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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCCCCAAGGTGGAAGAGATGCAATAACTAAGAACCCCATCCTTCGTGAGGATCAACTTCCTCAGAAGGTTCTTCATCCTAAACTGAAGAAGTCAAACAAGgttagtgcgctagcatttttttaggcataacttaaaagtgtattctcaataaagcaatgagacaaaaaaaaggtttatgttatcctgtggtatattatat...

Basic information

species Zea mays
transcript GRMZM2G160996_T02
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G160996_T02 (Zea mays), 5'ss of exon 5
lower sequence: LOC_Os02g02360.1 (Oryza sativa), 5'ss of exon 4
GCCCCAAGGTGGAAGAGATGCAATAACTAAGAACCCCATCCTTCGTGAGGATCAACTTCCTCAGAAGGTTCTTCATCCTAAACTGAAGAAGTCAAACAAG-
   |||||||||||||||||| ||||||||||| |||||  | ||||| || || ||||| ||||||||||| || ||||||  ||||||||||||||||  | ||    ||      | || |  |  | ||| |||||  |  | | | ||| |      |         |  |  ||   |   ||     |  || | | 
---CCAAGGTGGAAGAGATGCCATAACTAAGAATCCCATTTTGCGTGAAGACCAGCTTCCCCAGAAGGTTCTGCACCCTAAATCGAAGAAGTCAAACAAGCAGgtaactagcccttgctattgttagatttactgaaaagcctcctttta-taaggatgcctgcttttcggcacttaaattcaacatctccaaaacgttctttt

upper sequence: GRMZM2G160996_T02 (Zea mays), 5'ss of exon 5
lower sequence: GLYMA05G37950.1 (Glycine max), 5'ss of exon 4
GCCCCAAGGTGGAAGAGATGCAATAACTAAGAACCCCATCCTTCGTGAGGATCAACTTCCTCAGAAGGTTCTTCATCCTAAACTGAAGAAGTCAAACAAG-
   ||||||||| || |||||| | || ||||||| ||| || ||||| |||||||||||||| | ||| ||| |||||||| |||||||  | || |||  | | ||| |   |  | |   ||| |   ||   | | |      |  || |||   |   |  | |         || || || |||| | |  |  |||  |                                         
---CCAAGGTGGGAGGGATGCAGTGACAAAGAACCTCATTCTCCGTGAAGATCAACTTCCTCAAAGGGTACTTTATCCTAAAATGAAGAAAGCCAATAAGCAGgttgtgtgtgtgtgtctgtatttaaactattgataatagccaactgatccatatcccttgggaatatggtgttctttcatttttatcccgagtcaatttagttagtttcataccaacccgagcttacttaattacactttgtag

upper sequence: GRMZM2G160996_T02 (Zea mays), 5'ss of exon 5
lower sequence: Vv02s0025g03690.t01 (Vitis vinifera), 5'ss of exon 4
GCCCCAAGGTGGAAGAGATGCAATAACTAAGAACCCCATCCTTCGTGAGGATCAACTTCCTCAGAAGGTTCTTCATCCTAAACTGAAGAAGTCAAACAA------Ggttagtgcgctagcatttttttaggcataacttaaaagtgtattctca-ataaagcaatgagacaaaaaaaaggtttatgttatcctgtggtatattatat---------------------------------
      ||||||||||||||| || ||||||||||| ||  | ||||| |||||||| ||||| ||| | || || || ||    ||||||  |   ||       ||||||    |  | ||||  |   |||   || |||  ||||| | |   |  |   |   |     |  |   ||    |||| |||  |  |||  |                                  
------AGGTGGAAGAGATGCCATTACTAAGAACCCGATTTTACGTGAAGATCAACTCCCTCACAAGCTCCTGCACCCCAAGACAAAGAAGAAAGCTAATAAACCAgttagttttattcccttttcctccccatttttttaaaa-gtattgttatgcatgggtttctcatttctattattgttcaaatatcttgtatttaattgaagtttaattcatacatttcctattgttttttctag

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|67023296|gb|CO452045.1|CO452045
EST:     ATCAACTTCCTCAGAAGGTTCTTCATCCTAAACTGAAGAAGTCAAACAAG                         GATGATGATTTTCTTGGGCGTGTTCGACATATTTTCGCATGTTGGTGAT
genomic: ATCAACTTCCTCAGAAGGTTCTTCATCCTAAACTGAAGAAGTCAAACAAGgttagtgcgc ... ttcactatagGATGATGATTT-CTTGGGCGTGGTCGACATATTTTCGCATGGTGGTGAT
EST: gi|211203702|gb|FL472025.1|FL472025
EST:     ATCAACTTCCTCAGAAGGTTCTTCATCCTAAACTGAAGAAGTCAAACAAG                         GATGATGATTTCTTGGGCGTGGTCGACATATTTTCGCATGGTGGTGATAAG
genomic: ATCAACTTCCTCAGAAGGTTCTTCATCCTAAACTGAAGAAGTCAAACAAGgttagtgcgc ... ttcactatagGATGATGATTTCTTGGGCGTGGTCGACATATTTTCGCATGGTGGTGATAAG
EST: gi|211260639|gb|FL352273.1|FL352273
EST:     ATCAACTTCCTCAGAAGGTTCTTCATCCTAAACTGAAGAAGTCAAACAAG                         GATGATGATTTCTTGGGCGTGGTCGACATATTTTCGCATGGTGGTGATAAG
genomic: ATCAACTTCCTCAGAAGGTTCTTCATCCTAAACTGAAGAAGTCAAACAAGgttagtgcgc ... ttcactatagGATGATGATTTCTTGGGCGTGGTCGACATATTTTCGCATGGTGGTGATAAG
EST: gi|60355783|gb|DN222756.1|DN222756
EST:     ATCAACTTCCTCAGAAGGTTCTTCATCCTAAACTGAAGAAGTCAAACAAG                         GATGATGATTTCTTGGGCGTGGTCGACATATTTTCGCATGGTGGTGATAAG
genomic: ATCAACTTCCTCAGAAGGTTCTTCATCCTAAACTGAAGAAGTCAAACAAGgttagtgcgc ... ttcactatagGATGATGATTTCTTGGGCGTGGTCGACATATTTTCGCATGGTGGTGATAAG
EST: gi|60394073|gb|DN226943.1|DN226943
EST:     ATCAACTTCCTCAGAAGGTTCTTCATCCTAAACTGAAGAAGTCAAACAAG                         GATGATGATTTCTTGGGCGTGGTCGACATATTTTCGCATGGTGGTGATAAG
genomic: ATCAACTTCCTCAGAAGGTTCTTCATCCTAAACTGAAGAAGTCAAACAAGgttagtgcgc ... ttcactatagGATGATGATTTCTTGGGCGTGGTCGACATATTTTCGCATGGTGGTGATAAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCCCCAAGGTGGAAGAGATGCAATAACTAAGAACCCCATCCTTCGTGAGGATCAACTTCCTCAGAAGGTTCTTCATCCTAAACTGAAGAAGTCAAACAAGgttagtgcgctagcatttttttaggcataacttaaaagtgtattctcaataaagcaatgagacaaaaaaaaggtttatgttatcctgtggtatattatat

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT