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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttgtttccgataaaaaaatatgaaaacggtaatggttttagtgtttaccgaccgtttccgaccgttttaatccctattcagtgatatgtctgtttcacagGAATCTTGCCCTTCTGTGAAGAACATTTTACTTCTGGATTCTGAAGGAAAGCGTGTTGCTGTAAAGTATTTCTCAGATGATTGGCCGACTAATGCATCAA

Basic information

species Zea mays
transcript GRMZM2G314679_T04
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G314679_T05 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os02g21250.1 (Oryza sativa), 3'ss of exon 2
ttgtttccgataaaaaaatatgaaa-acggtaatggttttagtgtttaccgaccgtttcc--gaccgttttaatccctattcagtgat-atgtctgtttcacagGAATCTTGCCCTTCTGTGAAGAACATTTTACTTCTGGATTCTGAAGGAAAGCGTGTTGCTGTAAAGTATTTCTCAGATGATTGGCCGACTAATGCATCAA
 || ||  | | |  ||  ||||||  | | | |   |  |   ||| | | || || |     |   | ||||   |  | | ||   || |  ||| |||||||||||||||||||||||||||||||||| ||||||||||||||||| || |||||||| || || || ||||| ||||||||| | | |||||| ||||
-tgcttttgttgatgaa-catgaaatgcagcattaagt--aactttttctgtcctttgcacaagctcatgtaatgattcatgattgtccattttcgttacacagGAATCTTGCCCTTCTGTGAAGAACATTTTGCTTCTGGATTCTGAAGGGAAACGTGTTGCCGTGAAATACTTCTCGGATGATTGGTCTAGTAATGCGTCAA

upper sequence: GRMZM2G314679_T05 (Zea mays), 3'ss of exon 2
lower sequence: AT3G09800.1 (Arabidopsis thaliana), 3'ss of exon 2
------------------------------ttgtttccgataaaaaaatatgaaaacggtaatggttttagtgtttaccgaccgtttccgaccgtttt------aatccctattcagtgat------atgtctgtttcacagGAATCTTGCCCTTCTGTGAAGAACATTTTACTTCTGGATTCTGAAGGAAAGCGTGTTGCTGTAAAGTATTTCTCAGATGATTGGCCGACTAATGCATCAA
                              | || | |  | | ||  | || |    |      |  ||  | ||       ||||    |  ||||          | || | | |||       ||||   ||  | |||| ||||| ||||  || ||||| ||| | ||||| || ||||||||||||||||| ||||| ||||||| ||| ||||| ||||| ||||||||  | |
gtaagtacatatgcattatatgattgtatttcgtattctgttagaatgtgtgtatgttgccgcaatcatacagctttgtaggagttttactctttttttggactggaacttaattactgactttccaatgtacattgaatagGATTCTTGTCCTTTGGTAAAGAAGATTCTTCTTCTAGACTCTGAAGGAAAGCGTGTGGCTGTCAAGTATTACTCGGATGACTGGCCAACTAATGCCGCCA

upper sequence: GRMZM2G314679_T05 (Zea mays), 3'ss of exon 2
lower sequence: AT4G08520.1 (Arabidopsis thaliana), 3'ss of exon 2
-ttgtttccgataaaaaaat--atgaaaacggtaatggttttagtgtttaccgaccgtttccgaccgttttaatccctattcagtgatatgtctgtttcacagGAATCTTGCCCTTCTGTGAAGAACATTTTACTTCTGGATTCTGAAGGAAAGCGTGTTGCTGTAAAGTATTTCTCAGATGATTGGCCGACTAATGCATCAA
   |||     | | |  ||  ||   || | |  | | ||  |  | | |    | | ||  |    ||  || |  | |   || | |      |  | |||| ||||| ||||  || ||||||||| | ||||| || ||||||||||||||||| ||||| ||||||| ||| ||||||||| | |||||||| || |
gaagttcaaacttacatgatccattttaaggattctcgcttctgcttgtgcttctc-tctcttagtacttacatgctgactatctggtcta--caatgaatagGATTCTTGTCCTTTGGTAAAGAACATTCTTCTTCTAGACTCTGAAGGAAAGCGTGTGGCTGTCAAGTATTACTCCGATGATTGGGCAACTAATGCTTCCA

upper sequence: GRMZM2G314679_T05 (Zea mays), 3'ss of exon 2
lower sequence: AT1G60970.1 (Arabidopsis thaliana), 3'ss of exon 1
ttgtttccgataaaaaaatatgaaaacggtaatggttttagtgtttaccgaccgtttccgaccgttttaatccctattcagtgatatgtctgtttcac--------agGAATCTTGCCCTTCTGTGAAGAACATTTTACTTCTGGATTCTGAAGGAAAGCGTGTTGCTGTAAAGTATTTCTCAGATGATTGGCCGACTAATGCATCAA
    || |  |  |   ||       | || |    |||  || ||   ||   ||||      | ||||||  |||||  |  | ||| |   | ||        ||||||    |||    ||||| ||||| || ||| |||||||||||||||||||||| || || ||||||| ||||||||| ||||| || ||| || |  
----ttactgttcactgattcatgttctgttacatcttt--tggttggtgat--tttcaatatctcttaatctttattctattctgtgttttcattacttacatttagGAATTGCCCCCAAAAGTGAAAAACATCTTGCTTTTGGATTCTGAAGGAAAGCGTGTAGCGGTTAAGTATTACTCAGATGACTGGCCAACAAATTCAGCTC

upper sequence: GRMZM2G314679_T05 (Zea mays), 3'ss of exon 2
lower sequence: Vv09s0002g01710.t01 (Vitis vinifera), 3'ss of exon 1
ttgtttccgataaaaaaatatgaaaacggtaatggtttta--gtgtttaccgaccgtttccgaccgttttaatccctattcagtgatatgtctgtttcacagGAATCTTGCCCTTCTGTGAAGAACATTTTACTTCTGGATTCTGAAGGAAAGCGTGTTGCTGTAAAGTATTTCTCAGATGATTGGCCGACTAATGCATCAA---
 |  || | ||         |      ||  |||  || |   |||| |  |     |||  | |  || |     | ||  ||  | | | | ||| | |||   ||||||| ||| | || |||||| | ||||||||||||||||| |||||||| || || || |||| ||| ||||||||||| || |||||  |||   
-ttctttcaatcttttttattttgtttggacatgcattcatcatgttaattgttttcttctaatcaattcagattttgttttgttttgt-tttcttttatagG---CTTGCCCCTCTATAAAAAACATTCTTCTTCTGGATTCTGAAGGGAAGCGTGTGGCAGTCAAATATTACTCCGATGATTGGCCAACAAATGCTGCAAAAT

upper sequence: GRMZM2G314679_T05 (Zea mays), 3'ss of exon 2
lower sequence: Vv10s0003g02760.t01 (Vitis vinifera), 3'ss of exon 2
--------ttgtttccgataaaaaaatatgaaaacggtaatggttttagtgtttaccgaccgtttccgaccgttttaatccctattcagtgatatgtctgtttcacagGAATCTTGCCCTTCTGTGAAGAACATTTTACTTCTGGATTCTGAAGGAAAGCGTGTTGCTGTAAAGTATTTCTCAGATGATTGGCCGACTAATGCATCAA
        |    |     |     || |   |   | |     |||||| || |   ||      || |   | | ||   |||  | |  | | | | ||||| |||| || ||||||||||| || |||||| | || ||||||||||||||||| ||||| ||||| ||||| |  |  || || ||||| || |||    | |
aaacaaattcaaatttatcattcctatgtagtagttg-agcacatttagttttcatgaact-----cgcctagtctgatatttatgtaat--tttttttttttcatagGAGTCATGCCCTTCTGTAAAAAACATTCTCCTCCTGGATTCTGAAGGAAAACGTGTAGCTGTCAAGTACTATTGTGACGACTGGCCAACAAATAATGCTA

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|211282262|gb|FL038864.1|FL038864
EST:     GGTGGAATAGGGAACGGCCATACACCATGGCGGATTTCTCCAAG                         GAATCTTGCCCTTCTGTGAAGAACATTTTACTTCTGGATTCTGAAGGAAAG
genomic: GGTGGAATAGGGAACGGCCATACACCATGGCGGATTTCTCCAAGgtgcgaagaa ... tgtttcacagGAATCTTGCCCTTCTGTGAAGAACATTTTACTTCTGGATTCTGAAGGAAAG
EST: gi|211282264|gb|FL038866.1|FL038866
EST:     GGTGGAATAGGGAACGGCCATACACCATGGCGGATTTCTCCAAG                         GAATCTTGCCCTTCTGTGAAGAACATTTTACTTCTGGATTCTGAAGGAAAG
genomic: GGTGGAATAGGGAACGGCCATACACCATGGCGGATTTCTCCAAGgtgcgaagaa ... tgtttcacagGAATCTTGCCCTTCTGTGAAGAACATTTTACTTCTGGATTCTGAAGGAAAG
EST: gi|87157301|gb|DY402090.1|DY402090
EST:     GGGTGGAATAGGGAACGGCCATACACCATGGCGGATTTCTCCAAG                         GAATCTTGCCCTTCTGTGAAGAACATTTTACTTCTGGATTCTGAAGGAAAG
genomic: GGGTGGAATAGGGAACGGCCATACACCATGGCGGATTTCTCCAAGgtgcgaagaa ... tgtttcacagGAATCTTGCCCTTCTGTGAAGAACATTTTACTTCTGGATTCTGAAGGAAAG
EST: gi|7137590|gb|AW499170.1|AW499170
EST:     GGGTGGAATAGGGAACGGCCATACACCATGGCGGATTTCTCCAAG                         GAATCTTGCCCTTCTGTGAAGAACATTTTACTTCTGGATTCTGAAGGAAAG
genomic: GGGTGGAATAGGGAACGGCCATACACCATGGCGGATTTCTCCAAGgtgcgaagaa ... tgtttcacagGAATCTTGCCCTTCTGTGAAGAACATTTTACTTCTGGATTCTGAAGGAAAG
EST: gi|28187926|gb|CB179536.1|CB179536
EST:     GGTGGAATAGGGAACGGCCATACACCATGGCGGATTTCTCCAAG                         GAATCTTGCCCTTCTGTGAAGAACATTTTACTTCTGGATTCTGAAGGAAAG
genomic: GGTGGAATAGGGAACGGCCATACACCATGGCGGATTTCTCCAAGgtgcgaagaa ... tgtttcacagGAATCTTGCCCTTCTGTGAAGAACATTTTACTTCTGGATTCTGAAGGAAAG
EST: gi|211282263|gb|FL038865.1|FL038865
EST:     GGTGGAATAGGGAACGGCCATACACCATGGCGGATTTCTCCAAG                         GAATCTTGCCCTTCTGTGAAGAACATTTTACTTCTGGATTCTGAAGGAAAG
genomic: GGTGGAATAGGGAACGGCCATACACCATGGCGGATTTCTCCAAGgtgcgaagaa ... tgtttcacagGAATCTTGCCCTTCTGTGAAGAACATTTTACTTCTGGATTCTGAAGGAAAG
EST: gi|15313043|gb|BI478532.1|BI478532
EST:     GGGTGGAATAGGGAACGGCCATACACCATGGCGGATTTCTCCAAG                         GAATCTTGCCCTTCTGTGAAGAACATTTTACTTCTGGATTCTGAAGGAAAG
genomic: GGGTGGAATAGGGAACGGCCATACACCATGGCGGATTTCTCCAAGgtgcgaagaa ... tgtttcacagGAATCTTGCCCTTCTGTGAAGAACATTTTACTTCTGGATTCTGAAGGAAAG
EST: gi|211282260|gb|FL038862.1|FL038862
EST:     GGTGGAATAGGGAACGGCCATACACCATGGCGGATTTCTCCAAG                         GAATCTTGCCCTTCTGTGAAGAACATTTTACTTCTGGATTCTGAAGGAAAG
genomic: GGTGGAATAGGGAACGGCCATACACCATGGCGGATTTCTCCAAGgtgcgaagaa ... tgtttcacagGAATCTTGCCCTTCTGTGAAGAACATTTTACTTCTGGATTCTGAAGGAAAG
EST: gi|22819508|gb|BU499598.1|BU499598
EST:     GGAATAGGGAACGGCCATACACCATGGCGGATTTCTCCAAG                         GAATCTTGCCCTTCTGTGAAGAACATTTTACTTCTGGATTCTGAAGGAAAG
genomic: GGAATAGGGAACGGCCATACACCATGGCGGATTTCTCCAAGgtgcgaagaa ... tgtttcacagGAATCTTGCCCTTCTGTGAAGAACATTTTACTTCTGGATTCTGAAGGAAAG
EST: gi|211344197|gb|FL190861.1|FL190861
EST:     GGGTGGAATAGGGAACGGCCATACACCATGGCGGATTTCTCCAAG                         GAATCTTGCCCTTCTGTGAAGAACATTTTACTTCTGGATTCTGAAGGAAAG
genomic: GGGTGGAATAGGGAACGGCCATACACCATGGCGGATTTCTCCAAGgtgcgaagaa ... tgtttcacagGAATCTTGCCCTTCTGTGAAGAACATTTTACTTCTGGATTCTGAAGGAAAG
EST: gi|5928724|gb|AW055941.1|AW055941
EST:     GGGTGGAATAGGGAACGGCCATACACCATGGCGGATTTCTCCAAG                         GAATCTTGCCCTTCTGTGAAGAACATTTTACTTCTGGATTCTGAAGGAAAG
genomic: GGGTGGAATAGGGAACGGCCATACACCATGGCGGATTTCTCCAAGgtgcgaagaa ... tgtttcacagGAATCTTGCCCTTCTGTGAAGAACATTTTACTTCTGGATTCTGAAGGAAAG
EST: gi|211006747|gb|FL429436.1|FL429436
EST:     GGTGGAATAGGGAACGGCCATACACCATGGCGGATTTCTCCAAG                         GAATCTTGCCCTTCTGTGAAGAACATTTTACTTCTGGATTCTGAAGGAAAG
genomic: GGTGGAATAGGGAACGGCCATACACCATGGCGGATTTCTCCAAGgtgcgaagaa ... tgtttcacagGAATCTTGCCCTTCTGTGAAGAACATTTTACTTCTGGATTCTGAAGGAAAG
EST: gi|211282261|gb|FL038863.1|FL038863
EST:     GGTGGAATAGGGAACGGCCATACACCATGGCGGATTTCTCCAAG                         GAATCTTGCCCTTCTGTGAAGAACATTTTACTTCTGGATTCTGAAGGAAAG
genomic: GGTGGAATAGGGAACGGCCATACACCATGGCGGATTTCTCCAAGgtgcgaagaa ... tgtttcacagGAATCTTGCCCTTCTGTGAAGAACATTTTACTTCTGGATTCTGAAGGAAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taccgaccgtttccgaccgttttaatccctattcagtgatatgtctgtttcacagGAATCTTGCCCTTCTGTGAAGAACATTTTACTTCTGGATTCTGAAGGAAAGCGTGTTGCTGTAAAGTATTTCTCAGATGATTGGCCGACTAATGCATCAA
                   ttttaat  putative branch site (score: 3)
                                           tctgtttc  putative PPT
                   ttttaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttgtttccgataaaaaaatatgaaaacggtaatggttttagtgtttaccgaccgtttccgaccgttttaatccctattcagtgatatgtctgtttcacagGAATCTTGCCCTTCTGTGAAGAACATTTTACTTCTGGATTCTGAAGGAAAGCGTGTTGCTGTAAAGTATTTCTCAGATGATTGGCCGACTAATGCATCAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGATG
- - - - - -aaaaaaa
- - - - - - - - - -atgaaaac