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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gcaaaaaccatggtgttcagtatttcagtagctaccattattctgtttggaaataaattatatccatttttcttcttgatttcagGCACGATATGGAACACGAAGCATGGTGGCACTAGCAGCGAAATTGGAAGGTGAGGTAACATTCTATGAAAGGTACTTGGAGAACAGTTTGTGGAAGGAGA

Basic information

species Zea mays
transcript GRMZM2G003057_T02
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G003057_T07 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os04g47680.1 (Oryza sativa), 3'ss of exon 3
gcaaaaaccatggtgttcagtatttcagtagctaccattattctgtttgg-------aaataaattatatccat---ttttcttcttgatttcagGCACGATATGGAACACGAAGCATGGTGGCACTAGCAGCGAAATTGGAAGGTGAGGTAACATTCTATGAAAGGTACTTGGAGAACAGTTTGTGGAAGGAGA
   ||||  |     |||||||||   |||  |||  |  |  |  |||        |||| | | | |   |     |||| |  || ||||||||||||||||||||||||||||||   || || || | ||| ||  | || || ||||| |||||||||||||||||||||| || | | ||||||||||
-gtaaaattagaagattcagtattg-ggtatatactgtcctgtttcttgatcctaccaaattagtgacaggtacaaaatttccttctggtttcagGCACGATATGGAACACGAAGCATGACTGCTCTTGCTGTGAAGTTCAACGGCGAAGTAACTTTCTATGAAAGGTACTTGGAGAGCAATCTATGGAAGGAGA
















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|211018568|gb|FL456864.1|FL456864
EST:     AGTGGGAGTMCAAGCTAAGCTCAATATTCATTGACACTGCAAAGGAACAG                         GCACGATATGGAACACGAAGCATGGTGGCGCTAGCAGCGAAATTGGAAGGT
genomic: AGTGGGAGTACAAGCTAAGCTCAATATTCATTGACACTGCAAAGGAACAGgcaaaaacca ... ttgatttcagGCACGATATGGAACACGAAGCATGGTGGCACTAGCAGCGAAATTGGAAGGT
EST: gi|32827371|gb|CD967049.1|CD967049
EST:     AGTGGGAGTACAAGCTAAGCTCAATATTCATTGACACTGCAAAGGAACAG                         GCACGATATGGAACACGAAGCATGGTGGCGCTAGCAGCGAAATTGGAAGGT
genomic: AGTGGGAGTACAAGCTAAGCTCAATATTCATTGACACTGCAAAGGAACAGgcaaaaacca ... ttgatttcagGCACGATATGGAACACGAAGCATGGTGGCACTAGCAGCGAAATTGGAAGGT
EST: gi|149100496|gb|EE186576.2|EE186576
EST:     AGTGGGAGTACAAGCTAAGCTCAATATTCATTGACACTGCAAAGGAACAG                         GCACGATATGGAACACGAAGCATGGTGGCACTAGCAGCGAAATTGGAAGGT
genomic: AGTGGGAGTACAAGCTAAGCTCAATATTCATTGACACTGCAAAGGAACAGgcaaaaacca ... ttgatttcagGCACGATATGGAACACGAAGCATGGTGGCACTAGCAGCGAAATTGGAAGGT
EST: gi|211532554|gb|FL475961.1|FL475961
EST:     AGTGGGAGTACAAGCTAAGCTCAATATTCATTGACACTGCAAAGGAACAG                         GCACGATATGGAACACGAAGCATGGTGGCGCTAGCAGCGAAATTGGAAGGT
genomic: AGTGGGAGTACAAGCTAAGCTCAATATTCATTGACACTGCAAAGGAACAGgcaaaaacca ... ttgatttcagGCACGATATGGAACACGAAGCATGGTGGCACTAGCAGCGAAATTGGAAGGT
EST: gi|211367475|gb|FL445555.1|FL445555
EST:     AGTGGGAGTACAAGCTAAGCTCAATATTCATTGACACTGCAAAGGAACAG                         GCACGATATGGAACACGAAGCATGGTGGCGCTAGCAGCGAAATTGGAAGGT
genomic: AGTGGGAGTACAAGCTAAGCTCAATATTCATTGACACTGCAAAGGAACAGgcaaaaacca ... ttgatttcagGCACGATATGGAACACGAAGCATGGTGGCACTAGCAGCGAAATTGGAAGGT
EST: gi|211532553|gb|FL475960.1|FL475960
EST:     AGTGGGAGTACAAGCTAAGCTCAATATTCATTGACACTGCAAAGGAACAG                         GCACGATATGGAACACGAAGCATGGTGGCGCTAGCAGCGAAATTGGAAGGT
genomic: AGTGGGAGTACAAGCTAAGCTCAATATTCATTGACACTGCAAAGGAACAGgcaaaaacca ... ttgatttcagGCACGATATGGAACACGAAGCATGGTGGCACTAGCAGCGAAATTGGAAGGT
EST: gi|60340900|gb|DN207873.1|DN207873
EST:     AGTGGGAGTACAAGCTAAGCTCAATATTCATTGACACTGCAAAGGAACAG                         GCACGATATGGAACACGAAGCATGGTGGCGCTAGCAGCGAAATTGGAAGGT
genomic: AGTGGGAGTACAAGCTAAGCTCAATATTCATTGACACTGCAAAGGAACAGgcaaaaacca ... ttgatttcagGCACGATATGGAACACGAAGCATGGTGGCACTAGCAGCGAAATTGGAAGGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gctaccattattctgtttggaaataaattatatccatttttcttcttgatttcagGCACGATATGGAACACGAAGCATGGTGGCACTAGCAGCGAAATTGGAAGGTGAGGTAACATTCTATGAAAGGTACTTGGAGAACAGTTTGTGGAAGGAGA
                                           tcttgat  putative branch site (score: 4)
                                tccatttttcttcttg  CT-rich tract
      attattctgtttggaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gcaaaaaccatggtgttcagtatttcagtagctaccattattctgtttggaaataaattatatccatttttcttcttgatttcagGCACGATATGGAACACGAAGCATGGTGGCACTAGCAGCGAAATTGGAAGGTGAGGTAACATTCTATGAAAGGTACTTGGAGAACAGTTTGTGGAAGGAGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA