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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttaacttctattaatctgcaccattgagtacctttctcctttgttaaaatgctactataatctgggcattaattttaatgagttttttctcttccaaaagCTCATAGGCTCTCCAGATGATGCAAGCCTGGGATTTCTTCGAAGTGATAATGCAAAAAGATACATGAAACAACTACCACAGTTTCCAAGACAGGACTTCC

Basic information

species Zea mays
transcript GRMZM2G127141_T01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G127141_T01 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os10g38950.1 (Oryza sativa), 3'ss of exon 4
ttaacttctattaatctgcaccattgagtacctttctcctttgttaaaatgctactataatctg---ggcattaattttaatgagttttttctct-tccaaaagCTCATAGGCTCTCCAGATGATGCAAGCCTGGGATTTCTTCGAAGTGATAATGCAAAAAGATACATGAAACAACTACCACAGTTTCCAAGACAGGACTTCC
     ||   |  || |       ||  | | || ||  | |   ||  |    || ||| |     || || ||| ||||| ||    || ||| | |||||||| ||||| || ||||||||  ||||||| || |||||||| ||||||||||||| ||||||||||||||| ||||||||||  ||||| ||||||||||
---ttttgggtccatttttttttctgttttctttgcttttctaa-aatgtatccctgtaacccaagtggtatcaatattaatcagacccttttctcttcaaaagCTGATAGGGTCGCCAGATGACTCAAGCCTAGGGTTTCTTCGGAGTGATAATGCAAGAAGATACATGAAACAGCTACCACAGTACCCAAGGCAGGACTTCC

upper sequence: GRMZM2G127141_T01 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA11G02420.1 (Glycine max), 3'ss of exon 4
ttaacttctattaatctgcaccattgagtacctttctcctttgttaaaatgctactataatctg-ggcattaattttaatgagttttttctcttcc--aaaagCTCATAGGCTCTCCAGATGATGCAAGCCTGGGATTTCTTCGAAGTGATAATGCAAAAAGATACATGAAACAACTACCACAGTTTCCAAGACAGGACTTCC
  ||  |  |   || ||||  |     |    |  |    ||| ||     || || ||  ||   ||  |  | |  |    |||| || || |  ||||| |  |||| || || | |||||| ||||| |||||||| | |||||| ||||||||||||||  |    || || ||||| | |   |  ||  | ||| 
--aaaatgaaaggat-tgcataagctgattttatagttacctgtaaattgattagtacaagttgtaacacgacatgtgtttgtgttttccttttgcttaaaagTTATTAGGTTCACCTGTTGATGCCAGCCTTGGATTTCTCCAAAGTGAAAATGCAAAAAGATATGTTCGCCAGCTTCCACAATATAGGAAGCAAAATTTCT

upper sequence: GRMZM2G127141_T01 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA08G02060.1 (Glycine max), 3'ss of exon 4
ttaacttctattaatctgcacc-attgagtacctttctcctttgttaaaatgctactataatctgggcattaattttaatgagttttttctcttc---caaaagCTCATAGGCTCTCCAGATGATGCAAGCCTGGGATTTCTTCGAAGTGATAATGCAAAAAGATACATGAAACAACTACCACAGTTTCCAAGACAGGACTTCC
   |     ||  || | |||  |||   ||  || |   |   ||||       ||||||  ||    | ||||   |    ||||||   ||    |||||| |  |||| || || |||||||||||||| | |||||| |||||||||||||| | |||||| || | ||| || |||||||  |  |  ||  | ||| 
---agagaaatgcatatacactgattttatag-ttgcgtgtaaattaatcaatggctataaattgtaactcaattcatacatttttttttctttggcacaaaagTTATTAGGTTCACCTGATGATGCAAGCCTTGAATTTCTCCGAAGTGATAATGCCAGAAGATATATTAGACAGCTTCCACAGTACCGGAAGCAAAAATTCT

upper sequence: GRMZM2G127141_T01 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA18G47140.1 (Glycine max), 3'ss of exon 4
-ttaacttctattaatctgcaccattgagtacctttctcctttgttaaaatgctac-tataatctgggcattaattttaatgagttttttctcttccaaaa-gCTCATAGGCTCTCCAGATGATGCAAGCCTGGGATTTCTTCGAAGTGATAATGCAAAAAGATACATGAAACAACTACCACAGTTTCCAAGACAGGACTTCC-
 ||  |  ||||  || |||| | |    |  ||   |    |  |||    | |  | |||     |  |||||||| |  | |||  |  |||  |||| |||||||||||| || |||||    ||||| |||||||| ||||||||||||||    |||||  ||| ||| || ||||| | |||||| ||  | ||   
atttccccctatagat-tgcaacttc---tttctcattttcatactaagtctccatgtttaaaaaatgatttaattttgacaaatttccttgcttttaaaaagcTCATAGGCTCACCTGATGACCATAGCCTTGGATTTCTACGAAGTGATAATGCTCGTAGATATGTGAGACAGCTTCCACAATATCCAAGGCAACAATTTGC

upper sequence: GRMZM2G127141_T01 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA07G07270.1 (Glycine max), 3'ss of exon 4
ttaacttctattaatctgcaccattgagtacctttctcctttgttaaaatgctacta---taatctgggcattaattttaatgagttttttctcttccaaaagCTCATAGGCTCTCCAGATGATGCAAGCCTGGGATTTCTTCGAAGTGATAATGCAAAAAGATACATGAAACAACTACCACAGTTTCCAAGACAGGACTTCC
     | ||  ||   ||||   |    | |     ||||||    |  |  | ||    |||  ||  |  ||   | |     || |||   ||| ||||||| ||||| || ||  ||||||| ||||| |||||||| ||||||||||||||    |||||  | ||||| || || || | |||||  ||  ||||  
---tttcctggtagaatgcaaattcccattctccgatccttttcagatctctttctgatttaaaatgaactctagcatgacaattttcttttctttcaaaaagCTGATAGGTTCACCCAATGATGCCAGCCTTGGATTTCTACGAAGTGATAATGCTCGTAGATATGTAAAACAGCTTCCCCAATATCCAAAGCAAAACTTTT

upper sequence: GRMZM2G127141_T01 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA05G37480.1 (Glycine max), 3'ss of exon 4
-ttaacttctattaatctgcaccattgagtacctttctcctttgttaaaatgctactataatctgggcattaattttaatgagttttttctcttc----caaaagCTCATAGGCTCTCCAGATGATGCAAGCCTGGGATTTCTTCGAAGTGATAATGCAAAAAGATACATGAAACAACTACCACAGTTTCCAAGACAGGACTTCC
   || | |   ||| |||    |||   ||  || |   |   ||||       ||||||  ||    |  |||   |     | |    |||     |||||| |  |||| || || |||||||||||||| | |||||| |||||||||||||| | |||||| || | ||| || |||||||  |  |  ||  | ||| 
gagaaatgcatataagctg----attttatag-ttgcgtgtaaattaattactggctataagttgtagctccattcatacattctgtactcctttggcacaaaagTTATTAGGTTCACCTGATGATGCAAGCCTTGAATTTCTCCGAAGTGATAATGCCAGAAGATATATTAGACAGCTTCCACAGTACCGGAAGCAAAAATTCT

upper sequence: GRMZM2G127141_T01 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA09G39190.1 (Glycine max), 3'ss of exon 4
-ttaacttctattaatctgcaccattgagtacctttctcctttgttaaaatgctac-tataatctgggcattaattttaatgagttttttct--cttccaaaagCTCATAGGCTCTCCAGATGATGCAAGCCTGGGATTTCTTCGAAGTGATAATGCAAAAAGATACATGAAACAACTACCACAGTTTCCAAGACAGGACTTCC
 ||  |  ||||  || |||| | |    |  ||   |    |  |||    | |  | |||     |  |||| ||| |  | ||||   |   ||  |||||||||||||||| || |||||  | ||||| |||||||| ||||||||||||||    |||||  ||| ||| || ||||| | |||||| ||  | ||  
attttcccctatagat-tgcaacttc---tttctcattttcatactaagtctccatgtttaaaaattgatttaagtttgacaaattttccttgcttttaaaaagCTCATAGGCTCACCTGATGACACTAGCCTTGGATTTCTACGAAGTGATAATGCTCGTAGATATGTGAGACAGCTTCCACAATATCCAAGGCAACAATTTG

upper sequence: GRMZM2G127141_T01 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA16G03670.1 (Glycine max), 3'ss of exon 4
ttaacttctattaatctgcaccattgagtacctttctcctttgttaaaatgctactataatctgggcattaatttta-----atgagttttttctcttccaaaa-gCTCATAGGCTCTCCAGATGATGCAAGCCTGGGATTTCTTCGAAGTGATAATGCAAAAAGATACATGAAACAACTACCACAGTTTCCAAGACAGGACTTCC
     | ||  ||   ||||   |    | |     |||||  || | ||     | | || |    ||||| | ||     |  | ||| || |||| ||||| ||| ||||| || ||||||||||| ||||| |||||||| ||||||||||||||    |||||| | ||||| || || |||| ||||| |||  ||||  
---tttcctggtagaatgcaaattctcattctccgatcctt--ttcagatctctttctgatttaaa-attaactctagcatgacaattttcttttctttcaaaaagCTGATAGGTTCGCCAGATGATGCCAGCCTTGGATTTCTACGAAGTGATAATGCTCGTAGATACGTAAAACAGCTTCCGCAGTATCCAAAACAAAACTTTT

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|67025602|gb|CO454351.1|CO454351
EST:     CCCTGTTTCCTGGACGGNAT-ACATCCAGCAATTAAAATTGATCACTGAG                         CTCATAGGCTCTCCAGATGATAGCA-GCCTGGGNATT-CTTCNNAGTGATA
genomic: CCCTGTTTCCTGGACGGGATTACATCCAGCAATTAAAATTGATCACTGAGgtaaatttat ... cttccaaaagCTCATAGGCTCTCCAGATGAT-GCAAGCCTGGG-ATTTCTTCGAAGTGATA
EST: gi|76010905|gb|DT938075.1|DT938075
EST:     CATCCAGCAATAAAAATTGATCACTGAG                         CTCATAGGCTCTCCAGATGATGCAAGCCTGGGATTTCTTCGAAGTGATAAT
genomic: CATCCAGCAATTAAAATTGATCACTGAGgtaaatttat ... cttccaaaagCTCATAGGCTCTCCAGATGATGCAAGCCTGGGATTTCTTCGAAGTGATAAT
EST: gi|32933341|gb|CF038153.1|CF038153
EST:     CCCTGTTTCCTGGACGGGATTACATCCAGCAATTAAAATTGATCACTGAG                         CTCATAGGCTCTCCAGATGATGCAAGCCTGGGATTTCTTCGAAGTGATAAT
genomic: CCCTGTTTCCTGGACGGGATTACATCCAGCAATTAAAATTGATCACTGAGgtaaatttat ... cttccaaaagCTCATAGGCTCTCCAGATGATGCAAGCCTGGGATTTCTTCGAAGTGATAAT
EST: gi|149042023|gb|EE046997.2|EE046997
EST:     CCTGTTTCCT-GAGCGGGATTACATCCAGCAATTAAAATTGATCACTGAG                         CTCATAGGCTCTCCAGATGATGCAAGCCTGGGATTTCTTCGAAGTGATAAT
genomic: CCTGTTTCCTGGA-CGGGATTACATCCAGCAATTAAAATTGATCACTGAGgtaaatttat ... cttccaaaagCTCATAGGCTCTCCAGATGATGCAAGCCTGGGATTTCTTCGAAGTGATAAT
EST: gi|101388156|gb|EB816092.1|EB816092
EST:     CCCTGTTTCCTGGACGGGATTACATCCAGCAATTAAAATTGATCACTGAG                         CTCATAGGCTCTCCAGATGATG
genomic: CCCTGTTTCCTGGACGGGATTACATCCAGCAATTAAAATTGATCACTGAGgtaaatttat ... cttccaaaagCTCATAGGCTCTCCAGATGATG
EST: gi|60356919|gb|DN223892.1|DN223892
EST:     CCCTGTTTCCTGGACGGGATTACATCCAGCAATTAAAATTGATCACTGAG                         CTCATAGGCTCTCCAGATGATGCAAGCCTGGGATTTCTTCGAAGTGATAAT
genomic: CCCTGTTTCCTGGACGGGATTACATCCAGCAATTAAAATTGATCACTGAGgtaaatttat ... cttccaaaagCTCATAGGCTCTCCAGATGATGCAAGCCTGGGATTTCTTCGAAGTGATAAT
EST: gi|74241511|gb|DT649425.1|DT649425
EST:     CCCTGTTTCCTGGACGGGATTACATCCAGCAATTAAAATTGATCACTGAG                         CTCATAGGCTCTCCAGATGATGCAAGCCTGGGATTTCTTCGAAGTGATAAT
genomic: CCCTGTTTCCTGGACGGGATTACATCCAGCAATTAAAATTGATCACTGAGgtaaatttat ... cttccaaaagCTCATAGGCTCTCCAGATGATGCAAGCCTGGGATTTCTTCGAAGTGATAAT
EST: gi|60399358|gb|DN232172.1|DN232172
EST:     CCCTGTTTCCTGGACGGGATTACATCCAGCAATTAAAATTGATCACTGAG                         CTCATAGGCTCTCCAGATGATGCAAGCCTGGGATTTCTTCGAAGTGATAAT
genomic: CCCTGTTTCCTGGACGGGATTACATCCAGCAATTAAAATTGATCACTGAGgtaaatttat ... cttccaaaagCTCATAGGCTCTCCAGATGATGCAAGCCTGGGATTTCTTCGAAGTGATAAT
EST: gi|19351124|gb|BM895656.1|BM895656
EST:     CCCTGTTTCCTGGACGGGATTACATCCAGCAATTAAAATTGATCACTGAG                         CTCATAGGCTCTCCAGATGATGCAAGCCTGGGATTTCTTCGAAGTGATAAT
genomic: CCCTGTTTCCTGGACGGGATTACATCCAGCAATTAAAATTGATCACTGAGgtaaatttat ... cttccaaaagCTCATAGGCTCTCCAGATGATGCAAGCCTGGGATTTCTTCGAAGTGATAAT
EST: gi|71771177|gb|DR969114.1|DR969114
EST:     CTGGACGGGATTACATCCAGCAATTAAAATTGATCACTGAG                         CTCATAGGCTCTCCAGATGATGCAAGCCTGGGATTTCTTCGAAGTGATAAT
genomic: CTGGACGGGATTACATCCAGCAATTAAAATTGATCACTGAGgtaaatttat ... cttccaaaagCTCATAGGCTCTCCAGATGATGCAAGCCTGGGATTTCTTCGAAGTGATAAT
EST: gi|110223138|gb|EC905036.1|EC905036
EST:     CCCTGTTTCCTGGACGGGATTACATCCAGCAATTAAAATTGATCACTGAG                         CTCATAGGCTCTCCAGATGATGCAAGCCTGGGATTTCTTCGAAGTGATAAT
genomic: CCCTGTTTCCTGGACGGGATTACATCCAGCAATTAAAATTGATCACTGAGgtaaatttat ... cttccaaaagCTCATAGGCTCTCCAGATGATGCAAGCCTGGGATTTCTTCGAAGTGATAAT
EST: gi|76917704|gb|DV166966.1|DV166966
EST:     GGATTACATCCAGCAATTAAAATTGATCACTGAG                         CTCATAGGCTCTCCAGATGATGCAAGCCTGGGATTTCTTCGAAGTGATAAT
genomic: GGATTACATCCAGCAATTAAAATTGATCACTGAGgtaaatttat ... cttccaaaagCTCATAGGCTCTCCAGATGATGCAAGCCTGGGATTTCTTCGAAGTGATAAT
EST: gi|50338933|gb|CO534059.1|CO534059
EST:     CCCTGTTTCCTGGACGGGATTACATCCAGCAATTAAAATTGATCACTGAG                         CTCATAGGCTCTCCAGATGATGCAAGCCTGGGATTTCTTCGAAGTGATAAT
genomic: CCCTGTTTCCTGGACGGGATTACATCCAGCAATTAAAATTGATCACTGAGgtaaatttat ... cttccaaaagCTCATAGGCTCTCCAGATGATGCAAGCCTGGGATTTCTTCGAAGTGATAAT
EST: gi|60359685|gb|DN226658.1|DN226658
EST:     CCCTGTTTCCTGGACGGGATTACATCCAGCAATTAAAATTGATCACTGAG                         CTCATAGGCTCTCCAGATGATGCAAGCCTGGGATTTCTTCGAAGTGATAAT
genomic: CCCTGTTTCCTGGACGGGATTACATCCAGCAATTAAAATTGATCACTGAGgtaaatttat ... cttccaaaagCTCATAGGCTCTCCAGATGATGCAAGCCTGGGATTTCTTCGAAGTGATAAT
EST: gi|78091136|gb|DV519510.1|DV519510
EST:     CCCTGTTTCCTGGACGGGATTACATCCAGCAATTAAAATTGATCACTGAG                         CTCATAGGCTCTCCAGATGATGCAAGCCTGGGATTTCTTCGAAGTGATAAT
genomic: CCCTGTTTCCTGGACGGGATTACATCCAGCAATTAAAATTGATCACTGAGgtaaatttat ... cttccaaaagCTCATAGGCTCTCCAGATGATGCAAGCCTGGGATTTCTTCGAAGTGATAAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaaatgctactataatctgggcattaattttaatgagttttttctcttccaaaagCTCATAGGCTCTCCAGATGATGCAAGCCTGGGATTTCTTCGAAGTGATAATGCAAAAAGATACATGAAACAACTACCACAGTTTCCAAGACAGGACTTCC
                           ttttaat  putative branch site (score: 3)
                                     ttttttctcttcc  putative PPT
                      attaattttaatgagt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttaacttctattaatctgcaccattgagtacctttctcctttgttaaaatgctactataatctgggcattaattttaatgagttttttctcttccaaaagCTCATAGGCTCTCCAGATGATGCAAGCCTGGGATTTCTTCGAAGTGATAATGCAAAAAGATACATGAAACAACTACCACAGTTTCCAAGACAGGACTTCC

- - - - - - - -ctgcacc
- - - - - - - - - - - - - - - - - - - - - - - - -tgctact