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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AACGGCCTTGCTACCAAGGTAGAGAAGTCACGAAAGCAGATGAAGGAACGTAAGAACAGGGCGAAGAAAATCCGTGGTGTGAAGAAGGTGAgtaccagtcaggaattgctactcgtattcccattgttctggtacatttcaattatgtttgctgcacaattttttgcag

Basic information

species Zea mays
transcript GRMZM2G029685_T02
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G029685_T01 (Zea mays), 5'ss of exon 3
lower sequence: GLYMA19G43190.1 (Glycine max), 5'ss of exon 4
AACGGCCTTGCTACCAAGGTAGAGAAGTCACGAAAGCAGATGAAGGAACGTAAGAACAGGGCGAAGAAAATCCGTGGTGTGAAGAAGGTGAgt-----accagtcaggaattgcta-----ctcgtattcccattgttctggtacatttcaattatgtttgctgcacaattttttgcag
||||||||||  ||||||||||| |||||| | ||||| ||||||||  | ||||| || || ||||| || ||||| || |||||||| | |      | ||  |  | || ||      ||  | |   | |||||    || | || ||  || |    || |   ||  | ||||
AACGGCCTTGACACCAAGGTAGAAAAGTCAAGGAAGCAAATGAAGGAGAGAAAGAATAGAGCTAAGAAGATTCGTGGAGTAAAGAAGgtaattttgtagctagctataattttctttacctcttatgtgatccttgtttcattaaaattaaaacatatggcatgtattgttcgt-gcag

upper sequence: GRMZM2G029685_T01 (Zea mays), 5'ss of exon 3
lower sequence: AT3G04920.1 (Arabidopsis thaliana), 5'ss of exon 4
AACGGCCTTGCTACCAAGGTAGAGAAGTCACGAAAGCAGATGAAGGAACGTAAGAACAGGGCGAAGAAAATCCGTGGTGTGAAGAAGGTGAgta--ccagtcaggaat--tgcta-ctcgtattccc-attgttctggtacatttcaattatgtttgctgcacaattttttgcag
|| || ||||  || ||| | ||||||||| | || || || |||||| | ||||||||||||||||||||||||||||| ||||||||  |||  |  ||      |  ||||| ||  | ||    |||||    |||   || ||  || | |  ||  |||| ||| ||||
AATGGACTTGACACTAAGATTGAGAAGTCAAGGAAACAAATTAAGGAAAGGAAGAACAGGGCGAAGAAAATCCGTGGTGTTAAGAAGgtatgtatactggttttccctcttgctatcttctgtttttgattgtgactgta-gctttaagaatctgttttgatcaatgttt-gcag

upper sequence: GRMZM2G029685_T01 (Zea mays), 5'ss of exon 3
lower sequence: AT5G28060.1 (Arabidopsis thaliana), 5'ss of exon 4
AACGGCCTTGCTACCAAGGTAGAGAAGTCACGAAAGCAGATGAAGGAACGTAAGAACAGGGCGAAGAAAATCCGTGGTGTGAAGAAGGTGAg---------taccagtcaggaattgctactcgtattcccattgttctggtacatttcaatt--atgtttgctgcacaattttttgcag----
|| || ||||  |||||| | ||||| ||| | || ||||| |||||  | ||||||||||||||||| ||||||||||| |||||||| ||          || |  ||| |||    | | |   |     ||||   |    |||    |  | | |   ||||   |||| ||       
AATGGACTTGACACCAAGATTGAGAAATCAAGGAAACAGATCAAGGAGAGGAAGAACAGGGCGAAGAAGATCCGTGGTGTTAAGAAGgtaagagagaccaacactaaccagaaatctacatttgctattgttatgtttgtgcctgttttgtcttaacgatatttgcattgttttgtgagtgtag

upper sequence: GRMZM2G029685_T01 (Zea mays), 5'ss of exon 3
lower sequence: Vv07s0151g00900.t01 (Vitis vinifera), 5'ss of exon 4
AACGGCCTTGCTACCAAGGTAGAGAAGTCACGAAAGCAGATGAAGGAACGTAAGAACAGGGCGAAGAAAATCCGTGGTGTGAAGAAGGTGAgta--------ccagtcaggaattgctact-cgtattcc--cattgttctggtacatttcaatta---tgtttgctgcacaattttttgcag---------------------------------------------------------------------------------
|| ||  | | ||||||||| || |||||| | ||||| ||||||||| | ||||||||||| |||||  |||| || ||||||||||| |  |         |  |      ||| |  |  | | ||   || |  |      | ||||||||    | ||||||| ||| |   || |                                                                                   
AATGGATTGGATACCAAGGTGGAAAAGTCAAGGAAGCAAATGAAGGAAAGGAAGAACAGGGCCAAGAAGGTCCGAGGAGTGAAGAAGgtaaagaaatcatcttccttttaaccttgttggtgtgcactctagcaatagtaccaggcctttcaatttccttttttgctgtacactgggttactattgccattcccattagccatattatttgccttcaaagatttgggaccttcacgttcattgtactactcgttactcttgcag

upper sequence: GRMZM2G029685_T01 (Zea mays), 5'ss of exon 3
lower sequence: PP1S13_236V6.1 (Physcomitrella patens), 5'ss of exon 4
AACGGCCTTGCTACCAAGGTAGAGAAGTCACGAAAGCAGATGAAGGAACGTAAGAACAGGGCGAAGAAAATCCGTGGTGTGAAGAAGGTGAgtaccagtcaggaattgctactcgtattcccattgttctggtacatttca----attatgtttgctgcacaatttt--ttgcag--------------------------------------------------------
|| || || ||||||||||| ||||||||  | |||||||| ||||| || |||||| |  ||||||| ||| | ||||||||||||||  ||     |  || ||||          |  |||       ||  | || |     | ||||    ||   |  ||   |||  |                                                        
AATGGTCTGGCTACCAAGGTCGAGAAGTCGAGGAAGCAGATCAAGGAGCGCAAGAACCGTTCGAAGAAGATCAGGGGTGTGAAGAAGgtatgttgatatgtggcattgtcttggaatgtggcatccagaaagtgaaatttacattgtcatgtaaattgtgtagcttcgattgatgcagacgagtgtgtatgtgatgaagtgtcttacaaccttcatttggcttgactgcag

upper sequence: GRMZM2G029685_T01 (Zea mays), 5'ss of exon 3
lower sequence: PP1S450_9V6.1 (Physcomitrella patens), 5'ss of exon 4
AACGGCCTTGCTACCAAGGTAGAGAAGTCACGAAAGCAGATGAAGGAACGTAAGAACAGGGCGAAGAAAATCCGTGGTGTGAAGAAGGTGAgtac-cagtca--ggaattgctactcgtattcccattgttctggtacatttcaattatgtttgctgcacaattttttgcag-------------------------------------------------------------------------------------
|| ||  | || |||||||| ||||||||  | |||||||| ||||| || |||||| |  ||||||| ||| | ||||||||||||||  ||   || ||   ||||||  |   |  | |   |||    |      |||  ||||     ||| | | |      |                                                                                        
AATGGATTGGCAACCAAGGTCGAGAAGTCGAGGAAGCAGATCAAGGAGCGCAAGAACCGATCGAAGAAGATCAGGGGTGTGAAGAAGgttcgttttcattcgttggaattattgtcctaagttatattaagttcaggtcttttcattactgaagctacgctaccggaggttatcatgttttctcctgcattcttattgtgcgtttatgagtatgtttacaatgaagtgtctcacgacctgcatttgcttggtcccag

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|60397441|gb|DN230257.1|DN230257
EST:     GAAGGAACGTAAGAACAGGGCGAAGAAAATCCGTGGTGTGAAGAAG---A                         -CAAAGGCTGGAGATGCCAAGAAGAAGTAAGGGAGGAAGTTACTTGCCTTG
genomic: GAAGGAACGTAAGAACAGGGCGAAGAAAATCCGTGGTGTGAAGAAGGTGAgtaccagtca ... ttttttgcagACAAAGGCTGGAGATGCCAAGAAGAAGTAAGGGAGGAAGTTACTTGCCTTG
EST: gi|15079941|gb|BI388886.1|BI388886
EST:     GAAGGAACGTAAGAACAGGGCGAAGAAAATCCGTGGTGTGAAGAAG---A                         -CAAAGGCTGGAGATGCCAAGAAGAAGTAAGGGAGGAAATTACTTGCCTTG
genomic: GAAGGAACGTAAGAACAGGGCGAAGAAAATCCGTGGTGTGAAGAAGGTGAgtaccagtca ... ttttttgcagACAAAGGCTGGAGATGCCAAGAAGAAGTAAGGGAGGAAGTTACTTGCCTTG
EST: gi|60355885|gb|DN222858.1|DN222858
EST:     GAAGGAACGTAAGAACAGGGCGAAGAAAATCCGTGGTGTGAAGAAG---A                         -CAAAGGCTGGAGATGCCAAGAAGAAGTAAGGGAGGAAGTTACTTGCCTTG
genomic: GAAGGAACGTAAGAACAGGGCGAAGAAAATCCGTGGTGTGAAGAAGGTGAgtaccagtca ... ttttttgcagACAAAGGCTGGAGATGCCAAGAAGAAGTAAGGGAGGAAGTTACTTGCCTTG
EST: gi|16926632|gb|BM079700.1|BM079700
EST:     GAAGGAACGTAAGAACAGGGCGAAGAAAATCCGTGGTGTGAAGAAG---A                         -CAAAGGCTGGAGATGCCAAGAAGAAGTAAGGGAGGAAGTTACTTGCCTTG
genomic: GAAGGAACGTAAGAACAGGGCGAAGAAAATCCGTGGTGTGAAGAAGGTGAgtaccagtca ... ttttttgcagACAAAGGCTGGAGATGCCAAGAAGAAGTAAGGGAGGAAGTTACTTGCCTTG
EST: gi|37376305|gb|CF624665.1|CF624665
EST:     GAAGGAACGTAAGAACAGGGCGAAGAAAATCCGTGGTGTGAAGAAG---A                         -CAAAGGCTGGAGATGCCAAGAAGAAGTAAGGGAGGAAGTTACTTGCCTTG
genomic: GAAGGAACGTAAGAACAGGGCGAAGAAAATCCGTGGTGTGAAGAAGGTGAgtaccagtca ... ttttttgcagACAAAGGCTGGAGATGCCAAGAAGAAGTAAGGGAGGAAGTTACTTGCCTTG
EST: gi|113701166|gb|EE678670.1|EE678670
EST:     AAGAACAGGGCGAAGAAAATCCGTGGTTTGAAGAA---G-                         ACAAAGGCTGGAGATGCCAAGAAGAAGTAAGGGAGGAAGTTACTTGCCTTG
genomic: AAGAACAGGGCGAAGAAAATCCGTGGTGTGAAGAAGGTGAgtaccagtca ... ttttttgcagACAAAGGCTGGAGATGCCAAGAAGAAGTAAGGGAGGAAGTTACTTGCCTTG
EST: gi|5761771|gb|AI966819.1|AI966819
EST:     GAAAATCCGTGGTGTGAAGAA---G-                         ACAAAGGCTGGAGATGCCAAGAAGAAGTAAGGGAGGAAGTTACTTGCCTTG
genomic: GAAAATCCGTGGTGTGAAGAAGGTGAgtaccagtca ... ttttttgcagACAAAGGCTGGAGATGCCAAGAAGAAGTAAGGGAGGAAGTTACTTGCCTTG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AACGGCCTTGCTACCAAGGTAGAGAAGTCACGAAAGCAGATGAAGGAACGTAAGAACAGGGCGAAGAAAATCCGTGGTGTGAAGAAGGTGAgtaccagtcaggaattgctactcgtattcccattgttctggtacatttcaattatgtttgctgcacaattttttgcag

- - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG