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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gttttgcattatctaattgtgtagttaattggaggttttgtttggtgatgagttatcaagcaagataatttcttagttaataatctttcttcgttttcagAACGATGGTTTAACAATCATCCCAGAGTATGATTGGAAGTTATTCTCTGAGGAGTGGAGTGCGACGCCTGGAAAAGGTATATCTGCTGAAATCGCTTTTA

Basic information

species Zea mays
transcript GRMZM2G376074_T02
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G376074_T01 (Zea mays), 3'ss of exon 10
lower sequence: LOC_Os03g09270.1 (Oryza sativa), 3'ss of exon 1
gttttgcattatctaattgtgtagttaattggaggttttgtt--tggtg---atgagttatcaagcaagataatttcttagttaataatctttcttcgttttcagAACGATGGTTTAACAATCATCCCAGAGTATGATTGGAAGTTATTCTCTGAGGAGTGGAGTGCGACGCCTGGAAAAGGTATATCTGCTGAAATCGCTTTTA
   |  | ||      || | |  || ||| | |   || ||  || |     |  | |   |   || | || ||   |     | |  | |||| |||||||||  ||||| |||||||| ||  |||| | ||||||||  ||||||||||| ||||||| ||   | | |||||||||| ||| ||||||||| | |||||
---tatcgttgct--gttatctgttttatttgggcccttattgctgatatatgtatgctgaaagataaaaaaaattgacaccgggttaattgtctttgttttcagACTGATGGATTAACAATGATATCAGAATCTGATTGGATTTTATTCTCTGAAGAGTGGAATGTAGCACATGGAAAAGGTTTATGTGCTGAAATTGTTTTTA
















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|211008051|gb|FL363351.1|FL363351
EST:     CTTTGGATCTTGTTTGTAAGCGCGGAAGCATCACTCAGAAAACATCAAAT                         AACGATGGTTTAACAATCATCCCAGAGTATGATTGGAAGTT
genomic: CTTTGGATCTTGTTTGTAAGCGCGGAAGCATCACTCAGAAAACATCAAATgtaagttcat ... tcgttttcagAACGATGGTTTAACAATCATCCCAGAGTATGATTGGAAGTT
EST: gi|67022296|gb|CO451045.1|CO451045
EST:     CTTTGGATCTTGTTTGTAAGCGCGGAAGCATCACTCAGAAAACATCAAAT                         AACGATGGTTTAACAATCATCCCAGAGTATGATTGGAAGTTATTCTCTGAG
genomic: CTTTGGATCTTGTTTGTAAGCGCGGAAGCATCACTCAGAAAACATCAAATgtaagttcat ... tcgttttcagAACGATGGTTTAACAATCATCCCAGAGTATGATTGGAAGTTATTCTCTGAG
EST: gi|32931325|gb|CF036137.1|CF036137
EST:     CTTTGGATCTTGTTTGTAAGCGCGGAAGCATCACTCAGAAAACATCAAAT                         AACGATGGTTTAACGATCATCCCAGAGTATGATTGGAAGTTATTCTCTGAG
genomic: CTTTGGATCTTGTTTGTAAGCGCGGAAGCATCACTCAGAAAACATCAAATgtaagttcat ... tcgttttcagAACGATGGTTTAACAATCATCCCAGAGTATGATTGGAAGTTATTCTCTGAG
EST: gi|211061749|gb|FL343242.1|FL343242
EST:     CTTTGGATCTTGTTTGTAAGCGCGGAAGCATCACTCAGAAAACATCAAAT                         AACGATGGTTTAACAATCATCCCAGAGTATGATTGGAAGTTATTCTCTGAG
genomic: CTTTGGATCTTGTTTGTAAGCGCGGAAGCATCACTCAGAAAACATCAAATgtaagttcat ... tcgttttcagAACGATGGTTTAACAATCATCCCAGAGTATGATTGGAAGTTATTCTCTGAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgatgagttatcaagcaagataatttcttagttaataatctttcttcgttttcagAACGATGGTTTAACAATCATCCCAGAGTATGATTGGAAGTTATTCTCTGAGGAGTGGAGTGCGACGCCTGGAAAAGGTATATCTGCTGAAATCGCTTTTA
                             agttaat  putative branch site (score: 4)
                                      tctttcttcgttttc  putative PPT
                aagataatttcttagt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttttgcattatctaattgtgtagttaattggaggttttgtttggtgatgagttatcaagcaagataatttcttagttaataatctttcttcgttttcagAACGATGGTTTAACAATCATCCCAGAGTATGATTGGAAGTTATTCTCTGAGGAGTGGAGTGCGACGCCTGGAAAAGGTATATCTGCTGAAATCGCTTTTA

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