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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGCTGGTGGAGGTGTTTTTAAGAACGATAAAGGTCTTAAGTGCCAAATTCCTGGGGCAAATCTTAATGACATTGCAAATCAGGCAGATGATCTAGTAGAGgtaagttgaaaagcatgagtacacatatcctttactgatggccttccatggaataacacaatcttcataacctgattctttgcaatggaacattttcttt...

Basic information

species Zea mays
transcript GRMZM2G079452_T02
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G079452_T02 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os11g23790.2 (Oryza sativa), 5'ss of exon 4
TGCTGGTGGAGGTGTTTTTAAGAACGATAAAGGTCTTAAGTGCCAAATTCCTGGGGCAAATCTTAATGACATTGCAAATCAGGCAGATGATCTAGTAGAGgtaagttgaaaagcatgagtacacatatcctttactgatggccttccatggaataacacaat-cttcataacctgattctttgcaatggaacattttcttt-
||||||||||||||| ||||| || |||||||| ||||||||||| ||||| ||||| ||||||||||| |||||||| ||||||||||||||  | |||||||| ||||  | || ||||||  | |  | |||| |||  ||| ||||          || || ||| || || ||| || ||  | ||||     |   
TGCTGGTGGAGGTGTGTTTAAAAATGATAAAGGCCTTAAGTGCCAGATTCCAGGGGCCAATCTTAATGATATTGCAAACCAGGCAGATGATCTCTTGGAGgtaagatgaagggtattagtacaattgtg-tatactaatgatcttacatgatgctctgggattctacatgacttg-ttcatttcagagtaacaaaaattgca
















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|71311108|gb|DR791867.1|DR791867
EST:     CTGGGGCAAATCTTAATGACATTGCAAATCAGGCAGATGATCTAGTAGAG                         TCAATGGAATCTAGGGACACCATTCCTGATCGAAAACTTCTTGCAAGATTA
genomic: CTGGGGCAAATCTTAATGACATTGCAAATCAGGCAGATGATCTAGTAGAGgtaagttgaa ... gttgttatagTCAATGGAATCTAGGGACACCATTCCTGATCGAAAACTTCTTGCAAGATTA
EST: gi|149112959|gb|EE295744.2|EE295744
EST:     CTGGGGCAAATCTTAATGACATTGCAAATCAGGCAGATGATCTAGTAGAG                         TCAATGGAATCTAGGGACACCATTCCTGATCGAAAACTTCTTGCA-GAATA
genomic: CTGGGGCAAATCTTAATGACATTGCAAATCAGGCAGATGATCTAGTAGAGgtaagttgaa ... gttgttatagTCAATGGAATCTAGGGACACCATTCCTGATCGAAAACTTCTTGCAAGATTA
EST: gi|76012260|gb|DT939430.1|DT939430
EST:     CTGGGGCAAATCTTAATGACATTGCAAATCAGGCAGATGATCTAGTAGAG                         TCAATGGAATCTAGGGACACCATTCCTGATCGAAAACTTCTTGCAAGATTA
genomic: CTGGGGCAAATCTTAATGACATTGCAAATCAGGCAGATGATCTAGTAGAGgtaagttgaa ... gttgttatagTCAATGGAATCTAGGGACACCATTCCTGATCGAAAACTTCTTGCAAGATTA
EST: gi|71429968|gb|DR811018.1|DR811018
EST:     CTGGGGCAAATCTTAATGACATTGCAAATCAGGCAGATGATCTAGTAGAG                         TCAATGGAATCTAGGGACACCATTCCTGATCGAAAACTTCTTGCAAGATTA
genomic: CTGGGGCAAATCTTAATGACATTGCAAATCAGGCAGATGATCTAGTAGAGgtaagttgaa ... gttgttatagTCAATGGAATCTAGGGACACCATTCCTGATCGAAAACTTCTTGCAAGATTA
EST: gi|149107701|gb|EE189577.2|EE189577
EST:     CTGTGGCACATCTTAATGACATTGCAGATCAGGCAGATGATCTAGTACAG                         TCAATGGAATCTA
genomic: CTGGGGCAAATCTTAATGACATTGCAAATCAGGCAGATGATCTAGTAGAGgtaagttgaa ... gttgttatagTCAATGGAATCTA
EST: gi|71774790|gb|DR972668.1|DR972668
EST:     CTGGGGCAAATCTTAATGACATTGCAAATCAGGCAGATGATCTAGTAGAG                         TCAATGGAATCT
genomic: CTGGGGCAAATCTTAATGACATTGCAAATCAGGCAGATGATCTAGTAGAGgtaagttgaa ... gttgttatagTCAATGGAATCT
EST: gi|78090608|gb|DV518982.1|DV518982
EST:     CTGGGGCAAATCTTAATGACATTGCAAATCAGGCAGATGATCTAGTAGAG                         TCAATGGAATCTAGGGACACCATTCCTGATCGAAAACTTCTTGCAAGATTA
genomic: CTGGGGCAAATCTTAATGACATTGCAAATCAGGCAGATGATCTAGTAGAGgtaagttgaa ... gttgttatagTCAATGGAATCTAGGGACACCATTCCTGATCGAAAACTTCTTGCAAGATTA
EST: gi|149096864|gb|EE182658.2|EE182658
EST:     CTGGGGCAAATCTTAATGACATTGCAAATCAGGCAGATGATCTAGTAGAG                         TCAATGGAATCTAGGGACACCATTCCTGATCGAAAACTTCTTGCAAGATTA
genomic: CTGGGGCAAATCTTAATGACATTGCAAATCAGGCAGATGATCTAGTAGAGgtaagttgaa ... gttgttatagTCAATGGAATCTAGGGACACCATTCCTGATCGAAAACTTCTTGCAAGATTA
EST: gi|71444932|gb|DR825982.1|DR825982
EST:     CTGGGGCAAATCTTAATGACATTGCAAATCAGGCAGATGATCTAGTAGAG                         TCAATGGAATCTAGGGACACCATTCCTGATCGAAAACTTCTTGCAAGATTA
genomic: CTGGGGCAAATCTTAATGACATTGCAAATCAGGCAGATGATCTAGTAGAGgtaagttgaa ... gttgttatagTCAATGGAATCTAGGGACACCATTCCTGATCGAAAACTTCTTGCAAGATTA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGCTGGTGGAGGTGTTTTTAAGAACGATAAAGGTCTTAAGTGCCAAATTCCTGGGGCAAATCTTAATGACATTGCAAATCAGGCAGATGATCTAGTAGAGgtaagttgaaaagcatgagtacacatatcctttactgatggccttccatggaataacacaatcttcataacctgattctttgcaatggaacattttcttt

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gaaaagca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gaataaca