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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aaactcagatttaggtcttaaagtggggacagccatgcatttatctctatgaaaatatgacttatttgttattaataacgacacgccgttttggatacagATATATGCACCGTGGTGTGGGCATTGTCAATCACTGGAGCCTACTTACAACAAACTAGCCAAGCATCTAAGTGGAGTTGACTCCCTTGTGATAGCCAAAA

Basic information

species Zea mays
transcript GRMZM2G033829_T03
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G033829_T03 (Zea mays), 3'ss of exon 9
lower sequence: LOC_Os02g01010.1 (Oryza sativa), 3'ss of exon 9
aaactcagatttaggtcttaaagtggggacagccatgca--tttatctctatgaaaatatgacttatttgttattaataacgacacgccgttttggatacagATATATGCACCGTGGTGTGGGCATTGTCAATCACTGGAGCCTACTTACAACAAACTAGCCAAGCATCTAAGTGGAGTTGACTCCCTTGTGATAGCCAAAA
                      ||  |  |  ||  | |  |  ||    |  |||||   | |||| |||  |  ||||      |  | | | | | |||||||||||||| |||||||||||||||||   |||||||||||| |||||||| ||||  ||||||||  ||||  ||||||||||||| ||||| ||||
----------------------gtatgttcttcctggaaggtaaattatgagaaaaatggtatttatatgtggtccataatcgt-tgttgctgttgttgcagATATATGCACCATGGTGTGGGCATTGTCAGGAACTGGAGCCTACCTACAACAAGCTAGGAAAGCATCTCCGTGGCATTGACTCCCTTGTAATAGCTAAAA

upper sequence: GRMZM2G033829_T03 (Zea mays), 3'ss of exon 9
lower sequence: EFJ24976 (Selaginella moellendorffii), 3'ss of exon 9
aaactcagatttaggtcttaaagtggggacagccatgcatttatctctatgaaaatatgacttatttgttattaataacgacacgccgttttggatacagATATATGCACCGTGGTGTGGGCATTGTCAATCACTGGAGCCTACTTACAACAAACTAGCCAAGCATCTAAGTGGAGTTGACTCCCTTGTGATAGCCAAAA
                                   | || |  | | | | |   | |   || |   || ||  |  || ||||   |        ||||| ||||| |||||||| |||||||||||| |||||||||| |  |||||||| || ||    |  ||  | | |||  | || || ||||| ||||| |
----------------------------------gtacactgctatatcttagcttgtatattctacattcttcctctcgccacga-atccccctcgcagATTTATGCTCCGTGGTGCGGGCATTGTCAAGCACTGGAGCCCATCTACAACAAGCTCGCAGCTCGGCTCCGAGAAGTCAAATCTCTGGTGATTGCCAAGA
















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|17970051|gb|BM276819.1|BM276819
EST:     GAATCTGGATGTAATAGTTTTGGATGAATCAAAAAGATGTACTTCTGGAG                         ATATATGCACCGTGGCGTGGGCATTGTCAATCACTGGAGCCTACTTACAAC
genomic: GAGTCTGGATGTAATAGTTTTGGATGAATCAAAA-GATGTACTTCTGGAGgtatgttcct ... ttggatacagATATATGCACCGTGGTGTGGGCATTGTCAATCACTGGAGCCTACTTACAAC
EST: gi|5525515|gb|AI861408.1|AI861408
EST:     AGAATCTGGATGTAATAGTTTTGGATGAATCAAAAGATGTACTTCTGGAG                         ATATATGCACCGTGGTGTGGGCATTGTCAATCACTGGAGCCTACTTACAAC
genomic: AGAGTCTGGATGTAATAGTTTTGGATGAATCAAAAGATGTACTTCTGGAGgtatgttcct ... ttggatacagATATATGCACCGTGGTGTGGGCATTGTCAATCACTGGAGCCTACTTACAAC
EST: gi|18385207|gb|BM418406.1|BM418406
EST:     AGAATCTGGATGTAATAGTTTTGGATGAATCAAAAGATGTACTTCTGGAG                         ATATATGCACC
genomic: AGAGTCTGGATGTAATAGTTTTGGATGAATCAAAAGATGTACTTCTGGAGgtatgttcct ... ttggatacagATATATGCACC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctatgaaaatatgacttatttgttattaataacgacacgccgttttggatacagATATATGCACCGTGGTGTGGGCATTGTCAATCACTGGAGCCTACTTACAACAAACTAGCCAAGCATCTAAGTGGAGTTGACTCCCTTGTGATAGCCAAAA
                           taataac  putative branch site (score: 1)
                                        ccgtttt  putative PPT
      aaaatatgacttattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aaactcagatttaggtcttaaagtggggacagccatgcatttatctctatgaaaatatgacttatttgttattaataacgacacgccgttttggatacagATATATGCACCGTGGTGTGGGCATTGTCAATCACTGGAGCCTACTTACAACAAACTAGCCAAGCATCTAAGTGGAGTTGACTCCCTTGTGATAGCCAAAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG