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 5'  3'   		2  
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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtagcaactaactgtgcacctctttttctcaagaacaaccatgtacagcatattctcctgttctggttcactgcgcgatgccgctgaatcgtttactaaatataatactgcaatacagtaatactgaatagaacagaatgatgaggtccctctgggtcaaaatgctttatttcagGAACCGACTTCACAAATGCAGTGATAGACCGCGTCAATTTTGAGAAGGCCGATCTCACAGGGGCGATCTTCAAGAACACGGTCTTGTCAGGATCGACCTT

Basic information

species Zea mays
transcript GRMZM2G436710_T01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G436710_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os10g35810.1 (Oryza sativa), 3'ss of exon 2
gtagcaactaactgtgcacctctttttctcaagaacaaccatgtacagcatattctcctgttctggttcactgcgcgatgccgctgaatcgtttactaaatataatactgcaatacagtaatactgaatagaacagaatgatgaggtccctctgggtcaaaatgctttatttcagGAACCGACTTCACAAATGCAGTGATAGACCGCGTCAATTTTGAGAAGGCCGATCTCACAGGGGCGATCTTCAAGAACACGGTCTTGTCAGGATCGACCTT
                                          ||| |  | | || |||  | |  ||||   | | ||   |||| ||  ||| | ||||    |||     |  | | |||   || ||||||        || | | | |   ||||     ||  |||||||||| || |||||||||||||| |||||||| ||||||||||||||||||||||||  |||||| ||||||| |||||| |||||||||||||| |||||
------------------------------------------gtaaacta-actcaccttctgtcattcatcacactat--tgctgcattatttccaaaatcatgtacctt--tgaattgata---aacagaaca------ctagatgcttatatctcaa-----ttgttttcagGAACGGATTTCACAAATGCAGTAATAGACCGTGTCAATTTTGAGAAGGCCGATCTCCAAGGGGCAATCTTCAGGAACACCGTCTTGTCAGGATCAACCTT
















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|32924220|gb|CF029032.1|CF029032
EST:     GTCTGAAGTTGTCATGTCCAAAGCCTATGCCGTTGGTGCAAGTTTCAAAG                         GAACCGACTTCACAAATGCAGTGATAGACCGCGTCAATTTTGAGAAGGCCG
genomic: GTCTGAAGTTGTCATGTCCAAAGCTTATGCTGTTGGTGCAAGTTTCAAAGgtagcaacta ... tttatttcagGAACCGACTTCACAAATGCAGTGATAGACCGCGTCAATTTTGAGAAGGCCG
EST: gi|32923644|gb|CF028456.1|CF028456
EST:     GTCTGAAGTTGTCATGTCCAAAGCCTATGCCGTTGGTGCAAGTTTCAAAG                         GAACCGACTTCACAAATGCAGTGATAGACCGCGTCAATTTTGAGAAGGCCG
genomic: GTCTGAAGTTGTCATGTCCAAAGCTTATGCTGTTGGTGCAAGTTTCAAAGgtagcaacta ... tttatttcagGAACCGACTTCACAAATGCAGTGATAGACCGCGTCAATTTTGAGAAGGCCG
EST: gi|149083816|gb|EE173188.2|EE173188
EST:     GTCTGAAGTTGTCATGTCCAAAGCTTATGCTGTTGGTGCAAGTTTCAAAG                         GAACCGACTTCACAAATGCAGTGATAGACCGCGTCAATTTTGAGAAGGCCG
genomic: GTCTGAAGTTGTCATGTCCAAAGCTTATGCTGTTGGTGCAAGTTTCAAAGgtagcaacta ... tttatttcagGAACCGACTTCACAAATGCAGTGATAGACCGCGTCAATTTTGAGAAGGCCG
EST: gi|45846974|gb|CN070917.1|CN070917
EST:     GTCTGAAGTTGTCATGTCCAAAGCTTATGCTGTTGGTGCAAGTTTCAAAG                         GAACCGACTTCACAAATGCAGTGATAGACCGCGTCAATTTTGAGAAGGCCG
genomic: GTCTGAAGTTGTCATGTCCAAAGCTTATGCTGTTGGTGCAAGTTTCAAAGgtagcaacta ... tttatttcagGAACCGACTTCACAAATGCAGTGATAGACCGCGTCAATTTTGAGAAGGCCG
EST: gi|76011249|gb|DT938419.1|DT938419
EST:     GTCTGAAGTTGTCATGTCCAAAGCTTATGCTGTTGGTGCAAGTTTCAAAG                         GAACCGACTTCACAAATGCAGTGATAGACCGCGTCAATTTTGAGAAGGCGG
genomic: GTCTGAAGTTGTCATGTCCAAAGCTTATGCTGTTGGTGCAAGTTTCAAAGgtagcaacta ... tttatttcagGAACCGACTTCACAAATGCAGTGATAGACCGCGTCAATTTTGAGAAGGCCG
EST: gi|32928756|gb|CF033568.1|CF033568
EST:     GTCTGAAGTTGTCATGTCCAAAGCCTATGCCGTTGGTGCAAGTTTCAAAG                         GAACCGACTTCACAAATGCAGTGATAGACCGCGTCAATTTTGAGAAGGCCG
genomic: GTCTGAAGTTGTCATGTCCAAAGCTTATGCTGTTGGTGCAAGTTTCAAAGgtagcaacta ... tttatttcagGAACCGACTTCACAAATGCAGTGATAGACCGCGTCAATTTTGAGAAGGCCG
EST: gi|32923654|gb|CF028466.1|CF028466
EST:     GTCTGAAGTTGTCATGTCCAAAGCCTATGCCGTTGGTGCAAGTTTCAAAG                         GAACCGACTTCACAAATGCAGTGATAGACCGCGTCAATTTTGAGAAGGCCG
genomic: GTCTGAAGTTGTCATGTCCAAAGCTTATGCTGTTGGTGCAAGTTTCAAAGgtagcaacta ... tttatttcagGAACCGACTTCACAAATGCAGTGATAGACCGCGTCAATTTTGAGAAGGCCG
EST: gi|16377617|gb|BI992022.1|BI992022
EST:     GTCTGAAGTTGTCATGTCCAAAGCTTATGCTGTTGGTGCAAGTTTCAAAG                         GAACCGACTTCACAAATGCAGTGATAGACCGCGTCAATTTTGAGAAGGCCG
genomic: GTCTGAAGTTGTCATGTCCAAAGCTTATGCTGTTGGTGCAAGTTTCAAAGgtagcaacta ... tttatttcagGAACCGACTTCACAAATGCAGTGATAGACCGCGTCAATTTTGAGAAGGCCG
EST: gi|91878788|gb|EB408745.1|EB408745
EST:     GTCTGAAGTTGTCATGTCCAAGGCTTATGCTGTTGGTGCCAGTTTCTAAG                         GAACCGACTTCCCCAATGCAGTGATAGACCGCGTCAATTT
genomic: GTCTGAAGTTGTCATGTCCAAAGCTTATGCTGTTGGTGCAAGTTTCAAAGgtagcaacta ... tttatttcagGAACCGACTTCACAAATGCAGTGATAGACCGCGTCAATTT
EST: gi|211222880|gb|FL457387.1|FL457387
EST:     GTSTGAAGTTGTCATGTCCAAAGCTTATGCTGTTGGTGCAAGTTTCAAAG                         GAACCGACTTCACAAATGCAGTGATAGACCGCGTCAATTTTGAGAAGGCCG
genomic: GTCTGAAGTTGTCATGTCCAAAGCTTATGCTGTTGGTGCAAGTTTCAAAGgtagcaacta ... tttatttcagGAACCGACTTCACAAATGCAGTGATAGACCGCGTCAATTTTGAGAAGGCCG
EST: gi|148960305|gb|EE153561.2|EE153561
EST:     GTCTGAAGTTGTCATGTCCAAAGCTTATGCTGTTGGTGCAAGTTTCAAAG                         GAACCGACTTCACAAATGCAGTGATAGACCGCGTCAATTTTGAGAAGGCCG
genomic: GTCTGAAGTTGTCATGTCCAAAGCTTATGCTGTTGGTGCAAGTTTCAAAGgtagcaacta ... tttatttcagGAACCGACTTCACAAATGCAGTGATAGACCGCGTCAATTTTGAGAAGGCCG
EST: gi|13126454|gb|BG317024.1|BG317024
EST:     GTCTGAAGTTGTCATGTCCAAAGCTTATGCTGTTGGTGCAAGTTTCAAAG                         GAACCGACTTCACAAATGCAGTGATAGACCGCGTCAATTTTGAGAAGGCCG
genomic: GTCTGAAGTTGTCATGTCCAAAGCTTATGCTGTTGGTGCAAGTTTCAAAGgtagcaacta ... tttatttcagGAACCGACTTCACAAATGCAGTGATAGACCGCGTCAATTTTGAGAAGGCCG
EST: gi|74244507|gb|DT652421.1|DT652421
EST:     GTCTGAAGTTGTCATGTCCAAAGCTTATGCTGTTGGTGCAAGTTTCAAAG                         GAACCGACTTCACAAATGCAGTGATAGACCGCGTCAATTTTGAGAAGGCCG
genomic: GTCTGAAGTTGTCATGTCCAAAGCTTATGCTGTTGGTGCAAGTTTCAAAGgtagcaacta ... tttatttcagGAACCGACTTCACAAATGCAGTGATAGACCGCGTCAATTTTGAGAAGGCCG
EST: gi|24934401|gb|CA452619.1|CA452619
EST:     GTCTGAAGTTGTCATGTCCAAAGCCTATGCCGTTGGTGCAAGTTTCAAAG                         GAACCGACTTCACAAATGCAGTGATAGACCGCGTCAATTTTGAGAAGGCCG
genomic: GTCTGAAGTTGTCATGTCCAAAGCTTATGCTGTTGGTGCAAGTTTCAAAGgtagcaacta ... tttatttcagGAACCGACTTCACAAATGCAGTGATAGACCGCGTCAATTTTGAGAAGGCCG
EST: gi|32929133|gb|CF033945.1|CF033945
EST:     GTCTGAAGTTGTCATGTCCAAAGCCTATGCCGTTGGTGCAAGTTTCAAAG                         GAACCGACTTCACAAATGCAGTGATAGACCGCGTCAATCTTGAGAAGGCCG
genomic: GTCTGAAGTTGTCATGTCCAAAGCTTATGCTGTTGGTGCAAGTTTCAAAGgtagcaacta ... tttatttcagGAACCGACTTCACAAATGCAGTGATAGACCGCGTCAATTTTGAGAAGGCCG
EST: gi|32859433|gb|CD999114.1|CD999114
EST:     GTCTGAAGTTGTCATGTCCAAAGCCTATGCCGTTGGTGCAAGTTTCAAAG                         GAACCGACTTCACAAATGCAGTGATAGACCGCGTCAATTTTGAGAAGGCCG
genomic: GTCTGAAGTTGTCATGTCCAAAGCTTATGCTGTTGGTGCAAGTTTCAAAGgtagcaacta ... tttatttcagGAACCGACTTCACAAATGCAGTGATAGACCGCGTCAATTTTGAGAAGGCCG

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 3 RNA-Seq libraries.


Block sizes: 47 (upstream exon), 34 (downstream exon)
Score: 5

TCTTTAGCTGCAGCGCTGATGTCCGAGGCAAAGTTCGACGGCGCTGACATGTCTGAAGTTGTCATGTCCAAAGCTTATGCTGTTGGTGCAAGTTTCAAAGgtagcaacta ... tttatttcagGAACCGACTTCACAAATGCAGTGATAGACCGCGTCAATTTTGAGAAGGCCGATCTCACAGGGGCGATCTTCAAGAACACGGTCTTGTCAGGATCGACCTT


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 157

TCTTTAGCTGCAGCGCTGATGTCCGAGGCAAAGTTCGACGGCGCTGACATGTCTGAAGTTGTCATGTCCAAAGCTTATGCTGTTGGTGCAAGTTTCAAAGgtagcaacta ... tttatttcagGAACCGACTTCACAAATGCAGTGATAGACCGCGTCAATTTTGAGAAGGCCGATCTCACAGGGGCGATCTTCAAGAACACGGTCTTGTCAGGATCGACCTT


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 43

TCTTTAGCTGCAGCGCTGATGTCCGAGGCAAAGTTCGACGGCGCTGACATGTCTGAAGTTGTCATGTCCAAAGCTTATGCTGTTGGTGCAAGTTTCAAAGgtagcaacta ... tttatttcagGAACCGACTTCACAAATGCAGTGATAGACCGCGTCAATTTTGAGAAGGCCGATCTCACAGGGGCGATCTTCAAGAACACGGTCTTGTCAGGATCGACCTT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atactgaatagaacagaatgatgaggtccctctgggtcaaaatgctttatttcagGAACCGACTTCACAAATGCAGTGATAGACCGCGTCAATTTTGAGAAGGCCGATCTCACAGGGGCGATCTTCAAGAACACGGTCTTGTCAGGATCGACCTT
                                            ctttatttc  CT-rich tract
                                      aaaatgctttattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtagcaactaactgtgcacctctttttctcaagaacaaccatgtacagcatattctcctgttctggttcactgcgcgatgccgctgaatcgtttactaaatataatactgcaatacagtaatactgaatagaacagaatgatgaggtccctctgggtcaaaatgctttatttcagGAACCGACTTCACAAATGCAGTGATAGACCGCGTCAATTTTGAGAAGGCCGATCTCACAGGGGCGATCTTCAAGAACACGGTCTTGTCAGGATCGACCTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC