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'   		16  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtactatactgctaatgtttgttttctttacaaattaacactactgataattattttgctgagcagCTTGCTCAAGGTGGAACTGCAGTTGGAACTGGCTTGAACACCAAGAAAGG

Basic information

species Zea mays
transcript GRMZM2G010823_T01
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G010823_T01 (Zea mays), 3'ss of exon 7
lower sequence: LOC_Os03g21950.1 (Oryza sativa), 3'ss of exon 7
gtactatactg----ctaatgtttgttttc---------tttacaaattaac--actactgataat-tattttgctgagcagCTTGCTCAAGGTGGAACTGCAGTTGGAACTGGCTTGAACACCAAGAAAGG
|||||| |||       ||| ||||||||          |  | || || |   | | ||||| || | |||||||||||||||||||||||||||||||||||||||||| ||||||||||| ||||||||
gtactacactaatgttcaatatttgtttttagaatgatatgcaaaagttgaatgatttctgatcatattttttgctgagcagCTTGCTCAAGGTGGAACTGCAGTTGGAACGGGCTTGAACACTAAGAAAGG

upper sequence: GRMZM2G010823_T01 (Zea mays), 3'ss of exon 7
lower sequence: AT2G47510.2 (Arabidopsis thaliana), 3'ss of exon 8
---------gtactatactgctaatgtttgttttctt-tacaaattaacacta--ctgataattattttgctgag----------cagCTTGCTCAAGGTGGAACTGCAGTTGGAACTGGCTTGAACACCAAGAAAGG
          |  |||  |       | || |||| | |||   |  |   ||  ||||    ||  ||||||            |||||||| |||||||||||||| ||||| || || || ||||| ||||||||
gtttgggaaatgatatcttttggggatctgatttcctgtacttctccagtttatactgaggtctaacttgctggaaatgtttggccagCTTGCACAAGGTGGAACTGCGGTTGGGACAGGATTAAACACTAAGAAAGG

upper sequence: GRMZM2G010823_T01 (Zea mays), 3'ss of exon 7
lower sequence: Vv07s0005g00880.t01 (Vitis vinifera), 3'ss of exon 8
--------------gtactatactgctaatgtttgttttctttacaaattaacactactgataattattttgctgagcagCTTGCTCAAGGTGGAACTGCAGTTGGAACTGGCTTGAACACCAAGAAAGG
              ||| ||   |  |||   || ||| |   || |  |   |  |      | | || |  |||||||||||| |||||||| ||||| || || ||||| |||||||| ||||||||
gtctgcaacttgaagtattaagtttttaactgttctttcccccactaggtctaatgaacagggaatgttgt-ttgagcagCTTGCACAAGGTGGCACTGCTGTAGGGACTGGATTGAACACAAAGAAAGG

upper sequence: GRMZM2G010823_T01 (Zea mays), 3'ss of exon 7
lower sequence: EFJ18116 (Selaginella moellendorffii), 3'ss of exon 6
gtactatactgctaatgtttgttttctttacaaattaacactactgataattattttgctgagcagCTTGCTCAAGGTGGAACTGCAGTTGGAACTGGCTTGAACACCAAGAAAGG
          |     |   | | |   | |  |||       ||   |||| || ||    ||||||||| |||||||||||||| || ||||||||| | ||||| ||||||||
----------gtaggagcgcgctcttacttctgattgct----ctctaaattcttgtg----gcagCTTGCACAAGGTGGAACTGCCGTGGGAACTGGCCTCAACACTAAGAAAGG

upper sequence: GRMZM2G010823_T01 (Zea mays), 3'ss of exon 7
lower sequence: EFJ09601 (Selaginella moellendorffii), 3'ss of exon 6
gtactatactgctaatgtttgttttctttacaaattaacactactgataattattttgctgagcagCTTGCTCAAGGTGGAACTGCAGTTGGAACTGGCTTGAACACCAAGAAAGG
          |     |   | |     | |  |||       ||   |||| || ||    ||||||||| |||||||||||||| || ||||||||| | ||||| ||||||||
----------gtaggagcgcgctcgtacttctgattgct----ctctaaattcttgtg----gcagCTTGCCCAAGGTGGAACTGCCGTGGGAACTGGCCTCAACACTAAGAAAGG

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|148999094|gb|EE030327.2|EE030327
EST:     TCAAATATGGAATTGACCGCATTAATTGTACATTACCTCGGATGTACCAG                         CTTGCTCAAGGGGGAACTGCAGT
genomic: TCAAATATGGAATTGACCGCATTAATTGTACATTACCTCGGATGTACCAGgtactatact ... tgctgagcagCTTGCTCAAGGTGGAACTGCAGT
EST: gi|78111379|gb|DV529776.1|DV529776
EST:     TCAAATATGGAATTGACCGCATTAATTGTACATTACCTCGGATGTACCAG                         CTTGCTCAAGGTGGAACTGCAGTTG
genomic: TCAAATATGGAATTGACCGCATTAATTGTACATTACCTCGGATGTACCAGgtactatact ... tgctgagcagCTTGCTCAAGGTGGAACTGCAGTTG

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: 106

GTCAAATATGGAATTGACCGCATTAATTGTACATTACCTCGGATGTACCAGgtactatact ... tgctgagcagCTTGCTCAAGGTGGAACTGCAGTTGGAACTGGCTTGAACACCAAGAAAGG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 234

GTCAAATATGGAATTGACCGCATTAATTGTACATTACCTCGGATGTACCAGgtactatact ... tgctgagcagCTTGCTCAAGGTGGAACTGCAGTTGGAACTGGCTTGAACACCAAGAAAGG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 168

GTCAAATATGGAATTGACCGCATTAATTGTACATTACCTCGGATGTACCAGgtactatact ... tgctgagcagCTTGCTCAAGGTGGAACTGCAGTTGGAACTGGCTTGAACACCAAGAAAGG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 150

GTCAAATATGGAATTGACCGCATTAATTGTACATTACCTCGGATGTACCAGgtactatact ... tgctgagcagCTTGCTCAAGGTGGAACTGCAGTTGGAACTGGCTTGAACACCAAGAAAGG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctaatgtttgttttctttacaaattaacactactgataattattttgctgagcagCTTGCTCAAGGTGGAACTGCAGTTGGAACTGGCTTGAACACCAAGAAAGG
                              tactgat  putative branch site (score: 150)
                                       ttatttt  putative PPT
      tttgttttctttacaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtactatactgctaatgtttgttttctttacaaattaacactactgataattattttgctgagcagCTTGCTCAAGGTGGAACTGCAGTTGGAACTGGCTTGAACACCAAGAAAGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA