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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cccacagaaatttgggaatacaataagtatgtgaagatagatttgttacatttagtaattctgctaacaaaaactgaatttattttttcctttttgctagGGCACCTAACACACATGACAATGCGGCATCAAATCTTCTGTCTGGAAGGAATGTTGACACAATAATTAACCAGCTAATGGAGATGGGTGGGGGCAGTTGG

Basic information

species Zea mays
transcript GRMZM2G143462_T04
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G143462_T06 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os02g08300.1 (Oryza sativa), 3'ss of exon 5
cccacagaaatttgggaatacaataagtatgtgaagatagatttgttacatttagtaattctgctaacaaaaactgaatttattt--------tttcctttttgctagGGCACCT---AACACACATGACAATGCGGCATCAAATCTTCTGTCTGGAAGGAATGTTGACACAATAATTAACCAGCTAATGGAGATGGGTGGGGGCAGTTGG
      | ||  | |   |  | |     | |||| || | ||       |||| |  ||||  | | | | |||  || |  ||        ||   ||| |  ||| || |||   ||| || |||   | || |||||||||||  |||| ||||| ||| ||||||| |  ||||||||||| ||||| |||||||| ||||||   
-----tggaagatagatctgaattggtcttatgaatatgggttccac-tgtttact--ttctaatgaaatatactttatatgcttgctaaaacttatttttattttagAGCCCCTTCAAACGCATATGGTCAAGCAGCATCAAATCTATTGTCGGGAAGCAATCTTGACACTACGATTAACCAGCTGATGGAAATGGGTGGTGGCAGT---
















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|211394218|gb|FL229512.1|FL229512
EST:     GGTGGCACCAATTACAACTTCTCAGCCTGAAGGACTTCCTGCACA                         GGCACCTAACACACATGACAATGCGGCATCAAATCTTCTGTCTGGAAGGAA
genomic: GGTGGCACCAATTACAACTTCTCAGCCTGAAGGACTTCCTGCACAgtatatttcc ... tttttgctagGGCACCTAACACACATGACAATGCGGCATCAAATCTTCTGTCTGGAAGGAA
EST: gi|149095756|gb|EE181396.2|EE181396
EST:     GGTGGCACCAATTACAACTTCTCAGCCTGAAGGACTTCCTGCACA                         GGCACCTAACACACATGACAATGCGGCATCAAATCTTCTGTCTGGAAGGAA
genomic: GGTGGCACCAATTACAACTTCTCAGCCTGAAGGACTTCCTGCACAgtatatttcc ... tttttgctagGGCACCTAACACACATGACAATGCGGCATCAAATCTTCTGTCTGGAAGGAA
EST: gi|148995692|gb|EE034914.2|EE034914
EST:     GGTGGCACCAATTACAACTTCTCAGCCTGAAGGACTTCCTGCACA                         GGCACCTAACACACATGACAATGCGGCATCAAATCTTCTGTCTGGAAGGAA
genomic: GGTGGCACCAATTACAACTTCTCAGCCTGAAGGACTTCCTGCACAgtatatttcc ... tttttgctagGGCACCTAACACACATGACAATGCGGCATCAAATCTTCTGTCTGGAAGGAA
EST: gi|89759371|gb|DY688230.1|DY688230
EST:     GGTGGCACCAATTACAACTTCTCAGCCTGAAGGACTTCCTGCACA                         GGCACCTAACACACATGACAATGCGGCATCAAATCTTCTGTCTGGAAGGAA
genomic: GGTGGCACCAATTACAACTTCTCAGCCTGAAGGACTTCCTGCACAgtatatttcc ... tttttgctagGGCACCTAACACACATGACAATGCGGCATCAAATCTTCTGTCTGGAAGGAA
EST: gi|30306905|gb|CD001578.1|CD001578
EST:     GGTGGCACCAATTACAACTTCTCAGCCTGAAGGACTTCCTGCACA                         GGCACCTAACACACATGACAATGCGGCATCAAA
genomic: GGTGGCACCAATTACAACTTCTCAGCCTGAAGGACTTCCTGCACAgtatatttcc ... tttttgctagGGCACCTAACACACATGACAATGCGGCATCAAA
EST: gi|74242202|gb|DT650116.1|DT650116
EST:     GGTGGCACCAATTACAACTTCTCAGCCTGAAGGACTTCCTGCACA                         GGCACCTAACACACATGACAATGCGGCATCAAATCTTCTGTCTGGAAGGAA
genomic: GGTGGCACCAATTACAACTTCTCAGCCTGAAGGACTTCCTGCACAgtatatttcc ... tttttgctagGGCACCTAACACACATGACAATGCGGCATCAAATCTTCTGTCTGGAAGGAA
EST: gi|148947026|gb|EC892323.2|EC892323
EST:     GGTGGCACCAATTACAACTTCTCAGCCTGAAGGACTTCCTGCACA                         GGCACCTAACACACATGACAATGCGGCATCAAATCTTCTGTCTGGAAGGAA
genomic: GGTGGCACCAATTACAACTTCTCAGCCTGAAGGACTTCCTGCACAgtatatttcc ... tttttgctagGGCACCTAACACACATGACAATGCGGCATCAAATCTTCTGTCTGGAAGGAA
EST: gi|89758471|gb|DY687642.1|DY687642
EST:     GGTGGCACCAATTACAACTTCTCAGCCTGAAGGACTTCCTGCACA                         GGCACCTAACACACATGACAATGCGGCATCAAATCTTCTGTCTGGAAGGAA
genomic: GGTGGCACCAATTACAACTTCTCAGCCTGAAGGACTTCCTGCACAgtatatttcc ... tttttgctagGGCACCTAACACACATGACAATGCGGCATCAAATCTTCTGTCTGGAAGGAA
EST: gi|89761592|gb|DY689541.1|DY689541
EST:     GGTGGCACCAATTACAACTTCTCAGCCTGAAGGACTTCCTGCACA                         GGCACCTAACACACATGACAATGCGGCATCAAATCTTCTGTCTGGAAGGAA
genomic: GGTGGCACCAATTACAACTTCTCAGCCTGAAGGACTTCCTGCACAgtatatttcc ... tttttgctagGGCACCTAACACACATGACAATGCGGCATCAAATCTTCTGTCTGGAAGGAA
EST: gi|9731840|gb|BE510592.1|BE510592
EST:     GGTGGCACCAATTACAACTTCTCAGCCTGAAGGACTTCCTGCACA                         GGCACCTAACACACATGACAATGCGGCATCAAATCTTCTGTCTGGAAGGAA
genomic: GGTGGCACCAATTACAACTTCTCAGCCTGAAGGACTTCCTGCACAgtatatttcc ... tttttgctagGGCACCTAACACACATGACAATGCGGCATCAAATCTTCTGTCTGGAAGGAA
EST: gi|211394220|gb|FL229514.1|FL229514
EST:     GGTGGCACCAATTACAACTTCTCAGCCTGAAGGACTTCCTGCACA                         GGCACCTAACACACATGACAATGCGGCATCAAATCTTCTGTCTGGAAGGAA
genomic: GGTGGCACCAATTACAACTTCTCAGCCTGAAGGACTTCCTGCACAgtatatttcc ... tttttgctagGGCACCTAACACACATGACAATGCGGCATCAAATCTTCTGTCTGGAAGGAA
EST: gi|211488314|gb|FK957004.1|FK957004
EST:     GGTGGCACCAATTACAACTTCTCAGCCTGAAGGACTTCCTGCACA                         GGCACCTAACACACATGACAATGCGGCATCAAATCTTCTGTCTGGAAGGAA
genomic: GGTGGCACCAATTACAACTTCTCAGCCTGAAGGACTTCCTGCACAgtatatttcc ... tttttgctagGGCACCTAACACACATGACAATGCGGCATCAAATCTTCTGTCTGGAAGGAA
EST: gi|78111156|gb|DV529553.1|DV529553
EST:     GGTGGCACCAATTACAACTTCTCAGCCTGAAGGACTTCCTGCACA                         GGCACCTAACACACATGACAATGCGGCATCAAATCTTCTGTCTGGAAGGAA
genomic: GGTGGCACCAATTACAACTTCTCAGCCTGAAGGACTTCCTGCACAgtatatttcc ... tttttgctagGGCACCTAACACACATGACAATGCGGCATCAAATCTTCTGTCTGGAAGGAA
EST: gi|148999208|gb|EE036127.2|EE036127
EST:     GGTGGCACCAATTACAACTTCTCAGCCTGAAGGACTTCCTGCACA                         GGCACCTAACACACATGACAATGCGGCATCAAATCTTCTGTCTGGAAGGAA
genomic: GGTGGCACCAATTACAACTTCTCAGCCTGAAGGACTTCCTGCACAgtatatttcc ... tttttgctagGGCACCTAACACACATGACAATGCGGCATCAAATCTTCTGTCTGGAAGGAA
EST: gi|211491194|gb|FK957015.1|FK957015
EST:     GGTGGCACCAATTACAACTTCTCAGCCTGAAGGACTTCCTGCACA                         GGCACCTAACACACATGACAATGCGGCATCAAATCTTCTGT
genomic: GGTGGCACCAATTACAACTTCTCAGCCTGAAGGACTTCCTGCACAgtatatttcc ... tttttgctagGGCACCTAACACACATGACAATGCGGCATCAAATCTTCTGT
EST: gi|93280956|gb|EB673220.1|EB673220
EST:     GGTGGCACCAATTACAACTTCTCAGCCTGAAGGACTTCCTGCACA                         GGCACCTAACACACATGACAATGCGGCATCAAATCTTCTGTCTGGAAGGAA
genomic: GGTGGCACCAATTACAACTTCTCAGCCTGAAGGACTTCCTGCACAgtatatttcc ... tttttgctagGGCACCTAACACACATGACAATGCGGCATCAAATCTTCTGTCTGGAAGGAA
EST: gi|71771539|gb|DR969476.1|DR969476
EST:     GGTGGCACCAATTACAACTTCTCAGCCTGAAGGACTTCCTGCACA                         GGCACCTAACACACATGACAATGCGGCATCAAATCTTCTGTCTGGAAGGAA
genomic: GGTGGCACCAATTACAACTTCTCAGCCTGAAGGACTTCCTGCACAgtatatttcc ... tttttgctagGGCACCTAACACACATGACAATGCGGCATCAAATCTTCTGTCTGGAAGGAA
EST: gi|32805412|gb|CD957648.1|CD957648
EST:     GGTGGCACCAATTACAACTTCTCAGCCTGAAGGACTTCCTGCACA                         GGCACCTAACACACATGACAATGCGGCATCAAATCTTCTGTCTGGAAGGAA
genomic: GGTGGCACCAATTACAACTTCTCAGCCTGAAGGACTTCCTGCACAgtatatttcc ... tttttgctagGGCACCTAACACACATGACAATGCGGCATCAAATCTTCTGTCTGGAAGGAA
EST: gi|76912415|gb|DV164721.1|DV164721
EST:     GGTGGCACCAATTACAACTTCTCAGCCTGAAGGACTTCCTGCACA                         GGCACCTAACACACATGACAATGCGGCATCAAATCTTCTGTCTGGAAGGAA
genomic: GGTGGCACCAATTACAACTTCTCAGCCTGAAGGACTTCCTGCACAgtatatttcc ... tttttgctagGGCACCTAACACACATGACAATGCGGCATCAAATCTTCTGTCTGGAAGGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttacatttagtaattctgctaacaaaaactgaatttattttttcctttttgctagGGCACCTAACACACATGACAATGCGGCATCAAATCTTCTGTCTGGAAGGAATGTTGACACAATAATTAACCAGCTAATGGAGATGGGTGGGGGCAGTTGG
                tgctaac  putative branch site (score: 1)
                                 tttattttttcctttt  putative PPT
                       aaaaactgaatttatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cccacagaaatttgggaatacaataagtatgtgaagatagatttgttacatttagtaattctgctaacaaaaactgaatttattttttcctttttgctagGGCACCTAACACACATGACAATGCGGCATCAAATCTTCTGTCTGGAAGGAATGTTGACACAATAATTAACCAGCTAATGGAGATGGGTGGGGGCAGTTGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATG