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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tagtttcccagattggctttcttttggagtttcttttgtctgtatttataaattctgaaagaaaaacaagtggtgaattaaattcttctgcaacatgcagGATGCTGTTGATTGCCCAGAATGGGTTGTTCCATTCCATCTCTTCAAATTATTGGCAGAGGAG

Basic information

species Zea mays
transcript GRMZM2G042398_T02
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G042398_T01 (Zea mays), 3'ss of exon 10
lower sequence: LOC_Os08g08200.2 (Oryza sativa), 3'ss of exon 9
tagtttcccagattggctttcttttggagtttcttttgtctgtatttataaattctgaaagaaaaacaagtggtgaattaaat-tcttctgcaacatgcagGATGCTGTTGATTGCCCAGAATGGGTTGTTCCATTCCATCTCTTCAAATTATTGGCAGAGGAG-------------------------------------
|      ||||| |||  ||| ||    || |  ||| |   |   |  |    |||   | |||   | || || || | |  |||   |||| ||||||||||||||||||||||| ||||||||||||||||||||||||||||||||  |||||||||||                                     
tttccctccagactggacttccttctttgtgttctttcttgttggctgcattggctgttgggaaactta-tgatgtataagacgtctatggcaatatgcagGATGCTGTTGATTGCCCGGAATGGGTTGTTCCATTCCATCTCTTCAAATTGCTGGCAGAGGAGGTATTCTCTTCCTTAAACTATTGCGAGTAACACTCTG

upper sequence: GRMZM2G042398_T01 (Zea mays), 3'ss of exon 10
lower sequence: LOC_Os08g08200.1 (Oryza sativa), 3'ss of exon 9
tagtttcccagattggctttcttttggagtttcttttgtctgtatttataaattctgaaagaaaaacaagtggtgaattaaat-tcttctgcaacatgcagGATGCTGTTGATTGCCCAGAATGGGTTGTTCCATTCCATCTCTTCAAATTATTGGCAGAGGAG
|      ||||| |||  ||| ||    || |  ||| |   |   |  |    |||   | |||   | || || || | |  |||   |||| ||||||||||||||||||||||| ||||||||||||||||||||||||||||||||  |||||||||||
tttccctccagactggacttccttctttgtgttctttcttgttggctgcattggctgttgggaaactta-tgatgtataagacgtctatggcaatatgcagGATGCTGTTGATTGCCCGGAATGGGTTGTTCCATTCCATCTCTTCAAATTGCTGGCAGAGGAG

upper sequence: GRMZM2G042398_T01 (Zea mays), 3'ss of exon 10
lower sequence: Vv19s0014g04740.t01 (Vitis vinifera), 3'ss of exon 9
---tagtttcccagattggctttcttttggagtttcttttgtctgtatttataaattctgaaagaaaaacaa-gtggtgaattaaattcttctgcaacatgcagGATGCTGTTGATTGCCCAGAATGGGTTGTTCCATTCCATCTCTTCAAATTATTGGCAGAGGAG
   |  |    | | |  ||| |   |||     |    |  | | |      ||| ||      |||| ||  | | |||  ||   ||| ||     ||||||||||||||||||| || |||||| |||| ||||| ||| ||||||||| ||||||||| |||
ttatgatcctgctgctcagctctaccttgattccttaagttacagaaccacacaatcctacccataaaataatattgagaagaaagagcttttgt----tgcagGATGCTGTTGATTGTCCTGAATGGATTGTCCCATTTCATGTCTTCAAATCATTGGCAGAAGAG

upper sequence: GRMZM2G042398_T01 (Zea mays), 3'ss of exon 10
lower sequence: PP1S49_100V6.1 (Physcomitrella patens), 3'ss of exon 10
tagtttcccagattggct--ttcttttggagtttcttttgtctgtatttataaattctgaaagaaaaacaagtggtgaattaaattcttctgcaa--catgcagGATGCTGTTGATTGCCCAGAATGGGTTGTTCCATTCCATCTCTTCAAATTATTGGCAGAGGAG
 || |||     ||   |  | ||   | ||||||   ||  |    || |  | |           |||    |    || | || || ||| |  ||||||||||||||| ||||| ||||| ||| ||||||| |||||   ||||||||  || ||||  |||
-agattcgactgttatttcatactcaagtagtttcacatgagttcgattctcgagttgccccctctgacagccagc---tttacttgttttgcgatgcatgcagGATGCTGTGGATTGTCCAGAGTGGCTTGTTCCCTTCCAGTGCTTCAAATCTTTAGCAGCAGAG

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|166478805|gb|EG300577.1|EG300577
EST:     ATTCCCTGCATCCAGACCGTTTGGTATCAAGTACAAGTTTCAACTTAGAG                         GATGCTGTTGATTGCCCAGAATGGGTTGTTCCATTCCATCTCTTCAAATT
genomic: ATTCCCTGCATCCAGACCGTTTGGTATCAAGTACAAGTTTC-ACTTAGAGgtaagtggga ... caacatgcagGATGCTGTTGATTGCCCAGAATGGGTTGTTCCATTCCATCTCTTCAAATT
EST: gi|26558555|gb|CA830790.1|CA830790
EST:     AATTCCCTGCATCCAGACCGTTTGGTATCAAGTACAAGTTTCACTTAGAG                         GATGCTGTTGATTGCCCAGAATGGGTTGTTCCATTCCATCTCTTCAAATTA
genomic: AATTCCCTGCATCCAGACCGTTTGGTATCAAGTACAAGTTTCACTTAGAGgtaagtggga ... caacatgcagGATGCTGTTGATTGCCCAGAATGGGTTGTTCCATTCCATCTCTTCAAATTA
EST: gi|18165055|gb|BM334900.1|BM334900
EST:     CTGCATCCAGACCGTTTGGTATCAAGTACAAGTTTCACTTAGAG                         GATGCTGTTGATTGCCCAGAATGGGTTGTTCCATTCCATCTCTTCAAATTA
genomic: CTGCATCCAGACCGTTTGGTATCAAGTACAAGTTTCACTTAGAGgtaagtggga ... caacatgcagGATGCTGTTGATTGCCCAGAATGGGTTGTTCCATTCCATCTCTTCAAATTA
EST: gi|22472517|gb|BU036997.1|BU036997
EST:     AATTCCCTGCATCCAGACCGTTTGGTATCAAGTACAAGTTTCACTTAGAG                         GATGCTGTTGATTGCCCAGAATGGGTTGTTCCATTCCATCTCTTCAAATTA
genomic: AATTCCCTGCATCCAGACCGTTTGGTATCAAGTACAAGTTTCACTTAGAGgtaagtggga ... caacatgcagGATGCTGTTGATTGCCCAGAATGGGTTGTTCCATTCCATCTCTTCAAATTA
EST: gi|211475864|gb|FL467329.1|FL467329
EST:     AATTCCCTGCATCCAGACCGTTTGGTATCAAGTACAAGTTTCACTTAGAG                         GATGCTGTTGATTGCCCAGAATGGGTTGTTCCATTCCATCTCTTCAAATTA
genomic: AATTCCCTGCATCCAGACCGTTTGGTATCAAGTACAAGTTTCACTTAGAGgtaagtggga ... caacatgcagGATGCTGTTGATTGCCCAGAATGGGTTGTTCCATTCCATCTCTTCAAATTA
EST: gi|87155667|gb|DY400456.1|DY400456
EST:     AATTCCCTGCATCCAGACCGTTTGGTATCAAGTACAAGTTTCACTTAGAG                         GATGCTGTTGATTGCCCAGAATGGGTTGTTCCATTCCATCTCTTCAAATTA
genomic: AATTCCCTGCATCCAGACCGTTTGGTATCAAGTACAAGTTTCACTTAGAGgtaagtggga ... caacatgcagGATGCTGTTGATTGCCCAGAATGGGTTGTTCCATTCCATCTCTTCAAATTA
EST: gi|18164178|gb|BM334017.1|BM334017
EST:     AATTCCCTGCATCCAGACCGTTTGGTATCAAGTACAAGTTTCACTTAGAG                         GATGCTGTTGATTGCCCAGAATGGGTTGTTCCATTCCATCTCTTCAAATTA
genomic: AATTCCCTGCATCCAGACCGTTTGGTATCAAGTACAAGTTTCACTTAGAGgtaagtggga ... caacatgcagGATGCTGTTGATTGCCCAGAATGGGTTGTTCCATTCCATCTCTTCAAATTA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttataaattctgaaagaaaaacaagtggtgaattaaattcttctgcaacatgcagGATGCTGTTGATTGCCCAGAATGGGTTGTTCCATTCCATCTCTTCAAATTATTGGCAGAGGAG
                                     ttcttctgc  CT-rich tract
                            tgaattaaattctt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tagtttcccagattggctttcttttggagtttcttttgtctgtatttataaattctgaaagaaaaacaagtggtgaattaaattcttctgcaacatgcagGATGCTGTTGATTGCCCAGAATGGGTTGTTCCATTCCATCTCTTCAAATTATTGGCAGAGGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG
- - - - - - - - - - - - - - - - - - - - tgtattt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - aagaaaa