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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtagattggacgttgatcttttaggttctgtagagtctgtcttctccatgttctttttggaagttttggatatcagttcttccttgacttctaactatctgcaactgcacaattttggtgtcagGTACTCTTAACAACAAGTGACTGGGACGAGTGCAACTTCTGGCTCGCGGCATTGAAGCGGATGATCAAGACAAGGCAGAATTTCAGAATGTAAACCTTGT

Basic information

species Zea mays
transcript GRMZM2G152963_T02
intron # 21
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G152963_T02 (Zea mays), 3'ss of exon 21
lower sequence: LOC_Os07g46370.1 (Oryza sativa), 3'ss of exon 21
gtagattggacgttgatcttttaggttctgtagagtctgtcttctccatgttctttttggaagttttggatatcagttcttccttgacttctaactatctgcaactgcacaattttggtgtcagGTACTCTTAACAACAAGTGACTGGGACGAGTGCAACTTCTGGCTCGCGGCATTGAAGCGGATGATCAAGACAAGGCAGAATTTCAGAATGTAAACCT-TGT
        ||||||  || |||    || | |  ||   | |  |  || | ||   |  || ||||   |||   || ||       | |||| |||     ||||  |||| ||||   ||||||||  | ||||| || |||||||||||||||||||||||||| || ||||||||||| ||||||||||| |||||||||||||||||||||||   || 
-------tgacgttagtcattt----tccgcactgtggatttgatagat-tgctgagtataattttt---tattgcttttta------tcctaattattaattactgttcaatgttgg---cagGTACTTCTGACAACGAGCGACTGGGACGAGTGCAACTTCTGGCTTGCCGCATTGAAGCGTATGATCAAGACGAGGCAGAATTTCAGAATGTAAACGAGTG-

upper sequence: GRMZM2G152963_T02 (Zea mays), 3'ss of exon 21
lower sequence: GLYMA12G01290.1 (Glycine max), 3'ss of exon 21
gtagattggacgttgatcttttaggttctgtagagtctgtcttctccatgttctttttggaagttttggatatcagttcttccttgacttctaactatctgcaactgcacaattttggtgt--cagGTACTCTTAACAACAAGTGACTGGGACGAGTGCAACTTCTGGCTCGCGGCATTGAAGCGGATGATCAAGACAAGGCAGAATTTCAGAATG---TAAACCTTGT
                             ||| |   |   ||    |||    || | | | ||     | | |     ||| | |  ||||  |    ||  ||      |||| ||||  ||||| ||  | || || | ||| |||||||| ||| | | |||| | |   || | |||||||||||||||||||||||||     ||| |    ||||      
-----------------------------gtaaa---tcaattgcaaatgcaaattatagtatttacctgtgtaaaaaactccatcaaatctacattctagcctctttttttttttcgtgttgcagGTTCTTCTTACTACTACTGAGTGGGACGAATGCCAATCCTGGTTAGGTTCACTCAAGCGGATGATCAAGACAAGGCAGAGCGCGAGACTAGGTTAAAAAA---

upper sequence: GRMZM2G152963_T02 (Zea mays), 3'ss of exon 21
lower sequence: Vv13s0158g00140.t01 (Vitis vinifera), 3'ss of exon 21
gtagattggacgttgatcttttaggttctgtagagtctgtcttctccatgttctttttggaagttttggatatcagttcttccttgacttctaactatctgcaactgcacaattttggtgtcagGTACTCTTAACAACAAGTGACTGGGACGAGTGCAACTTCTGGCTCGCGGCATTGAAGCGGATGATCAAGACAAGGCAGAATTTCAGAATGTAAACCTTGT---
           ||  || || | ||   |  |   |    |||   ||  | |   |  ||| |    || ||       |  |||   | |   |||              ||   | |  |||||||  | || || ||||| ||||| ||||||||||||||||| ||  || | ||| ||||||||||||||||||||||| | ||| |   ||  | |    
-----------gtatat-ttctggggattaaaatattcaacttaggcaactccaaatgagaaat----gacattg-----tatttggtctttttttattc------------ttcctgggatagGTACTTCTTACGACCAGTGAGTGGGATGAGTGCAACTTCTGGCTAGCAACACTAAAGAGGATGATCAAGACAAGGCAGAATGTGAGATT---AAGTTAGAGAG

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|67010339|gb|CO439088.1|CO439088
EST:     TGTGCAGTGCAATTGATGCTAGTGATTTTGCCACTGCGATGCACCTCCAG                         GTACTCTTAACAACAAGTGACTGGGACGAGTGTAACTTCTGGCTCGCGGCA
genomic: TGTGCAGTGCAATTGATGCTAGCGATTTTGCCACTGCGATGCACCTCCAGgtagattgga ... ttggtgtcagGTACTCTTAACAACAAGTGACTGGGACGAGTGCAACTTCTGGCTCGCGGCA
EST: gi|60396836|gb|DN229660.1|DN229660
EST:     TGTGCAGTGCAATTGATGCTAGCGATTTTGCCACTGCGATGCACCTCCAG                         GTACTCTTAACAACAAGTGACTGGGACGAGTGCAACTTCTGGCTCGCGGCA
genomic: TGTGCAGTGCAATTGATGCTAGCGATTTTGCCACTGCGATGCACCTCCAGgtagattgga ... ttggtgtcagGTACTCTTAACAACAAGTGACTGGGACGAGTGCAACTTCTGGCTCGCGGCA
EST: gi|211125222|gb|FL004310.1|FL004310
EST:     TGTGCAGTGCAATTGATGCTAGCGATTTTGCCACTGCGATGCACCTCCAG                         GTACTCTTGACAACAAGTGACTGGGACGAGTGCAACTTCTGGCTCGCGGCA
genomic: TGTGCAGTGCAATTGATGCTAGCGATTTTGCCACTGCGATGCACCTCCAGgtagattgga ... ttggtgtcagGTACTCTTAACAACAAGTGACTGGGACGAGTGCAACTTCTGGCTCGCGGCA
EST: gi|18171779|gb|BM341619.1|BM341619
EST:     TGTGCAGTGCAATTGATGCTAGCGATTTTGCCACTGCGATGCACCTCCAG                         GTACTCTTAACAACAAGTGACTGGGACGAGTGCAACTTCTGGCTCGCGGCA
genomic: TGTGCAGTGCAATTGATGCTAGCGATTTTGCCACTGCGATGCACCTCCAGgtagattgga ... ttggtgtcagGTACTCTTAACAACAAGTGACTGGGACGAGTGCAACTTCTGGCTCGCGGCA
EST: gi|4966636|gb|AI691492.1|AI691492
EST:     TGTGCAGTGCAATTGATGCTAGCGATTTTGCCACTGCGATGCACCTCCAG                         GTACTCTTGACAACAAGTGACTGGGACGAGTGCAACTTCTGGCTCGCGGCA
genomic: TGTGCAGTGCAATTGATGCTAGCGATTTTGCCACTGCGATGCACCTCCAGgtagattgga ... ttggtgtcagGTACTCTTAACAACAAGTGACTGGGACGAGTGCAACTTCTGGCTCGCGGCA
EST: gi|16926753|gb|BM079821.1|BM079821
EST:     TGTGCAGTGCAATTGATGCTAGCGATTTTGCCACTGCGATGCACCTCCAG                         GTACTCTTAACAACAAGTGACTGGGACGAGTGCAACTTCTGGCTCGCGGCA
genomic: TGTGCAGTGCAATTGATGCTAGCGATTTTGCCACTGCGATGCACCTCCAGgtagattgga ... ttggtgtcagGTACTCTTAACAACAAGTGACTGGGACGAGTGCAACTTCTGGCTCGCGGCA
EST: gi|60358633|gb|DN225606.1|DN225606
EST:     TGTGCAGTGCAATTGATGCTAGCGATTTTGCCACTGCGATGCACCTCCAG                         GTACTCTTAACAACAAGTGACTGGGACGAGTGCAACTTCTGGCTCGCGGCA
genomic: TGTGCAGTGCAATTGATGCTAGCGATTTTGCCACTGCGATGCACCTCCAGgtagattgga ... ttggtgtcagGTACTCTTAACAACAAGTGACTGGGACGAGTGCAACTTCTGGCTCGCGGCA
EST: gi|14204166|gb|BG837843.1|BG837843
EST:     TGTGCAGTGCAATTGATGCTAGCGATTTTGCCACTGCGATGCACCTCCAG                         GTACTCTTGACAACAAGTGACTGGGACGAGTGCAACTTCTGGCTCGCGGCA
genomic: TGTGCAGTGCAATTGATGCTAGCGATTTTGCCACTGCGATGCACCTCCAGgtagattgga ... ttggtgtcagGTACTCTTAACAACAAGTGACTGGGACGAGTGCAACTTCTGGCTCGCGGCA
EST: gi|60352525|gb|DN219498.1|DN219498
EST:     TGTGCAGTGCAATTGATGCTAGCGATTTTGCCACTGCGATGCACCTCCAG                         GTACTCTTAACAACAAGTGACTGGGACGAGTGCAACTTCTGGCTCGCGGCA
genomic: TGTGCAGTGCAATTGATGCTAGCGATTTTGCCACTGCGATGCACCTCCAGgtagattgga ... ttggtgtcagGTACTCTTAACAACAAGTGACTGGGACGAGTGCAACTTCTGGCTCGCGGCA
EST: gi|213167833|gb|FM183398.1|FM183398
EST:     TGTGCAGTGCAATTGATGCTAGTGATTTTGCCACTGCGATGCACCTCCAG                         GTACTCTTAACAACAAGTGACTGGGACGAGTGTAACTTCTGGCTCGCGGCA
genomic: TGTGCAGTGCAATTGATGCTAGCGATTTTGCCACTGCGATGCACCTCCAGgtagattgga ... ttggtgtcagGTACTCTTAACAACAAGTGACTGGGACGAGTGCAACTTCTGGCTCGCGGCA
EST: gi|37398725|gb|CF636680.1|CF636680
EST:     TGTGCAGTGCAATTGATGCTAGCGATTTTGCCACTGCGATGCACCTCCAG                         GTACTCTTAACAACAAGTGACTGGGACGAGTGCAACTTTTGGCTCGCGGCA
genomic: TGTGCAGTGCAATTGATGCTAGCGATTTTGCCACTGCGATGCACCTCCAGgtagattgga ... ttggtgtcagGTACTCTTAACAACAAGTGACTGGGACGAGTGCAACTTCTGGCTCGCGGCA
EST: gi|6095621|gb|AW120288.1|AW120288
EST:     TGTGCAGTGCAATTGATGCTAGCGATTTTGCCCCTGCGATGCACCTCCAG                         GTACTCTTGACAACAAGTGACTGGGACGAGTGCAACTTTTGGCTCGCGGCA
genomic: TGTGCAGTGCAATTGATGCTAGCGATTTTGCCACTGCGATGCACCTCCAGgtagattgga ... ttggtgtcagGTACTCTTAACAACAAGTGACTGGGACGAGTGCAACTTCTGGCTCGCGGCA
EST: gi|5804662|gb|AI979632.1|AI979632
EST:     GTGCAGTGCAATTGATGCTAGCGATTTTGCC-CNTGCGATGCNCCTCCAG                         GTACTCTTGACAACAAGTGACTGGGACGAGTGCAACTTCTGGCTCGCGGCA
genomic: GTGCAGTGCAATTGATGCTAGCGATTTTGCCAC-TGCGATGCACCTCCAGgtagattgga ... ttggtgtcagGTACTCTTAACAACAAGTGACTGGGACGAGTGCAACTTCTGGCTCGCGGCA
EST: gi|18176571|gb|BM351504.1|BM351504
EST:     TGTGCAGTGCAATTGATGCTAGCGATTTTGCCACTGCGATGCACTTCCAG                         GTACTCTTAACAACAAGTGACTGGGACGAGTGCAACTTCTGGCTCGCGGCA
genomic: TGTGCAGTGCAATTGATGCTAGCGATTTTGCCACTGCGATGCACCTCCAGgtagattgga ... ttggtgtcagGTACTCTTAACAACAAGTGACTGGGACGAGTGCAACTTCTGGCTCGCGGCA
EST: gi|60672490|gb|DN475196.1|DN475196
EST:     TGTGCAGTGCAATTGATGCTAGCGATTTTGCCACTGCGATGCACCTCCAG                         GTACTCTTGACAACAAGTGACTGGGACGAGTGCAACTTCTGGCTCGCGGCA
genomic: TGTGCAGTGCAATTGATGCTAGCGATTTTGCCACTGCGATGCACCTCCAGgtagattgga ... ttggtgtcagGTACTCTTAACAACAAGTGACTGGGACGAGTGCAACTTCTGGCTCGCGGCA
EST: gi|6194805|gb|AW146909.1|AW146909
EST:     TGTGCAGTGCAATTGATGCTAGCGATTTTGCCACTGCGATGCACCTCCAG                         GTACTCTTGACAACAAGTGACTGGGACGAGTGCAACTTCTGGCTCGCGGCA
genomic: TGTGCAGTGCAATTGATGCTAGCGATTTTGCCACTGCGATGCACCTCCAGgtagattgga ... ttggtgtcagGTACTCTTAACAACAAGTGACTGGGACGAGTGCAACTTCTGGCTCGCGGCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atatcagttcttccttgacttctaactatctgcaactgcacaattttggtgtcagGTACTCTTAACAACAAGTGACTGGGACGAGTGCAACTTCTGGCTCGCGGCATTGAAGCGGATGATCAAGACAAGGCAGAATTTCAGAATGTAAACCTTGT
                   ttctaac  putative branch site (score: 1)
                                       acaatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtagattggacgttgatcttttaggttctgtagagtctgtcttctccatgttctttttggaagttttggatatcagttcttccttgacttctaactatctgcaactgcacaattttggtgtcagGTACTCTTAACAACAAGTGACTGGGACGAGTGCAACTTCTGGCTCGCGGCATTGAAGCGGATGATCAAGACAAGGCAGAATTTCAGAATGTAAACCTTGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC