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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cgatcactatgatgcctttgcagcttttgctcaatctcttcgtgattgttgattgtgcatctgcttataattcttgattgctccttgacttgactattagATAAATACCATGCTTGGGTAAATGCAGAGTTCCTCCTGGAGAAGTGCCTTGTCGGATTCCTTGATCCCACCGCGTAGATATCCAGGTCTCATGGCATTTT

Basic information

species Zea mays
transcript GRMZM2G152438_T02
intron # 6
splice site 3'
intron type U12 (go to U12 genes for details)

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G152438_T02 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os07g12830.3 (Oryza sativa), 3'ss of exon 4
cgatcactatgatgcctttgcagct--tttgct-caatctcttcgtgattgttgattgtgcatctgcttataattcttgatt--gctccttgacttgactattagATAAATACCATGCTTGGGTAAATGCAGAGTTCCTCCTGGAGAAGTGCCTTGTCGGATTCCTTGATCCCACCGCGTAGATATCC----AGGTCTCATGGCATTTT
 || |  ||||    | |||  |||   | |||   || ||| |  |   |||  |||| |||     |||||||||||||   | ||||| |||   |||| ||| ||||| ||||| |||||||||   || ||||||||||||||||||||||| |||||||| |||||||  | ||||||   |      | || | | ||    
-gaac-ttatgtgcaccttgaggctagctagctgtcatatctgcagggaggtt--ttgtccatgaatatataattcttgatatggttccttcactcccctat-agACAAATATCATGCATGGGTAAATTTTGAATTCCTCCTGGAGAAGTGCCTTGTTGGATTCCTCGATCCCAATGAGTAGATGCGCCATTGAGCCTGAGGCCA----

upper sequence: GRMZM2G152438_T02 (Zea mays), 3'ss of exon 6
lower sequence: EFJ04902 (Selaginella moellendorffii), 3'ss of exon 3
cgatcactatgatgcctttgcagcttttgctcaatctcttcgtgattgttgattgtgcatctgcttataattcttgattgctccttgacttgactattagATAAATACCATGCTTGGGTAAATGCAGAGTTCCTCCTGGAGAAGTGCCTTGTCGGATTCCTTGATCCCACCGCGTAGATATCCAGGTCTCATGGCATTTT
                                         || |  |||||||     | | |||        || |     |||   |||      ||| |||||||| |||||||| ||||| ||||||||||||||||  |||||  | ||   |  |    | |  |                            
-----------------------------------------gtaa--gttgatt---tgttttcttg-gccctgtgctcaaagctttgtttgct--ccagACAAATACCACGCTTGGGTGAATGCCGAGTTCCTCCTGGAGAGATGCCTC-TTGGGCGCTCTAGAACAATAG----------------------------

upper sequence: GRMZM2G152438_T02 (Zea mays), 3'ss of exon 6
lower sequence: EFJ11012 (Selaginella moellendorffii), 3'ss of exon 3
cgatcactatgatgcctttgcagcttttgctcaatctcttcgtgattgttgattgtgcatctgcttataattcttgattgctccttgacttgactatt--agATAAATACCATGCTTGGGTAAATGCAGAGTTCCTCCTGGAGAAGTGCCTTGTCGGATTCCTTGATCCCACCGCGTAGATATCCAGGTCTCATGGCATTTT
                                               ||   |||   || || ||      | ||  |||||   |  |||  |  |  ||| |||||||| |||||||| ||||| ||||||||||||||||  |||||  | ||   |  |    | |  |                            
-----------------------------------------------gtaagttg---atttgttttcttcccctg--tgctcaaagctttgtttgctccagACAAATACCACGCTTGGGTGAATGCCGAGTTCCTCCTGGAGAGATGCCTC-TTGGGCGCTCTAGAACAATAG----------------------------

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|78077673|gb|DV506107.1|DV506107
EST:     TGTTGATATGCTTATGAAAGCCGCTGGGAAAGACTGCACTGCTTTGTTCA                         ATAAATACCATGCTTGGGTAAATGCAGAGTTCCTCCTGGAGAAGTGCCTTG
genomic: TGTTGATATGCTTATGAAAGCCGCTGGGAAAGACTGCACTGCTTTGTTCAgtatccttct ... tgactattagATAAATACCATGCTTGGGTAAATGCAGAGTTCCTCCTGGAGAAGTGCCTTG
EST: gi|50328462|gb|CO523588.1|CO523588
EST:     TGTTGATATGCTTATGAAAGCCGCTGGGAAAGACTGCACTGCTTTGTTCA                         ATAAATACCATGCTTGGGTAAATGCAGAGTTCCTCCTGGAGAAGTGCCTTG
genomic: TGTTGATATGCTTATGAAAGCCGCTGGGAAAGACTGCACTGCTTTGTTCAgtatccttct ... tgactattagATAAATACCATGCTTGGGTAAATGCAGAGTTCCTCCTGGAGAAGTGCCTTG
EST: gi|78122153|gb|DV540537.1|DV540537
EST:     TGTTGATATGCTTATGAAAGCCGCTGGGAAAGACTGCACTGCTTTGTTCA                         ATAAATACCATGCTTGGGTAAATGCAGAGTTCCTCCTGGAGAAGTGCCTTG
genomic: TGTTGATATGCTTATGAAAGCCGCTGGGAAAGACTGCACTGCTTTGTTCAgtatccttct ... tgactattagATAAATACCATGCTTGGGTAAATGCAGAGTTCCTCCTGGAGAAGTGCCTTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgttgattgtgcatctgcttataattcttgattgctccttgacttgactattagATAAATACCATGCTTGGGTAAATGCAGAGTTCCTCCTGGAGAAGTGCCTTGTCGGATTCCTTGATCCCACCGCGTAGATATCCAGGTCTCATGGCATTTT
                                   ctccttgac  putative branch site 
                   ttataattcttgatt  TA-rich tract