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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtactgtattactgtttcaagaaacgcgtactattcaattcaatctgatgtcatagcaggctaaaccttacagtggttttatctgtagGGTATTGTTGACTCGGACACGCTGCCCCTGAACGTGTCACGAGAAATGCTTCAACAACATAGCAGTCTCAAGACCATCAAGAAGAAGCTGATCCGCAAAG

Basic information

species Zea mays
transcript GRMZM2G141931_T01
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G141931_T02 (Zea mays), 3'ss of exon 10
lower sequence: LOC_Os06g50300.1 (Oryza sativa), 3'ss of exon 10
gtactgtattactgtttcaagaaacgcgtactattcaattcaatctgatgtcatagcaggctaaaccttacagtggttttatctgtagGGTATTGTTGACTCGGACACGCTGCCCCTGAACGTGTCACGAGAAATGCTTCAACAACATAGCAGTCTCAAGACCATCAAGAAGAAGCTGATCCGCAAAG
|||||  |||||| ||||| |||   |    ||||| |||||   |||  | || |||| ||||||||   ||   | ||||||||||||| | || |||||||||||  |||| || || || |||||||||||||| |||||||||||||| || ||||||||||||||||| || ||||||||||
gtactagattactatttcatgaacgacacggtattccattca--ttgac-ttat-gcagcctaaacctataagc--tattatctgtagGGTCTCGTCGACTCGGACACATTGCCTCTCAATGTATCACGAGAAATGCTCCAACAACATAGCAGCCTGAAGACCATCAAGAAGAAACTAATCCGCAAAG

upper sequence: GRMZM2G141931_T02 (Zea mays), 3'ss of exon 10
lower sequence: GLYMA14G40320.3 (Glycine max), 3'ss of exon 10
---------gtactgtattactgtttcaag-aaacgcgtactattcaattcaatctgatgtcatagcaggctaaaccttacagtggttttatctgtagGGTATTGTTGACTCGGACACGCTGCCCCTGAACGTGTCACGAGAAATGCTTCAACAACATAGCAGTCTCAAGACCATCAAGAAGAAGCTGATCCGCAAAG
         ||  ||  ||  | || ||   |||    |  |||     |||   | || |  | ||   | ||   ||    ||   ||      ||||| ||||||| || |||||  |||| || || || |||||||||||||||||||||||||| ||||| ||||| ||||||||||| || ||  | ||||
gtaggcattgttgtgctttgttattgcagataaatatattttatgaggatcataataattt--ttgctaacaaatgtttcttttgacgttgggaacagGGTCTTGTTGATTCTGACACTTTGCCACTTAATGTATCACGAGAAATGCTTCAACAACATAGTAGTCTGAAGACAATCAAGAAGAAACTTATTAGGAAAG

upper sequence: GRMZM2G141931_T02 (Zea mays), 3'ss of exon 10
lower sequence: GLYMA17G37820.1 (Glycine max), 3'ss of exon 10
----------gtactgtattactgtttcaagaaacgcgtactattcaat--tcaatctgatgtcatagcaggctaaaccttacagt-ggttttatctgtagGGTATTGTTGACTCGGACACGCTGCCCCTGAACGTGTCACGAGAAATGCTTCAACAACATAGCAGTCTCAAGACCATCAAGAAGAAGCTGATCCGCAAAG
          ||  ||  ||  | || ||   ||    || | |   ||  |||   | || |  | ||    ||||  ||||  | |   ||      ||||| ||||||| || |||||  |||| || || || || |||||||||||||| |||||||| ||||| ||||| ||||||||||| || ||  | ||| 
ggtaggaattgttgtgctttgttattgcagataaaatatattttatgatgatcagaataattt--ttgctaa-taaatgttacttttgacgttgggaacaGGGTCTTGTTGATTCTGACACATTGCCACTTAATGTATCGCGAGAAATGCTTCAGCAACATAGTAGTCTAAAGACAATCAAGAAGAAACTTATTAGGAAA-

upper sequence: GRMZM2G141931_T02 (Zea mays), 3'ss of exon 10
lower sequence: AT4G24190.2 (Arabidopsis thaliana), 3'ss of exon 10
gtactgtattactgtttcaagaaacgcgtactattcaattcaatctgatgtcatagcaggctaaa--ccttacagtggttttatctgtagGGTATTGTTGACTCGGACACGCTGCCCCTGAACGTGTCACGAGAAATGCTTCAACAACATAGCAGTCTCAAGACCATCAAGAAGAAGCTGATCCGCAAAG
    |  | |||  ||  |||| |  |  |    |   ||||||   |  | ||    |||||||  ||| ||    |||   | || ||||| |||||||||| |||||  |||| || || || ||| ||||||||||||||||||| |||||  | ||||| || ||||||||||| ||||| || |
---gtaaactac--ttgaaagacaaactaaggggttctttcaatacaaatttatg---ggctaaatccctaacgtgagttgcttttgcagGGTCTTGTTGACTCTGACACATTGCCTCTAAATGTATCAAGAGAAATGCTTCAACAACACAGCAGCTTAAAGACAATTAAGAAGAAGCTTATCCGAAAGG

upper sequence: GRMZM2G141931_T02 (Zea mays), 3'ss of exon 10
lower sequence: Vv18s0001g14500.t01 (Vitis vinifera), 3'ss of exon 10
gtactgtattactgtttcaaga---aacgcgtactattcaattcaat--ctgatgtcatag---caggctaaaccttaca---gtggttttatctgtagGGTATTGTTGACTCGGACACGCTGCCCCTGAACGTGTCACGAGAAATGCTTCAACAACATAGCAGTCTCAAGACCATCAAGAAGAAGCTGATCCGCAAAG
||  |  || | | | | ||     |  | || ||  | || |  |    | |||   |||    ||     |   || |   |||   || |  | ||||| |||| || || |||||| | || || || || ||||||||||||||||||||||| |||||| | || || || ||||||||||| |||||||| |
gttataaatcaatttataaattcctattgggttcttgtaaactggagaatttatgaattaggtttagaagtgattctaaatgggtgacgttttgagcagGGTCTTGTAGATTCCGACACGTTACCTCTTAATGTTTCACGAGAAATGCTTCAACAACACAGCAGTTTGAAAACAATTAAGAAGAAGCTTATCCGCAAGG

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|211354989|gb|FL245114.1|FL245114
EST:     TCTCTGACGAATTTGATGATCTTCTTCCCAAGTACCTGAGCTTTTTGAAG                         GGTATTGTTGACTCGGACACGCTGCCCCTGAATGTGTCACGAGAAATGCTT
genomic: TCTCTGACGAATTTGATGATCTTCTTCCCAAGTACCTGAGCTTTTTGAAGgtactgtatt ... ttatctgtagGGTATTGTTGACTCGGACACGCTGCCCCTGAACGTGTCACGAGAAATGCTT
EST: gi|31354312|gb|CD438669.1|CD438669
EST:     TCTCTGACGAATTTGATGATCTTCTTCCCAAGTACCTGAGCTTTTTGAAG                         GGTATTGTTGACTCGGACACGCTGCCCCTGAACGTGTCACGAGAAATGCTT
genomic: TCTCTGACGAATTTGATGATCTTCTTCCCAAGTACCTGAGCTTTTTGAAGgtactgtatt ... ttatctgtagGGTATTGTTGACTCGGACACGCTGCCCCTGAACGTGTCACGAGAAATGCTT
EST: gi|32847287|gb|CD986968.1|CD986968
EST:     ACCTGAGCTTTTTGAAG                         GGTATTGTTGACTCGGACACGCTGCCCCTGAACGTGTCACGAGAAATGCTT
genomic: ACCTGAGCTTTTTGAAGgtactgtatt ... ttatctgtagGGTATTGTTGACTCGGACACGCTGCCCCTGAACGTGTCACGAGAAATGCTT
EST: gi|67017884|gb|CO446633.1|CO446633
EST:     TCTCTGACGAATTTGATGATCTTCTTCCCAAGTACCTGAGCTTTTTGAAG                         GGTATTGTTGACTCGGACACGCTGCCCCTGAACGTGTCACGAGAAATGCTT
genomic: TCTCTGACGAATTTGATGATCTTCTTCCCAAGTACCTGAGCTTTTTGAAGgtactgtatt ... ttatctgtagGGTATTGTTGACTCGGACACGCTGCCCCTGAACGTGTCACGAGAAATGCTT
EST: gi|60344141|gb|DN211114.1|DN211114
EST:     TCTCTGACGAATTTGATGATCTTCTTCCCAAGTACCTGAGCTTTTTGAAG                         GGTATTGTTGACTCGGACACGCTGCCCCTGAACGTGTCACGAGAAATGCTT
genomic: TCTCTGACGAATTTGATGATCTTCTTCCCAAGTACCTGAGCTTTTTGAAGgtactgtatt ... ttatctgtagGGTATTGTTGACTCGGACACGCTGCCCCTGAACGTGTCACGAGAAATGCTT
EST: gi|31356123|gb|CD440480.1|CD440480
EST:     TCTCTGACGAATTTGATGATCTTCTTCCCAAGTACCTGAGCTTTTTGAAG                         GGTATTGTTGACTCGGACACGCTGCCCCTGAACGTGTCACGAGAAATGCTT
genomic: TCTCTGACGAATTTGATGATCTTCTTCCCAAGTACCTGAGCTTTTTGAAGgtactgtatt ... ttatctgtagGGTATTGTTGACTCGGACACGCTGCCCCTGAACGTGTCACGAGAAATGCTT
EST: gi|21987199|gb|BQ778727.1|BQ778727
EST:     TCTCTGACGAATTTGATGATCTTCTTCCCAAGTACCTGAGCTTTTTGAAG                         GGTATTGTTGACTCGGACACCCTGCCCCTGAACGTGTCACGAGAAATGCTT
genomic: TCTCTGACGAATTTGATGATCTTCTTCCCAAGTACCTGAGCTTTTTGAAGgtactgtatt ... ttatctgtagGGTATTGTTGACTCGGACACGCTGCCCCTGAACGTGTCACGAGAAATGCTT
EST: gi|26456287|gb|CA827870.1|CA827870
EST:     TCTCTGACGAATTTGATGATCTTCTTCCCAAGTACCTGAGCTTTTTGAAG                         GGTATTGTTGACTCGGACACGCTGCCCCTGAACGTGTCACGAGAAATGCTT
genomic: TCTCTGACGAATTTGATGATCTTCTTCCCAAGTACCTGAGCTTTTTGAAGgtactgtatt ... ttatctgtagGGTATTGTTGACTCGGACACGCTGCCCCTGAACGTGTCACGAGAAATGCTT
EST: gi|7227450|gb|AW566091.1|AW566091
EST:     TCTCTGACGAATTTGATGATCTTCTTCCCAAGTACCTGAGCTTTTTGAAG                         GGTATTGTTGACTCGGACACGCTGCCCCTGAACGTGTCACGAGAAATGCTT
genomic: TCTCTGACGAATTTGATGATCTTCTTCCCAAGTACCTGAGCTTTTTGAAGgtactgtatt ... ttatctgtagGGTATTGTTGACTCGGACACGCTGCCCCTGAACGTGTCACGAGAAATGCTT
EST: gi|21987561|gb|BQ779089.1|BQ779089
EST:     TCTCTGACGAATTTGATGATCTTCTTCCCAAGTACCTGAGCTTTTTGAAG                         GGTATTGTTGACTCGGACACCCTGCCCCTGAACGTGTCACGAGAAATGCTT
genomic: TCTCTGACGAATTTGATGATCTTCTTCCCAAGTACCTGAGCTTTTTGAAGgtactgtatt ... ttatctgtagGGTATTGTTGACTCGGACACGCTGCCCCTGAACGTGTCACGAGAAATGCTT
EST: gi|67040100|gb|CO466355.1|CO466355
EST:     TCTCTGACGAATTTGATGATCTTCTTCCCAAGTACCTGAGCTTTTTGAAG                         GGTATTGTTGACTCGGACACGCTGCCCCTGAACGTGTCACGAGAAATGCTT
genomic: TCTCTGACGAATTTGATGATCTTCTTCCCAAGTACCTGAGCTTTTTGAAGgtactgtatt ... ttatctgtagGGTATTGTTGACTCGGACACGCTGCCCCTGAACGTGTCACGAGAAATGCTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcaattcaatctgatgtcatagcaggctaaaccttacagtggttttatctgtagGGTATTGTTGACTCGGACACGCTGCCCCTGAACGTGTCACGAGAAATGCTTCAACAACATAGCAGTCTCAAGACCATCAAGAAGAAGCTGATCCGCAAAG
                               accttac  putative branch site (score: 3)
                                           ttttatct  putative PPT
                                           ttttatct  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtactgtattactgtttcaagaaacgcgtactattcaattcaatctgatgtcatagcaggctaaaccttacagtggttttatctgtagGGTATTGTTGACTCGGACACGCTGCCCCTGAACGTGTCACGAGAAATGCTTCAACAACATAGCAGTCTCAAGACCATCAAGAAGAAGCTGATCCGCAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG