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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgaaactgccttcatcccttgtgcccacacataccctgtatattcatagtacttttgtacttcatttgaaatccttaccaatttatctattcatatgcagTTGCAAAAACAGTACTTTGGGAAGATGCGAAGCAAACTGTGACAGTGCTTCTACTGTTGGCTGTTATCTACTACCACTTATTTACATGTGGTTACACCTT

Basic information

species Zea mays
transcript GRMZM2G149224_T02
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G149224_T01 (Zea mays), 3'ss of exon 8
lower sequence: LOC_Os03g29170.1 (Oryza sativa), 3'ss of exon 8
gtatgaaactgccttcatcccttgtgcccacacataccctgtatattcatagtacttttgtacttcatttgaaatccttaccaatttatctattcatatgcagTTGCAAAAACAGTACTTTGGGAAGATGCGAAGCAAACTGTGACAGTGCTTCTACTGTTGGCTGTTATCTACTACCACTTATTTACATGTGGTTACACCTT
          |  |  ||  ||    | ||||||| |  || ||   |||    | ||   ||     |||| ||  | |  ||| |   | ||    ||||||||| || ||||| || ||||||||   |||||||||  |||| || || || ||  |||||||||||||||| || |||||||||||||||||||||||
----------gtatgaatatctctcacacacacatgca-tgcatgcccatg---ccttcacacccttcttgagattataatgaatattgatcttggc-tgcagTTGCGAAGACAGTTCTCTGGGAAGACATGAAGCAAACAATGACTGTACTACTGCTACTGGCTGTTATCTACTATCATTTATTTACATGTGGTTACACCTT
















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|87151705|gb|DY396494.1|DY396494
EST:     GAATCATAGGAGTATATCAAAGGCTTCAATTTTCCTCGGGAATGGAAATC                         TTGCAAAAACAGTACTTTGGGAAGATGCGAAGCAAACTGTGACAGTGCTTC
genomic: GAATCATAGGAGTATATCAAAGGCTTCAATTTTCCTCGGGAATGGAAATCgtatgaaact ... tcatatgcagTTGCAAAAACAGTACTTTGGGAAGATGCGAAGCAAACTGTGACAGTGCTTC
EST: gi|32863056|gb|CF002738.1|CF002738
EST:     GAATCATAGGAGTATATCAAAGGCTTCAATTTTCCTCGGGAATGGAAATC                         TTGCAAAAACAGTACTTTGGGAAGATGCGAAGCAAACTGTGACAGTGCTTC
genomic: GAATCATAGGAGTATATCAAAGGCTTCAATTTTCCTCGGGAATGGAAATCgtatgaaact ... tcatatgcagTTGCAAAAACAGTACTTTGGGAAGATGCGAAGCAAACTGTGACAGTGCTTC
EST: gi|166483903|gb|EG135197.1|EG135197
EST:     GAATCATAGGAGTATATCAAAGGCTTCAATTTTCCTCGGGAATGGAAATC                         TTGCAAAAACNGTACTTTGGGAAGA
genomic: GAATCATAGGAGTATATCAAAGGCTTCAATTTTCCTCGGGAATGGAAATCgtatgaaact ... tcatatgcagTTGCAAAAACAGTACTTTGGGAAGA
EST: gi|22489855|gb|BU049778.1|BU049778
EST:     GAATCATAGGAGTATATCAAAGGCTTCAATTTTCCTCGGGAATGGAAATC                         TTGCAAAAACAGTACTTTGGGAAGATGCGAAGCAAACTGTGACAGTGCTTC
genomic: GAATCATAGGAGTATATCAAAGGCTTCAATTTTCCTCGGGAATGGAAATCgtatgaaact ... tcatatgcagTTGCAAAAACAGTACTTTGGGAAGATGCGAAGCAAACTGTGACAGTGCTTC
EST: gi|60337162|gb|DN204135.1|DN204135
EST:     TTCCTCGGGAATGGAAATC                         TTGCAAAAACAGTACTTTGGGAAGATGCGAAGCAAACTGTGACAGTGCTTC
genomic: TTCCTCGGGAATGGAAATCgtatgaaact ... tcatatgcagTTGCAAAAACAGTACTTTGGGAAGATGCGAAGCAAACTGTGACAGTGCTTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atagtacttttgtacttcatttgaaatccttaccaatttatctattcatatgcagTTGCAAAAACAGTACTTTGGGAAGATGCGAAGCAAACTGTGACAGTGCTTCTACTGTTGGCTGTTATCTACTACCACTTATTTACATGTGGTTACACCTT
                          tccttac  putative branch site (score: 2)
                                        tctattc  putative PPT
                                  aatttatctattcata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgaaactgccttcatcccttgtgcccacacataccctgtatattcatagtacttttgtacttcatttgaaatccttaccaatttatctattcatatgcagTTGCAAAAACAGTACTTTGGGAAGATGCGAAGCAAACTGTGACAGTGCTTCTACTGTTGGCTGTTATCTACTACCACTTATTTACATGTGGTTACACCTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT