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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atttttccatgtgtgccataatatcctttgtcactttgtacatttttcttaaaatcaaacctggacaaagcttgttttaagtaatacaaactgtcatcagGTTGCAGAACCACTGAGAGCTATGGTTATGGGAGCTCCTTTGGAGGATGCCCGCCACCTCGCCCAAAGGTACGACAGAATGCGTCAAGAAGCTGAAGCGC

Basic information

species Zea mays
transcript GRMZM2G123624_T01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G123624_T01 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os10g36870.1 (Oryza sativa), 3'ss of exon 4
atttttccatgtgtgccataatatcctt------tgtcactttgtacatttttcttaaaatcaaacctggacaaagcttgttttaagtaatacaaactgtcatcagGTTGCAGAACCACTGAGAGCTATGGTTATGGGAGCTCCTTTGGAGGATGCCCGCCACCTCGCCCAAAGGTACGACAGAATGCGTCAAGAAGCTGAAGCGC
    | | |||  |||||||||  ||||      ||| |  |||| ||| | | |||   ||||| ||| |  |  ||  | | |  ||      | | |||| |||| ||||||||  |||| |||||||| ||||||||||||||||| ||||| ||||| || |||||||| |||||||| |||||||| ||||| ||||| |
----tgcaatgaatgccataatgcccttgcaaattgtaatcttgtgcatatattttac--tcaaatctgcatgagactgttctgacatatggattaatatcattagGTGGCAGAACCGTTGAGGGCTATGGTGATGGGAGCTCCTTTGGAAGATGCTCGCCATCTTGCCCAAAGATACGACAGGATGCGTCAGGAAGCCGAAGCAC

upper sequence: GRMZM2G123624_T01 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA12G04210.1 (Glycine max), 3'ss of exon 4
----atttttccatgtgtgccataatatcctttgtcactttgtacatttttcttaaaatcaaacctggacaaagcttgttttaagtaatacaaactgtc-atcagGTTGCAGAACCACTGAGAGCTATGGTTATGGGAGCTCCTTTGGAGGATGCCCGCCACCTCGCCCAAAGGTACGACAGAATGCGTCAAGAAGCTGAAGCGC
    || | | |  |||   |||| | |   |  | || | ||   | || |    |    | |||    |     || || |||| ||    | ||   || |||||||||| ||| | || || |||||  |||||||||| ||||||||||| || || || || ||| | || ||||||||||| || ||||||||||| |
ctctatctatactggtggctcatattgttgat--ttacctagtgtgtgttgcc---atcttagcctaataattatgtgattgaagtcatggtcaatgctgattagGTTGCAGAGCCATTAAGGGCAATGGTGGTGGGAGCTCCATTGGAGGATGCTCGGCATCTTGCTCAACGTTATGACAGAATGCGACAGGAAGCTGAAGCCC

upper sequence: GRMZM2G123624_T01 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA04G01100.2 (Glycine max), 3'ss of exon 4
-atttttccatgtgtgccataatatcc--tttgtcactttgtacatttttcttaaaatcaaacctggacaaa-gcttgttttaagtaatacaaactgtcatcagGTTGCAGAACCACTGAGAGCTATGGTTATGGGAGCTCCTTTGGAGGATGCCCGCCACCTCGCCCAAAGGTACGACAGAATGCGTCAAGAAGCTGAAGCGC
 ||  |  |   | || ||   |||||  |||||  |||  |   ||||   |   || |    |   | |  |    ||||||||| | |    ||   | |||||||||| ||  ||||||| ||||| ||||||||||| |||||||||||||| || || || ||| | || ||||||||||| || ||||| ||||| |
tatgctggctcat-tgtcaatttatccaatttgt-gcttgattttttttatctggcataatgtttctgcgagtgaacattttaagtattgcttgatgc--ttagGTTGCAGAGCCCTTGAGAGCAATGGTGATGGGAGCTCCATTGGAGGATGCCCGGCATCTTGCTCAACGTTATGACAGAATGCGGCAGGAAGCCGAAGCAC

upper sequence: GRMZM2G123624_T01 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA06G01120.2 (Glycine max), 3'ss of exon 4
--atttttccatgtgtgccataatatcctttgtcactttgtacatttttcttaaaatcaaacctggacaaa-gcttgttttaagtaatacaaactgtcatcagGTTGCAGAACCACTGAGAGCTATGGTTATGGGAGCTCCTTTGGAGGATGCCCGCCACCTCGCCCAAAGGTACGACAGAATGCGTCAAGAAGCTGAAGCGC
  ||  |  |   | || ||   |||||  | |    |||    ||||   | | || |    |   | |  |    ||||||| | | |    ||   | |||||||||| ||  | ||||| ||||| ||||||||||| |||||||||||||| || || || ||| | || ||||||||||| || ||||| ||||| |
atatgctggctcat-tgtcaatttatccagtttgtgcttgatttttttatctgacataatgtttctgcgagtgaacattttaagaattgcttgatgc--ttagGTTGCAGAGCCCTTAAGAGCAATGGTGATGGGAGCTCCATTGGAGGATGCCCGGCATCTTGCTCAACGTTATGACAGAATGCGGCAGGAAGCCGAAGCCC

upper sequence: GRMZM2G123624_T01 (Zea mays), 3'ss of exon 4
lower sequence: AT4G34660.2 (Arabidopsis thaliana), 3'ss of exon 4
-atttttccatgtgtgccataatatcctttgtcactttgtacatttttcttaaaatcaaacctggacaaagcttgttttaagtaatacaaactgtcatcagGTTGCAGAACCACTGAGAGCTATGGTTATGGGAGCTCCTTTGGAGGATGCCCGCCACCTCGCCCAAAGGTACGACAGAATGCGTCAAGAAGCTGAAGCGC
   |  ||  |    | ||    ||    ||    |   |   || ||  |  | |      |||  |   |     |     ||| |  | | |  | ||||||| || ||| |  | || |||||| |||||||||| |||||||||||  | || || || ||| | || ||||||||||| |||||||||||||| |
acatactctttaaaagtcaattaatgtcatggtgttcacttggttctttctttattgcggtttggctactacaatcatatgtcaatcctgaat-ttgttagGTTGCTGAGCCATTACGGGCAATGGTTTTGGGAGCTCCATTGGAGGATGCTAGACATCTTGCTCAACGCTATGACAGAATGCGCCAAGAAGCTGAAGCTC

upper sequence: GRMZM2G123624_T01 (Zea mays), 3'ss of exon 4
lower sequence: Vv18s0001g13530.t01 (Vitis vinifera), 3'ss of exon 4
atttttccatgtgtgccataatatcctttgtcactttgtacatttttcttaaaatcaaacctggacaaagc----ttgttttaagtaatacaaactgtcatcagGTTGCAGAACCACTGAGAGCTATGGTTATGGGAGCTCCTTTGGAGGATGCCCGCCACCTCGCCCAAAGGTACGACAGAATGCGTCAAGAAGCTGAAGCGC
   ||   |  | |   | | |||| ||    | | |  |  |  |  | |   |   ||||  | || |     || |     ||   |     | |   ||||||| ||||||  | ||||| ||||| ||||||||||| ||||||||||| || || || || ||| | || || ||||||||    ||||||||||| |
---ttaagacatat-ttacattatcattctaaattctccatttaatagtcagtttttcacctttataatgtgtagttatccagtgtttgattctttatttccagGTTGGAGAACCCTTAAGAGCAATGGTAATGGGAGCTCCCTTGGAGGATGCTCGACATCTTGCTCAACGATATGAGAGAATGCGAATGGAAGCTGAAGCTC

upper sequence: GRMZM2G123624_T01 (Zea mays), 3'ss of exon 4
lower sequence: Vv03s0038g00460.t01 (Vitis vinifera), 3'ss of exon 4
atttttccatgtgtgccataatatcctttgtcactttgtacatttttcttaaaatcaaacctggacaaagcttgttttaagtaatacaaactgtcat------cagGTTGCAGAACCACTGAGAGCTATGGTTATGGGAGCTCCTTTGGAGGATGCCCGCCACCTCGCCCAAAGGTACGACAGAATGCGTCAAGAAGCTGAAGCGC
    | |||  | | |   | | ||  || |  ||     | | |||  ||  | ||  | | |  |     || |  | ||  | |  | || | |       |||||||||| ||| | ||||| ||||| ||||||||||| ||||||||||| || || || || ||| | || || |||||||| |||||||||||||| |
--cgtgccactttttc---attttcaattattgctcctctcctatttgctatca-caggcgttgtaatcatgtgctcgatgtggtgctgaatgccttgatttctagGTTGCAGAGCCATTAAGAGCGATGGTAATGGGAGCTCCATTGGAGGATGCTCGACATCTTGCTCAACGCTATGAAAGAATGCGACAAGAAGCTGAAGCTC

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|19822322|gb|BQ048346.1|BQ048346
EST:     CCATGATGGAAAAGGAAAGGGGTAACCTGCTGAAAGCCCTTGGCACACAG                         GTTGCAGAACCACTGAGAGCTATGGTTATGGGAGCTCCTTTGGAGGATGCC
genomic: CCATGATGGAAAAGGAAAGGGGTAACCTGCTGAAAGCCCTTGGCACACAGgtattgccca ... ctgtcatcagGTTGCAGAACCACTGAGAGCTATGGTTATGGGAGCTCCTTTGGAGGATGCC
EST: gi|76935690|gb|DV174431.1|DV174431
EST:     CCATGATGGAAAAGGAAAGGGGTAACCTGCTGAAAGCCCTTGGCACACAG                         GTTGCAGAACCACTGAGAGCTATGGTTATGGGAGCTCCTTTGGAGGATGCC
genomic: CCATGATGGAAAAGGAAAGGGGTAACCTGCTGAAAGCCCTTGGCACACAGgtattgccca ... ctgtcatcagGTTGCAGAACCACTGAGAGCTATGGTTATGGGAGCTCCTTTGGAGGATGCC
EST: gi|149085095|gb|EE174602.2|EE174602
EST:     CCATGATGGAAAAGGAAAGGGGTAACCTGCTGAAAGCCCTTGGCACACAG                         GTTGCAGAACCACTGAGAGCTATGGTTATGGGAGCTCCTTTGGAGGATGCC
genomic: CCATGATGGAAAAGGAAAGGGGTAACCTGCTGAAAGCCCTTGGCACACAGgtattgccca ... ctgtcatcagGTTGCAGAACCACTGAGAGCTATGGTTATGGGAGCTCCTTTGGAGGATGCC
EST: gi|71765024|gb|DR962961.1|DR962961
EST:     CCATGATGGAAAAGGAAAGGGGTAACCTGCTGAAAGCCCTTGGCACACAG                         GTTGCAGAACCACTGAGAGCTATGGTTATGGGAGCTCCTTTGGAGGATGCC
genomic: CCATGATGGAAAAGGAAAGGGGTAACCTGCTGAAAGCCCTTGGCACACAGgtattgccca ... ctgtcatcagGTTGCAGAACCACTGAGAGCTATGGTTATGGGAGCTCCTTTGGAGGATGCC
EST: gi|71768414|gb|DR966351.1|DR966351
EST:     CCATGATGGAAAAGGAAAGGGGTAACCTGCTGAAAGCCCTTGGCACACAG                         GTTGCAGAACCACTGAGAGCTATGGTTATGGGAGCTCCTTTGGAGGATGCC
genomic: CCATGATGGAAAAGGAAAGGGGTAACCTGCTGAAAGCCCTTGGCACACAGgtattgccca ... ctgtcatcagGTTGCAGAACCACTGAGAGCTATGGTTATGGGAGCTCCTTTGGAGGATGCC
EST: gi|33102856|gb|CF062816.1|CF062816
EST:     CCATGATGGAAAAGGAAAGGGGTAACCTGCTGAAAGCCCTTGGCACACAG                         GTTGCAGAACCACTGAGAGCTATGGTTATGGGAGCTCCTTTGGAGGATGCC
genomic: CCATGATGGAAAAGGAAAGGGGTAACCTGCTGAAAGCCCTTGGCACACAGgtattgccca ... ctgtcatcagGTTGCAGAACCACTGAGAGCTATGGTTATGGGAGCTCCTTTGGAGGATGCC
EST: gi|71434707|gb|DR815757.1|DR815757
EST:     CCATGATGGAAAAGGAAAGGGGTAACCTGCTGAAAGCCCTTGGCACACAG                         GTTGCAGAACCACTGAGAGCTATGGTTATGGGAGCTCCTTTGGAGGATGCC
genomic: CCATGATGGAAAAGGAAAGGGGTAACCTGCTGAAAGCCCTTGGCACACAGgtattgccca ... ctgtcatcagGTTGCAGAACCACTGAGAGCTATGGTTATGGGAGCTCCTTTGGAGGATGCC
EST: gi|211244356|gb|FL352760.1|FL352760
EST:     CCATGATGGAAAAGGAAAGGGGTAACCTGCTGAAAGCCCTTGGCACACAG                         GTTGCAGAACCACTGAGAGCTATGGTTATGGGAGCTCCTTTGGAGGATGCC
genomic: CCATGATGGAAAAGGAAAGGGGTAACCTGCTGAAAGCCCTTGGCACACAGgtattgccca ... ctgtcatcagGTTGCAGAACCACTGAGAGCTATGGTTATGGGAGCTCCTTTGGAGGATGCC
EST: gi|20506722|gb|BQ279315.1|BQ279315
EST:     CCATGATGGAAAAGGAAAGGGGTAACCTGCTGAAAGCCCTTGGCACACAG                         GTTGCAGAACCACTGAGAGCTATGGTTATGGGAGCTCCTTTGGAGGATGCC
genomic: CCATGATGGAAAAGGAAAGGGGTAACCTGCTGAAAGCCCTTGGCACACAGgtattgccca ... ctgtcatcagGTTGCAGAACCACTGAGAGCTATGGTTATGGGAGCTCCTTTGGAGGATGCC
EST: gi|33102965|gb|CF062925.1|CF062925
EST:     CCATGATGGAAAAGGAAAGGGGTAACCTGCTGAAAGCCCTTGGCACACAG                         GTTGCAGAACCACTGAGAGCTATGGTTATGGGAGCTCCTTTGGAGGATGCC
genomic: CCATGATGGAAAAGGAAAGGGGTAACCTGCTGAAAGCCCTTGGCACACAGgtattgccca ... ctgtcatcagGTTGCAGAACCACTGAGAGCTATGGTTATGGGAGCTCCTTTGGAGGATGCC
EST: gi|71328410|gb|DR800842.1|DR800842
EST:     CCATGATGGAAAAGGAAAGGGGTAACCTGCTGAAAGCCCTTGGCACACAG                         GTTGCAGAACCACTGAGAGCTATGGTTATGGGAGCTCCTTTGGAGGATGCC
genomic: CCATGATGGAAAAGGAAAGGGGTAACCTGCTGAAAGCCCTTGGCACACAGgtattgccca ... ctgtcatcagGTTGCAGAACCACTGAGAGCTATGGTTATGGGAGCTCCTTTGGAGGATGCC
EST: gi|74244904|gb|DT652818.1|DT652818
EST:     CCATGATGGAAAAGGAAAGGGGTAACCTGCTGAAAGCCCTTGGCACACAG                         GTTGCAGAACCACTGAGAGCTATGGTTATGGGAGCTCCTTTGGAGGATGCC
genomic: CCATGATGGAAAAGGAAAGGGGTAACCTGCTGAAAGCCCTTGGCACACAGgtattgccca ... ctgtcatcagGTTGCAGAACCACTGAGAGCTATGGTTATGGGAGCTCCTTTGGAGGATGCC
EST: gi|74239024|gb|DT646938.1|DT646938
EST:     CCATGATGGAAAAGGAAAGGGGTAACCTGCTGAAAGCCCTTGGCACACAG                         GTTGCAGAACCACTGAGAGCTATGGTTATGGGAGCTCCTTTGGAGGATGCC
genomic: CCATGATGGAAAAGGAAAGGGGTAACCTGCTGAAAGCCCTTGGCACACAGgtattgccca ... ctgtcatcagGTTGCAGAACCACTGAGAGCTATGGTTATGGGAGCTCCTTTGGAGGATGCC
EST: gi|211529255|gb|FL011602.1|FL011602
EST:     CCATGATGGAAAAGGAAAGGGGTAACCTGCTGAAAGCCCTTGGCACACAG                         GTTGCAGAACCACTGAGAGCTATGGTTATGGGAGCTCCTTTGGAGGATGCC
genomic: CCATGATGGAAAAGGAAAGGGGTAACCTGCTGAAAGCCCTTGGCACACAGgtattgccca ... ctgtcatcagGTTGCAGAACCACTGAGAGCTATGGTTATGGGAGCTCCTTTGGAGGATGCC
EST: gi|211250291|gb|FL313176.1|FL313176
EST:     CCATGATGGAAAAGGAAAGGGGTAACCTGCTGAAASSCCTTGGCACACAG                         GTTGCAGAACCACTGAGAGCTATGGTTATGGGAG
genomic: CCATGATGGAAAAGGAAAGGGGTAACCTGCTGAAAGCCCTTGGCACACAGgtattgccca ... ctgtcatcagGTTGCAGAACCACTGAGAGCTATGGTTATGGGAG

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: 314

CAGTGGTAGCACACTGTCGAAGGCGGCATTAAGTTTTGCTAAGGCACGGTCCATGATGGAAAAGGAAAGGGGTAACCTGCTGAAAGCCCTTGGCACACAGgtattgccca ... ctgtcatcagGTTGCAGAACCACTGAGAGCTATGGTTATGGGAGCTCCTTTGGAGGATGCCCGCCACCTCGCCCAAAGGTACGACAGAATGCGTCAAGAAGCTGAAGCGC


Block sizes: 45 (upstream exon), 49 (downstream exon)
Score: 182

CAGTGGTAGCACACTGTCGAAGGCGGCATTAAGTTTTGCTAAGGCACGGTCCATGATGGAAAAGGAAAGGGGTAACCTGCTGAAAGCCCTTGGCACACAGgtattgccca ... ctgtcatcagGTTGCAGAACCACTGAGAGCTATGGTTATGGGAGCTCCTTTGGAGGATGCCCGCCACCTCGCCCAAAGGTACGACAGAATGCGTCAAGAAGCTGAAGCGC


Block sizes: 46 (upstream exon), 47 (downstream exon)
Score: 96

CAGTGGTAGCACACTGTCGAAGGCGGCATTAAGTTTTGCTAAGGCACGGTCCATGATGGAAAAGGAAAGGGGTAACCTGCTGAAAGCCCTTGGCACACAGgtattgccca ... ctgtcatcagGTTGCAGAACCACTGAGAGCTATGGTTATGGGAGCTCCTTTGGAGGATGCCCGCCACCTCGCCCAAAGGTACGACAGAATGCGTCAAGAAGCTGAAGCGC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 223

CAGTGGTAGCACACTGTCGAAGGCGGCATTAAGTTTTGCTAAGGCACGGTCCATGATGGAAAAGGAAAGGGGTAACCTGCTGAAAGCCCTTGGCACACAGgtattgccca ... ctgtcatcagGTTGCAGAACCACTGAGAGCTATGGTTATGGGAGCTCCTTTGGAGGATGCCCGCCACCTCGCCCAAAGGTACGACAGAATGCGTCAAGAAGCTGAAGCGC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcttaaaatcaaacctggacaaagcttgttttaagtaatacaaactgtcatcagGTTGCAGAACCACTGAGAGCTATGGTTATGGGAGCTCCTTTGGAGGATGCCCGCCACCTCGCCCAAAGGTACGACAGAATGCGTCAAGAAGCTGAAGCGC
                             ttttaagtaatacaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atttttccatgtgtgccataatatcctttgtcactttgtacatttttcttaaaatcaaacctggacaaagcttgttttaagtaatacaaactgtcatcagGTTGCAGAACCACTGAGAGCTATGGTTATGGGAGCTCCTTTGGAGGATGCCCGCCACCTCGCCCAAAGGTACGACAGAATGCGTCAAGAAGCTGAAGCGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - -catgtgt
- - - - - - - - - - - - - - - - - - - - - - - - - aaaatcaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - acctgga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cttgttt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -atacaaa