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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCCTCAAGGTGGAAGAGATGCCATAACTAAGAACCCCATTCTACGTGAGGACCAGCTTCCTCAGAAGGTTCTTCATCCTAAATTGAAGAAGTCCAGCAAGgttagtgctctagcatttctttctttttttcgtgtactgaaaagtcatttcagaataaggtaatgaggatacatgcacaacaaactgtggactacttaat...

Basic information

species Zea mays
transcript GRMZM2G079143_T01
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G079143_T01 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os02g02360.1 (Oryza sativa), 5'ss of exon 4
GCCTCAAGGTGGAAGAGATGCCATAACTAAGAACCCCATTCTACGTGAGGACCAGCTTCCTCAGAAGGTTCTTCATCCTAAATTGAAGAAGTCCAGCAAGgttagtgctctagcatttctttctttttttcgtgtactgaaaagtcatttcagaataaggtaatgaggatacatgcacaacaaactgtggactacttaat--------
    ||||||||||||||||||||||||||||| |||||| | ||||| ||||||||||| ||||||||||| || ||||||| ||||||||| | ||||   ||    |||||  ||  |   || ||   | |||||||||| |   |   | |||||      |  |    ||||   ||        || |  ||         
---CCAAGGTGGAAGAGATGCCATAACTAAGAATCCCATTTTGCGTGAAGACCAGCTTCCCCAGAAGGTTCTGCACCCTAAATCGAAGAAGTCAAACAAG--CAGgtaactagcccttgcta--ttgttagatttactgaaaagcctcctttta-taaggatgcctgcttttcggcacttaaattcaacatctccaaaacgttctttt

upper sequence: GRMZM2G079143_T01 (Zea mays), 5'ss of exon 4
lower sequence: Vv02s0025g03690.t01 (Vitis vinifera), 5'ss of exon 4
GCCTCAAGGTGGAAGAGATGCCATAACTAAGAACCCCATTCTACGTGAGGACCAGCTTCCTCAGAAGGTTCTTCATCCTAAATTGAAGAAGT---CCAGCAAGgttagtgctctagcatttctttctttttttcgtgtactgaaaagtcatttcagaataaggtaatgaggatacatgcacaacaaactgtggactacttaat--------------------------------------
      |||||||||||||||||| ||||||||||| ||| ||||||| || || || ||||| ||| | || || || ||    ||||||    | |  ||      |  | |   ||| | || |  |   | | |  | ||||||  | | |      |||        |  ||        || | |    || |||||                                      
------AGGTGGAAGAGATGCCATTACTAAGAACCCGATTTTACGTGAAGATCAACTCCCTCACAAGCTCCTGCACCCCAAGACAAAGAAGAAAGCTAATAAACCAgttagttt--tattcccttttcctccccatttttttaaaagtattgttatgcatgggtttctcatttctattattgttcaaatatcttgtatttaattgaagtttaattcatacatttcctattgttttttctag
















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|88753974|gb|DY538115.1|DY538115
EST:     ACCAGCTTCCTCAGAAGGTTCTTCTTCCTAAATTGAAGAAGTCCAGCAAG                         GCGGATGATTTTTTGGGCGTTGAGGACATATTTTCGCACAGTGGTGATAAG
genomic: ACCAGCTTCCTCAGAAGGTTCTTCATCCTAAATTGAAGAAGTCCAGCAAGgttagtgctc ... ttcactatagGCGGATGATTTCTTGGGCGTTGAGGACATATTTTCGCACAGTGGTGATAAG
EST: gi|211345612|gb|FL479622.1|FL479622
EST:     ACCAGCTTCCTCAGAAGGTTCTTCATCCTAAATTGAAGAAGTCCAGCAAG                         GCGGATGATTTCTTGGGCGTTGAGGACATATTTTCGCACAGTGGTGATAAG
genomic: ACCAGCTTCCTCAGAAGGTTCTTCATCCTAAATTGAAGAAGTCCAGCAAGgttagtgctc ... ttcactatagGCGGATGATTTCTTGGGCGTTGAGGACATATTTTCGCACAGTGGTGATAAG
EST: gi|111433439|gb|EE297756.1|EE297756
EST:     ACCAGCTTCCTCAGAAGGTTCTTCATCCTAAATTGAAGAAGTCCAGCAAG                         GCGGATGATTTCTTGGGCGTTGAGGACATATTTTCGCACAGTGGTGATAAG
genomic: ACCAGCTTCCTCAGAAGGTTCTTCATCCTAAATTGAAGAAGTCCAGCAAGgttagtgctc ... ttcactatagGCGGATGATTTCTTGGGCGTTGAGGACATATTTTCGCACAGTGGTGATAAG
EST: gi|12046018|gb|BF728053.1|BF728053
EST:     CAGCTTTCCTCANGAAGGTTCTTCATCCTAAATTGAAGAAGTCCAGCAAGG                         GCGGATGATTTCTTGGGCGTTGAAGACATATTCTCGCACAGTGGTGATAA
genomic: CAGC-TTCCTCA-GAAGGTTCTTCATCCTAAATTGAAGAAGTCCAGCAA-Ggttagtgctc ... ttcactatagGCGGATGATTTCTTGGGCGTTGAGGACATATTTTCGCACAGTGGTGATAA
EST: gi|60348779|gb|DN215752.1|DN215752
EST:     ACCAGCTTCCTCAGAAGGTTCTTCATCCTAAATTGAAGAAGTCCAGCAAG                         GCGGATGATTTCTTGGGCGTTGAGGACATATTTTCGCACAGTGGTGATAAG
genomic: ACCAGCTTCCTCAGAAGGTTCTTCATCCTAAATTGAAGAAGTCCAGCAAGgttagtgctc ... ttcactatagGCGGATGATTTCTTGGGCGTTGAGGACATATTTTCGCACAGTGGTGATAAG
EST: gi|45567461|gb|CK985583.1|CK985583
EST:     ACCAGCTTCCTCAGAAGGTTCTTCATCCTAAATTGAAGAAGTCCAGCAAG                         GCGGATGATTTCTTGGGCGTTGAGGACATATTCTCGCACAGTGGTGATAAG
genomic: ACCAGCTTCCTCAGAAGGTTCTTCATCCTAAATTGAAGAAGTCCAGCAAGgttagtgctc ... ttcactatagGCGGATGATTTCTTGGGCGTTGAGGACATATTTTCGCACAGTGGTGATAAG

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
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---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCCTCAAGGTGGAAGAGATGCCATAACTAAGAACCCCATTCTACGTGAGGACCAGCTTCCTCAGAAGGTTCTTCATCCTAAATTGAAGAAGTCCAGCAAGgttagtgctctagcatttctttctttttttcgtgtactgaaaagtcatttcagaataaggtaatgaggatacatgcacaacaaactgtggactacttaat

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -agaataag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - acaacaaa