Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   		8  
 5'  3'   		9  
 5'  3'   		10  
 5'  3'   		11  
 5'  3'   		12  
 5'  3'   		13  
 5'  3'   		14  
 5'  3'   		15  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aactcatggagtccccctttaacattgcattaggctctttttaaatgctctgcgcttctgcttacgtggcactgagacacctcatctttattacgttcagGTCGCAGCAGAAAACAATAATCAATTCAATGGCTGTAAATGAGGATGGTGTCTTGGCAACTGGAG

Basic information

species Zea mays
transcript GRMZM2G017089_T01
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G017089_T01 (Zea mays), 3'ss of exon 13
lower sequence: LOC_Os03g21990.1 (Oryza sativa), 3'ss of exon 15
aactcatggagtccccctttaacattgcattaggctct---ttttaaatgctctgcgcttctgcttacgtggcactgagacacctcatct-ttattacgtt-cagGTCGCAGCAGAAAACAATAATCAATTCAATGGCTGTAAATGAGGATGGTGTCTTGGCAACTGGAG
 |   |||   |  |       | |||| |   | | |   || |||| |  |      |  | | |  |   ||| | ||   ||| |  || | || || |||||| ||||||||||| || || || ||||||||||||||||| ||||||||||||||||||||||
-agcaatgtgatttcaag--ggctttgcttactgttgtaacttgtaaacgaacaatagctaggatcatata--acttaaacttgtcaccgattgtcacctttcagGTCCCAGCAGAAAACCATCATAAACTCAATGGCTGTAAATGAAGATGGTGTCTTGGCAACTGGAG

upper sequence: GRMZM2G017089_T01 (Zea mays), 3'ss of exon 13
lower sequence: AT4G15900.1 (Arabidopsis thaliana), 3'ss of exon 14
----aactcatggagtccccctttaacattgcatta--ggctctttttaaat--gctctg-cgcttctgcttacgtg------gcactgagacacc--tcatctttatt-acgttcagGT-CGCAGCAGAAAACAATAATCAATTCAATGGCTGTAAATGAGGATGGTGTCTTGGCAACTGGAG
      |||    ||       |  || ||||||     |  ||||| ||||  |  ||| |  |  |  ||| ||       |   |   |||    | |||||| |  | |   | || |||| |||||||| ||||| ||| ||||||||||||| |||||||||||  |||  |||||||
gtaagtctctgctagataattatatactttgcatctccagtgcttttgaaataggagctgtcattattaattatgtaattgatgtgtttgaacaatgtttatctttttccatggaaaagTTCGCAACAGAAAACCATAATTAATGCAATGGCTGTAAACGAGGATGGTGTGATGGTCACTGGAG
















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|78021762|gb|DV490149.1|DV490149
EST:     AACGTAAAGAAGTTTAACCTTCCCAAAGGCGAATTTCTGCACAACATGCT                         GTCGCAGCAGAAAACAATAATCAATTCAATGGCTGTAAATGAGGATGGTGT
genomic: AACGTAAAGAAGTTTAACCTTCCCAAAGGCGAATTTCTGCACAACATGCTgtgagtcttc ... ttacgttcagGTCGCAGCAGAAAACAATAATCAATTCAATGGCTGTAAATGAGGATGGTGT
EST: gi|148951459|gb|EC897184.2|EC897184
EST:     AACGTAAAGAAGTTTAACCTTCCCAAAGGCGAATTTCTGCACAACATGCT                         GTCGCAGCAGAAAACAATAATCAATTCAATGGCTGTAAATGAGGATGGTGT
genomic: AACGTAAAGAAGTTTAACCTTCCCAAAGGCGAATTTCTGCACAACATGCTgtgagtcttc ... ttacgttcagGTCGCAGCAGAAAACAATAATCAATTCAATGGCTGTAAATGAGGATGGTGT
EST: gi|60342895|gb|DN209868.1|DN209868
EST:     CCAAAGGCGAATTTATGCACAACATGCT                         GTCGCAGCAGAAAACAATAATCAATTCAATGGCTGTAAATGAGGATGGTGT
genomic: CCAAAGGCGAATTTCTGCACAACATGCTgtgagtcttc ... ttacgttcagGTCGCAGCAGAAAACAATAATCAATTCAATGGCTGTAAATGAGGATGGTGT
EST: gi|37376961|gb|CF625047.1|CF625047
EST:     AACGTAAAGAAGTTTAACCTTCCCAAAGGCGAATTTCTGCACAACATGCT                         GTCGCAGCAGAAAACAATAATCAATTCAATGGCTGTAAATGAGGATGGTGT
genomic: AACGTAAAGAAGTTTAACCTTCCCAAAGGCGAATTTCTGCACAACATGCTgtgagtcttc ... ttacgttcagGTCGCAGCAGAAAACAATAATCAATTCAATGGCTGTAAATGAGGATGGTGT
EST: gi|116814103|gb|EC856623.1|EC856623
EST:     AACGTAAAGAAGTTTAACCTTCCCAAAGGCGAATTTCTGCACAACATGCT                         GTCGCAGCAGAAAACAATAATCAATTCAATGGCTGTAAATGAGGATGGTGT
genomic: AACGTAAAGAAGTTTAACCTTCCCAAAGGCGAATTTCTGCACAACATGCTgtgagtcttc ... ttacgttcagGTCGCAGCAGAAAACAATAATCAATTCAATGGCTGTAAATGAGGATGGTGT
EST: gi|71432304|gb|DR813354.1|DR813354
EST:     AACGTAAAGAAGTTTAACCTTCCCAAAGGCGAATTTCTGCACAACATGCT                         GTCGCAGCAGAAAACAATAATCAATTCAATGGCTGTAAATGAGGATGGTGT
genomic: AACGTAAAGAAGTTTAACCTTCCCAAAGGCGAATTTCTGCACAACATGCTgtgagtcttc ... ttacgttcagGTCGCAGCAGAAAACAATAATCAATTCAATGGCTGTAAATGAGGATGGTGT
EST: gi|31406178|gb|CD484910.1|CD484910
EST:     AACGTAAAGAAGTTTAACCTTCCCAAAGGCGAATTTCTGCACAACATGCT                         GTCGCAGCAGAAAACAATAATCAATTCAATGGCTGTAAATGAGGATGGTGT
genomic: AACGTAAAGAAGTTTAACCTTCCCAAAGGCGAATTTCTGCACAACATGCTgtgagtcttc ... ttacgttcagGTCGCAGCAGAAAACAATAATCAATTCAATGGCTGTAAATGAGGATGGTGT
EST: gi|32933315|gb|CF038127.1|CF038127
EST:     AACGTAAAGAAGTTTAACCTTCCCAAAGGCGAATTTCTGCACAACATGCT                         GTCGCAGCAGAAAACAATAATCAATTCAATGGCTGTAAATGAGGATGGTGT
genomic: AACGTAAAGAAGTTTAACCTTCCCAAAGGCGAATTTCTGCACAACATGCTgtgagtcttc ... ttacgttcagGTCGCAGCAGAAAACAATAATCAATTCAATGGCTGTAAATGAGGATGGTGT
EST: gi|60357310|gb|DN224283.1|DN224283
EST:     AACGTAAAGAAGTTTAACCTTCCCAAAGGCGAATTTCTGCACAACATGCT                         GTCGCAGCAGAAAACAATAATCAATTCAATGGCTGTAAATGAGGATGGTGT
genomic: AACGTAAAGAAGTTTAACCTTCCCAAAGGCGAATTTCTGCACAACATGCTgtgagtcttc ... ttacgttcagGTCGCAGCAGAAAACAATAATCAATTCAATGGCTGTAAATGAGGATGGTGT
EST: gi|93012802|gb|EB638322.1|EB638322
EST:     AACGTAAAGAAGTTTAACCTTCCCAAAGGCGAATTTCTGCACAACATGCT                         GTCGCAGCAGAAAACAATAATCAATTCAATGGCTGTAAATGAGGATGGTGT
genomic: AACGTAAAGAAGTTTAACCTTCCCAAAGGCGAATTTCTGCACAACATGCTgtgagtcttc ... ttacgttcagGTCGCAGCAGAAAACAATAATCAATTCAATGGCTGTAAATGAGGATGGTGT
EST: gi|110491423|gb|EE013510.1|EE013510
EST:     AACGTAAAGAAGTTTAACCTTCCCAAAGGCGAATTTCTGCACAACATGCT                         GTCGCAGCAGAAAACAATAATCAATTCAATGGCTGTAAATGAGGATGGTGT
genomic: AACGTAAAGAAGTTTAACCTTCCCAAAGGCGAATTTCTGCACAACATGCTgtgagtcttc ... ttacgttcagGTCGCAGCAGAAAACAATAATCAATTCAATGGCTGTAAATGAGGATGGTGT
EST: gi|6538870|gb|AW225009.1|AW225009
EST:     AACGTAAAGAAGTTTAACCTTCCCAAAGGCGAATTTTTGCCCAACATGCT                         GTCGCAGCAGAAAACAATAATCAATTCAATGGCTGTAAATGAGGATGGTGT
genomic: AACGTAAAGAAGTTTAACCTTCCCAAAGGCGAATTTCTGCACAACATGCTgtgagtcttc ... ttacgttcagGTCGCAGCAGAAAACAATAATCAATTCAATGGCTGTAAATGAGGATGGTGT
EST: gi|71757914|gb|DR955851.1|DR955851
EST:     AACGTAAAGAAGTTTAACCTTCCCAAAGGCGAATTTCTGCACAACATGCT                         GTCGCAGCAGAAAACAATAATCAATTCAATGGCTGTAAATGAGGATGGTGT
genomic: AACGTAAAGAAGTTTAACCTTCCCAAAGGCGAATTTCTGCACAACATGCTgtgagtcttc ... ttacgttcagGTCGCAGCAGAAAACAATAATCAATTCAATGGCTGTAAATGAGGATGGTGT
EST: gi|33093989|gb|CF053983.1|CF053983
EST:     AACGTAAAGAAGTTTAACCTTCCCAAAGGCGAATTTCTGCACAACATGCT                         GTCGCAGCAGAAAACAATAATCAATTCAATGGCTGTAAATGAGGATGGTGT
genomic: AACGTAAAGAAGTTTAACCTTCCCAAAGGCGAATTTCTGCACAACATGCTgtgagtcttc ... ttacgttcagGTCGCAGCAGAAAACAATAATCAATTCAATGGCTGTAAATGAGGATGGTGT
EST: gi|4967045|gb|AI691809.1|AI691809
EST:     GTAAA-AAGTTTAACCTTCCCAAAGGCGAATTTCTGCNCANCATGCT                         GTCGCAGCAGAAACCAATAATCAATTCAATGGCTGTAAATGAGGATGGTGT
genomic: GTAAAGAAGTTTAACCTTCCCAAAGGCGAATTTCTGCACAACATGCTgtgagtcttc ... ttacgttcagGTCGCAGCAGAAAACAATAATCAATTCAATGGCTGTAAATGAGGATGGTGT
EST: gi|33091991|gb|CF051985.1|CF051985
EST:     AACGTAAAGAAGTTTAACCTTCCCAAAGGCGAATTTCTGCACAACATGCT                         GTCGCAGCAGAAAACAATAATCAATTCAATGGCTGTAAATGAGGATGGTGT
genomic: AACGTAAAGAAGTTTAACCTTCCCAAAGGCGAATTTCTGCACAACATGCTgtgagtcttc ... ttacgttcagGTCGCAGCAGAAAACAATAATCAATTCAATGGCTGTAAATGAGGATGGTGT
EST: gi|5055899|gb|AI734786.1|AI734786
EST:     AAGAAGTTTAACCTTCCCAAAGGCGAATTTCTGCNCAACATGCT                         GTCGCAGCAGAAACCAATAATCAATTCAATGGCTGTAAATGAGGATGGTGT
genomic: AAGAAGTTTAACCTTCCCAAAGGCGAATTTCTGCACAACATGCTgtgagtcttc ... ttacgttcagGTCGCAGCAGAAAACAATAATCAATTCAATGGCTGTAAATGAGGATGGTGT
EST: gi|101383542|gb|EB813827.1|EB813827
EST:     AACGTAAAGAAGTTTAACCTTCCCAAAGGCGAATTTCTGCACAACATGCT                         GTCGCAGCAGAAAACAATAATCAATTCAATGGCTGTAAATGAGGATGGTGT
genomic: AACGTAAAGAAGTTTAACCTTCCCAAAGGCGAATTTCTGCACAACATGCTgtgagtcttc ... ttacgttcagGTCGCAGCAGAAAACAATAATCAATTCAATGGCTGTAAATGAGGATGGTGT
EST: gi|148950912|gb|EC896542.2|EC896542
EST:     AACGTAAAGAAGTTTAACCTTCCCAAAGGCGAATTTCTGCACAACATGCT                         GTCGCAGCAGAAAACAATAATCAATTCAATGGCTGTAAATGAGGATGGTGT
genomic: AACGTAAAGAAGTTTAACCTTCCCAAAGGCGAATTTCTGCACAACATGCTgtgagtcttc ... ttacgttcagGTCGCAGCAGAAAACAATAATCAATTCAATGGCTGTAAATGAGGATGGTGT
EST: gi|37382890|gb|CF628417.1|CF628417
EST:     AACGTAAAGAAGTTTAACCTTCCCAAAGGCG-ATTTCTGCACAACATGCT                         GTCGCAGCAGAAAACAATAATCAATTCAATGGCTGTAAATGAGGATGGTGT
genomic: AACGTAAAGAAGTTTAACCTTCCCAAAGGCGAATTTCTGCACAACATGCTgtgagtcttc ... ttacgttcagGTCGCAGCAGAAAACAATAATCAATTCAATGGCTGTAAATGAGGATGGTGT
EST: gi|148943610|gb|EC888673.2|EC888673
EST:     AACGTAAAGAAGTTTAACCTTCCCAAAGGCGAATTTCTGCACAACATGCT                         GTCGCAGCAGAAAACAATAATCAATTCAATGGCTGTAAATGAGGATGGTGT
genomic: AACGTAAAGAAGTTTAACCTTCCCAAAGGCGAATTTCTGCACAACATGCTgtgagtcttc ... ttacgttcagGTCGCAGCAGAAAACAATAATCAATTCAATGGCTGTAAATGAGGATGGTGT
EST: gi|71432303|gb|DR813353.1|DR813353
EST:     AACGTAAAGAAGTTTAACCTTCCCAAAGGCGAATTTCTGCACAACATGCT                         GTCGCAGCAGAAAACAATAATCAATTCAATGGCTGTAAATGAGGATGGTGT
genomic: AACGTAAAGAAGTTTAACCTTCCCAAAGGCGAATTTCTGCACAACATGCTgtgagtcttc ... ttacgttcagGTCGCAGCAGAAAACAATAATCAATTCAATGGCTGTAAATGAGGATGGTGT
EST: gi|33091976|gb|CF051970.1|CF051970
EST:     AACGTAAAGAAGTTTAACCTTCCCAAAGGCGAATTTCTGCACAACATGCT                         GTCGCAGCAGAAAACAATAATCAATTCAATGGCTGTAAATGAGGATGGTGT
genomic: AACGTAAAGAAGTTTAACCTTCCCAAAGGCGAATTTCTGCACAACATGCTgtgagtcttc ... ttacgttcagGTCGCAGCAGAAAACAATAATCAATTCAATGGCTGTAAATGAGGATGGTGT
EST: gi|33091634|gb|CF051628.1|CF051628
EST:     AACGTAAAGAAGTTTAACCTTCCCAAAGGCGAATTTCTGCACAACATGCT                         GTCGCAGCAGAAAACAATAATCAATTCAATGGCTGTAAATGAGGATGGTGT
genomic: AACGTAAAGAAGTTTAACCTTCCCAAAGGCGAATTTCTGCACAACATGCTgtgagtcttc ... ttacgttcagGTCGCAGCAGAAAACAATAATCAATTCAATGGCTGTAAATGAGGATGGTGT
EST: gi|31909551|gb|CD650975.1|CD650975
EST:     AACGTAAAGAAGTTTAACCTTCCCAAAGGCGAATTTCTGCACAACATGCT                         GTCGCAGCAGAAAACAATAATCAATTCAATGGCTGTAAATGAGGATGGTGT
genomic: AACGTAAAGAAGTTTAACCTTCCCAAAGGCGAATTTCTGCACAACATGCTgtgagtcttc ... ttacgttcagGTCGCAGCAGAAAACAATAATCAATTCAATGGCTGTAAATGAGGATGGTGT

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), 49 (downstream exon)
Score: 222

GAAAGCATTTGCATCAGCATCAGCAGACAACGTAAAGAAGTTTAACCTTCCCAAAGGCGAATTTCTGCACAACATGCTgtgagtcttc ... ttacgttcagGTCGCAGCAGAAAACAATAATCAATTCAATGGCTGTAAATGAGGATGGTGTCTTGGCAACTGGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 147

GAAAGCATTTGCATCAGCATCAGCAGACAACGTAAAGAAGTTTAACCTTCCCAAAGGCGAATTTCTGCACAACATGCTgtgagtcttc ... ttacgttcagGTCGCAGCAGAAAACAATAATCAATTCAATGGCTGTAAATGAGGATGGTGTCTTGGCAACTGGAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 118

GAAAGCATTTGCATCAGCATCAGCAGACAACGTAAAGAAGTTTAACCTTCCCAAAGGCGAATTTCTGCACAACATGCTgtgagtcttc ... ttacgttcagGTCGCAGCAGAAAACAATAATCAATTCAATGGCTGTAAATGAGGATGGTGTCTTGGCAACTGGAG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 128

GAAAGCATTTGCATCAGCATCAGCAGACAACGTAAAGAAGTTTAACCTTCCCAAAGGCGAATTTCTGCACAACATGCTgtgagtcttc ... ttacgttcagGTCGCAGCAGAAAACAATAATCAATTCAATGGCTGTAAATGAGGATGGTGTCTTGGCAACTGGAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgctctgcgcttctgcttacgtggcactgagacacctcatctttattacgttcagGTCGCAGCAGAAAACAATAATCAATTCAATGGCTGTAAATGAGGATGGTGTCTTGGCAACTGGAG
             tgcttac  putative branch site (score: 128)
                                       tctttatt  putative PPT
                                      atctttatta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aactcatggagtccccctttaacattgcattaggctctttttaaatgctctgcgcttctgcttacgtggcactgagacacctcatctttattacgttcagGTCGCAGCAGAAAACAATAATCAATTCAATGGCTGTAAATGAGGATGGTGTCTTGGCAACTGGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGATG
- - catggag
- - - - - - - - - - - - ttgcatt
- - - - - - - - - - - - - - - - - - - - - -aatgctc
- - - - - - - - - - - - - - - - - - - - - - - - - - -gcttctg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gcactga