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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgcgttccctgctcaagattatcttaattaattgccacaccacgtaacattgaacttagtccttttcacaaacttgctagATGGAAGAACGTATGACACTATGCAACATGGTTGTTGAAGCTGGTGGAAAGAACGGTGTCGTGCCTGCTGATGAAACTACATTTAAATACCTTGAG

Basic information

species Zea mays
transcript GRMZM2G370852_T02
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G370852_T03 (Zea mays), 3'ss of exon 8
lower sequence: LOC_Os02g03260.1 (Oryza sativa), 3'ss of exon 7
gtgcgttccctgctcaagattatcttaattaattg---ccacaccacgtaacattgaacttagtccttttcacaaacttgctagATGGAAGAACGTATGACACTATGCAACATGGTTGTTGAAGCTGGTGGAAAGAACGGTGTCGTGCCTGCTGATGAAACTACATTTAAATACCTTGAG
||  | ||| ||||||  | ||  || || ||||     ||     | |  | || ||| || |  ||| | |||||||| ||||||||||| || |||||||| |||||||||||| ||||||||||||| ||||| ||||| |||||||| ||| ||||||||||||| || ||||||
gtatgctccgtgctcataactagattgatcaattattttcatctttcatggcttttaacctaata-tttccgcaaacttggtagATGGAAGAGCGAATGACACTGTGCAACATGGTTATTGAAGCTGGTGGCAAGAATGGTGTTGTGCCTGCCGATCAAACTACATTTAACTATCTTGAG

upper sequence: GRMZM2G370852_T03 (Zea mays), 3'ss of exon 8
lower sequence: GLYMA20G34160.1 (Glycine max), 3'ss of exon 9
--gtgcgttccctgctcaagattatcttaattaat----tgccacaccacgtaacattgaacttagtccttttcacaaact-tgctagATGGAAGAACGTATGACACTATGCAACATGGTTGTTGAAGCTGGTGGAAAGAACGGTGTCGTGCCTGCTGATGAAACTACATTTAAATACCTTGAG
   ||| | |  |   ||   || ||||  |  ||    ||  |       ||  ||   ||||     || |   |   | |  |||||||||||| | |||||||| |||||||||||| | |||||||| || || |||||| | ||  ||||||||  ||| ||||  ||||||||||||
gtatgcatacttttaacactgttttctttctatatggtatgttatttgcactagtataagacttttgaattgttgtattgtattgtagATGGAAGAAAGGATGACACTGTGCAACATGGTTATAGAAGCTGGAGGGAAAAACGGTATTGTTGCTGCTGATAGAACCACATACAAATACCTTGAG

upper sequence: GRMZM2G370852_T03 (Zea mays), 3'ss of exon 8
lower sequence: GLYMA17G37540.1 (Glycine max), 3'ss of exon 8
--------------------gtgcgttccctgctcaagattatc-ttaattaattgccacaccacgtaacattgaacttagtccttttcacaaacttgctagATGGAAGAACGTATGACACTATGCAACATGGTTGTTGAAGCTGGTGGAAAGAACGGTGTCGTGCCTGCTGATGAAACTACATTTAAATACCTTGAG
                     |   ||      ||||  | |    |  ||  ||   |    |  ||| | |    || ||  |||   |    | | |||||||||||||| |||||| | |||||||||||||||||||||||||||||||| ||||| || ||||||||    |||||||||||||| ||||| 
aaaacacaagtaaacgggccataaatttttc-ttcaatctcagaactctttcttttttattataaataaaagttgttttggtaatttgttcctcttggataGATGGAAGAACGGATGACATTGTGCAACATGGTTGTTGAAGCTGGTGGAAAGAATGGTGTTGTTCCTGCTGACAGCACTACATTTAAATATCTTGA-

upper sequence: GRMZM2G370852_T03 (Zea mays), 3'ss of exon 8
lower sequence: GLYMA14G40570.1 (Glycine max), 3'ss of exon 8
--------------------gtgcgttccctgctcaagattatcttaattaattgccacaccacgtaacattgaacttagtccttttcacaaacttgctagATGGAAGAACGTATGACACTATGCAACATGGTTGTTGAAGCTGGTGGAAAGAACGGTGTCGTGCCTGCTGATGAAACTACATTTAAATACCTTGAG
                          |   |  ||||  |        ||  ||   |    |  ||| ||||   || ||  |||   |    | | |||||||||||||| |||||| | |||||||||||||||||||||||||||||||| ||||| || ||||||||    |||||||||||||| ||||||
gaaaacacaagtaaacgggccctaaatttttcttcaatctcggaactctttcttttgattataaataaaattgt-tttggtaatttgttcctcttggatagATGGAAGAACGGATGACATTGTGCAACATGGTTGTTGAAGCTGGTGGAAAGAATGGTGTTGTTCCTGCTGACAGCACTACATTTAAATATCTTGAG

upper sequence: GRMZM2G370852_T03 (Zea mays), 3'ss of exon 8
lower sequence: AT4G13430.1 (Arabidopsis thaliana), 3'ss of exon 8
-----------------------------gtgcgttccctg-ctcaagattatcttaattaattgc--cacaccacgtaa-cattgaact-tagtccttttcacaaactt---------gctagATGGAAGAACGTATGACACTATGCAACATGGTTGTTGAAGCTGGTGGAAAGAACGGTGTCGTGCCTGCTGATGAAACTACATTTAAATACCTTGAG
                              || || || |  || |     ||   ||||||| ||  || |  | || | ||||||  | ||     || |   ||  |         |||||||||||||| | |||||| | |||||||||||||| |||||||| |||||||| |||||| | ||| ||||||  || ||||| || ||  |||||
gtaagaaatcattctatatttcctacattatgggtcccttctcttatagaaataaaaattaatagctgcatatgatgttatcattgatttataaatggttgcttgaatcttttttggctgctagATGGAAGAAAGAATGACATTGTGCAACATGGTTGTGGAAGCTGGGGGAAAGAATGGTGTCATCCCTCCTGATGCGACGACATTAAATTATGTTGAG

upper sequence: GRMZM2G370852_T03 (Zea mays), 3'ss of exon 8
lower sequence: Vv05s0049g01980.t01 (Vitis vinifera), 3'ss of exon 8
----------------------------------------------gtgcgttccctgctcaagattatcttaattaat-tgccacaccacgtaacattgaacttagtccttttcacaaacttgctagATGGAAGAACGTATGACACTATGCAACATGGTTGTTGAAGCTGGTGGAAAGAACGGTGTCGTGCCTGCTGATGAAACTACATTTAAATACCTTGAG
                                              || | || | ||      |||   ||||| |   ||        |  |   ||||  |   || || |   |||||    ||||||||||| | |||||| |||||||||||||| |||||||||| |||||||| ||||| || |||||||||   ||||||  ||| |||||||||
gtaggtgcacttttatagatcttccactgcaagtatctaaatcactgttcatttc-tgtgtggaatttgtttaatcagcctgttctggatcacagttttga-ttgtttcattgttctaaactgaaaagATGGAAGAAAGAATGACATTATGCAACATGGTTATTGAAGCTGGGGGAAAGAATGGTGTTGTCCCTGCTGATAGTACTACACATAAGTACCTTGAG

upper sequence: GRMZM2G370852_T03 (Zea mays), 3'ss of exon 8
lower sequence: Vv08s0056g01640.t01 (Vitis vinifera), 3'ss of exon 8
-----------------------------------------------gtgcgttccctgctcaagattatcttaattaattgccacaccacgtaacattgaacttagtccttttcacaaacttgctagATGGAAGAACGTATGACACTATGCAACATGGTTGTTGAAGCTGGTGGAAAGAACGGTGTCGTGCCTGCTGATGAAACTACATTTAAATACCTTGAG
                                                ||| || | | || ||  || | | |   || |||         |    || |   |  |  |  || ||| ||    ||||||||||| | |||||| ||||||||||||||||||||||||| |||||||| ||||| || |||||||||   ||||||  ||| |||||||||
gtaagttcacttttacagatcttcccctgcaaaaatctcaagtcattctgcatttctttctgaaatttgtataatcaaactgcactggattatggttttaattgttttattcctctcaa-ctgaaaagATGGAAGAAAGGATGACATTATGCAACATGGTTGTTGAAGCTGGAGGAAAGAATGGTGTTGTTCCTGCTGATAGTACTACACATAAGTACCTTGAG

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|32840108|gb|CD979789.1|CD979789
EST:     CAACCTACAAATCGATGGAGTTTGTTGGATCAACTGTAGAAAGTCTAACC                         ATGGAAGAACGTATGACACTATGCAACATGGTTGTTGAAGCTGGTGGAAAG
genomic: CAACCTACAAATCGATGGAGTTTGTTGGATCAACTGTAGAAAGTCTAACCgtgcgttccc ... aacttgctagATGGAAGAACGTATGACACTATGCAACATGGTTGTTGAAGCTGGTGGAAAG
EST: gi|32846022|gb|CD985703.1|CD985703
EST:     CAACCTACAAATCGATGGAGTTTGTTGGATCAACTGTAGAAAGTCTAACC                         ATGGAAGAACGTATGACACTATGCGACATGGTTGTTGAAGCTGGTGGAAAG
genomic: CAACCTACAAATCGATGGAGTTTGTTGGATCAACTGTAGAAAGTCTAACCgtgcgttccc ... aacttgctagATGGAAGAACGTATGACACTATGCAACATGGTTGTTGAAGCTGGTGGAAAG
EST: gi|32840107|gb|CD979788.1|CD979788
EST:     CAACCTACAAATCGATGGAGTTTGTTGGATCAACTGTAGAAAGTCTAACC                         ATGGAAGAACGTATGACACTATGCAACATGGTTGTTGAAGCTGGTGGAAAG
genomic: CAACCTACAAATCGATGGAGTTTGTTGGATCAACTGTAGAAAGTCTAACCgtgcgttccc ... aacttgctagATGGAAGAACGTATGACACTATGCAACATGGTTGTTGAAGCTGGTGGAAAG
EST: gi|32840106|gb|CD979787.1|CD979787
EST:     CAACCTACAAATCGATGGAGTTTGTTGGATCAACTGTAGAAAGTCTAACCC                         ATGGAAGAACGTATGACACTATGCAACATGGTTGTTGAAGCTGGTGGAAA
genomic: CAACCTACAAATCGATGGAGTTTGTTGGATCAACTGTAGAAAGTCTAA-CCgtgcgttccc ... aacttgctagATGGAAGAACGTATGACACTATGCAACATGGTTGTTGAAGCTGGTGGAAA
EST: gi|211524232|gb|FL397627.1|FL397627
EST:     CAACCTACAAATCGATGGAGTTTGTTGGATCAACTGTAGAAAGTCTAACC                         ATGGAAGAACGTATGACACTATGCAACATGGTTGTTGAAGCTGGTGGAAAG
genomic: CAACCTACAAATCGATGGAGTTTGTTGGATCAACTGTAGAAAGTCTAACCgtgcgttccc ... aacttgctagATGGAAGAACGTATGACACTATGCAACATGGTTGTTGAAGCTGGTGGAAAG

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: 45 (upstream exon), 47 (downstream exon)
Score: 131

ATTATTGGTGAGATTTCAGTATCTGGTGCAACCTACAAATCGATGGAGTTTGTTGGATCAACTGTAGAAAGTCTAACCgtgcgttccc ... aacttgctagATGGAAGAACGTATGACACTATGCAACATGGTTGTTGAAGCTGGTGGAAAGAACGGTGTCGTGCCTGCTGATGAAACTACATTTAAATACCTTGAG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 228

ATTATTGGTGAGATTTCAGTATCTGGTGCAACCTACAAATCGATGGAGTTTGTTGGATCAACTGTAGAAAGTCTAACCgtgcgttccc ... aacttgctagATGGAAGAACGTATGACACTATGCAACATGGTTGTTGAAGCTGGTGGAAAGAACGGTGTCGTGCCTGCTGATGAAACTACATTTAAATACCTTGAG


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 143

ATTATTGGTGAGATTTCAGTATCTGGTGCAACCTACAAATCGATGGAGTTTGTTGGATCAACTGTAGAAAGTCTAACCgtgcgttccc ... aacttgctagATGGAAGAACGTATGACACTATGCAACATGGTTGTTGAAGCTGGTGGAAAGAACGGTGTCGTGCCTGCTGATGAAACTACATTTAAATACCTTGAG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 138

ATTATTGGTGAGATTTCAGTATCTGGTGCAACCTACAAATCGATGGAGTTTGTTGGATCAACTGTAGAAAGTCTAACCgtgcgttccc ... aacttgctagATGGAAGAACGTATGACACTATGCAACATGGTTGTTGAAGCTGGTGGAAAGAACGGTGTCGTGCCTGCTGATGAAACTACATTTAAATACCTTGAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aattaattgccacaccacgtaacattgaacttagtccttttcacaaacttgctagATGGAAGAACGTATGACACTATGCAACATGGTTGTTGAAGCTGGTGGAAAGAACGGTGTCGTGCCTGCTGATGAAACTACATTTAAATACCTTGAG
                acgtaac  putative branch site (score: 138)
                   taacatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgcgttccctgctcaagattatcttaattaattgccacaccacgtaacattgaacttagtccttttcacaaacttgctagATGGAAGAACGTATGACACTATGCAACATGGTTGTTGAAGCTGGTGGAAAGAACGGTGTCGTGCCTGCTGATGAAACTACATTTAAATACCTTGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGAT