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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaggatctcaagcacaaagcattatttttttccactcgtttagtgcaatgtatctcaaatataatgttctgtgctaccagGAAGCCAAAGAGAAGTTTCAGCAGCTGCAGAAGGTTATATCCATTCTTGGAGATGCAGAGAAAAGAGCTTTATATGATGAGACTGGCATTACTGATGATG

Basic information

species Zea mays
transcript GRMZM2G129987_T01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G129987_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os02g10220.1 (Oryza sativa), 3'ss of exon 2
gtaggatctcaagcacaaagcattatttttttccactcgtttagtgcaatgtatctcaaatataatgttctgtgctaccagGAAGCCAAAGAGAAGTTTCAGCAGCTGCAGAAGGTTATATCCATTCTTGGAGATGCAGAGAAAAGAGCTTTATATGATGAGACTGGCATTACTGATGATG
|||||||||      ||||       |||||||||    || ||||| || | |||||| |    |||| |||| |  ||||||||||| ||||| ||||||||||| |||||||| ||||| |||||||| ||||  |||||||| || ||||||||||||||||| ||| |||||||||
gtaggatcttgtttccaaa-------ttttttccatggattaagtgccatttgtctcaattgagctgttatgtgatgtcagGAAGCCAAGGAGAAATTTCAGCAGCTTCAGAAGGTGATATCTATTCTTGGGGATGAGGAGAAAAGGGCATTATATGATGAGACTGGAATTGCTGATGATG

upper sequence: GRMZM2G129987_T01 (Zea mays), 3'ss of exon 2
lower sequence: AT3G12170.1 (Arabidopsis thaliana), 3'ss of exon 2
--------gtaggatctcaagcacaaagcatt----atttttt-----tccactcgtttagtgcaatgtatctcaaata--taatgttctgtgctac--cagGAAGCCAAAGAGAAGTTTCAGCAGCTGCAGAAGGTTATATCCATTCTTGGAGATGCAGAGAAAAGAGCTTTATATGATGAGACTGGCATTACTGATGATG
        |  || | |      |    | ||    | |||||     || | ||  ||  | || |||| |   |||   |  | ||||   | |   ||||| || |||||||| ||||||||| |||| |||||||| || ||||| || |||| ||||||||||||  | |||||| | ||||||     ||||||||
gtttaactgaggggttttggtttctttacttttcttagtttttaggggtctattcaattt-tacattgtaaccggaattcttgtttttcttatccaatacagGATGCTAAAGAGAAATTTCAGCAGTTGCAAAAGGTTATTTCGATTCTCGGTGATGAAGAGAAAAGAGCAGTCTATGATCAAACTGGCTCAGTTGATGATG

upper sequence: GRMZM2G129987_T01 (Zea mays), 3'ss of exon 2
lower sequence: AT5G06910.1 (Arabidopsis thaliana), 3'ss of exon 2
gtaggatctcaagcacaaagcattatttttttccactcgtttagtgcaatgtatctcaaa--tataatgttctgtgctaccagGAAGCCAAAGAGAAGTTTCAGCAGCTGCAGAAGGTTATATCCATTCTTGGAGATGCAGAGAAAAGAGCTTTATATGATGAGACTGGCATTACTGATGATG
        | ||  ||| |   || |  ||      |  ||| |    || ||  | ||   | || | || | |  |  |||||||| ||||| ||||| ||||||||||| || || ||||| |||||||| |||| ||||||||| ||  | |||||| | ||||||   | ||||||||
-------gttaaatacacactcttttacttgagatattttttggattcatttacatgaagattctactattgttttgttacagGAAGCTAAAGACAAGTTCCAGCAGCTGCAAAAAGTGATATCAATTCTTGGTGATGAAGAGAAAAGGGCAGTCTATGATCAAACTGGCTCAATTGATGATG

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|78111290|gb|DV529687.1|DV529687
EST:     ATCACAAATTGGCTCTGCGCCTCCATCCAGATAAGAATCCTGGGGATGAG                         GAAGCCAAAGAGAAGTTTCAGCAGCTGCAGAAGGTTATATCCATTCTTGGA
genomic: ATCACAAATTGGCTCTGCGCCTCCATCCAGATAAGAATCCTGGGGATGAGgtaggatctc ... gtgctaccagGAAGCCAAAGAGAAGTTTCAGCAGCTGCAGAAGGTTATATCCATTCTTGGA
EST: gi|31628006|gb|CD526397.1|CD526397
EST:     ATCACAAATTGGCTCTGCGCCTCCATCCAGATAAGAATCCTGGGGATGAG                         GAAGCGAAAGAGAAGTTTCAGCAGCTGCAGAAGGTTATATCCATTCTTGGA
genomic: ATCACAAATTGGCTCTGCGCCTCCATCCAGATAAGAATCCTGGGGATGAGgtaggatctc ... gtgctaccagGAAGCCAAAGAGAAGTTTCAGCAGCTGCAGAAGGTTATATCCATTCTTGGA
EST: gi|31664549|gb|CD573482.1|CD573482
EST:     ATCACAAATTGGCTCTGCGCCTCCATCCAGATAAGAATCCTGGGGATGAG                         GAAGCCAAAGAGAAGTTTCAGCAGCTGCAGAAGGTTATATCCATTCTTGGA
genomic: ATCACAAATTGGCTCTGCGCCTCCATCCAGATAAGAATCCTGGGGATGAGgtaggatctc ... gtgctaccagGAAGCCAAAGAGAAGTTTCAGCAGCTGCAGAAGGTTATATCCATTCTTGGA
EST: gi|19436724|gb|BM953134.1|BM953134
EST:     ATCACAAATTGGCTCTGCGCCTCCATCCAGATAAGAATCCTGGGGATGAG                         GAAGCCAAAGAGAAGTTTCAGCAGCTGCAGAAGGTTATATCCATTCTTGGA
genomic: ATCACAAATTGGCTCTGCGCCTCCATCCAGATAAGAATCCTGGGGATGAGgtaggatctc ... gtgctaccagGAAGCCAAAGAGAAGTTTCAGCAGCTGCAGAAGGTTATATCCATTCTTGGA
EST: gi|149009177|gb|EE041301.2|EE041301
EST:     ATCACAAATTGGCTCTGCGCCTCCATCCAGATAAGAATCCTGGGGATGAG                         GAAGCCAAAGAGAAGTTTCAGCAGCTGCAGAAGGTTATATCCATTCTTGGA
genomic: ATCACAAATTGGCTCTGCGCCTCCATCCAGATAAGAATCCTGGGGATGAGgtaggatctc ... gtgctaccagGAAGCCAAAGAGAAGTTTCAGCAGCTGCAGAAGGTTATATCCATTCTTGGA
EST: gi|91053239|gb|EB163657.1|EB163657
EST:     ATCACAAATTGGCTCTGCGCCTCCATCCAGATAAGAATCCTGGGGATGAG                         GAAGCCAAAGAGAAGTTTCAGCAGCTGCAGAAGGTTATATCCATTCTTGGA
genomic: ATCACAAATTGGCTCTGCGCCTCCATCCAGATAAGAATCCTGGGGATGAGgtaggatctc ... gtgctaccagGAAGCCAAAGAGAAGTTTCAGCAGCTGCAGAAGGTTATATCCATTCTTGGA
EST: gi|76011893|gb|DT939063.1|DT939063
EST:     ATCACAAATTGGCTCTGCGCCTCCATCCAGATAAGAATCCTGGGGATGAG                         GAAGCCAAAGAGAAGTTTCAGCAGCTGCAGAAGGTTATATCCATTCTTGGA
genomic: ATCACAAATTGGCTCTGCGCCTCCATCCAGATAAGAATCCTGGGGATGAGgtaggatctc ... gtgctaccagGAAGCCAAAGAGAAGTTTCAGCAGCTGCAGAAGGTTATATCCATTCTTGGA
EST: gi|71771230|gb|DR969167.1|DR969167
EST:     ATCACAAATTGGCTCTGCGCCTCCATCCAGATAAGAATCCTGGGGATGAG                         GAAGCCAAAGAGAAGTTTCAGCAGCTGCAGAAGGTTATATCCATTCTTGGA
genomic: ATCACAAATTGGCTCTGCGCCTCCATCCAGATAAGAATCCTGGGGATGAGgtaggatctc ... gtgctaccagGAAGCCAAAGAGAAGTTTCAGCAGCTGCAGAAGGTTATATCCATTCTTGGA
EST: gi|78082398|gb|DV510810.1|DV510810
EST:     ATCACAAATTGGCTCTGCGCCTCCATCCAGATAAGAATCCTGGGGATGAG                         GAAGCCAAAGAGAAGTTTCAGCAGCTGCAGAAGGTTATATCCATTCTTGGA
genomic: ATCACAAATTGGCTCTGCGCCTCCATCCAGATAAGAATCCTGGGGATGAGgtaggatctc ... gtgctaccagGAAGCCAAAGAGAAGTTTCAGCAGCTGCAGAAGGTTATATCCATTCTTGGA
EST: gi|211448244|gb|FK956529.1|FK956529
EST:     ATCACAAATTGGCTCTGCGCCTCCATCCAGATAAGAATCCTGGGGATGAG                         GAAGCCAAAGAGAAGTTTCAGCAGCTGCAGAAGGTTATATCCATTCTTGGA
genomic: ATCACAAATTGGCTCTGCGCCTCCATCCAGATAAGAATCCTGGGGATGAGgtaggatctc ... gtgctaccagGAAGCCAAAGAGAAGTTTCAGCAGCTGCAGAAGGTTATATCCATTCTTGGA
EST: gi|19057616|gb|BM736283.1|BM736283
EST:     ATCACAAATTGGCTCTGCGCCTCCATCCAGATAAGAATCCTGGGGATGAG                         GAAGCCAAAGAGAAGTTTCAGCAGCTGCAGAAGGTTATATCCATTCTTGGA
genomic: ATCACAAATTGGCTCTGCGCCTCCATCCAGATAAGAATCCTGGGGATGAGgtaggatctc ... gtgctaccagGAAGCCAAAGAGAAGTTTCAGCAGCTGCAGAAGGTTATATCCATTCTTGGA
EST: gi|19436292|gb|BM952702.1|BM952702
EST:     ATCACAAATTGGCTCTGCGCCTCCATCCAGATAAGAATCCTGGGGATGAG                         GAAGCCAAAGAGAAGTTTCAGCAGCTGCAGAAGGTTATATCCATTCTTGGA
genomic: ATCACAAATTGGCTCTGCGCCTCCATCCAGATAAGAATCCTGGGGATGAGgtaggatctc ... gtgctaccagGAAGCCAAAGAGAAGTTTCAGCAGCTGCAGAAGGTTATATCCATTCTTGGA
EST: gi|71320398|gb|DR796949.1|DR796949
EST:     ATCACAAATTGGCTCTGCGCCTCCATCCAGATAAGAATCCTGGGGATGAG                         GAAGCCAAAGAGAAGTTTCAGCAGCTGCAGAAGGTTATATCCATTCTTGGA
genomic: ATCACAAATTGGCTCTGCGCCTCCATCCAGATAAGAATCCTGGGGATGAGgtaggatctc ... gtgctaccagGAAGCCAAAGAGAAGTTTCAGCAGCTGCAGAAGGTTATATCCATTCTTGGA
EST: gi|211448242|gb|FK956527.1|FK956527
EST:     ATCACAAATTGGCTCTGCGCCTCCATCCAGATAAGAATCCTGGGGATGAG                         GAAGCCAAAGAGAAGTTTCAGCAGCTGCAGAAGGTTATATCCATTCTTGGA
genomic: ATCACAAATTGGCTCTGCGCCTCCATCCAGATAAGAATCCTGGGGATGAGgtaggatctc ... gtgctaccagGAAGCCAAAGAGAAGTTTCAGCAGCTGCAGAAGGTTATATCCATTCTTGGA
EST: gi|211450351|gb|FK956532.1|FK956532
EST:     ATCACAAATTGGCTCTGCGCCTCCATCCAGATAAGAATCCTGGGGATGAG                         GAAGCCAAAGAGAAGTTTCAGCAGCTGCAGAAGGTTATATCCATTCTTGGA
genomic: ATCACAAATTGGCTCTGCGCCTCCATCCAGATAAGAATCCTGGGGATGAGgtaggatctc ... gtgctaccagGAAGCCAAAGAGAAGTTTCAGCAGCTGCAGAAGGTTATATCCATTCTTGGA
EST: gi|19436725|gb|BM953135.1|BM953135
EST:     ATCACAAATTGGCTCTGCGCCTCCATCCAGATAAGAATCCTGGGGATGAG                         GAAGCCAAAGAGAAGTTTCAGCAGCTGCAGAAGGTTATATCCATTCTTGGA
genomic: ATCACAAATTGGCTCTGCGCCTCCATCCAGATAAGAATCCTGGGGATGAGgtaggatctc ... gtgctaccagGAAGCCAAAGAGAAGTTTCAGCAGCTGCAGAAGGTTATATCCATTCTTGGA
EST: gi|91054843|gb|EB165261.1|EB165261
EST:     ATCACAAATTGGCTCTGCGCCTCCATCCAGATAAGAATCCTGGGGATGAG                         GAAGCCAAAGAGAAGTTTCAGCAGCTGCAGAAGGTTATATCCATTCTTGGA
genomic: ATCACAAATTGGCTCTGCGCCTCCATCCAGATAAGAATCCTGGGGATGAGgtaggatctc ... gtgctaccagGAAGCCAAAGAGAAGTTTCAGCAGCTGCAGAAGGTTATATCCATTCTTGGA
EST: gi|211448245|gb|FK956530.1|FK956530
EST:     ATCACAAATTGGCTCTGCGCCTCCATCCAGATAAGAATCCTGGGGATGAG                         GAAGCGAAAGAGAAGTTTCAGCAGCTGCAGAAGGTTATATCCATTCTTGGA
genomic: ATCACAAATTGGCTCTGCGCCTCCATCCAGATAAGAATCCTGGGGATGAGgtaggatctc ... gtgctaccagGAAGCCAAAGAGAAGTTTCAGCAGCTGCAGAAGGTTATATCCATTCTTGGA
EST: gi|76924244|gb|DV169873.1|DV169873
EST:     ATCACAAATTGGCTCTGCGCCTCCATCCAGATAAGAATCCTGGGGATGAG                         GAAGCCAAAGAGAAGTTTCAGCAGCTGCAGAAGGTTATATCCATTCTTGGA
genomic: ATCACAAATTGGCTCTGCGCCTCCATCCAGATAAGAATCCTGGGGATGAGgtaggatctc ... gtgctaccagGAAGCCAAAGAGAAGTTTCAGCAGCTGCAGAAGGTTATATCCATTCTTGGA
EST: gi|71315532|gb|DR794370.1|DR794370
EST:     ATCACAAATTGGCTCTGCGCCTCCATCCAGATAAGAATCCTGGGGATGAG                         GAAGCCAAAGAGAAGTTTCAGCAGCTGCAGAAGGTTATATCCATTCTTGGA
genomic: ATCACAAATTGGCTCTGCGCCTCCATCCAGATAAGAATCCTGGGGATGAGgtaggatctc ... gtgctaccagGAAGCCAAAGAGAAGTTTCAGCAGCTGCAGAAGGTTATATCCATTCTTGGA

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 4 RNA-Seq libraries.


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 198

ATCTTGGGAGTTGAGAAGACTGCTTCACAACAAGAAATAAAGAAGGCATATCACAAATTGGCTCTGCGCCTCCATCCAGATAAGAATCCTGGGGATGAGgtaggatctc ... gtgctaccagGAAGCCAAAGAGAAGTTTCAGCAGCTGCAGAAGGTTATATCCATTCTTGGAGATGCAGAGAAAAGAGCTTTATATGATGAGACTGGCATTACTGATGATG


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 56

ATCTTGGGAGTTGAGAAGACTGCTTCACAACAAGAAATAAAGAAGGCATATCACAAATTGGCTCTGCGCCTCCATCCAGATAAGAATCCTGGGGATGAGgtaggatctc ... gtgctaccagGAAGCCAAAGAGAAGTTTCAGCAGCTGCAGAAGGTTATATCCATTCTTGGAGATGCAGAGAAAAGAGCTTTATATGATGAGACTGGCATTACTGATGATG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 78

ATCTTGGGAGTTGAGAAGACTGCTTCACAACAAGAAATAAAGAAGGCATATCACAAATTGGCTCTGCGCCTCCATCCAGATAAGAATCCTGGGGATGAGgtaggatctc ... gtgctaccagGAAGCCAAAGAGAAGTTTCAGCAGCTGCAGAAGGTTATATCCATTCTTGGAGATGCAGAGAAAAGAGCTTTATATGATGAGACTGGCATTACTGATGATG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 40

ATCTTGGGAGTTGAGAAGACTGCTTCACAACAAGAAATAAAGAAGGCATATCACAAATTGGCTCTGCGCCTCCATCCAGATAAGAATCCTGGGGATGAGgtaggatctc ... gtgctaccagGAAGCCAAAGAGAAGTTTCAGCAGCTGCAGAAGGTTATATCCATTCTTGGAGATGCAGAGAAAAGAGCTTTATATGATGAGACTGGCATTACTGATGATG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttttccactcgtttagtgcaatgtatctcaaatataatgttctgtgctaccagGAAGCCAAAGAGAAGTTTCAGCAGCTGCAGAAGGTTATATCCATTCTTGGAGATGCAGAGAAAAGAGCTTTATATGATGAGACTGGCATTACTGATGATG
                         tatctcaaatataat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaggatctcaagcacaaagcattatttttttccactcgtttagtgcaatgtatctcaaatataatgttctgtgctaccagGAAGCCAAAGAGAAGTTTCAGCAGCTGCAGAAGGTTATATCCATTCTTGGAGATGCAGAGAAAAGAGCTTTATATGATGAGACTGGCATTACTGATGATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCTT