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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagctgatattttacaagttaataaactgttatcatatcatatactgtacataccatgccatttgtgtcagcttgtttctgtcccaggcagGAGATGGAGAGTGCAGCTGTGGAGGAAACGTGGTCAAAGGATTGTGTGTTAAGCCAAACAAAGGGGACGCTGTTCTCTTCTGGAGCATG

Basic information

species Zea mays
transcript GRMZM2G028004_T04
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G028004_T05 (Zea mays), 3'ss of exon 9
lower sequence: LOC_Os04g27850.1 (Oryza sativa), 3'ss of exon 9
-------gttag-ctgatattttacaagttaataaactgttat--catatca--tatactgtacataccatgccatttgtgtcagcttgtttctgtcccaggcagGAGATGGAGAGTGCAGCTGTGGAGGAAACGTGGTCAAAGGATTGTGTGTTAAGCCAAACAAAGGGGACGCTGTTCTCTTCTGGAGCATG
       ||  | ||| |   |      ||  | | || ||||   |||| |  | |  ||| | | ||      | ||  |    |    ||||| ||||||||||||||| || || |||||||| || ||  ||||||||||||| ||||| |||||||||||||| || ||||| || || |||||||||
acatgtcgtggggctgcttcatccgtctttgtttagcttttatgttatatgatttgtggtgtgcttgcctgatattctgaattta-tcacctctgttccagGCAGGAGATGGTGAATGTAGCTGTGGCGGGAAGATGGTCAAAGGATTATGTGTCAAGCCAAACAAAGGAGATGCTGTGCTATTTTGGAGCATG
















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|5901353|gb|AW042453.1|AW042453
EST:     TTATGTATTTGACAGATGGCGTTGTAGGTGGTGAAACTCACTTTCCGCAG                         GCAGGAGATGGAGAGTGCAGCTGTGGAGGAAACGTGGTCAAAGGATTGTGT
genomic: TTATGTATTTGACAGATGGCGTTGTAGGTGGTGAAACTCACTTTCCGCAGgttagctgat ... tcccaggcagG-AG-A--TGGAGAGTGCAGCTGTGGAGGAAACGTGGTCAAAGGATTGTGT
EST: gi|31363979|gb|CD448334.1|CD448334
EST:     TTATGTATTTGACAGATGGCGTTGTAGGTGGTGAAACTCACTTTCCGCAGGCAG                      
genomic: TTATGTATTTGACAGATGGCGTTGTAGGTGGTGAAACTCACTTT-C-C--GCAGgttagctgat ... tcccagg
EST: gi|18650084|gb|BM498903.1|BM498903
EST:     TTATGTATTTGACAGATGGCGTTGTAGGTGGTGAAACTCACTTTCCGCAGGCAG                      
genomic: TTATGTATTTGACAGATGGCGTTGTAGGTGGTGAAACTCACTTT-C-C--GCAGgttagctgat ... tcccagg
EST: gi|31353632|gb|CD437989.1|CD437989
EST:     TTATGTATTTGACAGATGGCGTTGTAGGTGGTGAAACTCACTTTCCGCAG                         GCAGGAGATGGAGAGTGCAGCTGTGGAGGAAACGTGGTCAAAGGATTGTGT
genomic: TTATGTATTTGACAGATGGCGTTGTAGGTGGTGAAACTCACTTTCCGCAGgttagctgat ... tcccaggcagG-AG-A--TGGAGAGTGCAGCTGTGGAGGAAACGTGGTCAAAGGATTGTGT
EST: gi|24768702|gb|CA403831.1|CA403831
EST:     TTATGTATTTGACAGATGGCGTTGTAGGTGGTGAAACTCACTTTCCGCAGGCAG                      
genomic: TTATGTATTTGACAGATGGCGTTGTAGGTGGTGAAACTCACTTT-C-C--GCAGgttagctgat ... tcccagg
EST: gi|211143817|gb|FL448468.1|FL448468
EST:     TTATGTATTTGACAGATGGCGTTGTAGGTGGTGAAACTCACTTTCCGCAG                         GAGATGGAGAGTGCAGCTGTGGAGGAAACGTGGTCAAAGGATTGTGTGTTA
genomic: TTATGTATTTGACAGATGGCGTTGTAGGTGGTGAAACTCACTTTCCGCAGgttagctgat ... tcccaggcagGAGATGGAGAGTGCAGCTGTGGAGGAAACGTGGTCAAAGGATTGTGTGTTA
EST: gi|67013387|gb|CO442136.1|CO442136
EST:     TTATGTATTTGACAGATGGCGTTGTAGGTGGTGAAACTCACTTTCCGCAG                         GAGATGGAGAGTGCANCTGTGNGAG-AAACGTGGTCAAAGGATTGTGTGTT
genomic: TTATGTATTTGACAGATGGCGTTGTAGGTGGTGAAACTCACTTTCCGCAGgttagctgat ... tcccaggcagGAGATGGAGAGTGCAGCTGTG-GAGGAAACGTGGTCAAAGGATTGTGTGTT
EST: gi|24768774|gb|CA403903.1|CA403903
EST:     TTATGTATTTGACAGATGGCGTTGTAGGTGGTGAAACTCACTTTCCGCAG                         GCAGGAGATGGAGAGTGCAGCTGTGGAGGAAACGTGGTCAAAGGATTGTGT
genomic: TTATGTATTTGACAGATGGCGTTGTAGGTGGTGAAACTCACTTTCCGCAGgttagctgat ... tcccaggcagG-AG-A--TGGAGAGTGCAGCTGTGGAGGAAACGTGGTCAAAGGATTGTGT
EST: gi|67013389|gb|CO442138.1|CO442138
EST:     TATGTATTTGACAGATGGCGTTGTAGGTGGTGAAACTCACTTTCCGCNAG                         -AGATGGAGAGTGCANCTGTGNGAG-AAACGTGGTCAAAGGATTGTGTGT
genomic: TATGTATTTGACAGATGGCGTTGTAGGTGGTGAAACTCACTTTCCGC-AGgttagctgat ... tcccaggcagGAGATGGAGAGTGCAGCTGTG-GAGGAAACGTGGTCAAAGGATTGTGTGT
EST: gi|211143816|gb|FL448467.1|FL448467
EST:     TTATGTATTTGACAGATGGCGTTGTAGGTGGTGAAACTCACTTTCCGCAG                         GAGATGGAGAGTGCAGCTGTGGAGGAAACGTGGTCAAAGGATTGTGTGTTA
genomic: TTATGTATTTGACAGATGGCGTTGTAGGTGGTGAAACTCACTTTCCGCAGgttagctgat ... tcccaggcagGAGATGGAGAGTGCAGCTGTGGAGGAAACGTGGTCAAAGGATTGTGTGTTA
EST: gi|31364601|gb|CD448956.1|CD448956
EST:     TTATGTATTTGACAGATGGCGTTGTAGGTGGTGAAACTCACTTTCCGCAG                         GCAGGAGATGGAGAGTGCAGCTGTGGAGGAAACGTGGTCAAAGGATTGTGT
genomic: TTATGTATTTGACAGATGGCGTTGTAGGTGGTGAAACTCACTTTCCGCAGgttagctgat ... tcccaggcagG-AG-A--TGGAGAGTGCAGCTGTGGAGGAAACGTGGTCAAAGGATTGTGT
EST: gi|37395929|gb|CF635251.1|CF635251
EST:     TTATGTATTTGACAGATGGCGTTGTAGGTGGTGAAACTCACTTTCCGCAGGCAG                      
genomic: TTATGTATTTGACAGATGGCGTTGTAGGTGGTGAAACTCACTTT-C-C--GCAGgttagctgat ... tcccagg
EST: gi|60355576|gb|DN222549.1|DN222549
EST:     TTATGTATTTGACAGATGGCGTTGTAGGTGGTGAAACTCACTTTCCGCAGGCAG                      
genomic: TTATGTATTTGACAGATGGCGTTGTAGGTGGTGAAACTCACTTT-C-C--GCAGgttagctgat ... tcccagg


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atcatatactgtacataccatgccatttgtgtcagcttgtttctgtcccaggcagGAGATGGAGAGTGCAGCTGTGGAGGAAACGTGGTCAAAGGATTGTGTGTTAAGCCAAACAAAGGGGACGCTGTTCTCTTCTGGAGCATG
                                   cttgtttctgtccc  CT-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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttagctgatattttacaagttaataaactgttatcatatcatatactgtacataccatgccatttgtgtcagcttgtttctgtcccaggcagGAGATGGAGAGTGCAGCTGTGGAGGAAACGTGGTCAAAGGATTGTGTGTTAAGCCAAACAAAGGGGACGCTGTTCTCTTCTGGAGCATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA