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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttcaaagggactgccagttccctattgctttactttgtaatattattataataccacaaagctgttccttgaagaaattgtaatacataatgttttgtagGATGCAAAATCTAAAGACATTGAAGATGTGCTGATTCTTTCTGGTGACCATCTCTACCGTATGGACTACATGGACTTTGTTCAG

Basic information

species Zea mays
transcript GRMZM2G391936_T02
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G391936_T02 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os03g52460.1 (Oryza sativa), 3'ss of exon 4
ttcaaagggactgccagttccctattgctttactttgtaatattattataataccacaaagctgttccttgaagaaattgtaatacataatg------ttttgtagGATGCAAAATCTAAAGACATTGAAGATGTGCTGATTCTTTCTGGTGACCATCTCTACCGTATGGACTACATGGACTTTGTTCAG
    ||           | || | ||  || |   |   ||  || |  || ||| ||    || |||||  | || || |||| |||  ||      ||||||||||||| ||| |||||||||| || ||||||||||||||||||||||| ||||||||||| ||||||||||||||||||||||||
----aacttttcaattatcccttgttatttgatcgtactattctactgaaaaacctcatca-tgctccttacataattt-taatgcatcgtgctatcgttttgtagGATGCCAAAGCTAAAGACATCGATGATGTGCTGATTCTTTCTGGTGATCATCTCTACCGCATGGACTACATGGACTTTGTTCAG

upper sequence: GRMZM2G391936_T02 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA07G38820.1 (Glycine max), 3'ss of exon 4
ttcaaagggactgccagttccctattgctttactttgtaatattattataa-taccacaaagctgttccttgaagaaat-tgtaataca-taatgttttgtagGATGCAAAATCTAAAGACATTGAAGATGTGCTGATTCTTTCTGGTGACCATCTCTACCGTATGGACTACATGGACTTTGTTCAG
      |  | | |   ||||  ||      |      || |  | | ||| | | |    | ||||   ||    ||| |  ||||   |  | | ||||||||| ||| |  ||| || ||||| |||||  |||||||||| || || || |||||||| |||||||| |||||||||||||| 
-cttttgctatttct--ttcctcatcataaaaaaggccaagaagaatctaaatgctagttgggtgttaaatgcgataatgtagaatatgcttctatgttgtagGATCCAAGAAGTAAGGATATTGAGGATGTCTTGATTCTTTCCGGGGATCACCTCTACCGAATGGACTATATGGACTTTGTTCAA

upper sequence: GRMZM2G391936_T02 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA17G01900.1 (Glycine max), 3'ss of exon 4
ttcaaagggactgccagttccctattgctttactttgtaatattattataa-taccacaaagctgttccttgaagaaat-tgtaataca-taatgttttgtagGATGCAAAATCTAAAGACATTGAAGATGTGCTGATTCTTTCTGGTGACCATCTCTACCGTATGGACTACATGGACTTTGTTCAG
      |  | | |   ||||  ||      |      || |  | | ||| | | |    | ||||   ||  | ||| |  ||||   |  | | ||||||||| ||| |  ||| || ||||| |||||  ||||||||||||| || || |||||||| |||||||| |||||||||||||| 
-cttttgttatttct--ttcctcatcatagcaaaggccaagaagaatctaaatgctagttggatgttaaatgtggtaatgtagaatatgcttctatgttgtagGATCCAAGAAGTAAGGATATTGAGGATGTCTTGATTCTTTCTGGAGATCACCTCTACCGAATGGACTATATGGACTTTGTTCAA

upper sequence: GRMZM2G391936_T02 (Zea mays), 3'ss of exon 4
lower sequence: Vv05s0020g02880.t01 (Vitis vinifera), 3'ss of exon 4
ttcaaagggactgccagttccctattgctttactttgtaatattattataataccacaaagctgttccttgaagaaattgtaatacataatgttttgtagGATGCAAAATCTAAAGACATTGAAGATGTGCTGATTCTTTCTGGTGACCATCTCTACCGTATGGACTACATGGACTTTGTTCAG
       | ||    | ||| ||  |  ||    || |    | |  |  | ||   |        ||  ||||   |  |||  | |    |  | ||||||  || |  ||| || ||||| |||||||||||||| ||||| || ||| | ||||| |||||||| |||||||||||||||
-------gtacccatatttcacttctagttaggattctggggtaaccaatagacggta---tcaaaccaagaaggg-tgttaaagcttttcatcctatagGATCAAAGAAGTAAGGAAATTGAGGATGTGCTGATTCTGTCTGGAGATCATTTATACCGAATGGACTATATGGACTTTGTTCAG

upper sequence: GRMZM2G391936_T02 (Zea mays), 3'ss of exon 4
lower sequence: PP1S389_5V6.1 (Physcomitrella patens), 3'ss of exon 3
--------------ttcaaagggactgccagttccctattgctttactttgtaatattattataataccacaaagctgttccttgaagaaattgta-------atacataatgttttgtagGATGCAAAATCTAAAGACATTGAAGATGTGCTGATTCTTTCTGGTGACCATCTCTACCGTATGGACTACATGGACTTTGTTCAG
              || ||    | | | |||| |  |  | || ||||  |      | |   | | |   ||  | |  |||| |   ||  ||        |   |    | ||  ||||||| ||   ||| |   | ||||| ||  | ||| | || || |||||| | ||||||||||||||||||||||||||||||
gtatcacccagcattttaatcttaat-ctagtttcaaaacg-ttcacttcatg----cacttggaaagcctgaatttatcgcttgtacgtatcttacaggctcgtctgttgaatgtttcagGATGCCAAGAATAAGGTTGTGGAAGACGTAGTAATTTTATCCGGAGACCATTTGTACCGTATGGACTACATGGACTTTGTTCAG

upper sequence: GRMZM2G391936_T02 (Zea mays), 3'ss of exon 4
lower sequence: PP1S347_12V6.1 (Physcomitrella patens), 3'ss of exon 4
------------------------------------------------ttcaaagggactgccagttcc-ctattgctttactttgtaatattattataataccacaaagctgttccttgaagaaattgta---atacataatgttttgtagGATGCAAAATCTAAAGACATTGAAGATGTGCTGATTCTTTCTGGTGACCATCTCTACCGTATGGACTACATGGACTTTGTTCAG----------------
                                                   |   |||      ||||  | ||| | || | |  | ||  ||    |  |  | ||   |   | |     |  ||  |   |    |    | ||| ||||||| ||   ||| |   | || || ||| | ||  | || || || || |||||||||||||| |||||||||||||| |||                
gtacactcttaattccattgcaactatgttttaaggattgttgtgtctactagttggaaaattcgttcggcaatttcattccatcttcattctaa-gcagcaatagaagcatcaccttcacttatgttccatccacgtgtttattgttgaagGATGCCAAGAATAAGGTGGTGGAGGACGTGGTTATCTTGTCCGGCGATCACCTCTACCGTATGGATTACATGGACTTTGTCCAGAAGCACAGGGACAGTG

upper sequence: GRMZM2G391936_T02 (Zea mays), 3'ss of exon 4
lower sequence: EFJ23417 (Selaginella moellendorffii), 3'ss of exon 5
ttcaaagggactgccagttccctattgctttactttgtaatattattataataccacaaagctgttccttgaagaaattgtaatacataatgttttgtagGATGCAAAATCTAAAGACATTGAAGATGTGCTGATTCTTTCTGGTGACCATCTCTACCGTATGGACTACATGGACTTTGTTCAG
                              |||| | ||  |||   |   |        |||  |      ||   | ||  |  || |        ||||||  | |   || ||| | ||  | |||||  |||| || ||||| || |||||||| |||||||||||||||||||| |||
-----------------------------gtactctttaccatttccaaggtgttg---ggctcgtatgctgaggtttcgttttgtatgaca------agGATGTGAGAAACAAGGACGTCGACTACGTGCTTGTTCTCTCCGGTGATCACCTCTACCGCATGGACTACATGGACTTTGTCCAG

upper sequence: GRMZM2G391936_T02 (Zea mays), 3'ss of exon 4
lower sequence: EFJ25399 (Selaginella moellendorffii), 3'ss of exon 4
ttcaaagggactgccagttccctattgctttactttgtaatattattataataccacaaagctgttccttgaagaaattgtaatacataatgttttgtagGATGCAAAATCTAAAGACATTGAAGATGTGCTGATTCTTTCTGGTGACCATCTCTACCGTATGGACTACATGGACTTTGTTCAG
                                    ||| | |||  ||  | |||    | ||  |    | |     ||      |  | |     ||||||  | |   || ||| | ||  | |||||  |||| || ||||| || |||||||| |||||||||||||||||||| |||
------------------------------------gtactcttaccat--ttccaaggtgttggactcgcatgctgaggtttcgttttgtatgaca-agGATGTGAGAAACAAGGACGTCGACTACGTGCTTGTTCTCTCCGGTGATCACCTCTACCGCATGGACTACATGGACTTTGTCCAG

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|149101455|gb|EE187574.2|EE187574
EST:     GGTTTCAGGGTACTGCTGATGCAGTTCGGCAGTTCGACTGGCTTTTCGAT                         GATGCAAAATCTAAAGACATTGAAGATGTGCTGATTCTTTCTGGTGACCAT
genomic: GGTTTCAGGGTACTGCTGATGCAGTTCGGCAGTTCGACTGGCTTTTCGATgtaagagttg ... tgttttgtagGATGCAAAATCTAAAGACATTGAAGATGTGCTGATTCTTTCTGGTGACCAT
EST: gi|71429963|gb|DR811013.1|DR811013
EST:     GGTTTCAGGGTACTGCTGATGCAGTTCGGCAGTTCGACTGGCTTTTCGAT                         GATGCAAAATCTAAAGACATTGAAGATGTGCTGATTCTTTCTGGGGACCAT
genomic: GGTTTCAGGGTACTGCTGATGCAGTTCGGCAGTTCGACTGGCTTTTCGATgtaagagttg ... tgttttgtagGATGCAAAATCTAAAGACATTGAAGATGTGCTGATTCTTTCTGGTGACCAT
EST: gi|71435811|gb|DR816861.1|DR816861
EST:     GGTTTCAGGGTACTGCTGATGCAGTTCGGCAGTTCGACTGGCTTTTCGAT                         GATGCAAAATCTAAAGACATTGAAGATGTGCTGATTCTTTCTGGTGACCAT
genomic: GGTTTCAGGGTACTGCTGATGCAGTTCGGCAGTTCGACTGGCTTTTCGATgtaagagttg ... tgttttgtagGATGCAAAATCTAAAGACATTGAAGATGTGCTGATTCTTTCTGGTGACCAT
EST: gi|211114649|gb|FL303211.1|FL303211
EST:     GGTTTCAGGGTACTGCTGATGCAGTTCGGCAGTTCGACTGGCTTTTCGAT                         GATGCAAA-TCTAA-GACATTGAAGATGTGCTGATTCTTTCTG-TGACCAT
genomic: GGTTTCAGGGTACTGCTGATGCAGTTCGGCAGTTCGACTGGCTTTTCGATgtaagagttg ... tgttttgtagGATGCAAAATCTAAAGACATTGAAGATGTGCTGATTCTTTCTGGTGACCAT
EST: gi|211118620|gb|FL303281.1|FL303281
EST:     GTTTTCAGGGTACTGCTGATGCAGTTCGGCAGTTCGACTGGCTTTTCGAT                         GATGCAAAATCTAA-GACTTTGAAGATGTGCTGAATTCTTTCTGGGGACCA
genomic: GTTT-CAGGGTACTGCTGATGCAGTTCGGCAGTTCGACTGGCTTTTCGATgtaagagttg ... tgttttgtagGATGCAAAATCTAAAGACATTGAAGATGTGCTGA-TTCTTTCTGGTGACCA
EST: gi|211116232|gb|FL303236.1|FL303236
EST:     GGTTTCAGGGTACTGCTGATGCAGTTCGGCAGTTCGACTGGCTTTTCGAT                         GATGCAAAATCTAAAGACATTGGAGATGTGCTGAATCCTTCTGGTGACCAT
genomic: GGTTTCAGGGTACTGCTGATGCAGTTCGGCAGTTCGACTGGCTTTTCGATgtaagagttg ... tgttttgtagGATGCAAAATCTAAAGACATTGAAGATGTGCTGATTCTTTCTGGTGACCAT
EST: gi|211117825|gb|FL303269.1|FL303269
EST:     GGTTTCAGGGTACTGCTGATGCAGTTCGGCAGTTCGACTGGCTTTTCGAT                         GATGCAAAATCTAAAGACATTGAAGATGTGCTGATTCTTT
genomic: GGTTTCAGGGTACTGCTGATGCAGTTCGGCAGTTCGACTGGCTTTTCGATgtaagagttg ... tgttttgtagGATGCAAAATCTAAAGACATTGAAGATGTGCTGATTCTTT
EST: gi|211115446|gb|FL303226.1|FL303226
EST:     GGTTTCAGGGTACTGCTGATGCAGTTCGGCAGTTCGACTGGCTTTTCGAT                         GATGCAAA-TCTAAAGACATTGAAGATGTGCTGATTC
genomic: GGTTTCAGGGTACTGCTGATGCAGTTCGGCAGTTCGACTGGCTTTTCGATgtaagagttg ... tgttttgtagGATGCAAAATCTAAAGACATTGAAGATGTGCTGATTC
EST: gi|76291271|gb|DV030839.1|DV030839
EST:     GGTTTCAGGGTACTGCTGATGCAGTTCGGCAGTTCGACTGGCTTTTCGAT                         GATGCAAAATCTAAAGACATTGAAGATGTGCTGATTCTTTCTGGTGACCAT
genomic: GGTTTCAGGGTACTGCTGATGCAGTTCGGCAGTTCGACTGGCTTTTCGATgtaagagttg ... tgttttgtagGATGCAAAATCTAAAGACATTGAAGATGTGCTGATTCTTTCTGGTGACCAT
EST: gi|211118623|gb|FL303284.1|FL303284
EST:     GTTTCAGGGTACTGCTGATGCAGTTCGGCAGTTCGACGGGCTTTTTCGAT                         GATGCAAAATCTAAA
genomic: GTTTCAGGGTACTGCTGATGCAGTTCGGCAGTTCGACTGGCTTTT-CGATgtaagagttg ... tgttttgtagGATGCAAAATCTAAA
EST: gi|50335822|gb|CO530948.1|CO530948
EST:     GGTTTCAGGGTACTGCTGATGCAGTTCGGCAGTTCGACTGGCTTTTCGAT                         GATGCAAAATCTAAAGACATTGAAGATGTGCTGATTCTTTCTGGTGACCAT
genomic: GGTTTCAGGGTACTGCTGATGCAGTTCGGCAGTTCGACTGGCTTTTCGATgtaagagttg ... tgttttgtagGATGCAAAATCTAAAGACATTGAAGATGTGCTGATTCTTTCTGGTGACCAT
EST: gi|211116234|gb|FL303238.1|FL303238
EST:     GGTTTCAGGGTACTGCTGATGCAGTTCGGCAGTTCGACTGGGTTTTCGAT                         GATGCAAAATCTAAAGACATGGAAGATGTGCTGATTTCTT-CTGGTGAACA
genomic: GGTTTCAGGGTACTGCTGATGCAGTTCGGCAGTTCGACTGGCTTTTCGATgtaagagttg ... tgttttgtagGATGCAAAATCTAAAGACATTGAAGATGTGCTGATT-CTTTCTGGTGACCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttataataccacaaagctgttccttgaagaaattgtaatacataatgttttgtagGATGCAAAATCTAAAGACATTGAAGATGTGCTGATTCTTTCTGGTGACCATCTCTACCGTATGGACTACATGGACTTTGTTCAG
                             aaattgtaatacataa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttcaaagggactgccagttccctattgctttactttgtaatattattataataccacaaagctgttccttgaagaaattgtaatacataatgttttgtagGATGCAAAATCTAAAGACATTGAAGATGTGCTGATTCTTTCTGGTGACCATCTCTACCGTATGGACTACATGGACTTTGTTCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA