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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cagttctctgtttctttatgttgagctgtacttgtgttgcttaaacaataaaccatttttttcaataattttccctttatcccctgcatttatgcaccagATAAATTTGGAGCTGCTATGGCAATTGTAAAGAATGATATCAGCGGCAATATCACA

Basic information

species Zea mays
transcript GRMZM2G060870_T01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G060870_T03 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os02g40890.2 (Oryza sativa), 3'ss of exon 2
----cagttct-ctgtttctttatgttgagctgtacttgtgttgcttaaacaataaaccatttttttcaataattttccctttatcccctgcatttatgcaccagATAAATTTGGAGCTGCTATGGCAATTGTAAAGAATGATATCAGCGGCAATATCACA
    || ||     |||| ||  | || ||        |  |    |||  | |    |    | |||  |  | |  ||||| | | |||  ||| |   ||||||||||||||||||||||||||| |||| |||| ||| ||  | || |||||||| 
acttcaattaaatcgtttgttagttttaagtcagg---gcatactctaactattgtggctaagtgttcctttgtct--cctttgttctctgactttgtattccagATAAATTTGGAGCTGCTATGGCACTTGTGAAGAGTGACATTGGTGGTAATATCACG

upper sequence: GRMZM2G060870_T03 (Zea mays), 3'ss of exon 2
lower sequence: Vv05s0049g01330.t01 (Vitis vinifera), 3'ss of exon 2
cagttctctgtttctttatgttgagctgtacttgtgttgcttaaacaataaaccatttttttcaa----taattt---------tccctttatcccctgcatttatgcaccagATAAATTTGGAGCTGCTATGGCAATTGTAAAGAATGATATCAGCGGCAATATCACA
             | ||||||| |  | ||| |||| |   || |||||      | || ||  |    ||   |         |   ||| ||   |  |||| |    ||||||| |||||||||||||||||| |||||||   ||||||  | || |||||| | 
-------------cattatgttcatttctacctgtgctctatatacaatttgagttcttatttgagtcctagcgtgttaatgggttgatttttcaattatatttttatggcagATAAGTTTGGAGCTGCTATGGCACTTGTAAAATCTGATATTGGTGGTAATATCTCG
















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|45567822|gb|CK985763.1|CK985763
EST:     TCTCACCAAGCCCTTCCTTGATGTCTGCAAGCAAATCTTGCCTGTCCTGG                         ATAAATTTGGAGCTGCTATGGCAATTGTAAAGAATGATATCAGCGGCAATA
genomic: TCTCACCAAGCCCTTCCTTGATGTCTGCAAGCAAATCTTGCCTGTCCTGGgtaacacatt ... tatgcaccagATAAATTTGGAGCTGCTATGGCAATTGTAAAGAATGATATCAGCGGCAATA
EST: gi|60401114|gb|DN233921.1|DN233921
EST:     TCTCACCAAGCCCTTCCTTGATGTCTGCAAGCAAATCTTGCCTGTCCTGG                         ATAAATTTGGAGCTGCTATGGCAATTGTAAAGAATGATATCAGCGGCAATA
genomic: TCTCACCAAGCCCTTCCTTGATGTCTGCAAGCAAATCTTGCCTGTCCTGGgtaacacatt ... tatgcaccagATAAATTTGGAGCTGCTATGGCAATTGTAAAGAATGATATCAGCGGCAATA
EST: gi|6223799|gb|AW154930.1|AW154930
EST:     TCTCACCAAGCCCTTCCTTGATGTCTGCAAGCATATCTTGCCTGTCCTGG                         ATAAATTTGGAGCTGCTATGGCAATTGTAAAGAATGATATCAGCGGCAATA
genomic: TCTCACCAAGCCCTTCCTTGATGTCTGCAAGCAAATCTTGCCTGTCCTGGgtaacacatt ... tatgcaccagATAAATTTGGAGCTGCTATGGCAATTGTAAAGAATGATATCAGCGGCAATA
EST: gi|22542222|gb|BU092660.1|BU092660
EST:     TCTCACCAAGCCCTTCCTTGATGTCTGCAAGCAAATCTTGCCTGTCCTGG                         ATAAATTTGGAGCTGCTATGGCAATTGTAAAGAATGATATCAGCGGCAATA
genomic: TCTCACCAAGCCCTTCCTTGATGTCTGCAAGCAAATCTTGCCTGTCCTGGgtaacacatt ... tatgcaccagATAAATTTGGAGCTGCTATGGCAATTGTAAAGAATGATATCAGCGGCAATA
EST: gi|60401080|gb|DN233887.1|DN233887
EST:     TCTCACCAAGCCCTTCCTTGATGTCTGCAAGCAAATCTTGCCTGTCCTGG                         ATAAATTTGGAGCTGCTATGGCAATTGTAAAGAATGATATCAGCGGCAATA
genomic: TCTCACCAAGCCCTTCCTTGATGTCTGCAAGCAAATCTTGCCTGTCCTGGgtaacacatt ... tatgcaccagATAAATTTGGAGCTGCTATGGCAATTGTAAAGAATGATATCAGCGGCAATA
EST: gi|31359252|gb|CD443609.1|CD443609
EST:     TCTCACCAAGCCCTTCCTTGATGTCTGCAAGCAAATCTTGCCTGTCCTGG                         ATAAATTTGGAGCTGCTATGGCAATTGTAAAGAATGATATCAGCGGCAATA
genomic: TCTCACCAAGCCCTTCCTTGATGTCTGCAAGCAAATCTTGCCTGTCCTGGgtaacacatt ... tatgcaccagATAAATTTGGAGCTGCTATGGCAATTGTAAAGAATGATATCAGCGGCAATA
EST: gi|6223801|gb|AW154932.1|AW154932
EST:     TCTCACCAAGCCCTTCCTTGATGTCTGCAAGCATATCTTGCCTGTCCTGG                         ATAAATTTGGAGCTGCTATGGCAATTGTAAAGAATGATATCAGCGGCAATA
genomic: TCTCACCAAGCCCTTCCTTGATGTCTGCAAGCAAATCTTGCCTGTCCTGGgtaacacatt ... tatgcaccagATAAATTTGGAGCTGCTATGGCAATTGTAAAGAATGATATCAGCGGCAATA
EST: gi|26559123|gb|CA831358.1|CA831358
EST:     CTCAACAAAGCCCTTCCTTGATGTCTGCAAGCAAATCTTGCCTGTCCTGG                         ATAAATTTGGAGCTGCTATGGCAATTGTAAAGAATGATATCAGCGGCAATA
genomic: CTC-ACCAAGCCCTTCCTTGATGTCTGCAAGCAAATCTTGCCTGTCCTGGgtaacacatt ... tatgcaccagATAAATTTGGAGCTGCTATGGCAATTGTAAAGAATGATATCAGCGGCAATA
EST: gi|211107786|gb|FL216766.1|FL216766
EST:     TCTCACCAAGCCCTTCCTTGATGTCTGCAAGCATATCTTGCCTGTCCTGG                         ATAAATTTGGAGCTGCTATGGCAATTGTAAAGAATGATATCAGCGGCAATA
genomic: TCTCACCAAGCCCTTCCTTGATGTCTGCAAGCAAATCTTGCCTGTCCTGGgtaacacatt ... tatgcaccagATAAATTTGGAGCTGCTATGGCAATTGTAAAGAATGATATCAGCGGCAATA
EST: gi|6223798|gb|AW154929.1|AW154929
EST:     TCTCACCAAGCCCTTCCTTGATGTCTGCAAGCATATCTTGCCTGTCCTGG                         ATAAATTTGGAGCTGCTATGGCAATTGTAAAGAATGATATCAGCGGCAATA
genomic: TCTCACCAAGCCCTTCCTTGATGTCTGCAAGCAAATCTTGCCTGTCCTGGgtaacacatt ... tatgcaccagATAAATTTGGAGCTGCTATGGCAATTGTAAAGAATGATATCAGCGGCAATA
EST: gi|211296159|gb|FL473353.1|FL473353
EST:     TCTTGCCTTTCCTGG                         ATAAATTTGGAGCTGGCTATGGCAATTGTAAAGAATGATATCAGCGGCAAT
genomic: TCTTGCCTGTCCTGGgtaacacatt ... tatgcaccagATAAATTTGGAGCT-GCTATGGCAATTGTAAAGAATGATATCAGCGGCAAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

caataaaccatttttttcaataattttccctttatcccctgcatttatgcaccagATAAATTTGGAGCTGCTATGGCAATTGTAAAGAATGATATCAGCGGCAATATCACA
                       ttttccctttatcccc  CT-rich tract
     aaccatttttttcaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cagttctctgtttctttatgttgagctgtacttgtgttgcttaaacaataaaccatttttttcaataattttccctttatcccctgcatttatgcaccagATAAATTTGGAGCTGCTATGGCAATTGTAAAGAATGATATCAGCGGCAATATCACA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA