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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtcatttagtttttcaccttggaaagttctgtctcatttctatcatcaatacgttatatatgctgaaggcacttgttttccttttacatgtaatcagGGAAGTTTTTACAACTTGGAGGCTATACGCAATGCTGGAGTCCAG

Basic information

species Zea mays
transcript GRMZM2G169516_T03
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G169516_T05 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os04g39270.1 (Oryza sativa), 3'ss of exon 4
gtcatttagtttttcaccttggaaagttctgtctcatttctat--catcaatacgttatatatgctgaaggcacttgttttccttttacatgtaatcagGGAAGTTTTTACAACTTGGAGGCTATACGCAATGCTGGAGTCCAG
|||| | |  ||||| | || || | ||  |   |   |||    ||| |  |  ||||  ||||||||     |||||| | |||   ||||||||||||||||||| || | ||||| |||||||||||||||||||| |||
gtcagtaatcttttcccttttgacaatttggctactcctctgatgcattacgaaattatgcatgctgaa----tttgtttccgtttgttatgtaatcagGGAAGTTTTGACTATTTGGATGCTATACGCAATGCTGGAGTACAG
















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|71318677|gb|DR796095.1|DR796095
EST:     AAAACGGAGCAGCATGCCTTAGTGTTCTTACAGATGAAAAGTACTTTCAG                         GGAAGTTTTTACAACTTGGAGGCTATACGCAATGCTGGAGTCCAG
genomic: AAAACGGAGCAGCATGCCTTAGTGTTCTTACAGATGAAAAGTACTTTCAGgtcatttagt ... atgtaatcagGGAAGTTTTTACAACTTGGAGGCTATACGCAATGCTGGAGTCCAG
EST: gi|71433348|gb|DR814398.1|DR814398
EST:     AAAACGGAGCAGCATGCCTTAGTGTTCTTACAGATGAAAAGTACTTTCAG                         GGAAGTTTTTACAACTTGGAGGCTATACGCAATGCTGGAGTC
genomic: AAAACGGAGCAGCATGCCTTAGTGTTCTTACAGATGAAAAGTACTTTCAGgtcatttagt ... atgtaatcagGGAAGTTTTTACAACTTGGAGGCTATACGCAATGCTGGAGTC
EST: gi|71324172|gb|DR798789.1|DR798789
EST:     AAAACGGAGCAGCATGCCTTAGTGTTCTTACAGATGAAAAGTACTTTCAG                         GGAAGTTTTTACAACTTGGAGGCTATACGCAATGCTGGAGTCCAG
genomic: AAAACGGAGCAGCATGCCTTAGTGTTCTTACAGATGAAAAGTACTTTCAGgtcatttagt ... atgtaatcagGGAAGTTTTTACAACTTGGAGGCTATACGCAATGCTGGAGTCCAG
EST: gi|148972168|gb|EE023038.2|EE023038
EST:     AAAACGGAGCAGCATGCCTTAGTGTTCTTACAGATGAAAAGTACTTTCAG                         GGAAGTTTTTACAACTTGGAGGCTATACGCAATGCTGGAGTCCAG
genomic: AAAACGGAGCAGCATGCCTTAGTGTTCTTACAGATGAAAAGTACTTTCAGgtcatttagt ... atgtaatcagGGAAGTTTTTACAACTTGGAGGCTATACGCAATGCTGGAGTCCAG
EST: gi|76926401|gb|DV170844.1|DV170844
EST:     AAAACGGAGCAGCATGCCTTAGTGTTCTTACAGATGAAAAGTACTTTCAG                         GGAAGTTTTTACAACTTGGAGGCTATACGCAATGCTGGAGTCCAG
genomic: AAAACGGAGCAGCATGCCTTAGTGTTCTTACAGATGAAAAGTACTTTCAGgtcatttagt ... atgtaatcagGGAAGTTTTTACAACTTGGAGGCTATACGCAATGCTGGAGTCCAG
EST: gi|149026795|gb|EE046156.2|EE046156
EST:     AAAACGGAGCAGCATGCCTTAGTGTTCTTACAGATGAAAAGTACTTTCAG                         GGAAGTTTTTACAACTTGGAGGCTATACGCAATGCTGGAGTCCAG
genomic: AAAACGGAGCAGCATGCCTTAGTGTTCTTACAGATGAAAAGTACTTTCAGgtcatttagt ... atgtaatcagGGAAGTTTTTACAACTTGGAGGCTATACGCAATGCTGGAGTCCAG
EST: gi|148950313|gb|EC895872.2|EC895872
EST:     AAAACGGAGCAGCATGCCTTAGTGTTCTTACAGATGAAAAGTACTTTCAG                         GGAAGTTTTTACAACTTGGAGGCT
genomic: AAAACGGAGCAGCATGCCTTAGTGTTCTTACAGATGAAAAGTACTTTCAGgtcatttagt ... atgtaatcagGGAAGTTTTTACAACTTGGAGGCT
EST: gi|71442934|gb|DR823984.1|DR823984
EST:     AAAACGGAGCAGCATGCCTTAGTGTTCTTACAGATGAAAAGTACTTTCAG                         GGAAGTTTTTACAACTTGGAGGCTATACGCAATGCTGGAGTCCAG
genomic: AAAACGGAGCAGCATGCCTTAGTGTTCTTACAGATGAAAAGTACTTTCAGgtcatttagt ... atgtaatcagGGAAGTTTTTACAACTTGGAGGCTATACGCAATGCTGGAGTCCAG
EST: gi|78121834|gb|DV540218.1|DV540218
EST:     AAAACGGAGCAGCATGCCTTAGTGTTCTTACAGATGAAAAGTACTTTCAG                         GGAAGTTTTTACAACTTGGAGGCTATACGCAATGCTGGAGTCCAG
genomic: AAAACGGAGCAGCATGCCTTAGTGTTCTTACAGATGAAAAGTACTTTCAGgtcatttagt ... atgtaatcagGGAAGTTTTTACAACTTGGAGGCTATACGCAATGCTGGAGTCCAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcatcaatacgttatatatgctgaaggcacttgttttccttttacatgtaatcagGGAAGTTTTTACAACTTGGAGGCTATACGCAATGCTGGAGTCCAG
                                 ttttccttttacat  CT-rich tract
     aatacgttatatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtcatttagtttttcaccttggaaagttctgtctcatttctatcatcaatacgttatatatgctgaaggcacttgttttccttttacatgtaatcagGGAAGTTTTTACAACTTGGAGGCTATACGCAATGCTGGAGTCCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA