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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aataaaacatctatttgccataacatctgtgaacagacatttttcaactatgaaatggtagtctccaatccatttgacagttcatttttcctttatgcagATGATTCCTGTTGCTGCAAATGATGTTGCTTTTTCACTGCATGCTGTAGCATTGACAGCCTTTACCGTTTTTCAAGTATTCATATATGAG

Basic information

species Zea mays
transcript GRMZM2G015869_T02
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G015869_T02 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os12g18110.1 (Oryza sativa), 3'ss of exon 2
aataaaac-atctatttgccataacatctgtgaacagacatttttcaactatgaaatggtagtctccaatccatttgacagttcatttttcctttatgcagATGATTCCTGTTGCTGCAAATGATGTTGCTTTTTCACTGCATGCTGTAGCATTGACAGCCTTTACCGTTTTTCAAGTATTCATATATGAG
||| | || | ||   || |||      |          |  ||| |||| | |  || ||  |   |||| |    |   ||   | |   || ||||||||||||||||| || |||||||||||||| |||||  | || || || || |||||||| |||||| |||||||||||||||| || |||
aatgagaccaccttggtgtcattcttcttcatgtttattagctttaaactgt-atttgctaagcctaaatcaaacatattattttgtatcatttgatgcagATGATTCCTGTCGCGGCAAATGATGTTGCCTTTTCTGTACACGCGGTTGCCTTGACAGCTTTTACCCTTTTTCAAGTATTCATCTACGAG

upper sequence: GRMZM2G015869_T02 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA19G07750.1 (Glycine max), 3'ss of exon 3
---------------------------------------------------------------aataaaacatctatttgccataacatctgtgaacagacatttttcaactatgaaatggtagtctccaatccatttgacagttcatttttcctttat-gcagATGATTCCTGTTGCTGCAAATGATGTTGCTTTTTCACTGCATGCTGTAGCATTGACAGCCTTTACCGTTTTTCAAGTATTCATATATGAG
                                                               || |||      | |   | |    | |||| | |  ||||    |   | |  ||  |||| |   | |  | |||    |  || ||  |  || ||||||||||||||| || || |||||||||||||| ||  | ||| | ||   ||| |      |||   | |  ||| | |  || | ||| 
gtgggacttgaatttttcaaatggctagcaaaataatacaacacgagtcaccaatgtactgccaacaaatatcaaaatcaactttgtctttgtgcaaaatcattagatattcacgttatc-tagttt---agctttatgatctcttgttattattgcattgcagATGATTCCTGTAGCCGCTAATGATGTTGCTTTCTCCATTCATTCAGTCATATTAAATTTAATTATACTGTCCCAAATTTCAATGTTTGAA

upper sequence: GRMZM2G015869_T02 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA16G07110.1 (Glycine max), 3'ss of exon 2
aataaaacatctatttgccataacatctgtgaacagacatttttcaactatgaaatggtagtctccaatccatt--tgacagttcatttttcctttatgcagATGATTCCTGTTGCTGCAAATGATGTTGCTTTTTCACTGCATGCTGTAGCATTGACAGCCTTTACCGTTTTTCAAGTATTCATATATGAG
 ||   |||     |   |  ||||      ||   |  | | |      | | ||     | |  | | |  |  ||    || | |||   ||  | |||||||| |||||||||||||||||||||||||| ||  | ||||||||   | |||||||  ||||  | || ||  |    || ||||| 
-attttacaaa-gctcatccaaacacacactaagtaatgtctgttcttatttatataaatatttggagttccctaatgtagttttagtttcatttgtttcagATGATACCTGTTGCTGCAAATGATGTTGCTTTCTCGATCCATGCTGTTCTACTGACAGCAATTACATTGTTCCAGATTGCAATCTATGAA

upper sequence: GRMZM2G015869_T02 (Zea mays), 3'ss of exon 2
lower sequence: Vv14s0219g00130.t01 (Vitis vinifera), 3'ss of exon 2
aataaaacatctatttgccataacatctgtgaacagacatttttcaactatgaaatggtagtctccaatccatttgacagttcatttttcctttatgcagATGATTCCTGTTGCTGCAAATGATGTTGCTTTTTCACTGCATGCTGTAGCATTGACAGCCTTTACCGTTTTTCAAGTATTCATATATGAG
           | |||    |    ||| | |       |||| |  |       |||   | |  |||  || ||       || ||| |||  |||||||||| ||||| |||||||||||||||||||| ||| | |||||||| |  |||| ||| |||||    || ||| |    || ||||||
----------gtttttattttcgggtctttcag-----gttttccctcctctttttgg--atttttaat--atgtggtgaa--atgttttcttgttgcagATGATACCTGTGGCTGCAAATGATGTTGCTTTCTCAATTCATGCTGTTGTCTTGATAGCATTTACTTGGTTCCAAATTGCAATCTATGAG

upper sequence: GRMZM2G015869_T02 (Zea mays), 3'ss of exon 2
lower sequence: Vv14s0219g00120.t01 (Vitis vinifera), 3'ss of exon 2
aataaaacatctatttgccataacatctgtgaacagacatttttcaactatgaaatggtagtctccaatc-catttgacagttcatttttcctttat-gcagATGATTCCTGTTGCTGCAAATGATGTTGCTTTTTCACTGCATGCTGTAGCATTGACAGCCTTTACCGTTTTTCAAGTATTCATATATGAG
  ||       ||| |   | |   |    ||  | |  || || || | |   ||  |   ||    |  ||  |    | | ||      |||||  |||||||| ||||| |||||||||||||||||||| ||| | ||||||||    |||||||| |||||  | |||||| |    || ||||||
-ttactttgcttatgt-taaaagggtggaagagaacaagttgtttaagtgttccattttttcctttttttacaaatatgtggtgatacgctttttattacagATGATACCTGTGGCTGCAAATGATGTTGCTTTCTCAATTCATGCTGTTATCTTGACAGCATTTACTTTGTTTCAAATTGCAATCTATGAG

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|50329144|gb|CO524270.1|CO524270
EST:     TCAGCCCATTCATCCAGCAACAGTATCATGACAAATATGGTGATAAAGAG                         ATGATTCCTGTTGCTGCAAATGATGTTGCTTTTTCACTGCATGCTGTAGCA
genomic: TCAGCCCATTCATCCAGCAACAGTATCATGACAAATATGGTGATAAAGAGgtttgtctta ... ctttatgcagATGATTCCTGTTGCTGCAAATGATGTTGCTTTTTCACTGCATGCTGTAGCA
EST: gi|37420119|gb|CF647747.1|CF647747
EST:     TCAGCCCATTCATCCAGCAACAGTATCATGACAAATATGGTGATAAAGAG                         ATGATTCCTGTTGCTGCAAATGATGTTGCTTTTTCACTGCATGCTGTAGCA
genomic: TCAGCCCATTCATCCAGCAACAGTATCATGACAAATATGGTGATAAAGAGgtttgtctta ... ctttatgcagATGATTCCTGTTGCTGCAAATGATGTTGCTTTTTCACTGCATGCTGTAGCA
EST: gi|78084914|gb|DV513307.1|DV513307
EST:     TCAGCCCATTCATCCAGCAACAGTATCATGACAAATATGGTGATAAAGAG                         ATGATTCCTGTTGCTGCAAATGATGTTGCTTTTTCACTGCATGCTGTAGCA
genomic: TCAGCCCATTCATCCAGCAACAGTATCATGACAAATATGGTGATAAAGAGgtttgtctta ... ctttatgcagATGATTCCTGTTGCTGCAAATGATGTTGCTTTTTCACTGCATGCTGTAGCA
EST: gi|211284538|gb|FL301650.1|FL301650
EST:     CAGCCCATTCATCCAGCAACAGTATCATGGACAAATATGGTGATAAAGAG                         ATGATTCCTGTTGCTGCAAATGATGTTGCTTTTTCACTGCATTCTGTAGCA
genomic: CAGCCCATTCATCCAGCAACAGTATCATG-ACAAATATGGTGATAAAGAGgtttgtctta ... ctttatgcagATGATTCCTGTTGCTGCAAATGATGTTGCTTTTTCACTGCATGCTGTAGCA
EST: gi|50334359|gb|CO529485.1|CO529485
EST:     TCAGCCCATTCATCCAGCAACAGTATCATGACAAATATGGTGATAAAGAG                         ATGATTCCTGTTGCTGCAAATGATGTTGCTTTTTCACTGCATGCTGTAGCA
genomic: TCAGCCCATTCATCCAGCAACAGTATCATGACAAATATGGTGATAAAGAGgtttgtctta ... ctttatgcagATGATTCCTGTTGCTGCAAATGATGTTGCTTTTTCACTGCATGCTGTAGCA
EST: gi|32918962|gb|CF023774.1|CF023774
EST:     TCAGCCCATTCATCCAGCAACAGTATCATGACAAATATGGTGACAAAGAG                         ATGATTCCAGTTGCTGCAAATGATGTTGCTTTTTCACTGCATGCTGTAGCA
genomic: TCAGCCCATTCATCCAGCAACAGTATCATGACAAATATGGTGATAAAGAGgtttgtctta ... ctttatgcagATGATTCCTGTTGCTGCAAATGATGTTGCTTTTTCACTGCATGCTGTAGCA
EST: gi|211284537|gb|FL301649.1|FL301649
EST:     TCAGCCCATTCATCCAGCAACAGTATCATGACAAATATGGTGATAAAGAG                         ATGATTCCTGTTGCTGCAAATGATGTTGCTTTTTCABSTGCATGCTGTAGC
genomic: TCAGCCCATTCATCCAGCAACAGTATCATGACAAATATGGTGATAAAGAGgtttgtctta ... ctttatgcagATGATTCCTGTTGCTGCAAATGATGTTGCTTTTTCAC-TGCATGCTGTAGC
EST: gi|211284533|gb|FL301645.1|FL301645
EST:     TCAGCCCATTCATCCAGCAACAGTATCATGACAAATATGGTGATAAAGAG                         ATGATTCCTGTTGCTGCAAATGATGTTGCTTTTTCA
genomic: TCAGCCCATTCATCCAGCAACAGTATCATGACAAATATGGTGATAAAGAGgtttgtctta ... ctttatgcagATGATTCCTGTTGCTGCAAATGATGTTGCTTTTTCA
EST: gi|211284534|gb|FL301646.1|FL301646
EST:     TCAGCCCATTCATCCAGCAACAGTATCATGACAAATATGGTGATAAAGAG                         ATGATTCCTGTTGCTGCAAATGATGTTGCTTTTTCACTGCATGCTGTAGCA
genomic: TCAGCCCATTCATCCAGCAACAGTATCATGACAAATATGGTGATAAAGAGgtttgtctta ... ctttatgcagATGATTCCTGTTGCTGCAAATGATGTTGCTTTTTCACTGCATGCTGTAGCA
EST: gi|211284540|gb|FL301652.1|FL301652
EST:     TCAGCCCATTCATCCAGCAACAGTATCATGACAAATATGGTGATAAAGAG                         ATGATTCCTGTTGCTGCAAATGATGTTGCTTTTTCACTGCATGCTGTAGCA
genomic: TCAGCCCATTCATCCAGCAACAGTATCATGACAAATATGGTGATAAAGAGgtttgtctta ... ctttatgcagATGATTCCTGTTGCTGCAAATGATGTTGCTTTTTCACTGCATGCTGTAGCA
EST: gi|78084875|gb|DV513268.1|DV513268
EST:     TCAGCCCATTCATCCAGCAACAGTATCATGACAAATATGGTGATAAAGAG                         ATGATTCCTGTTGCTGCAAATGATGTTGCTTTTTCACTGCATGCTGTAGCA
genomic: TCAGCCCATTCATCCAGCAACAGTATCATGACAAATATGGTGATAAAGAGgtttgtctta ... ctttatgcagATGATTCCTGTTGCTGCAAATGATGTTGCTTTTTCACTGCATGCTGTAGCA
EST: gi|71772025|gb|DR969962.1|DR969962
EST:     TCAGCCCATTCATCCAGCAACAGTATCATGACAAATATGGTGATAAAGAG                         ATGATTCCTGTTGCTGCAAATGATGTTGCTTTTTCACTGCATGCTGTAGCA
genomic: TCAGCCCATTCATCCAGCAACAGTATCATGACAAATATGGTGATAAAGAGgtttgtctta ... ctttatgcagATGATTCCTGTTGCTGCAAATGATGTTGCTTTTTCACTGCATGCTGTAGCA
EST: gi|9732652|gb|BE511404.1|BE511404
EST:     TCAGCCCATTCATCCAGCAACAGTATCATGACAAATATGGTGATAAAGAG                         ATGATTCCTGTTGCTGCAAATGATGTTGCTTTTTCACTGCATGCTGTAGCA
genomic: TCAGCCCATTCATCCAGCAACAGTATCATGACAAATATGGTGATAAAGAGgtttgtctta ... ctttatgcagATGATTCCTGTTGCTGCAAATGATGTTGCTTTTTCACTGCATGCTGTAGCA
EST: gi|211284535|gb|FL301647.1|FL301647
EST:     TCAGCCCATTCATCCAGCAACAGTATCATGACAAATATGGTGATAAAGAG                         ATGATTCCTGTT
genomic: TCAGCCCATTCATCCAGCAACAGTATCATGACAAATATGGTGATAAAGAGgtttgtctta ... ctttatgcagATGATTCCTGTT
EST: gi|211284536|gb|FL301648.1|FL301648
EST:     TCAGCCCATTCATTCAGCAACAGTATCATGACAAATATGGTGACAAAGAG                         ATGATTCCAGTTGCTGCAAATGATGTTGCTTTTTCACTGCATGCTGTAGCA
genomic: TCAGCCCATTCATCCAGCAACAGTATCATGACAAATATGGTGATAAAGAGgtttgtctta ... ctttatgcagATGATTCCTGTTGCTGCAAATGATGTTGCTTTTTCACTGCATGCTGTAGCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aactatgaaatggtagtctccaatccatttgacagttcatttttcctttatgcagATGATTCCTGTTGCTGCAAATGATGTTGCTTTTTCACTGCATGCTGTAGCATTGACAGCCTTTACCGTTTTTCAAGTATTCATATATGAG
                          atttgac  putative branch site (score: 4)
                                   ttcatttttcctttat  putative PPT
                                   ttcattttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aataaaacatctatttgccataacatctgtgaacagacatttttcaactatgaaatggtagtctccaatccatttgacagttcatttttcctttatgcagATGATTCCTGTTGCTGCAAATGATGTTGCTTTTTCACTGCATGCTGTAGCATTGACAGCCTTTACCGTTTTTCAAGTATTCATATATGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
aataaaa
- - - - - - - -tgccata
- - - - - - - - - - - - - - - gaacaga
- - - - - - - - - - - - - - - - - - - - - - - - - tgaaatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ccatttg