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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AAACAAAGGCCTCTACTGATTGTTGCAGAAGATGTGGAAAGTGAAGCATTAGGTACTCTGATTATTAACAAGCTTCGTGCAGGCATCAAGgtaggttctgtcaagtttctctgtttggtaccatttctgttctaattggaacaacattcag

Basic information

species Zea mays
transcript GRMZM2G416120_T01
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G416120_T01 (Zea mays), 5'ss of exon 8
lower sequence: LOC_Os10g32550.1 (Oryza sativa), 5'ss of exon 9
AAACAAAGGCCTCTACTGATTGTTGCAGAAGATGTGGAAAGTGAAGCATTAGGTACTCTGATTATTAACAAGCTTCGTGCAGGCATCAAGgtaggttc-tgtcaagtttctctgtttggtacc---atttctgttctaattggaa----caacattcag
|| ||||||||||| ||||||||||| |||||||| || || || ||||| |||||||||||||||||||||||||||||||||||||||||  ||   |     |  | | || || | | |    |   ||| |||| ||            |||||
AAGCAAAGGCCTCTGCTGATTGTTGCTGAAGATGTAGAGAGCGAGGCATTGGGTACTCTGATTATTAACAAGCTTCGTGCAGGCATCAAGgtcagtaaatactgggcatttgtgatttgaatctgtgtagttgtcctaaatgagggatgtgttgttcag

upper sequence: GRMZM2G416120_T01 (Zea mays), 5'ss of exon 8
lower sequence: GLYMA10G33680.1 (Glycine max), 5'ss of exon 9
AAACAAAGGCCTCTACTGATTGTTGCAGAAGATGTGGAAAGTGAAGCATTAGGTACTCTGATTATTAACAAGCTTCGTGCAGGCATCAAGgtaggttctgtcaa------gtttctctgtttggtaccatttctgttctaattggaacaacattcag---------------
| |||||||||| |||||||||| || || |||||||||||||| ||  | |  ||||| ||| | || || |||||||| || |||||||| |||| || | |      ||||  |  ||| || |     |   |  ||||     | | || |                
AGACAAAGGCCTTTACTGATTGTCGCTGAGGATGTGGAAAGTGATGCCCTTGCAACTCTTATTCTAAATAAACTTCGTGCTGGAATCAAGgttggttttgcctatctgtagttttacattttagttcttaggcgcattaaatttttggatcgttgatttttctgtcctttag

upper sequence: GRMZM2G416120_T01 (Zea mays), 5'ss of exon 8
lower sequence: Vv05s0051g00340.t01 (Vitis vinifera), 5'ss of exon 9
AAACAAAGGCCTCTACTGATTGTTGCAGAAGATGTGGAAAGTGAAGCATTAGGTACTCTGATTATTAACAAGCTTCGTGCAGGCATCAAGgtaggttctgtc----------------aagtttctctgtttggtaccatttctgttctaattggaaca---acattcag------------------------------------
|  || |||||| ||||||||||||| |||||||||||||| |||||| | |  ||||| ||| | || ||||||||||| || ||||||||||||  |||                 | || | | | | |   |  |||||| || |||||  |  |   | ||  |                                     
ACTCAGAGGCCTTTACTGATTGTTGCTGAAGATGTGGAAAGCGAAGCACTGGCCACTCTTATTCTAAATAAGCTTCGTGCTGGAATCAAGgtaggtgttgtttctttagatacagataatgtatttttatgttaaattatttctcttttaattaaaggatttatatataatttggatcttatatggattgtgcattatctctaaag

upper sequence: GRMZM2G416120_T01 (Zea mays), 5'ss of exon 8
lower sequence: PP1S378_9V6.2 (Physcomitrella patens), 5'ss of exon 9
AAACAAAGGCCTCTACTGATTGTTGCAGAAGATGTGGAAAGTGAAGCATTAGGTACTCTGATTATTAACAAGCTTCGTGCAGGCATCAAGgtaggtt-----ctgtcaagtttctctgtttggtaccatt---tctgttctaa-ttggaacaacattcag------------------------------
 | ||||||||||| ||||||||||| |||||||||||||||||||| || | ||| |||||  | || |||||| | |  ||  | |||||| |||     |  |    || || | |||  ||   |    | ||  ||    ||| | ||   ||                                
GATCAAAGGCCTCTCCTGATTGTTGCTGAAGATGTGGAAAGTGAAGCTTTGGCTACGCTGATAGTCAATAAGCTTAGGGGTGGTGTGAAGgtatgttaacagccattgtattcctttttttcctagtttggggtttgcgctgggctgggataaatctccttcgacgtagtaatagttcaaaggatgacca

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|50328354|gb|CO523480.1|CO523480
EST:     GTGAAGCATTAGGTACTCTGATTATTAACAAGCTTCGTGCAGGCATCAAG                         GTCTGTGCTGTCAAAGCTCCTGGTTTTGGGGAAAACAGGAAGGCAAACTTA
genomic: GTGAAGCATTAGGTACTCTGATTATTAACAAGCTTCGTGCAGGCATCAAGgtaggttctg ... caacattcagGTCTGTGCTGTCAAAGCTCCTGGTTTTGGGGAAAACAGGAAGGCAAACTTA
EST: gi|31349659|gb|CD434016.1|CD434016
EST:     GTGAAGCATTGGGTACTCTGATTATTAACAAGCTTCGTGCAGGCATCTCG                         GTCTGTGCTGTCAAAGCTCCTGGTTTTGGGGAAAACAGGAAGGCAAACTTA
genomic: GTGAAGCATTAGGTACTCTGATTATTAACAAGCTTCGTGCAGGCATCAAGgtaggttctg ... caacattcagGTCTGTGCTGTCAAAGCTCCTGGTTTTGGGGAAAACAGGAAGGCAAACTTA
EST: gi|71425566|gb|DR806758.1|DR806758
EST:     GTGAAGCATTAGGTACTCTGATTATTAACAAGCTTCGTGCAGGCATCAAG                         GTCTGTGCTGTCAAAGCTCCTGGTTTTGGGGAAAACAGGAAGGCAAACTTA
genomic: GTGAAGCATTAGGTACTCTGATTATTAACAAGCTTCGTGCAGGCATCAAGgtaggttctg ... caacattcagGTCTGTGCTGTCAAAGCTCCTGGTTTTGGGGAAAACAGGAAGGCAAACTTA
EST: gi|78078493|gb|DV506906.1|DV506906
EST:     GTGAAGCATTAGGTACTCTGATTATTAACAAGCTTCGTGCAGGCATCAAG                         GTCTGTGCTGTCAAAGCTCCTGGTTTTGGGGAAAACAGGAAGGCAAACTTA
genomic: GTGAAGCATTAGGTACTCTGATTATTAACAAGCTTCGTGCAGGCATCAAGgtaggttctg ... caacattcagGTCTGTGCTGTCAAAGCTCCTGGTTTTGGGGAAAACAGGAAGGCAAACTTA
EST: gi|32929020|gb|CF033832.1|CF033832
EST:     ACTCTGATTATTAACAAGCTTCGTGCAGGCATCAAG                         GTCTGTGCTGTCAAAGCTCCTGGTTTTGGGGAAAACAGGAAGGCAAACTTA
genomic: ACTCTGATTATTAACAAGCTTCGTGCAGGCATCAAGgtaggttctg ... caacattcagGTCTGTGCTGTCAAAGCTCCTGGTTTTGGGGAAAACAGGAAGGCAAACTTA
EST: gi|18450761|gb|BM429039.1|BM429039
EST:     GTGAAGCATTAGGTACTCTGATTATTAACAAGCTTCGTGCAGGCATCAAG                         GTCTGTGCTGTCAAAGCTCCTGGTTTTGGGGAAAACAGGAAGGCAAACTTA
genomic: GTGAAGCATTAGGTACTCTGATTATTAACAAGCTTCGTGCAGGCATCAAGgtaggttctg ... caacattcagGTCTGTGCTGTCAAAGCTCCTGGTTTTGGGGAAAACAGGAAGGCAAACTTA
EST: gi|87152342|gb|DY397131.1|DY397131
EST:     GTGAAGCATTAGGTACTCTGATTATTAACAAGCTTCGTGCAGGCATCAAG                         GTCTGTGCTGTCAAAGCTCCTGGTTTTGGGGAAAACAGGAAGGCAAACTTA
genomic: GTGAAGCATTAGGTACTCTGATTATTAACAAGCTTCGTGCAGGCATCAAGgtaggttctg ... caacattcagGTCTGTGCTGTCAAAGCTCCTGGTTTTGGGGAAAACAGGAAGGCAAACTTA
EST: gi|32944170|gb|CF048989.1|CF048989
EST:     ACTCTGATTATTAACAAGCTTCGTGCAGGCATCAAG                         GTCTGTGCTGTCAAAGCTCCTGGTTTTGGGGAAAACAGGAAGGCAAACTTA
genomic: ACTCTGATTATTAACAAGCTTCGTGCAGGCATCAAGgtaggttctg ... caacattcagGTCTGTGCTGTCAAAGCTCCTGGTTTTGGGGAAAACAGGAAGGCAAACTTA
EST: gi|32932633|gb|CF037445.1|CF037445
EST:     GTGCAGCATTAGGTACTCTGATTATTAACAAGCTTCGTGCAGGCATCAAG                         GTCTGTGCTGTCAAAGCTCCTGGTTTTGGGGAAAACAGGAAGGCAAACTTA
genomic: GTGAAGCATTAGGTACTCTGATTATTAACAAGCTTCGTGCAGGCATCAAGgtaggttctg ... caacattcagGTCTGTGCTGTCAAAGCTCCTGGTTTTGGGGAAAACAGGAAGGCAAACTTA
EST: gi|67019174|gb|CO447923.1|CO447923
EST:     GTGAAGCATTGGGTACTCTGATTAT-AACAAGCTTCGTGCAGGCATCAAG                         GTCTGTGCTGTCAAAGCTCCTGGTTTTGGGGAAAACANGAAGGCANACTTA
genomic: GTGAAGCATTAGGTACTCTGATTATTAACAAGCTTCGTGCAGGCATCAAGgtaggttctg ... caacattcagGTCTGTGCTGTCAAAGCTCCTGGTTTTGGGGAAAACAGGAAGGCAAACTTA
EST: gi|32931719|gb|CF036531.1|CF036531
EST:     AGGTACTCTGATTATTAACAAGCTTCGTGCAGGCATCAAG                         GTCTGTGCTGTCAAAGCTCCTGGTTTTGGGGAAAACAGGAAGGCAAACTTA
genomic: AGGTACTCTGATTATTAACAAGCTTCGTGCAGGCATCAAGgtaggttctg ... caacattcagGTCTGTGCTGTCAAAGCTCCTGGTTTTGGGGAAAACAGGAAGGCAAACTTA
EST: gi|33103385|gb|CF063345.1|CF063345
EST:     ACTCTGATTATTAACAAGCTTCGTGCAGGCATCAAG                         GTCTGTGCTGTCAAAGCTCCTGGTTTTGGGGAAAACAGGAAGGCAAACTTA
genomic: ACTCTGATTATTAACAAGCTTCGTGCAGGCATCAAGgtaggttctg ... caacattcagGTCTGTGCTGTCAAAGCTCCTGGTTTTGGGGAAAACAGGAAGGCAAACTTA
EST: gi|22489874|gb|BU049797.1|BU049797
EST:     GTGAAGCATTAGGTACTCTGATTATTAACAAGCTTCGTGCAGGCATCAAG                         GTCTGTGCTGTCAAAGCTCCTGGTTTTGGGGAAAACAGGAAGGCAAACTTA
genomic: GTGAAGCATTAGGTACTCTGATTATTAACAAGCTTCGTGCAGGCATCAAGgtaggttctg ... caacattcagGTCTGTGCTGTCAAAGCTCCTGGTTTTGGGGAAAACAGGAAGGCAAACTTA

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: 258

AAACAAAGGCCTCTACTGATTGTTGCAGAAGATGTGGAAAGTGAAGCATTAGGTACTCTGATTATTAACAAGCTTCGTGCAGGCATCAAGgtaggttctg ... caacattcagGTCTGTGCTGTCAAAGCTCCTGGTTTTGGGGAAAACAGGAAGGCAAACTTACAGGACCTCGCTATCCTTACCGGAGGAGAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 114

AAACAAAGGCCTCTACTGATTGTTGCAGAAGATGTGGAAAGTGAAGCATTAGGTACTCTGATTATTAACAAGCTTCGTGCAGGCATCAAGgtaggttctg ... caacattcagGTCTGTGCTGTCAAAGCTCCTGGTTTTGGGGAAAACAGGAAGGCAAACTTACAGGACCTCGCTATCCTTACCGGAGGAGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 101

AAACAAAGGCCTCTACTGATTGTTGCAGAAGATGTGGAAAGTGAAGCATTAGGTACTCTGATTATTAACAAGCTTCGTGCAGGCATCAAGgtaggttctg ... caacattcagGTCTGTGCTGTCAAAGCTCCTGGTTTTGGGGAAAACAGGAAGGCAAACTTACAGGACCTCGCTATCCTTACCGGAGGAGAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 180

AAACAAAGGCCTCTACTGATTGTTGCAGAAGATGTGGAAAGTGAAGCATTAGGTACTCTGATTATTAACAAGCTTCGTGCAGGCATCAAGgtaggttctg ... caacattcagGTCTGTGCTGTCAAAGCTCCTGGTTTTGGGGAAAACAGGAAGGCAAACTTACAGGACCTCGCTATCCTTACCGGAGGAGAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AAACAAAGGCCTCTACTGATTGTTGCAGAAGATGTGGAAAGTGAAGCATTAGGTACTCTGATTATTAACAAGCTTCGTGCAGGCATCAAGgtaggttctgtcaagtttctctgtttggtaccatttctgttctaattggaacaacattcag

- - - - - - - - - - - - - - - - - - - -  TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT