Skip to another splice site:
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 5'  3'   		2  
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 5'  3'   		5  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatatcactgcagaaatgttactatgactctctgtttcaatacagaaaatcagaaatccaataatatatgcctgagcatccggcctcatctcttgcagGAACAAATGCTGCAAGATGCAAACAGGGTTCTGAAAAGGAAG

Basic information

species Zea mays
transcript GRMZM2G087095_T02
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G087095_T02 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os03g54170.1 (Oryza sativa), 3'ss of exon 5
---------------------------------gtaatatcactgcagaaatgttactatgactctctgtttcaatacagaaaatcagaaatccaataatata--tgcctgagcatccggcctcatctcttgcagGAACAAATGCTGCAAGATGCAAACAGGGTTCTGAAAAGGAAG
                                  | |||| ||| ||  |  || | ||    |  || ||||| |   | ||||  |   |    | || ||  |||   |  ||    | |    |  | |||||||||||||| ||||||||||||||||| ||||||||||||
gtaacactgaaatatcttcttcaatgccgccaaatgatat-actacactacagtgaatacttgtacctctttcagtg--gcaaattcggtttgtttttatctaattgctccaatattgaactt----ttcttcagGAACAAATGCTACAAGATGCAAACAGGGTCCTGAAAAGGAAG
















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|211463197|gb|FL126646.1|FL126646
EST:     ACTCAAGTGTTACTTGATGAACTTTGTGACTTAAAGAGAAAG                         GAACAAATGCTGCAAGATGCAAACAGGGTTCTGAAAAGGAAG
genomic: ACTCAAGTGTTACTTGATGAACTTTGTGACTTAAAGAGAAAGgtaatatcac ... tctcttgcagGAACAAATGCTGCAAGATGCAAACAGGGTTCTGAAAAGGAAG
EST: gi|32808460|gb|CD960694.1|CD960694
EST:     TAAAGAGAAAG                         GAACAAATGCTGCAAGATGCAAACAGGGTTCTGAAAAGGAAG
genomic: TAAAGAGAAAGgtaatatcac ... tctcttgcagGAACAAATGCTGCAAGATGCAAACAGGGTTCTGAAAAGGAAG
EST: gi|76285511|gb|DV025079.1|DV025079
EST:     ACTCAAGTGTTACTTGATGAACTTTGTGACTTAAAGAGAAAG                         GAACAAATGCTGCAAGATGCAAACAGGGTTCTGAAAAGGAAG
genomic: ACTCAAGTGTTACTTGATGAACTTTGTGACTTAAAGAGAAAGgtaatatcac ... tctcttgcagGAACAAATGCTGCAAGATGCAAACAGGGTTCTGAAAAGGAAG
EST: gi|71421466|gb|DR805441.1|DR805441
EST:     ACTCAAGTGTTACTTGATGAACTTTGTGACTTAAAGAGAAAG                         GAACAAATGCTGCAAGATGCAAACAGGGTTCTGAAAAGGAAG
genomic: ACTCAAGTGTTACTTGATGAACTTTGTGACTTAAAGAGAAAGgtaatatcac ... tctcttgcagGAACAAATGCTGCAAGATGCAAACAGGGTTCTGAAAAGGAAG
EST: gi|32847296|gb|CD986977.1|CD986977
EST:     ACTCAAGTGTTACTTGATGAACTTTGTGACTTAAAGAGAAAG                         GAACAAATGCTGCAAGATGCAAACAGGGTTCTGAAAAGGAAG
genomic: ACTCAAGTGTTACTTGATGAACTTTGTGACTTAAAGAGAAAGgtaatatcac ... tctcttgcagGAACAAATGCTGCAAGATGCAAACAGGGTTCTGAAAAGGAAG
EST: gi|50331175|gb|CO526301.1|CO526301
EST:     ACTCAAGTGTTACTTGATGAACTTTGTGACTTAAAGAGAAAG                         GAACAAATGCTGCAAGATGCAAACAGGGTTCTGAAAAGGAAG
genomic: ACTCAAGTGTTACTTGATGAACTTTGTGACTTAAAGAGAAAGgtaatatcac ... tctcttgcagGAACAAATGCTGCAAGATGCAAACAGGGTTCTGAAAAGGAAG
EST: gi|18383542|gb|BM416742.1|BM416742
EST:     TTAAAGAGAAAG                         GACCAAATGCTGCAAGATGCAAACAGGGTTCTGAAAAGGAAG
genomic: TTAAAGAGAAAGgtaatatcac ... tctcttgcagGAACAAATGCTGCAAGATGCAAACAGGGTTCTGAAAAGGAAG
EST: gi|78112770|gb|DV531164.1|DV531164
EST:     ACTCAAGTGTTACTTGATGAACTTTGTGACTTAAAGAGAAAG                         GAACAAATGCTGCAAGATGCAAACAGGGTTCTGAAAAGGAAG
genomic: ACTCAAGTGTTACTTGATGAACTTTGTGACTTAAAGAGAAAGgtaatatcac ... tctcttgcagGAACAAATGCTGCAAGATGCAAACAGGGTTCTGAAAAGGAAG
EST: gi|32832220|gb|CD971898.1|CD971898
EST:     ACTCAAGTGTTACCTGATGAACTTTGTGACTTAAAGAGAAAG                         GAACGAATGCTGCAAGATGCAAACAGGGTTCTGAAAAGGAAG
genomic: ACTCAAGTGTTACTTGATGAACTTTGTGACTTAAAGAGAAAGgtaatatcac ... tctcttgcagGAACAAATGCTGCAAGATGCAAACAGGGTTCTGAAAAGGAAG
EST: gi|71425163|gb|DR806564.1|DR806564
EST:     ACTCAAGTGTTACTTGATGAACTTTGTGACTTAAAGAGAAAG                         GAACAAATGCTGCAAGATGCAAACAGGGTTCTGAAAAGGAAG
genomic: ACTCAAGTGTTACTTGATGAACTTTGTGACTTAAAGAGAAAGgtaatatcac ... tctcttgcagGAACAAATGCTGCAAGATGCAAACAGGGTTCTGAAAAGGAAG
EST: gi|148951816|gb|EC897579.2|EC897579
EST:     AAGAAAGACTCAAAGTGTTACTTGATGAACTTTGTGACTTAAAGAGAAAG                         GAACAAATGCTGCAAGATGCAAACAGGGTTCTGAAAAGGAAG
genomic: AAGAAAGACTC-AAGTGTTACTTGATGAACTTTGTGACTTAAAGAGAAAGgtaatatcac ... tctcttgcagGAACAAATGCTGCAAGATGCAAACAGGGTTCTGAAAAGGAAG
EST: gi|26557907|gb|CA830142.1|CA830142
EST:     CTTTGTGACTTAAAGAGAAAG                         GAACAAATGCTGCAAGATGCAAACAGGGTTCTGAAAAGGAAG
genomic: CTTTGTGACTTAAAGAGAAAGgtaatatcac ... tctcttgcagGAACAAATGCTGCAAGATGCAAACAGGGTTCTGAAAAGGAAG
EST: gi|5055580|gb|AI734467.1|AI734467
EST:     ACTCAAGTGTTACTTGATGAACTTTGTGACTTAAAGAGAAAG                         GAACAAATGCTGCAAGATGCAAACAGGGTTCTGAAAAGGAAG
genomic: ACTCAAGTGTTACTTGATGAACTTTGTGACTTAAAGAGAAAGgtaatatcac ... tctcttgcagGAACAAATGCTGCAAGATGCAAACAGGGTTCTGAAAAGGAAG
EST: gi|32832432|gb|CD972110.1|CD972110
EST:     ACTCAAGTGTTACTTGATGAACTTTGTGACTTAAAGAGAAAG                         GAACAAATGCTGCAAGATGCAAACAGGGTTCTGAAAAGGAAG
genomic: ACTCAAGTGTTACTTGATGAACTTTGTGACTTAAAGAGAAAGgtaatatcac ... tctcttgcagGAACAAATGCTGCAAGATGCAAACAGGGTTCTGAAAAGGAAG
EST: gi|5030602|gb|AI714796.1|AI714796
EST:     GAACTTTGTGACTTAAAGAGAAAG                         GAACAAATGCTGCAAGATGCAAACAGGGTTCTGAAAAGGAAG
genomic: GAACTTTGTGACTTAAAGAGAAAGgtaatatcac ... tctcttgcagGAACAAATGCTGCAAGATGCAAACAGGGTTCTGAAAAGGAAG
EST: gi|21809509|gb|BQ667827.1|BQ667827
EST:     AGACTCAAGTGTTACTTGATGAACTTTGTGACTTAAAGAGAAAG                         GAACAAATGCTGCAAGATGCAAGCAGGGTTCTGAAAAGGAAG
genomic: AGACTCAAGTGTTACTTGATGAACTTTGTGACTTAAAGAGAAAGgtaatatcac ... tctcttgcagGAACAAATGCTGCAAGATGCAAACAGGGTTCTGAAAAGGAAG
EST: gi|78122333|gb|DV540717.1|DV540717
EST:     ACTCAAGTGTTACTTGATGAACTTTGTGACTTAAAGAGAAAG                         GAACAAATGCTGCAAGATGCAAACAGGGTTCTGAAAAGGAAG
genomic: ACTCAAGTGTTACTTGATGAACTTTGTGACTTAAAGAGAAAGgtaatatcac ... tctcttgcagGAACAAATGCTGCAAGATGCAAACAGGGTTCTGAAAAGGAAG
EST: gi|32835484|gb|CD975162.1|CD975162
EST:     ACTCAAGTGTTACTTGATGAACTTTGTGACTTAAAGAGAAAG                         GAACAAATGCTGCAAGATGCAAACAGGGTTCTGAAAAGGAAG
genomic: ACTCAAGTGTTACTTGATGAACTTTGTGACTTAAAGAGAAAGgtaatatcac ... tctcttgcagGAACAAATGCTGCAAGATGCAAACAGGGTTCTGAAAAGGAAG
EST: gi|71330054|gb|DR801766.1|DR801766
EST:     ACTCAAGTGTTACTTGATGAACTTTGTGACTTAAAGAGAAAG                         GAACAAATGCTGCAAGATGCAAACAGGGTTCTGAAAAGGAAG
genomic: ACTCAAGTGTTACTTGATGAACTTTGTGACTTAAAGAGAAAGgtaatatcac ... tctcttgcagGAACAAATGCTGCAAGATGCAAACAGGGTTCTGAAAAGGAAG
EST: gi|87157198|gb|DY401987.1|DY401987
EST:     AGACTCAAGTGTTACTTGATGAACTTTGTGACTTAAAGAGAAAG                         GAACAAATGCTGCAAGATGCAAACAGGGTTCTGAAAAGGAAG
genomic: AGACTCAAGTGTTACTTGATGAACTTTGTGACTTAAAGAGAAAGgtaatatcac ... tctcttgcagGAACAAATGCTGCAAGATGCAAACAGGGTTCTGAAAAGGAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agaaaatcagaaatccaataatatatgcctgagcatccggcctcatctcttgcagGAACAAATGCTGCAAGATGCAAACAGGGTTCTGAAAAGGAAG
                                        cctcatctctt  CT-rich tract
          aaatccaataatatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaatatcactgcagaaatgttactatgactctctgtttcaatacagaaaatcagaaatccaataatatatgcctgagcatccggcctcatctcttgcagGAACAAATGCTGCAAGATGCAAACAGGGTTCTGAAAAGGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA