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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGCAAAGAAACTCGAGCATTTTTTCTGCCAGACCTGTACAGCTGAAAATGGTAAGATGGTTGAGAATTCACATGAAGCTACAGCGCAATCAGAAGAAAAGgtaagccacacatgatgttagtttctgcttatcattggtgtaagcttgctatctaagggggtgattggttccaagggactaaaccgtcatatcgggtgtc...

Basic information

species Zea mays
transcript GRMZM2G097726_T01
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G097726_T02 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os07g08880.2 (Oryza sativa), 5'ss of exon 4
AGCAAAGAAACTCGAGCATTTTTTCTGCCAGACCTGTACAGCTGAAAATGGTAAGATGGTTGAGAATTCACATGAAGCTACAGCGCAATCAGAAGAAAAGgtaagccac-acatgatgttagtttctgcttatcattggtg--taagcttgctatc--taagggggtgattggttccaagggactaaaccgtcatatcgggtgtc
 ||||| ||||| ||||||||||||||||||| |||||| || |||||||| ||||||| ||||||||| |||||||||||||||||||| |||||||||||||   |  | ||| ||  | |      ||||||||  ||  |    | ||||||  ||  | | || |        | || |     |  |    |||||   
TGCAAAAAAACTAGAGCATTTTTTCTGCCAGAGCTGTACTGCGGAAAATGGAAAGATGGCTGAGAATTCTCATGAAGCTACAGCGCAATCCGAAGAAAAGgtaaaatatgatatgttgggattactgaattatcattaatgatttgtttagctatcagtagtgcgatggtaatacatcaaggccagggtctcc----cgggttc-
















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|211224876|gb|FL455272.1|FL455272
EST:     GTAAGATGGTTGAGAATTCACATGAAGCTACAGCGCAATCAGAAGAAAAG                         CCGGTGGAGTCAAAAAGGCGGCGAAGGTGATGGCCGTGCTGATTAAATTTA
genomic: GTAAGATGGTTGAGAATTCACATGAAGCTACAGCGCAATCAGAAGAAAAGgtaagccaca ... atctcttcagCCGGTGGAGTCAAAAAGGCGGCGAAGGTGATGGCCGTGCTGATTAAATTTA
EST: gi|78180631|gb|DV550959.1|DV550959
EST:     GTAAGATGGTTGAGAATTCACATGAAGCTACAGCGCAATCAGAAGAAAAG                         CCGGTGGAGTCAAAAAGGCGGCGAAGGTGATGGCCGTGCTGATTAAATTTA
genomic: GTAAGATGGTTGAGAATTCACATGAAGCTACAGCGCAATCAGAAGAAAAGgtaagccaca ... atctcttcagCCGGTGGAGTCAAAAAGGCGGCGAAGGTGATGGCCGTGCTGATTAAATTTA
EST: gi|67017898|gb|CO446647.1|CO446647
EST:     GTAAGATGGTTGAGAATTCACATGAAGCTACAGCGCAATCAGAAGAAAAG                         CCGGTGGAGTCAAAAAGGCGGCGAAGGTGATGGCCGTGCTGATTAAATTTA
genomic: GTAAGATGGTTGAGAATTCACATGAAGCTACAGCGCAATCAGAAGAAAAGgtaagccaca ... atctcttcagCCGGTGGAGTCAAAAAGGCGGCGAAGGTGATGGCCGTGCTGATTAAATTTA
EST: gi|78074294|gb|DV502728.1|DV502728
EST:     GTAAGATGGTTGAGAATTCACATGAAGCTACAGCGCAATCAGAAGAAAAG                         CCGGTGGAGTCAAAAAGGCGGCGAAGGTGATGGCCGTGCTGATTAAATTTA
genomic: GTAAGATGGTTGAGAATTCACATGAAGCTACAGCGCAATCAGAAGAAAAGgtaagccaca ... atctcttcagCCGGTGGAGTCAAAAAGGCGGCGAAGGTGATGGCCGTGCTGATTAAATTTA
EST: gi|4967167|gb|AI691875.1|AI691875
EST:     GTAAGATGGTTGAGAATTCACATGAAGCTACAGCGCAATCAGAAGAAAAG                         CTGGTGGAGTCAAAAAGGCGGCGAAGGTGATGGCCGTGCTGATTAAATTTA
genomic: GTAAGATGGTTGAGAATTCACATGAAGCTACAGCGCAATCAGAAGAAAAGgtaagccaca ... atctcttcagCCGGTGGAGTCAAAAAGGCGGCGAAGGTGATGGCCGTGCTGATTAAATTTA
EST: gi|19822612|gb|BQ048636.1|BQ048636
EST:     GTAAGATGGTTGAGAATTCACATGAAGCTACAGCGCAATCAGAAGAAAAG                         CCGGTGGAGTCAAAAAGGCGGCGAAGGTGATGGCCGTGCTGATTAAATTTA
genomic: GTAAGATGGTTGAGAATTCACATGAAGCTACAGCGCAATCAGAAGAAAAGgtaagccaca ... atctcttcagCCGGTGGAGTCAAAAAGGCGGCGAAGGTGATGGCCGTGCTGATTAAATTTA
EST: gi|28909803|gb|CB331108.1|CB331108
EST:     GTAAGATGGTTGAGAATTCACATGAAGCTACAGCGCAATCAGAAGAAAAG                         CCGGTGGAGTCAAAAAGGCGGCGAAGGTGATGGCCGTGCTGATTAAATTTA
genomic: GTAAGATGGTTGAGAATTCACATGAAGCTACAGCGCAATCAGAAGAAAAGgtaagccaca ... atctcttcagCCGGTGGAGTCAAAAAGGCGGCGAAGGTGATGGCCGTGCTGATTAAATTTA
EST: gi|18648816|gb|BM497635.1|BM497635
EST:     GCAAGATGGTTGAGAATTCACATGAAGCTACAGCGCAATCAGAAGAAAAG                         CCGGTGGAGTCAAAAAGGCGGCGAAGGTGATGGC
genomic: GTAAGATGGTTGAGAATTCACATGAAGCTACAGCGCAATCAGAAGAAAAGgtaagccaca ... atctcttcagCCGGTGGAGTCAAAAAGGCGGCGAAGGTGATGGC
EST: gi|8551650|gb|BE128821.1|BE128821
EST:     GTAAGATGGTTGAGAATTCACATGAAGCTACAGCGCAATCAGAAGAAAAG                         CCGGTGGAGTCAAAAAGGCGGCGAAGGTGATGGCCGTGCTGATTAAATTTA
genomic: GTAAGATGGTTGAGAATTCACATGAAGCTACAGCGCAATCAGAAGAAAAGgtaagccaca ... atctcttcagCCGGTGGAGTCAAAAAGGCGGCGAAGGTGATGGCCGTGCTGATTAAATTTA
EST: gi|60354816|gb|DN221789.1|DN221789
EST:     GTAAGATGGTTGAGAATTCACATGAAGCTACAGCGCAATCAGAAGAAAAG                         CCGGTGGAGTCAAAAAGGCGGCGAAGGTGATGGCCGTGCTGATTAAATTTA
genomic: GTAAGATGGTTGAGAATTCACATGAAGCTACAGCGCAATCAGAAGAAAAGgtaagccaca ... atctcttcagCCGGTGGAGTCAAAAAGGCGGCGAAGGTGATGGCCGTGCTGATTAAATTTA
EST: gi|60399583|gb|DN232394.1|DN232394
EST:     GTAAGATGGTTGAGAATTCACATGAAGCTACAGCGCAATCAGAAGAAAAG                         CCGGTGGAGTCAAAAAGGCGGCGAAGGTGATGGCCGTGCTGATTAAATTTA
genomic: GTAAGATGGTTGAGAATTCACATGAAGCTACAGCGCAATCAGAAGAAAAGgtaagccaca ... atctcttcagCCGGTGGAGTCAAAAAGGCGGCGAAGGTGATGGCCGTGCTGATTAAATTTA
EST: gi|9733234|gb|BE511986.1|BE511986
EST:     GTAAGATGGTTGAGAATTCACATGAAGCTACAGCGCAATCAGAAGAAAAG                         CTGGTGGAGTCAAAAAGGCGGCGAAGGTGATGGCCGTGCTGATTAAATTTA
genomic: GTAAGATGGTTGAGAATTCACATGAAGCTACAGCGCAATCAGAAGAAAAGgtaagccaca ... atctcttcagCCGGTGGAGTCAAAAAGGCGGCGAAGGTGATGGCCGTGCTGATTAAATTTA
EST: gi|18649399|gb|BM498218.1|BM498218
EST:     GTAAGATGGTTGAGAATTCACATGAAGCTACAGCGCAATCAGAAGATAAG                         CCGGTGGAGTCAAAAAGGCGGCGAAGGTGATGGCCGTGCTGATTAAA
genomic: GTAAGATGGTTGAGAATTCACATGAAGCTACAGCGCAATCAGAAGAAAAGgtaagccaca ... atctcttcagCCGGTGGAGTCAAAAAGGCGGCGAAGGTGATGGCCGTGCTGATTAAA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGCAAAGAAACTCGAGCATTTTTTCTGCCAGACCTGTACAGCTGAAAATGGTAAGATGGTTGAGAATTCACATGAAGCTACAGCGCAATCAGAAGAAAAGgtaagccacacatgatgttagtttctgcttatcattggtgtaagcttgctatctaagggggtgattggttccaagggactaaaccgtcatatcgggtgtc

- - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA