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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtccaaggatggtttattttatcaccacagtaattcttttaccctttttgtctgcattcttggataatgacatttttcatttgttttatagTACGAACCAGAACTCTTTCCTGGCCTTATCTATCGGATGAAACAACCAAAGATTGTTCTTTTAATTTTTGTTTCAGGCAAGATTGTTTTGACTGGAGCAA

Basic information

species Zea mays
transcript GRMZM2G161418_T06
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G161418_T05 (Zea mays), 3'ss of exon 7
lower sequence: LOC_Os03g45410.1 (Oryza sativa), 3'ss of exon 7
gtatgtccaaggatggtttattttatcaccacagtaattcttttaccctttttgtctgcattcttggataatgacatttttcatttgtttta-tagTACGAACCAGAACTCTTTCCTGGCCTTATCTATCGGATGAAACAACCAAAGATTGTTCTTTTAATTTTTGTTTCAGGCAAGATTGTTTTGACTGGAGCAA
||| ||  |    | |  |   || | |  ||       |||| ||  || || | |   |||||     ||| | | |  | ||||| |||  |||| || ||||||||||||||||| || || ||||||||||| |||||||||||||||||| | ||||||||||||||||||||||||||||| |||||||
gtaagttgagtccttgcatgcctttttaggacg-----cctttcacatttgttatgt-tgttctt-----atgtcctgtgccttttgtgttaacagTATGAGCCAGAACTCTTTCCTGGTCTGATATATCGGATGAAGCAACCAAAGATTGTTCTTCTGATTTTTGTTTCAGGCAAGATTGTTTTGACCGGAGCAA

upper sequence: GRMZM2G161418_T05 (Zea mays), 3'ss of exon 7
lower sequence: LOC_Os12g39070.1 (Oryza sativa), 3'ss of exon 6
gtatgtccaaggatggtttattttatcaccacagtaattcttttaccctttttgtctgcattcttggataatgacatttttcatttgttttatagTACGAACCAGAACTCTTTCCTGGCCTTATCTATCGGATGAAACAACCAAAGATTGTTCTTTTAATTTTTGTTTCAGGCAAGATTGTTTTGACTGGAGCAA
||| ||  ||   | |  | |||| | |  |   || |||||| ||   | || |    |||||      ||| | | |  | ||||| ||  |||| || || |||||||||||||| || || ||||||||||| ||||| |||||||||||| | ||||||||||||||||||||||||||||| |||||||
gtaagttgaatccttgcatgtttttttagga---tatttctttcacatatgttatgc-tattctc-----atgtcttgtgccttttgtcttccagTATGAGCCTGAACTCTTTCCTGGTCTGATATATCGGATGAAGCAACCGAAGATTGTTCTTCTGATTTTTGTTTCAGGCAAGATTGTTTTGACCGGAGCAA

upper sequence: GRMZM2G161418_T05 (Zea mays), 3'ss of exon 7
lower sequence: Vv06s0004g00180.t01 (Vitis vinifera), 3'ss of exon 7
----gtatgtccaaggatggtttattttatcaccacagtaattcttttaccctttttgtctgcattcttggat--aatgacatttttcatttgttttatagTACGAACCAGAACTCTTTCCTGGCCTTATCTATCGGATGAAACAACCAAAGATTGTTCTTTTAATTTTTGTTTCAGGCAAGATTGTTTTGACTGGAGCAA
     ||  |  ||  ||  |  |    ||||    | |  |   | |   || |   | ||| || ||| ||  |||    |||    ||||||    |||| ||||||||| | || |||||| | |||||||| |||||||||||||||||||| ||  | || ||||| ||||| || |||||| | |||||||| |
aaatttaaattgaatcattttaaaaaaaatcatgtaaatgttgtctgtgttctctac-tgtgccttattgtattgaatatagtttggattttgttgggcagTATGAACCAGAATTGTTCCCTGGCTTGATCTATCGAATGAAACAACCAAAGATTGTGCTGCTTATCTTTGTGTCAGGGAAAATTGTTCTCACTGGAGCTA

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|18163021|gb|BM332860.1|BM332860
EST:     TTCCAATTAGGCTTGAGGGCCTTGCATATTCTCATGGTGCCTTCTCAAGT                         TACGAACCAGAACTCTTTCCTGGCCTTATCTATCGGATGAAACAACCAAAG
genomic: TTCCAATTAGGCTTGAGGGCCTTGCATATTCTCATGGTGCCTTCTCAAGTgtatgtccaa ... tgttttatagTACGAACCAGAACTCTTTCCTGGCCTTATCTATCGGATGAAACAACCAAAG
EST: gi|32914682|gb|CF019494.1|CF019494
EST:     TTCCAATTAGGCTTGAGGGCCTTGCATATTCTCATGGTGCCTTCTCAAGT                         TACGAACCCGAACTCTTTCTTTTTCTTATCTATCGGATGAAACAACCAAAG
genomic: TTCCAATTAGGCTTGAGGGCCTTGCATATTCTCATGGTGCCTTCTCAAGTgtatgtccaa ... tgttttatagTACGAACCAGAACTCTTTCCTGGCCTTATCTATCGGATGAAACAACCAAAG
EST: gi|7137809|gb|AW499281.1|AW499281
EST:     TCCAATTAGGCTTGAGGGCCTTGCATATTCTCATGGTGCCTTCTCAAGT                         TACGAACCAGAACTCTTTCCTGCCCTTATCTATCGGATGAAACAACCAAAG
genomic: TCCAATTAGGCTTGAGGGCCTTGCATATTCTCATGGTGCCTTCTCAAGTgtatgtccaa ... tgttttatagTACGAACCAGAACTCTTTCCTGGCCTTATCTATCGGATGAAACAACCAAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttaccctttttgtctgcattcttggataatgacatttttcatttgttttatagTACGAACCAGAACTCTTTCCTGGCCTTATCTATCGGATGAAACAACCAAAGATTGTTCTTTTAATTTTTGTTTCAGGCAAGATTGTTTTGACTGGAGCAA
                                    tttttcatttgtttt  CT-rich tract
                           ataatgacatttttca  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgtccaaggatggtttattttatcaccacagtaattcttttaccctttttgtctgcattcttggataatgacatttttcatttgttttatagTACGAACCAGAACTCTTTCCTGGCCTTATCTATCGGATGAAACAACCAAAGATTGTTCTTTTAATTTTTGTTTCAGGCAAGATTGTTTTGACTGGAGCAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA