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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatgtgctcccgtctcttgccccccatcagacttcgtcattgtctgctacacctccgaattaatcattcagcttgctttcttcagTGGCCCAGAGGGTTGCTGCTCCATGGCCCCCCTGGCACCGGAAAG

Basic information

species Zea mays
transcript GRMZM2G149994_T05
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G149994_T05 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os04g42110.1 (Oryza sativa), 3'ss of exon 1
gtaatgtgctcccgtctcttgccccccatcagacttcgtcattgtctgctacacctcc---gaattaatcattcagctt------gctttcttcagTGG--------CCCAGAGGGTTGCTGCTCCATGGCCCCCCTGGCACCGGAAAG
||| ||| | ||  || | |   | |  |  | | |  | ||  ||   | ||||| |    || ||   || ||  ||        | | | || |||        |||||||| ||||||||||| |||||| ||||||| ||||||
gtattgt-cgcctatcccctcttctc--ttcgtccttattatcatcaagtgcacctgcttgtaaatagcaatccatttttgaaataatctttgcattggtgcagTTTCCCAGAGGATTGCTGCTCCACGGCCCCTCTGGCACTGGAAAG
















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|211510550|gb|FL129059.1|FL129059
EST:     TGCTCGGCCTCAAG                         TGGCCCAGAGGGTTGCTACTCCACGGCCCCCCTGGCACCGGAAAG
genomic: TGCTCGGCCTCAAGgtaatgtgct ... ctttcttcagTGGCCCAGAGGGTTGCTGCTCCATGGCCCCCCTGGCACCGGAAAG
EST: gi|211510555|gb|FL129064.1|FL129064
EST:     TGCTCGGCCTCAAG                         TGGCCCAGAGGGTTGCTACTCCACGGCCCCCCTGGCACCGGAAAG
genomic: TGCTCGGCCTCAAGgtaatgtgct ... ctttcttcagTGGCCCAGAGGGTTGCTGCTCCATGGCCCCCCTGGCACCGGAAAG
EST: gi|211510558|gb|FL129067.1|FL129067
EST:     TGCTCGGCCTCAAG                         TGGCCCAGAGGGTTGCTACTCCACGGCCCCCCTGGCACCGGAAAG
genomic: TGCTCGGCCTCAAGgtaatgtgct ... ctttcttcagTGGCCCAGAGGGTTGCTGCTCCATGGCCCCCCTGGCACCGGAAAG
EST: gi|211510556|gb|FL129065.1|FL129065
EST:     TGCTCGGCCTCAAG                         TGGCCCAGAGGGTTGCTACTCCACGGCCCCCCTGGCACCGGAAAG
genomic: TGCTCGGCCTCAAGgtaatgtgct ... ctttcttcagTGGCCCAGAGGGTTGCTGCTCCATGGCCCCCCTGGCACCGGAAAG
EST: gi|211512912|gb|FL129068.1|FL129068
EST:     TGCTCGGCCTCAAG                         TGGCCCAGAGGGTTGCTACTCCACGGCCCCCCTGGCACCGGAAAG
genomic: TGCTCGGCCTCAAGgtaatgtgct ... ctttcttcagTGGCCCAGAGGGTTGCTGCTCCATGGCCCCCCTGGCACCGGAAAG
EST: gi|71445517|gb|DR826567.1|DR826567
EST:     TGGCTTATCCTTTCCTCTACGCCCGCGAGTCCCGTTTGCTCGGCCTCAAG                         TGGCCCAGAGGGTTGCTGCTCCATGGCCCCCCTGGCACCGGAAAG
genomic: TGGCTTATCCTTTCCTCTACGCCCGCGAGTCCCGTTTGCTCGGCCTCAAGgtaatgtgct ... ctttcttcagTGGCCCAGAGGGTTGCTGCTCCATGGCCCCCCTGGCACCGGAAAG
EST: gi|211512914|gb|FL129070.1|FL129070
EST:     TGCTCGGCCTCAAG                         TGGCCCAGAGGGTTGCTACTCCACGGCCCCCCTGGCACCGGAAAG
genomic: TGCTCGGCCTCAAGgtaatgtgct ... ctttcttcagTGGCCCAGAGGGTTGCTGCTCCATGGCCCCCCTGGCACCGGAAAG
EST: gi|211510557|gb|FL129066.1|FL129066
EST:     TGCTCGGCCTCAAG                         TGGCCCAGAGGGTTGCTACTCCACGGCCCCCCTGGCACCGGAAAG
genomic: TGCTCGGCCTCAAGgtaatgtgct ... ctttcttcagTGGCCCAGAGGGTTGCTGCTCCATGGCCCCCCTGGCACCGGAAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acttcgtcattgtctgctacacctccgaattaatcattcagcttgctttcttcagTGGCCCAGAGGGTTGCTGCTCCATGGCCCCCCTGGCACCGGAAAG
                           aattaat  putative branch site (score: 3)
                                         cttgctttcttc  putative PPT
                           aattaatcatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaatgtgctcccgtctcttgccccccatcagacttcgtcattgtctgctacacctccgaattaatcattcagcttgctttcttcagTGGCCCAGAGGGTTGCTGCTCCATGGCCCCCCTGGCACCGGAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT