTTTGGGAACA
genomic: TAGGGGATAATGTACATTCCACAAGGATTGCTTTTGTTGAATTTGTCCATgtaagaacaa ... tgaatcacagGCTGAGGGTGCCATCATGGCTCTGAATTGCAGCGGGATGATTTTGGGAACA
EST: gi|28983351|gb|BQ538610.2|BQ538610
EST:     TAGGGGATAATGTACATTCCACAAGGATTGCTTTTGTTGAATTTGTCCAT                         GCTGAGGGTGCCATCATGGCTCTGAATTGCAGCGGGATGATTTTGGGAACA
genomic: TAGGGGATAATGTACATTCCACAAGGATTGCTTTTGTTGAATTTGTCCATgtaagaacaa ... tgaatcacagGCTGAGGGTGCCATCATGGCTCTGAATTGCAGCGGGATGATTTTGGGAACA
EST: gi|38502629|gb|CF972489.1|CF972489
EST:     TAGGGGATAATGTACATTCCACAAGGATTGCTTTTGTTGAATTTGTCCAT                         GCTGAGGGTGCCATCATGGCTCTGAATTGCAGCGGGATGATTTTGGGAAC-
genomic: TAGGGGATAATGTACATTCCACAAGGATTGCTTTTGTTGAATTTGTCCATgtaagaacaa ... tgaatcacagGCTGAGGGTGCCATCATGGCTCTGAATTGCAGCGGGATGATTTTGGGAACA
EST: gi|33771172|gb|CF272833.1|CF272833
EST:     TAGGGGATAATGTACATTCCACAAGGATTGCTTTTGTTGAATTTGTCCGT                         GCTGAGGGTGCCATCATGGCTCTGA
genomic: TAGGGGATAATGTACATTCCACAAGGATTGCTTTTGTTGAATTTGTCCATgtaagaacaa ... tgaatcacagGCTGAGGGTGCCATCATGGCTCTGA
EST: gi|4804027|gb|AI665893.1|AI665893
EST:     AGGATTGCTTTTGTTGAATTTGTCCAT                         GCTGAGGGTGCCATCATGGCTTTGAATTGCAGCGGGATGATTTTGGGAACA
genomic: AGGATTGCTTTTGTTGAATTTGTCCATgtaagaacaa ... tgaatcacagGCTGAGGGTGCCATCATGGCTCTGAATTGCAGCGGGATGATTTTGGGAACA
EST: gi|211050111|gb|FL461721.1|FL461721
EST:     GATAATGTACATTCCACAAGGATTGCTTTTGTTGAATTTGTCCAT                         GCTGAGGGTGCCATCATGGCTCTGAATTGCAGCGGGATGATTTTGGGAACA
genomic: GATAATGTACATTCCACAAGGATTGCTTTTGTTGAATTTGTCCATgtaagaacaa ... tgaatcacagGCTGAGGGTGCCATCATGGCTCTGAATTGCAGCGGGATGATTTTGGGAACA
EST: gi|109179585|gb|EC380089.1|EC380089
EST:     GGGATAATGTACATTCCACAAGGATTGCTTTTGTTGAATTTGTCCAT                         GCTGAGGGTGCCATCATGGCTCTGAATTGCAGCGGGATGATTTTGGGAACA
genomic: GGGATAATGTACATTCCACAAGGATTGCTTTTGTTGAATTTGTCCATgtaagaacaa ... tgaatcacagGCTGAGGGTGCCATCATGGCTCTGAATTGCAGCGGGATGATTTTGGGAACA
EST: gi|6827432|gb|AW331075.1|AW331075
EST:     TAGGGGATAATGTACATTCCACAAGGATTGCTTTTGNTGAATTTGTCCAT                         GCTGAGGGTGCCATCATGGCTCTGAATTGCAGCGGGATGATTTTGGGAACA
genomic: TAGGGGATAATGTACATTCCACAAGGATTGCTTTTGTTGAATTTGTCCATgtaagaacaa ... tgaatcacagGCTGAGGGTGCCATCATGGCTCTGAATTGCAGCGGGATGATTTTGGGAACA

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: 46 (upstream exon), 46 (downstream exon)
Score: 77

GTCTCTCGGTTGAGGCTTCTAGGGGATAATGTACATTCCACAAGGATTGCTTTTGTTGAATTTGTCCATgtaagaacaa ... tgaatcacagGCTGAGGGTGCCATCATGGCTCTGAATTGCAGCGGGATGATTTTGGGAACACTGCCTGTCAG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 108

GTCTCTCGGTTGAGGCTTCTAGGGGATAATGTACATTCCACAAGGATTGCTTTTGTTGAATTTGTCCATgtaagaacaa ... tgaatcacagGCTGAGGGTGCCATCATGGCTCTGAATTGCAGCGGGATGATTTTGGGAACACTGCCTGTCAG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 177

GTCTCTCGGTTGAGGCTTCTAGGGGATAATGTACATTCCACAAGGATTGCTTTTGTTGAATTTGTCCATgtaagaacaa ... tgaatcacagGCTGAGGGTGCCATCATGGCTCTGAATTGCAGCGGGATGATTTTGGGAACACTGCCTGTCAG


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

GTCTCTCGGTTGAGGCTTCTAGGGGATAATGTACATTCCACAAGGATTGCTTTTGTTGAATTTGTCCATgtaagaacaa ... tgaatcacagGCTGAGGGTGCCATCATGGCTCTGAATTGCAGCGGGATGATTTTGGGAACACTGCCTGTCAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gagtatccgcttaagatggagatattgattctaacttttgaactctgaatcacagGCTGAGGGTGCCATCATGGCTCTGAATTGCAGCGGGATGATTTTGGGAACACTGCCTGTCAG
                            ttctaac  putative branch site (score: 140)
                     atattgatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gattgtgctcgtacaggcatgccttctatttgttccttccatactgagtatccgcttaagatggagatattgattctaacttttgaactctgaatcacagGCTGAGGGTGCCATCATGGCTCTGAATTGCAGCGGGATGATTTTGGGAACACTGCCTGTCAG

- -tgtgctc
- - - - - - - -ggcatgc
- - - - - - - - - - - - - - - tgttcct
- - - - - - - - - - - - - - - - - - - -catactg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgattct