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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tccattttttacaatctttgtattttctaaaaatcagcaatatccccatccactatcacgaagatgcgtacttgatggattttatttttcttgtttgcagATTTTCTTATACTATTCTTTACCGAGGCTTTATTTTATGGAGGAGTTGCAATTTTTGTCTTCTTGATTGATAAAGTCTGGAGACCTTTGCAGCAAGTAGC

Basic information

species Zea mays
transcript GRMZM2G034975_T01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G034975_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os01g50830.2 (Oryza sativa), 3'ss of exon 3
tccattttttacaatctttgtattttctaaaaatcag-caatatccccatccactatca-cgaagatgcgta-cttgatggattttatttttcttgtttgcagATTTTCTTATACTATTCTTTACCGAGGCTTTATTTTATGGAGGAGTTGCAATTTTTGTCTTCTTGATTGATAAAGTCTGGAGACCTTTGCAGCAAGTAGC
   |  | |||  |   | |   |  || |    ||  | | ||    ||  |   | | |   |  || || | |||||| ||||    |  ||| || |||||||||||||||||||||||||||||||| |||||||||||||||| |||||||||||| | |||||||||||||||||||| |||||||||||||||||
-ttaaatcttaagacactagatgtccctgattcccattccacatttggatgaagcctaagcatggcagcataacctgatggttttt--cataattgcttacagATTTTCTTATACTATTCTTTACCGAGGCTCTATTTTATGGAGGAGTCGCAATTTTTGTCCTGTTGATTGATAAAGTCTGGAGGCCTTTGCAGCAAGTAGC
















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|76010384|gb|DT937554.1|DT937554
EST:     TTACTTGCGCAAAGTACTCTCAGCAGTGTTTGAAGATTCCTTGTTGACAG                         ATTTTCTTATACTATTCTTTACCGAGGCTTTATTTTATGGAGGAGTTGCAA
genomic: TTACTTGCGCAAAGTACTCTCAGCAGTGTTTGAAGATTCCTTGTTGACAGgtatcctttc ... ttgtttgcagATTTTCTTATACTATTCTTTACCGAGGCTTTATTTTATGGAGGAGTTGCAA
EST: gi|76010385|gb|DT937555.1|DT937555
EST:     TTACTTGCGCAAAGTACTCTCAGCAGTGTTTGAAGATTCCTTGTTGACAG                         ATTTTCTTATACTATTCTTTTAC-GAGGCTTTATTTTATGGAGGAGTTGCA
genomic: TTACTTGCGCAAAGTACTCTCAGCAGTGTTTGAAGATTCCTTGTTGACAGgtatcctttc ... ttgtttgcagATTTTCTTATACTATTCTTT-ACCGAGGCTTTATTTTATGGAGGAGTTGCA
EST: gi|78079427|gb|DV507839.1|DV507839
EST:     TTACTTGCGCAAAGTACTCTCAGCAGTGTTTGAAGATTCCTTGTTGACAG                         ATTTTCTTATACTATTCTTTACCCGAG-CTTTATTTTTATGGAGGAGTTGC
genomic: TTACTTGCGCAAAGTACTCTCAGCAGTGTTTGAAGATTCCTTGTTGACAGgtatcctttc ... ttgtttgcagATTTTCTTATACTATTCTTTACC-GAGGCTTTATTTT-ATGGAGGAGTTGC
EST: gi|71326147|gb|DR799760.1|DR799760
EST:     TTACTTGCGCAAAGTACTCTCAGCAGTGTTTGAAGATTCCTTGTTGACAG                         ATTTTCTTATACTATTCTTTACCGAGGCTTTATTTTATGGAGGAGTTGCAA
genomic: TTACTTGCGCAAAGTACTCTCAGCAGTGTTTGAAGATTCCTTGTTGACAGgtatcctttc ... ttgtttgcagATTTTCTTATACTATTCTTTACCGAGGCTTTATTTTATGGAGGAGTTGCAA
EST: gi|78082089|gb|DV510501.1|DV510501
EST:     TTACTTGCGCAAAGTACTCTCAGCAGTGTTTGAAGATTCCTTGTTGACAG                         ATTTTCTTATACTATTCTTTACCGAGGCTTTATTTTATGGAGGAGTTGCAA
genomic: TTACTTGCGCAAAGTACTCTCAGCAGTGTTTGAAGATTCCTTGTTGACAGgtatcctttc ... ttgtttgcagATTTTCTTATACTATTCTTTACCGAGGCTTTATTTTATGGAGGAGTTGCAA
EST: gi|50325253|gb|CO520379.1|CO520379
EST:     TTACTTGCGCAAAGTACTCTCAGCAGTGTTTGAAGATTCCTTGTTGACAG                         ATTTTCTTATACTATTCTTTACCGAGGCTTTATTTTATGGAGGAGTTGCAA
genomic: TTACTTGCGCAAAGTACTCTCAGCAGTGTTTGAAGATTCCTTGTTGACAGgtatcctttc ... ttgtttgcagATTTTCTTATACTATTCTTTACCGAGGCTTTATTTTATGGAGGAGTTGCAA
EST: gi|76933226|gb|DV173377.1|DV173377
EST:     TTACTTGCGCAAAGTACTCTCAGCAGTGTTTGAAGATTCCTTGTTGACAG                         ATTTTCTTATACTATTCTT
genomic: TTACTTGCGCAAAGTACTCTCAGCAGTGTTTGAAGATTCCTTGTTGACAGgtatcctttc ... ttgtttgcagATTTTCTTATACTATTCTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccatccactatcacgaagatgcgtacttgatggattttatttttcttgtttgcagATTTTCTTATACTATTCTTTACCGAGGCTTTATTTTATGGAGGAGTTGCAATTTTTGTCTTCTTGATTGATAAAGTCTGGAGACCTTTGCAGCAAGTAGC
                        acttgat  putative branch site (score: 5)
                                  ttttatttttcttgtt  putative PPT
                                 attttatttttcttgt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tccattttttacaatctttgtattttctaaaaatcagcaatatccccatccactatcacgaagatgcgtacttgatggattttatttttcttgtttgcagATTTTCTTATACTATTCTTTACCGAGGCTTTATTTTATGGAGGAGTTGCAATTTTTGTCTTCTTGATTGATAAAGTCTGGAGACCTTTGCAGCAAGTAGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG