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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaggcataattccaagtttcgctgatatttattttggttcctgcagtgtaatgattgaacttggcttttgcaatgcagCTATATACCATCACAACTCTAATTCTTACCGTACAGACGATATACTATAGCCACATCTACCATCGTCTTGAAGCAAAAAAATCCAGGGCAGCTAGCAAG

Basic information

species Zea mays
transcript GRMZM2G024733_T02
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G024733_T02 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os01g16170.4 (Oryza sativa), 3'ss of exon 4
gtaaggcataattccaagtttcg------ctgatatttattttggttcctgcagtg--taatgattgaa--cttggcttttgcaatgcagCTATATACCATCACAACTCTAATTCTTACCGTACAGACGATATACTATAGCCACATCTACCATCGTCTTGAAGCAAAAAAATCCAGGGCAGCTAGCAAG
||||||    |   || |||||       ||| | |||| |||  ||| ||  ||   | |      ||  |||| | |||| |||||||||||| |||||||||||| | ||||| || | ||||||  |||||||||||||||| || || |||||| ||||||||||| |||||||| | ||||||
gtaaggtgccaaatcaggtttctggatttctgctgtttaatttc-ttcttgtggttgttgacacccaaaaacttgccatttggaatgcagCTATACACCATCACAACTGTTATTCTCACTGGACAGACAGTATACTATAGCCACATATATCACCGTCTTAAAGCAAAAAAAGCCAGGGCAACAAGCAAG
















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|71426414|gb|DR807464.1|DR807464
EST:     CTGCCAACTCAGATGTACATGGCACTG                         CTATATACCATCACAACTCTAATTCTTACCGTACAGACGATATACTATAGC
genomic: CTGCCAACTCAGATGTACATGGCACTGgtaaggcata ... tgcaatgcagCTATATACCATCACAACTCTAATTCTTACCGTACAGACGATATACTATAGC
EST: gi|71432685|gb|DR813735.1|DR813735
EST:     CTGCCAACTCAGATGTACATGGCACTG                         CTATATACCATCACAACTCTAATTCTTACCGTACAGACGATATACTATAGC
genomic: CTGCCAACTCAGATGTACATGGCACTGgtaaggcata ... tgcaatgcagCTATATACCATCACAACTCTAATTCTTACCGTACAGACGATATACTATAGC
EST: gi|71770193|gb|DR968130.1|DR968130
EST:     CTGCCAACTCAGATGTACATGGCACTG                         CTATATACCATCACAACTCTAATTCTTACCGTACAGACGATATACTATAGC
genomic: CTGCCAACTCAGATGTACATGGCACTGgtaaggcata ... tgcaatgcagCTATATACCATCACAACTCTAATTCTTACCGTACAGACGATATACTATAGC
EST: gi|94472307|gb|EB701265.1|EB701265
EST:     CTGCCAACTCAGATGTACATGGCACTG                         CTATATACCATCACAACTCTAATTCTTACCGTACAGACGATATACTATAG
genomic: CTGCCAACTCAGATGTACATGGCACTGgtaaggcata ... tgcaatgcagCTATATACCATCACAACTCTAATTCTTACCGTACAGACGATATACTATAG
EST: gi|76288325|gb|DV027893.1|DV027893
EST:     CTGCCAACTCAGATGTACATGGCACTG                         CTATATACCATCACAACTCTAATTCTTACCGTACAGACGATATACTATAGC
genomic: CTGCCAACTCAGATGTACATGGCACTGgtaaggcata ... tgcaatgcagCTATATACCATCACAACTCTAATTCTTACCGTACAGACGATATACTATAGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gatatttattttggttcctgcagtgtaatgattgaacttggcttttgcaatgcagCTATATACCATCACAACTCTAATTCTTACCGTACAGACGATATACTATAGCCACATCTACCATCGTCTTGAAGCAAAAAAATCCAGGGCAGCTAGCAAG
 cgctgat  putative branch site (score: 4)
                                         cttttgc  putative PPT
     ttatttt  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaggcataattccaagtttcgctgatatttattttggttcctgcagtgtaatgattgaacttggcttttgcaatgcagCTATATACCATCACAACTCTAATTCTTACCGTACAGACGATATACTATAGCCACATCTACCATCGTCTTGAAGCAAAAAAATCCAGGGCAGCTAGCAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCAAG