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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atatcatttcatgcacttgatctgtacctttgacatttgtagcataccttctagtttcttttactttatggggtcatcttacatgaatttgggtttctagGATGGATATTGACTACTCACCAACAGGGCGTGAATTTGTCACTGGTTCATATGATAGAACA

Basic information

species Zea mays
transcript GRMZM2G590033_T01
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G590033_T01 (Zea mays), 3'ss of exon 12
lower sequence: LOC_Os01g13730.1 (Oryza sativa), 3'ss of exon 12
-atatcatttcatgcacttgatctgtacctttgacatttgtagcatacctt-ctagtttcttttactttatggggtcatcttacatgaatttgggtttctagGATGGATATTGACTACTCACCAACAGGGCGTGAATTTGTCACTGGTTCATATGATAGAACA
 ||      | |   |    ||             || |   ||||   || ||| | |  || | | |  |  ||||| |||||||||  |   ||   |||||||| ||||| || ||||||||||||||||||||||| || ||||| || |||||||||
catgcagagtta-atatcccatgcaatttcccattatatcctgcatcttttgctactcttcttgattctgggaagtcattttacatgaacgttc-ttcacagGATGGACATTGATTATTCACCAACAGGGCGTGAATTTGTTACGGGTTCCTACGATAGAACA

upper sequence: GRMZM2G590033_T01 (Zea mays), 3'ss of exon 12
lower sequence: GLYMA14G07070.1 (Glycine max), 3'ss of exon 12
atatcatttcatgcacttgatctgtacctttgacatttgtagcataccttctagtttcttttactttatggggtcatcttacatgaatttgggtttctagGATGGATATTGACTACTCACCAACAGGGCGTGAATTTGTCACTGGTTCATATGATAGAACA
                 | |   ||   ||  | |  | | ||||   |  || ||   |  | | |||     |  | |   |  ||||   | |  ||||||||| |||||||||||||||| || || || |||||||||||||| ||||||||||||
----------------gtaagaagttttttctataaatattgcatttttggtaattc--tagaatgtatcatacctgcatttttatatttcattctacagGATGGATGTTGACTACTCACCAACTGGACGAGAGTTTGTCACTGGTTCTTATGATAGAACA

upper sequence: GRMZM2G590033_T01 (Zea mays), 3'ss of exon 12
lower sequence: GLYMA02G41900.1 (Glycine max), 3'ss of exon 12
atatcatttcatgcacttgatctgtacctttgacatttgtagcataccttctagtttcttttactttatggggtcatcttacatgaatttgggtttctagGATGGATATTGACTACTCACCAACAGGGCGTGAATTTGTCACTGGTTCATATGATAGAACA
                 | |   |    ||  | |  | | |  |   |  || ||   | || ||||      || | |   |  ||||   | |  ||||||||| |||||||||||||||| || || || ||||||||||| || ||||||||||||
----------------gtaagaagatttttctataaatattgtgtttttggtaattc--tataatttagcataccagcatgtttttatttctttctacagGATGGATGTTGACTACTCACCAACCGGACGGGAGTTTGTCACTGGATCTTATGATAGAACA

upper sequence: GRMZM2G590033_T01 (Zea mays), 3'ss of exon 12
lower sequence: Vv12s0028g03140.t01 (Vitis vinifera), 3'ss of exon 12
-------atatcatttcatgcacttgatctgtacctttgacatttgtagcataccttctagtttcttttactttatggggtcatcttacatga-atttgggtttctagGATGGATATTGACTACTCACCAACAGGGCGTGAATTTGTCACTGGTTCATATGATAGAACA
        |  | |||  |   |||||    |    ||    | ||  |   |  |  || ||||||   | ||  ||    |||||  |  | | || | ||   |||||||||||||| |||||||| || || || |||||||| || || || ||||||||||||
gtaagatgtgacctttttttttcttgagacatgagattc---tctgctgttcatttgatattttcttgatcatttaggaaatatctttaagaatactttgtttctcagGATGGATATTGATTACTCACCCACTGGTCGGGAATTTGTAACCGGATCTTATGATAGAACA

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|78026076|gb|DV494463.1|DV494463
EST:     AGAAAATTAGATGAAGCAAAAATTGTTCACAAAGGCCATGTTTCAGCAGT                         GATGGATATTGACTACTCACCAACAGGGCGTGAATTTGTCACTGGTTCATA
genomic: AGAAAATTAGATGAAGCAAAAATTGTTCACAAAGGCCATGTTTCAGCAGTgtaagtgtat ... gggtttctagGATGGATATTGACTACTCACCAACAGGGCGTGAATTTGTCACTGGTTCATA
EST: gi|6526884|gb|AW216143.1|AW216143
EST:     AAAAAATTAGATGAAGCAAAAATTGTTCACAAAGGCCATGTTTCAGCAGT                         GATGGATATTGACTACTCACCAACAGGGCGTGAATTTGTCACTGGTTCATA
genomic: AGAAAATTAGATGAAGCAAAAATTGTTCACAAAGGCCATGTTTCAGCAGTgtaagtgtat ... gggtttctagGATGGATATTGACTACTCACCAACAGGGCGTGAATTTGTCACTGGTTCATA
EST: gi|76020036|gb|DT947206.1|DT947206
EST:     AAAATTAGATGAAGCAAAAATTGTTCACAAAGGCCATGTTTCAGCAGT                         GATGGATATTGACTACTCACCAACAGGGCGTGAATTTGTCACTGGTTCATA
genomic: AAAATTAGATGAAGCAAAAATTGTTCACAAAGGCCATGTTTCAGCAGTgtaagtgtat ... gggtttctagGATGGATATTGACTACTCACCAACAGGGCGTGAATTTGTCACTGGTTCATA
EST: gi|71772084|gb|DR970021.1|DR970021
EST:     AGAAAATTAGATGAAGCAAAAATTGTTCACAAAGGCCATGTTTCAGCAGT                         GATGGATATTGACTACTCACCAACAGGGCGTGAATTTGTCACTGGTTCATA
genomic: AGAAAATTAGATGAAGCAAAAATTGTTCACAAAGGCCATGTTTCAGCAGTgtaagtgtat ... gggtttctagGATGGATATTGACTACTCACCAACAGGGCGTGAATTTGTCACTGGTTCATA
EST: gi|9742841|gb|BE518989.1|BE518989
EST:     AGAAAATTAGATGAAGCAAAAATTGTTCACAAAGGCCATGTTTCAGCAGT                         GATGGATATTGACTACTCACCAACAGGGCGTGAATTTGTCACTGGTTCATA
genomic: AGAAAATTAGATGAAGCAAAAATTGTTCACAAAGGCCATGTTTCAGCAGTgtaagtgtat ... gggtttctagGATGGATATTGACTACTCACCAACAGGGCGTGAATTTGTCACTGGTTCATA
EST: gi|32933250|gb|CF038062.1|CF038062
EST:     AGAAAATTAGATGAAGCAAAAATTGTTCACAAAGGCCATGTTTCTGCAGT                         GATGGATATTGACTACTCACCAACAGGGCGTGAATTTGTCACTGGTTCATA
genomic: AGAAAATTAGATGAAGCAAAAATTGTTCACAAAGGCCATGTTTCAGCAGTgtaagtgtat ... gggtttctagGATGGATATTGACTACTCACCAACAGGGCGTGAATTTGTCACTGGTTCATA

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), 48 (downstream exon)
Score: 184

GCAAATGAAGACACAAACTGTTACTCCTTTGATGCTAGAAAATTAGATGAAGCAAAAATTGTTCACAAAGGCCATGTTTCAGCAGTgtaagtgtat ... gggtttctagGATGGATATTGACTACTCACCAACAGGGCGTGAATTTGTCACTGGTTCATATGATAGAACA


Block sizes: 46 (upstream exon), 48 (downstream exon)
Score: 205

GCAAATGAAGACACAAACTGTTACTCCTTTGATGCTAGAAAATTAGATGAAGCAAAAATTGTTCACAAAGGCCATGTTTCAGCAGTgtaagtgtat ... gggtttctagGATGGATATTGACTACTCACCAACAGGGCGTGAATTTGTCACTGGTTCATATGATAGAACA


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 193

GCAAATGAAGACACAAACTGTTACTCCTTTGATGCTAGAAAATTAGATGAAGCAAAAATTGTTCACAAAGGCCATGTTTCAGCAGTgtaagtgtat ... gggtttctagGATGGATATTGACTACTCACCAACAGGGCGTGAATTTGTCACTGGTTCATATGATAGAACA


Block sizes: 49 (upstream exon), 43 (downstream exon)
Score: 128

GCAAATGAAGACACAAACTGTTACTCCTTTGATGCTAGAAAATTAGATGAAGCAAAAATTGTTCACAAAGGCCATGTTTCAGCAGTgtaagtgtat ... gggtttctagGATGGATATTGACTACTCACCAACAGGGCGTGAATTTGTCACTGGTTCATATGATAGAACA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

accttctagtttcttttactttatggggtcatcttacatgaatttgggtttctagGATGGATATTGACTACTCACCAACAGGGCGTGAATTTGTCACTGGTTCATATGATAGAACA
                              atcttac  putative branch site (score: 128)
                                                tttct  putative PPT
         tttcttttactttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atatcatttcatgcacttgatctgtacctttgacatttgtagcataccttctagtttcttttactttatggggtcatcttacatgaatttgggtttctagGATGGATATTGACTACTCACCAACAGGGCGTGAATTTGTCACTGGTTCATATGATAGAACA

- - - -ttcatgc
- - - - - - - - - - -ctgtacc
- - - - - - - - - - - - - - - tgacatt
- - - - - - - - - - - - - - - - - - -tgtagca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - acatgaa