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

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagctctttcctcttggtgatgatgctgggttgctgccgcggattatattggtggaatagcttgcgcatgattttgatttcagatttctccctgtgctgccggtggcggttgtttctgaatggctgtactgaccgaaccgttggtgttgcatgctctgcagctcAAGAACGGGGCCGACAAGTCGGAGGACAAGAAGAGGAAGAAGAGGTCGTGAGCGCGTCGAGAAGGGAAGCTCTTCCACTTCCACATATGCATAGGAGTAA

Basic information

species Zea mays
transcript GRMZM2G029087_T04
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G029087_T04 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os02g03280.3 (Oryza sativa), 3'ss of exon 5
gtgagctctttcctcttggtgatgatgctgggttgctgccgcggattatattggtggaatagcttgcgcatgattttgatttcagatttctccctgtgctgccggtggcggttgtttctgaatggctgtactgaccg-aaccgttggtgttgcatgctctgcagctcAAGAACGGGGCCGACAAGTCGGAGGACAAGAAGAGGAAGAAGAGGTCGTGAGCGCGTCGAGAAGGGAAGCTCTTCCACTTCCACATATGCATAGGAGTAA---------
                            || ||   || | | | |||   || |     |  |||| ||| ||  |     |  ||   |  | | | | | | | |     | || ||||  ||||  |||||    | |        ||  | |  ||||||||||||||| | | |||||||||||||| |||||||||||||||||||| |||| || ||            ||||||   |   || ||    |  |   |         
---------------------------gtgagtacatgactcagcttac--tgct----caatttgctcatcatcct----ccgtatgcattgccgcgattcggtttgattcggcttttgaaatgctgacctgacgatgaacacccacaatgtctccgttgcagCTCAAGAACGCGTCTGACAAGTCGGAGGAGAAGAAGAGGAAGAAGAGGTCTTGAGAGCTTC------------TCTTCCCGCTTTGCACATAAGAAAAAACCACCGCGGCTA
















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|71432249|gb|DR813299.1|DR813299
EST:     CTTCACAGACTTCGTGGCCGTCCTCGTCCGCGTCCTCGTCATCATGCTCA                         A-GAACGGGGCCGACAAGTCGGAGGACAAGAAGAGAAAGA-GAAGTCGTGA
genomic: CTTCACAGACTTCGTGGCCGTCCTCGTCCGCGTCCTCGTCATCATGGTGAgtgagctctt ... tctgcagctcAAGAACGGGGCCGACAAGTCGGAGGACAAGAAGAGGAAGAAGAGGTCGTGA
EST: gi|149046683|gb|EE048073.2|EE048073
EST:     CTTCACAGACTTCGTGGGCGTCCTCGTCCGCGTCCTCGTCATCATGCTCA                         A-GAACGGGGCCG
genomic: CTTCACAGACTTCGTGGCCGTCCTCGTCCGCGTCCTCGTCATCATGGTGAgtgagctctt ... tctgcagctcAAGAACGGGGCCG
EST: gi|74244275|gb|DT652189.1|DT652189
EST:     CTTCACAGACTTCGTGGCCGTCCTCGTCCGCGTCCTCGTCATCATGCTNC                         A-GAACGGGGCCGACAAGTCGG
genomic: CTTCACAGACTTCGTGGCCGTCCTCGTCCGCGTCCTCGTCATCATGGTGAgtgagctctt ... tctgcagctcAAGAACGGGGCCGACAAGTCGG
EST: gi|76288415|gb|DV027983.1|DV027983
EST:     CTTCACAGACTTCGTGGCCGTCCTCGTCCGCGTCCTCGTCATCATGCTCA                         A-GAACGGGGCCGACAAGTCGGAGGACAAGAAGAGGAAGAAGAGGTCGTGA
genomic: CTTCACAGACTTCGTGGCCGTCCTCGTCCGCGTCCTCGTCATCATGGTGAgtgagctctt ... tctgcagctcAAGAACGGGGCCGACAAGTCGGAGGACAAGAAGAGGAAGAAGAGGTCGTGA
EST: gi|67014096|gb|CO442845.1|CO442845
EST:     CTTCACAGACTTCGTGGCCGTCCTCGTCCGCGTCCTCGTCATCATGCT-C                         AAGAACGGGGCCGACAAGTCGGAGGACAAGAAGAGGAAGAAGAGGTCGTGA
genomic: CTTCACAGACTTCGTGGCCGTCCTCGTCCGCGTCCTCGTCATCATGGTGAgtgagctctt ... tctgcagctcAAGAACGGGGCCGACAAGTCGGAGGACAAGAAGAGGAAGAAGAGGTCGTGA
EST: gi|76011040|gb|DT938210.1|DT938210
EST:     CTTCACAGACTTCGTGGCCGTCCTCGTCCGCGTCCTCGTCATCATGCTCA                         A-GAACGGGGCCGACAAGTCGGAGGACAAGAAGAGGAAGAAGAGGTCGTGA
genomic: CTTCACAGACTTCGTGGCCGTCCTCGTCCGCGTCCTCGTCATCATGGTGAgtgagctctt ... tctgcagctcAAGAACGGGGCCGACAAGTCGGAGGACAAGAAGAGGAAGAAGAGGTCGTGA
EST: gi|78105316|gb|DV523734.1|DV523734
EST:     CTTCACAGACTTCGTGGCCGTCCTCGTCCGCGTCCTCGTCATCATGCTCA                         A-GAACGGGGCCGACAAGTCGGAGGACAAGAAGAGGAAGAAGAGGTCGTGA
genomic: CTTCACAGACTTCGTGGCCGTCCTCGTCCGCGTCCTCGTCATCATGGTGAgtgagctctt ... tctgcagctcAAGAACGGGGCCGACAAGTCGGAGGACAAGAAGAGGAAGAAGAGGTCGTGA
EST: gi|149048849|gb|EE048352.2|EE048352
EST:     CTTCACAGACTTCGTGGCCGTCCTCGTCCGCGTCCTCGTCATCATGCTCA                         A-GAACGGGGCCGACCAGTCGGAGGACAAGAAGAGGAAGAAGAGGTCGTGA
genomic: CTTCACAGACTTCGTGGCCGTCCTCGTCCGCGTCCTCGTCATCATGGTGAgtgagctctt ... tctgcagctcAAGAACGGGGCCGACAAGTCGGAGGACAAGAAGAGGAAGAAGAGGTCGTGA
EST: gi|149008168|gb|EE040356.2|EE040356
EST:     CTTCACAGACTTCGTGGCCGTCCTCGTCCGCGTCCTCGTCATCATGCTCA                         A-GAACGGGGCCGCCAAGTCGGAGGACAAGAAGAGGAAGAAGAGGTCGTGA
genomic: CTTCACAGACTTCGTGGCCGTCCTCGTCCGCGTCCTCGTCATCATGGTGAgtgagctctt ... tctgcagctcAAGAACGGGGCCGACAAGTCGGAGGACAAGAAGAGGAAGAAGAGGTCGTGA
EST: gi|149008169|gb|EE040357.2|EE040357
EST:     CTTCACAGACTTCGTGGCCGTCCTCGTCCGCGTCCTCGTCATCATGCTCA                         A-GAACGGGGGCGACAAGTC
genomic: CTTCACAGACTTCGTGGCCGTCCTCGTCCGCGTCCTCGTCATCATGGTGAgtgagctctt ... tctgcagctcAAGAACGGGGCCGACAAGTC
EST: gi|149103195|gb|EE288568.2|EE288568
EST:     CTTCACAGACTTCGTGGCCGTCCTCGTCCGCGTCCTCGTCATCATGCTCA                         A-GAACGGGGCCGACAAGTC
genomic: CTTCACAGACTTCGTGGCCGTCCTCGTCCGCGTCCTCGTCATCATGGTGAgtgagctctt ... tctgcagctcAAGAACGGGGCCGACAAGTC
EST: gi|111190431|gb|EE288567.1|EE288567
EST:     CTTCACAGACTTCGTGGCCGTCCTCGTCCGCGTCCTCGTCATCATGCTCA                         A-GAACGGGGCCGCCAAGTCGGAGGACAAGAAGAGGAAGAAGAGGTCGTGA
genomic: CTTCACAGACTTCGTGGCCGTCCTCGTCCGCGTCCTCGTCATCATGGTGAgtgagctctt ... tctgcagctcAAGAACGGGGCCGACAAGTCGGAGGACAAGAAGAGGAAGAAGAGGTCGTGA
EST: gi|76013720|gb|DT940890.1|DT940890
EST:     CTTCACAGACTTCGTGGCCGTCCTCGTCCGCGTCCTCGTCATCATGCTCA                         A-GAACGGGGCCGACAAGTCGGAGGACAAGAAAAGGAAGAAGAGGTCGTGA
genomic: CTTCACAGACTTCGTGGCCGTCCTCGTCCGCGTCCTCGTCATCATGGTGAgtgagctctt ... tctgcagctcAAGAACGGGGCCGACAAGTCGGAGGACAAGAAGAGGAAGAAGAGGTCGTGA
EST: gi|149110917|gb|EE294415.2|EE294415
EST:     CTTCACAGACTTCGTGGCCGTCTTCGTCCGCGTCCTGGTCATCATGCTCA                         A-GAACGGGGCCGACAAGTCGGAGGACAAGAAGAGGAAGAAGAGGTCGTGA
genomic: CTTCACAGACTTCGTGGCCGTCCTCGTCCGCGTCCTCGTCATCATGGTGAgtgagctctt ... tctgcagctcAAGAACGGGGCCGACAAGTCGGAGGACAAGAAGAGGAAGAAGAGGTCGTGA
EST: gi|109637514|gb|EC591059.1|EC591059
EST:     CTTCACAGACTTCGTGGCCGTCCTCGTCCGCGTCCTCGTCATCATGCT-C                         AAGAACGGGGCCGACAAGTCGGAGGACAAGAAGAGGAAGAAGAGGTCGTGA
genomic: CTTCACAGACTTCGTGGCCGTCCTCGTCCGCGTCCTCGTCATCATGGTGAgtgagctctt ... tctgcagctcAAGAACGGGGCCGACAAGTCGGAGGACAAGAAGAGGAAGAAGAGGTCGTGA
EST: gi|148954442|gb|EC899865.2|EC899865
EST:     CTTCACAGACTTCGTGGCCGTCCTCGTCCGCGTCCTCGTCATCATGCTCA                         A-GAACGGGGCCGACAAGTCGGAGGACAAGAAGAGGAAGAAGAGGTCGTGA
genomic: CTTCACAGACTTCGTGGCCGTCCTCGTCCGCGTCCTCGTCATCATGGTGAgtgagctctt ... tctgcagctcAAGAACGGGGCCGACAAGTCGGAGGACAAGAAGAGGAAGAAGAGGTCGTGA
EST: gi|50328016|gb|CO523142.1|CO523142
EST:     TTTCACAGACTTGGTGGCCGTCCTCGTCCGCGTCCTGGTCATCATGCT-C                         AAGAACGGGGCCGACAAGTCGGAGGACAAGAAGAGGAAGAAGAGGTCGTGA
genomic: CTTCACAGACTTCGTGGCCGTCCTCGTCCGCGTCCTCGTCATCATGGTGAgtgagctctt ... tctgcagctcAAGAACGGGGCCGACAAGTCGGAGGACAAGAAGAGGAAGAAGAGGTCGTGA
EST: gi|18178570|gb|BM379780.1|BM379780
EST:     CTTCACAGACTTCGTGGCCGTCCTCGTCCGCGTCCTCGTCATCATGCT-C                         AAGAACGGGGCCGACAAGTCGGAGGACAAGAAGAGGAAGAAGAGGTCGTGA
genomic: CTTCACAGACTTCGTGGCCGTCCTCGTCCGCGTCCTCGTCATCATGGTGAgtgagctctt ... tctgcagctcAAGAACGGGGCCGACAAGTCGGAGGACAAGAAGAGGAAGAAGAGGTCGTGA
EST: gi|71432248|gb|DR813298.1|DR813298
EST:     CTTCACAGACTTCGTGGCCGTCCTCGTCCGCGTCCTCGTCATCATGCTCA                         A-GAACGGGGCCGACAAGTCGGAGGACAAGAAGAGGAAGAAGAGGTCGTGA
genomic: CTTCACAGACTTCGTGGCCGTCCTCGTCCGCGTCCTCGTCATCATGGTGAgtgagctctt ... tctgcagctcAAGAACGGGGCCGACAAGTCGGAGGACAAGAAGAGGAAGAAGAGGTCGTGA
EST: gi|76288416|gb|DV027984.1|DV027984
EST:     CTTCACAGACTTCGTGGCCGTCCTCGTCCGCGTCTTCGTCATCATGCTCA                         A-GAACGGGGCCGACAAGTC
genomic: CTTCACAGACTTCGTGGCCGTCCTCGTCCGCGTCCTCGTCATCATGGTGAgtgagctctt ... tctgcagctcAAGAACGGGGCCGACAAGTC
EST: gi|51592969|gb|CV072115.1|CV072115
EST:     CTTCACAGACTTCGTGGCCGTCCTCGTCCGCGTCCTCGTCATCATGCTCA                         A-GAACGGGGCCGACAAGTCGGAGGACAAGAAGAGGAAGAAGAGGTCGTGA
genomic: CTTCACAGACTTCGTGGCCGTCCTCGTCCGCGTCCTCGTCATCATGGTGAgtgagctctt ... tctgcagctcAAGAACGGGGCCGACAAGTCGGAGGACAAGAAGAGGAAGAAGAGGTCGTGA
EST: gi|47961573|gb|CN844282.1|CN844282
EST:     CTTCACAGACTTCGTGGCCGTCCTCGTCCGCGTCCTCGTCATCATGCT-C                         AAGAACGGGGCCGACAAGTCGGAGGACAAGAAGAGGAAGAAGAGGTCGTGA
genomic: CTTCACAGACTTCGTGGCCGTCCTCGTCCGCGTCCTCGTCATCATGGTGAgtgagctctt ... tctgcagctcAAGAACGGGGCCGACAAGTCGGAGGACAAGAAGAGGAAGAAGAGGTCGTGA
EST: gi|149086320|gb|EE175861.2|EE175861
EST:     CTTCACAGACTTGGTGGCCGTCCTCGTCCGCGTCCTCGTCATCATGCT-C                         AAGAACGGGGCCGACAAGTCGGAGGACAAGAAGAGGAAGAAGAGGTCGTGA
genomic: CTTCACAGACTTCGTGGCCGTCCTCGTCCGCGTCCTCGTCATCATGGTGAgtgagctctt ... tctgcagctcAAGAACGGGGCCGACAAGTCGGAGGACAAGAAGAGGAAGAAGAGGTCGTGA
EST: gi|148964263|gb|EE015455.2|EE015455
EST:     CTTCACAGACTTCGTGGCCGTCCTCGTCCGCGTCCTCGTCATCATGCTCA                         A-GAACGGGGCCGAACA-GTCGGAGG
genomic: CTTCACAGACTTCGTGGCCGTCCTCGTCCGCGTCCTCGTCATCATGGTGAgtgagctctt ... tctgcagctcAAGAACGGGGCCGA-CAAGTCGGAGG
EST: gi|78110664|gb|DV529067.1|DV529067
EST:     CTTCACAGACTTCGTGGCCGTCCTCGTCCGCGTCCTCGTCATCATGCTCA                         A-GAACGGGGCCGACAAGTCGGAGGACAAGAAGAGGAAGAAGAGGTCGTGA
genomic: CTTCACAGACTTCGTGGCCGTCCTCGTCCGCGTCCTCGTCATCATGGTGAgtgagctctt ... tctgcagctcAAGAACGGGGCCGACAAGTCGGAGGACAAGAAGAGGAAGAAGAGGTCGTGA
EST: gi|51593042|gb|CV072188.1|CV072188
EST:     CTTCACAGACTTCGTGGCCGTCCTCGTCCGCGTCCTCGTCATCATGCTCA                         A-GAACGGGGCCGACAAGTCGGAGGACAAGAAGAGGAAGAAGAGGTCGTGA
genomic: CTTCACAGACTTCGTGGCCGTCCTCGTCCGCGTCCTCGTCATCATGGTGAgtgagctctt ... tctgcagctcAAGAACGGGGCCGACAAGTCGGAGGACAAGAAGAGGAAGAAGAGGTCGTGA
EST: gi|32863120|gb|CF002802.1|CF002802
EST:     CTTCACAGACTTCGTGGCCGTCCTCGTCCGCGTCCTCGTCATCATGCT-C                         AAGAACGGGGCCGACAAGTCGGAGGACAAGAAGAGGAAGAAGAGGTCGTGA
genomic: CTTCACAGACTTCGTGGCCGTCCTCGTCCGCGTCCTCGTCATCATGGTGAgtgagctctt ... tctgcagctcAAGAACGGGGCCGACAAGTCGGAGGACAAGAAGAGGAAGAAGAGGTCGTGA
EST: gi|74232622|gb|DT640536.1|DT640536
EST:     CTTCACAGACTTCGTGGCCGTCCTCGTCCGCGTCCTCGTCATCATGCTCA                         A-GAACGGGGCCGACAAGTCGGAGGACAAGAAGAGGAAGAAGAGGTCGTGA
genomic: CTTCACAGACTTCGTGGCCGTCCTCGTCCGCGTCCTCGTCATCATGGTGAgtgagctctt ... tctgcagctcAAGAACGGGGCCGACAAGTCGGAGGACAAGAAGAGGAAGAAGAGGTCGTGA
EST: gi|67041238|gb|CO467493.1|CO467493
EST:     CTTCACAGACTTCGTGGCCGTCCTCGTCCGCGTCCTCGTCATCATGCTCA                         A-GAACGGGGCCCGACA-GTCGGAGGACAAGA
genomic: CTTCACAGACTTCGTGGCCGTCCTCGTCCGCGTCCTCGTCATCATGGTGAgtgagctctt ... tctgcagctcAAGAACGGGGCC-GACAAGTCGGAGGACAAGA
EST: gi|76013719|gb|DT940889.1|DT940889
EST:     CTTCACAGACTTCGTGGCCGTCCTCGTCCGCGTCCTCGTCATCATGCTCA                         A-GAACGGGGCCGACAAGTCGGAGGACAAGAAGAGGAAGAAGAGGTCGTGA
genomic: CTTCACAGACTTCGTGGCCGTCCTCGTCCGCGTCCTCGTCATCATGGTGAgtgagctctt ... tctgcagctcAAGAACGGGGCCGACAAGTCGGAGGACAAGAAGAGGAAGAAGAGGTCGTGA
EST: gi|149108187|gb|EE292532.2|EE292532
EST:     CTTCACAGACTTCGTGGCCGTCCTCGTCCGCGTCCTCGTCATCATGCTCA                         A-GAACGGGGCCGACAAGTCGGAGGACAAGAAGAGGAAGAAGAGGTCGTGA
genomic: CTTCACAGACTTCGTGGCCGTCCTCGTCCGCGTCCTCGTCATCATGGTGAgtgagctctt ... tctgcagctcAAGAACGGGGCCGACAAGTCGGAGGACAAGAAGAGGAAGAAGAGGTCGTGA
EST: gi|148997294|gb|EE035788.2|EE035788
EST:     CTTCACAGACTTCGTGGCCGTCCTCGTCCGCGTCCTCGTCATCATGCTCA                         A-GAACGGGGCCGACAAGTCGGAGGACAAGAAGAGGAAGAAGAGGTCGTGA
genomic: CTTCACAGACTTCGTGGCCGTCCTCGTCCGCGTCCTCGTCATCATGGTGAgtgagctctt ... tctgcagctcAAGAACGGGGCCGACAAGTCGGAGGACAAGAAGAGGAAGAAGAGGTCGTGA
EST: gi|50323899|gb|CO519025.1|CO519025
EST:     CTTCACAGACTTGGTGGCCGTCCTCGTCCGCGTCCTCGTCATCATGCT-C                         AAGAACGGGGCCGACAAGTCGGAGGACAAGAAGAGGAAGAAGAGGTCGTGA
genomic: CTTCACAGACTTCGTGGCCGTCCTCGTCCGCGTCCTCGTCATCATGGTGAgtgagctctt ... tctgcagctcAAGAACGGGGCCGACAAGTCGGAGGACAAGAAGAGGAAGAAGAGGTCGTGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgtttctgaatggctgtactgaccgaaccgttggtgttgcatgctctgcagctcAAGAACGGGGCCGACAAGTCGGAGGACAAGAAGAGGAAGAAGAGGTCGTGAGCGCGTCGAGAAGGGAAGCTCTTCCACTTCCACATATGCATAGGAGTAA
                 tactgac  putative branch site (score: 1)
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagctctttcctcttggtgatgatgctgggttgctgccgcggattatattggtggaatagcttgcgcatgattttgatttcagatttctccctgtgctgccggtggcggttgtttctgaatggctgtactgaccgaaccgttggtgttgcatgctctgcagctcAAGAACGGGGCCGACAAGTCGGAGGACAAGAAGAGGAAGAAGAGGTCGTGAGCGCGTCGAGAAGGGAAGCTCTTCCACTTCCACATATGCATAGGAGTAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -CGGGGCCG