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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CGCTGGGAGGCACACCCCTGGTACCTTCACTAACCAGCTCCAGACCTCCTTCAGCGAGCCTCGGCTGCTCATCCTTACCGACCCAAGGACTGACCATCAGgtgaacagaatttcagtttcaaagttcagaaatatttagtgagtggaccctgcagtgtgatggtgaactaattgttatggtggtgattgtttgcag

Basic information

species Zea mays
transcript GRMZM2G126821_T02
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G126821_T02 (Zea mays), 5'ss of exon 1
lower sequence: LOC_Os03g08440.1 (Oryza sativa), 5'ss of exon 2
CGCTGGGAGGCACACCCCTGGTACCTTCACTAACCAGCTCCAGACCTCCTTCAGCGAGCCTCGGCTGCTCATCCTTACCGACCCAAGGACTGACCATCAGgtgaacagaatttcagtttcaaagttcagaaatatttagtgagtggaccctgcagtgtgatggtgaactaat--tgttatggtggtgattgtttgcag
 ||||| ||||| || |||||||| || || || |||||||||||||||||||||||||| || ||||||||||| || ||||||||||| || || |||||||| |  ||  |  | |||  ||   |      || |||| | |    | ||||   || ||  ||| ||  ||||||  ||     ||| |||||
TGCTGGAAGGCATACGCCTGGTACATTTACCAATCAGCTCCAGACCTCCTTCAGCGAGCCCCGTCTGCTCATCCTCACTGACCCAAGGACCGATCACCAGgtgaaaatgatcaccatgtcacggtagtgcg----ttggtgaattggg--tacagt---attgtttactgatcgtgttatcctgaattatgtctgcag

upper sequence: GRMZM2G126821_T02 (Zea mays), 5'ss of exon 1
lower sequence: GLYMA16G01460.1 (Glycine max), 5'ss of exon 2
CGCTGGGAGGCACACCCCTGGTACCTTCACTAACCAGCTCCAGACCTCCTTCAGCGAGCCTCGGCTGCTCATCCTTACCGACCCAAGGACTGACCATCAGgtgaacaga-atttcagtttcaaagttcagaaata--tttagtgagtggaccctgcagtgtgatggtgaactaattgttatggtggtgattgtttgcag-----------------------------------------------------------
 ||||| |||||||| || ||||||||||| || ||||| ||||| || ||||| |||||||| || || ||||| || || ||||| || || || |||||| | |   |  |||| ||||||    | |  |   |||||| | | |  | |  | ||   || |||  | |||  | |  ||    |||||||| |                                                           
TGCTGGAAGGCACACTCCCGGTACCTTCACCAATCAGCTTCAGACTTCGTTCAGTGAGCCTCGTCTCCTTATCCTCACTGATCCAAGAACAGATCACCAGgtggatacccaaatcagcttcaaatgatatatttgattttagttacttgtgctttgattg-attgttgacatgatttatgttatgtatgttgtttgcggttgttgtggtgttgactgtgttgtgttgttaatgtgtgtgtttgttcgtttgtgtgcag

upper sequence: GRMZM2G126821_T02 (Zea mays), 5'ss of exon 1
lower sequence: GLYMA07G04890.1 (Glycine max), 5'ss of exon 2
CGCTGGGAGGCACACCCCTGGTACCTTCACTAACCAGCTCCAGACCTCCTTCAGCGAGCCTCGGCTGCTCATCCTTACCGACCCAAGGACTGACCATCAGgtgaacag---aatttcagtttca---aagttcagaaatatttagtgagtggaccct-gcagtgtgatggtgaactaattgttatggtggt---------gattgtttgcag----------------------------------------------------------
 ||||| |||||||| |||||||||||||| || ||||| || || ||||||||||||||||| || || || |||||||| ||||| || || || ||||| |  |    | |||||  | ||   |  |  ||||| |   |   | | ||  || |     ||  | |  | | ||||||   || ||         |||||||||                                                             
TGCTGGAAGGCACACTCCTGGTACCTTCACCAATCAGCTTCAAACTTCCTTCAGCGAGCCTCGTCTCCTTATTCTTACCGATCCAAGAACAGATCACCAGgttagtaccctattttcatatgcagttatatgaagaaaaaaagatacatttgattctagtcacatgtggtttgattgattgttgatgtagtttatggtgtgattgtttgtttagggttgttgtattgcccgtgttgtgttgttaatgtatgtttgttggtttgtgtgcag

upper sequence: GRMZM2G126821_T02 (Zea mays), 5'ss of exon 1
lower sequence: AT3G04770.1 (Arabidopsis thaliana), 5'ss of exon 2
CGCTGGGAGGCACACCCCTGGTACCTTCACTAACCAGCTCCAGACCTCCTTCAGCGAGCCTCGGCTGCTCATCCTTACCGACCCAAGGACTGACCATCAGgtgaacagaatttcagtttcaaagttcagaaatatttagtgagtggaccctgcagtgtgatggtgaactaattgttatggtggtgattgtttgcag-
 ||||| || ||||| |||||||| |||||||||||  | ||||| || ||||| |||||| || || | || || ||||||||||| || |||||||||||  |  |||| |  |||| |    |||  | |     |||| |  ||  || ||  |  ||||      | ||   |  ||||   |||||||   
TGCTGGAAGACACACTCCTGGTACTTTCACTAACCAAATGCAGACTTCTTTCAGTGAGCCTAGGTTGTTGATTCTCACCGACCCAAGAACCGACCATCAGgtatattgaatgt--gttttac--ctcatcagtt----gtgatttaactgtgtaggtttttggttttgctaatgcggttttggtttgtgtttgccag

upper sequence: GRMZM2G126821_T02 (Zea mays), 5'ss of exon 1
lower sequence: AT1G72370.2 (Arabidopsis thaliana), 5'ss of exon 2
CGCTGGGAGGCACACCCCTGGTACCTTCACTAACCAGCTCCAGACCTCCTTCAGCGAGCCTCGGCTGCTCATCCTTACCGACCCAAGGACTGACCATCAGgtgaacagaatttcagtttcaaagttcagaaatatttagtgagtggaccctgcagtgtgatggtgaactaattgttatggtggtgattgtttgcag
 ||||| || ||||| |||||||||||||| || ||| | ||||| |||||||| || ||  ||||| | || ||||| |||||||| |||||||| ||||| |||     ||||     |   |||| | |    |||||| ||     ||   | || |  |||  ||| |||  ||   |||     ||||||
TGCTGGAAGACACACTCCTGGTACCTTCACCAATCAGATGCAGACATCCTTCAGTGAACCAAGGCTGTTGATTCTTACTGACCCAAGAACTGACCACCAGgtaaact---cttca----tatgattcatatac---tagtgattgattaatgatttttgttattga--taaatgtcttgtgtgtg-----ttgcag

upper sequence: GRMZM2G126821_T02 (Zea mays), 5'ss of exon 1
lower sequence: Vv09s0002g00610.t01 (Vitis vinifera), 5'ss of exon 2
CGCTGGGAGGCACACCCCTGGTACCTTCACTAACCAGCTCCAGACCTCCTTCAGCGAGCCTCGGCTGCTCATCCTTACCGACCCAAGGACTGACCATCAGgt----gaacagaatttcagtttcaaagttcagaaat--atttagtgagtggaccctgcagtgtgatggtgaactaattgttatggtggtgattgtttgcag
 ||||| |||||||| || ||||| ||||| || ||||||||||| || ||||| ||||| || || |||||||| || |||||||| ||||| || |||||    ||| |  |      |||  || ||| |   |   ||| |    | |        |   |   ||  |||| || || | |     |        | 
TGCTGGAAGGCACACACCAGGTACATTCACCAATCAGCTCCAGACATCTTTCAGTGAGCCCCGTCTTCTCATCCTCACAGACCCAAGAACTGATCACCAGgtaagtgaataacacacatctttataaattctgtttttagtttgggttttagggttcaaggaaggtgcgtagactactttttctagc--caaccagggaaat

upper sequence: GRMZM2G126821_T02 (Zea mays), 5'ss of exon 1
lower sequence: EFJ20712 (Selaginella moellendorffii), 5'ss of exon 2
CGCTGGGAGGCACACCCCTGGTACCTTCACTAACCAGCTCCAGACCTCCTTCAGCGAGCCTCGGCTGCTCATCCTTACCGACCCAAGGACTGACCATCAGgtgaacagaatttcagtttcaaagttcagaaatatttagtgagtggaccctgcagtgtgatggtgaactaattgttatggtggtgattgtttgcag
||| ||||||||||||||||| || ||||| || |||||||||| |||||||   |||||||| || ||||| || || || ||  | || || || ||||| |      |  |    || |      ||  | |||  | | |||   |     | || |      ||   |||| |    |             
CGCCGGGAGGCACACCCCTGGAACTTTCACCAATCAGCTCCAGAACTCCTTCTCGGAGCCTCGCCTCCTCATTCTCACGGATCCGCGCACCGATCACCAGgtaagtttgctcgctcgatctag--cacgacttttttcctcattggtttccttcttttgttttgtgtctgtgtgttcttccag-------------

upper sequence: GRMZM2G126821_T02 (Zea mays), 5'ss of exon 1
lower sequence: EFJ32709 (Selaginella moellendorffii), 5'ss of exon 2
CGCTGGGAGGCACACCCCTGGTACCTTCACTAACCAGCTCCAGACCTCCTTCAGCGAGCCTCGGCTGCTCATCCTTACCGACCCAAGGACTGACCATCAGgtgaacagaatt--tcagtttcaaagttcagaaatatttagtgagtggaccctgcagtgtgatggtgaactaattgttatggtggtgattgtttgcag
||| ||||||||||||||||| || ||||| || |||||||||| |||||||   |||||||| || ||||| || || || ||  | || || || ||||| |      |   ||  | |   |   |     |  | | ||  |     ||   || |  || ||      || ||   |                
CGCCGGGAGGCACACCCCTGGAACTTTCACCAATCAGCTCCAGAACTCCTTCTCGGAGCCTCGCCTCCTCATTCTCACGGATCCGCGCACAGATCACCAGgtaagtttgctcgctcgatctagcacgacttttttcctcattggtttccttcttttgttttgtg-tgtgtgtgttcttccag----------------

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|33101681|gb|CF061641.1|CF061641
EST:     TCAGCGAGCCTCGGCTGCTCATCCTTACCGACCCAAGGACTGACCATCAG                         CCAATTAAGGAGTCTGCTCTGGGGAACCATCCCCACCATTGCCTTCTGTGA
genomic: TCAGCGAGCCTCGGCTGCTCATCCTTACCGACCCAAGGACTGACCATCAGgtgaacagaa ... ttgtttgcagCCAATTAAGGAGTCTGCTCTGGGGAAC-ATCCCCACCATTGCCTTCTGTGA
EST: gi|30306590|gb|CD001263.1|CD001263
EST:     TCAGCGAGCCTCGGCTGCTCATCCTTACCGACCCAAGGACTGACCATCAG                         CCAATTAAGGAGTCTGCTCTGGGGAACATCCCCACCATTGCCTTCTGTGAT
genomic: TCAGCGAGCCTCGGCTGCTCATCCTTACCGACCCAAGGACTGACCATCAGgtgaacagaa ... ttgtttgcagCCAATTAAGGAGTCTGCTCTGGGGAACATCCCCACCATTGCCTTCTGTGAT
EST: gi|32850981|gb|CD990662.1|CD990662
EST:     TCAGCGAGCCTCGACTGCTCATCCTTACCGACCCAAGGACTGACCATCAG                         CCAATTAAGGAGTCTGCTCTGGGGAACCATCCCCACCATTGCCTTCTGTGA
genomic: TCAGCGAGCCTCGGCTGCTCATCCTTACCGACCCAAGGACTGACCATCAGgtgaacagaa ... ttgtttgcagCCAATTAAGGAGTCTGCTCTGGGGAAC-ATCCCCACCATTGCCTTCTGTGA
EST: gi|211540690|gb|FL218505.1|FL218505
EST:     TCAGCGAGCCTCGGCTGCTCATCCTTACCGACCCAAGGACTGACCATCAG                         CCAATTAAGGAGTCTGCTCTGGGGAACATCCCCACCATTGCCTTCTGTGAT
genomic: TCAGCGAGCCTCGGCTGCTCATCCTTACCGACCCAAGGACTGACCATCAGgtgaacagaa ... ttgtttgcagCCAATTAAGGAGTCTGCTCTGGGGAACATCCCCACCATTGCCTTCTGTGAT
EST: gi|18964153|gb|BM660841.1|BM660841
EST:     TCAGCGAGCCTCGACTGCTCATCCTTACCGACCCAAGGACTGACCATCAG                         CCAATTAAGGAGTCTGCTCTGGGGAACATCCCCACCATTGCCTTCTGTGAT
genomic: TCAGCGAGCCTCGGCTGCTCATCCTTACCGACCCAAGGACTGACCATCAGgtgaacagaa ... ttgtttgcagCCAATTAAGGAGTCTGCTCTGGGGAACATCCCCACCATTGCCTTCTGTGAT
EST: gi|28987078|gb|CB351453.1|CB351453
EST:     TCAGCGAGCCTCGGCTGCTCATCCTTACCGACCCAAGGACTGACCATCAG                         CCAATTAAGGAGTCTGCTCTGGGGAACATCCCCACCATTGCCTTCTGTGAT
genomic: TCAGCGAGCCTCGGCTGCTCATCCTTACCGACCCAAGGACTGACCATCAGgtgaacagaa ... ttgtttgcagCCAATTAAGGAGTCTGCTCTGGGGAACATCCCCACCATTGCCTTCTGTGAT
EST: gi|24768430|gb|CA403559.1|CA403559
EST:     GCTGCTCATCCTTACCGACCCAAGGACTGACCATCAG                         CCAATTAAGGAGTCTGCTCTGGGGAACATCCCCACCATTGCCTTCTGTGAT
genomic: GCTGCTCATCCTTACCGACCCAAGGACTGACCATCAGgtgaacagaa ... ttgtttgcagCCAATTAAGGAGTCTGCTCTGGGGAACATCCCCACCATTGCCTTCTGTGAT
EST: gi|7216530|gb|AW562652.1|AW562652
EST:     TCAGCGAGCCTCGGCTGCTCATCCTTACCGACCCAAGGACTGACCATCAG                         CCAATTAAGGAGTCTGCTCTGGGGAACATCCCCACCATTGCCTTCTGTGAT
genomic: TCAGCGAGCCTCGGCTGCTCATCCTTACCGACCCAAGGACTGACCATCAGgtgaacagaa ... ttgtttgcagCCAATTAAGGAGTCTGCTCTGGGGAACATCCCCACCATTGCCTTCTGTGAT
EST: gi|21330457|gb|BQ485838.1|BQ485838
EST:     TCAGCGAGCCTCGGCTGCTCATCCTTACCGACCCAAGGACTGACCATCAG                         CCAATTAAGGAGTCTGCTCTGGGGAACATCCCCACCATTGCCTTCTGTGAT
genomic: TCAGCGAGCCTCGGCTGCTCATCCTTACCGACCCAAGGACTGACCATCAGgtgaacagaa ... ttgtttgcagCCAATTAAGGAGTCTGCTCTGGGGAACATCCCCACCATTGCCTTCTGTGAT
EST: gi|31353712|gb|CD438069.1|CD438069
EST:     TCAGCGAGCCTCGGCTGCTCATCCTTACCGACCCAAGGACTGACCATCAG                         CCAATTAAGGAGTCTGCTCTGGGGAACATCCCCACCATTGCCTTCTGTGAT
genomic: TCAGCGAGCCTCGGCTGCTCATCCTTACCGACCCAAGGACTGACCATCAGgtgaacagaa ... ttgtttgcagCCAATTAAGGAGTCTGCTCTGGGGAACATCCCCACCATTGCCTTCTGTGAT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CGCTGGGAGGCACACCCCTGGTACCTTCACTAACCAGCTCCAGACCTCCTTCAGCGAGCCTCGGCTGCTCATCCTTACCGACCCAAGGACTGACCATCAGgtgaacagaatttcagtttcaaagttcagaaatatttagtgagtggaccctgcagtgtgatggtgaactaattgttatggtggtgattgtttgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT