Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   		8  
 5'  3'   		9  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTCAGATCGCTCAGGCATATGAGAAAAACGGAGCAGCATGCCTTAGTGTTCTTACAGATGAAAAGTACTTTCAGgtcatttagtttttcaccttggaaagttctgtctcatttctatcatcaatacgttatatatgctgaaggcacttgttttccttttacatgtaatcag

Basic information

species Zea mays
transcript GRMZM2G169516_T02
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G169516_T02 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os04g39270.1 (Oryza sativa), 5'ss of exon 4
GTTCAGATCGCTCAGGCATATGAGAAAAACGGAGCAGCATGCCTTAGTGTTCTTACAGATGAAAAGTACTTTCAGgtcatttagtttttcaccttggaaagttctgtctcatttctat--catcaatacgttatatatgctgaaggcacttgttttccttttacatgtaatcag
||||||||||| ||  ||||||||||||| |||||||||||| | |||||||| ||||||| ||| ||||||||||||| | |  ||||| | || || | ||  |   |   |||    ||| |  |  ||||  ||||||||     |||||| | |||   ||||||||||
GTTCAGATCGCCCAAACATATGAGAAAAATGGAGCAGCATGCTTAAGTGTTCTCACAGATGCAAAATACTTTCAGgtcagtaatcttttcccttttgacaatttggctactcctctgatgcattacgaaattatgcatgctgaa----tttgtttccgtttgttatgtaatcag
















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|15312691|gb|BI478322.1|BI478322
EST:     GTGTTCTTACAGATGAAAAGTACTTTCAG                         GGAAGTTTTTACAACTTGGAGGCTATACGCAATGCTGGAGTCCAG
genomic: GTGTTCTTACAGATGAAAAGTACTTTCAGgtcatttagt ... atgtaatcagGGAAGTTTTTACAACTTGGAGGCTATACGCAATGCTGGAGTCCAG
EST: gi|71430054|gb|DR811104.1|DR811104
EST:     AAAACGGAGCAGCATGCCTTAGTGTTCTTACAGATGAAAAGTACTTTCAG                         GGAAGTTTTTACAACTTGGAGGCTATACGCAATGCTGGAGTCCAG
genomic: AAAACGGAGCAGCATGCCTTAGTGTTCTTACAGATGAAAAGTACTTTCAGgtcatttagt ... atgtaatcagGGAAGTTTTTACAACTTGGAGGCTATACGCAATGCTGGAGTCCAG
EST: gi|71438048|gb|DR819098.1|DR819098
EST:     AAAACGGAGCAGCATGCCTTAGTGTTCTTACAGATGAAAAGTACTTTCAG                         GGAAGTTTTTACAACTTGGAGGCTATACGCAATGCTGGAGTCCAG
genomic: AAAACGGAGCAGCATGCCTTAGTGTTCTTACAGATGAAAAGTACTTTCAGgtcatttagt ... atgtaatcagGGAAGTTTTTACAACTTGGAGGCTATACGCAATGCTGGAGTCCAG
EST: gi|148972168|gb|EE023038.2|EE023038
EST:     AAAACGGAGCAGCATGCCTTAGTGTTCTTACAGATGAAAAGTACTTTCAG                         GGAAGTTTTTACAACTTGGAGGCTATACGCAATGCTGGAGTCCAG
genomic: AAAACGGAGCAGCATGCCTTAGTGTTCTTACAGATGAAAAGTACTTTCAGgtcatttagt ... atgtaatcagGGAAGTTTTTACAACTTGGAGGCTATACGCAATGCTGGAGTCCAG
EST: gi|149026795|gb|EE046156.2|EE046156
EST:     AAAACGGAGCAGCATGCCTTAGTGTTCTTACAGATGAAAAGTACTTTCAG                         GGAAGTTTTTACAACTTGGAGGCTATACGCAATGCTGGAGTCCAG
genomic: AAAACGGAGCAGCATGCCTTAGTGTTCTTACAGATGAAAAGTACTTTCAGgtcatttagt ... atgtaatcagGGAAGTTTTTACAACTTGGAGGCTATACGCAATGCTGGAGTCCAG
EST: gi|71324172|gb|DR798789.1|DR798789
EST:     AAAACGGAGCAGCATGCCTTAGTGTTCTTACAGATGAAAAGTACTTTCAG                         GGAAGTTTTTACAACTTGGAGGCTATACGCAATGCTGGAGTCCAG
genomic: AAAACGGAGCAGCATGCCTTAGTGTTCTTACAGATGAAAAGTACTTTCAGgtcatttagt ... atgtaatcagGGAAGTTTTTACAACTTGGAGGCTATACGCAATGCTGGAGTCCAG
EST: gi|24765189|gb|CA400348.1|CA400348
EST:     AAAACGGAGCAGCATGCCTTAGTGTTCTTACAGATGAAAAGTACTTTCAG                         GGAAGTTTTTACAACTTGGAGGCTATACGCAATGCTGGAGTCCAG
genomic: AAAACGGAGCAGCATGCCTTAGTGTTCTTACAGATGAAAAGTACTTTCAGgtcatttagt ... atgtaatcagGGAAGTTTTTACAACTTGGAGGCTATACGCAATGCTGGAGTCCAG
EST: gi|71442934|gb|DR823984.1|DR823984
EST:     AAAACGGAGCAGCATGCCTTAGTGTTCTTACAGATGAAAAGTACTTTCAG                         GGAAGTTTTTACAACTTGGAGGCTATACGCAATGCTGGAGTCCAG
genomic: AAAACGGAGCAGCATGCCTTAGTGTTCTTACAGATGAAAAGTACTTTCAGgtcatttagt ... atgtaatcagGGAAGTTTTTACAACTTGGAGGCTATACGCAATGCTGGAGTCCAG
EST: gi|76926401|gb|DV170844.1|DV170844
EST:     AAAACGGAGCAGCATGCCTTAGTGTTCTTACAGATGAAAAGTACTTTCAG                         GGAAGTTTTTACAACTTGGAGGCTATACGCAATGCTGGAGTCCAGTGC
genomic: AAAACGGAGCAGCATGCCTTAGTGTTCTTACAGATGAAAAGTACTTTCAGgtcatttagt ... atgtaatcagGGAAGTTTTTACAACTTGGAGGCTATACGCAATGCTGGAGTCCAGTGC
EST: gi|148950313|gb|EC895872.2|EC895872
EST:     AAAACGGAGCAGCATGCCTTAGTGTTCTTACAGATGAAAAGTACTTTCAG                         GGAAGTTTTTACAACTTGGAGGCT
genomic: AAAACGGAGCAGCATGCCTTAGTGTTCTTACAGATGAAAAGTACTTTCAGgtcatttagt ... atgtaatcagGGAAGTTTTTACAACTTGGAGGCT
EST: gi|71433348|gb|DR814398.1|DR814398
EST:     AAAACGGAGCAGCATGCCTTAGTGTTCTTACAGATGAAAAGTACTTTCAG                         GGAAGTTTTTACAACTTGGAGGCTATACGCAATGCTGGAGTCTAG
genomic: AAAACGGAGCAGCATGCCTTAGTGTTCTTACAGATGAAAAGTACTTTCAGgtcatttagt ... atgtaatcagGGAAGTTTTTACAACTTGGAGGCTATACGCAATGCTGGAGTCCAG
EST: gi|71431465|gb|DR812515.1|DR812515
EST:     CAGATGAAAAGTACTTTCAG                         GGAAGTTTTTACAAC-TGGAGGGCTATACGCAATGCTGGAGTCCAG
genomic: CAGATGAAAAGTACTTTCAGgtcatttagt ... atgtaatcagGGAAGTTTTTACAACTTGGA-GGCTATACGCAATGCTGGAGTCCAG
EST: gi|71318677|gb|DR796095.1|DR796095
EST:     AAAACGGAGCAGCATGCCTTAGTGTTCTTACAGATGAAAAGTACTTTCAG                         GGAAGTTTTTACAACTTGGAGGCTATACGCAATGCTGGAGTCCAG
genomic: AAAACGGAGCAGCATGCCTTAGTGTTCTTACAGATGAAAAGTACTTTCAGgtcatttagt ... atgtaatcagGGAAGTTTTTACAACTTGGAGGCTATACGCAATGCTGGAGTCCAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTTCAGATCGCTCAGGCATATGAGAAAAACGGAGCAGCATGCCTTAGTGTTCTTACAGATGAAAAGTACTTTCAGgtcatttagtttttcaccttggaaagttctgtctcatttctatcatcaatacgttatatatgctgaaggcacttgttttccttttacatgtaatcag

- - - - - - - - - - - - - - - GGAGCA
- - - - - - - - - - - - - - -  GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGATG