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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctgttacttttaacagctaatgcaatctggatgagtcacctatgaattccatactggaatctgttgcgcttttgttgatcattattattttgcaatccagGCTAGGGGATTGAAGAAGCACTTGAAGAGGCTCAATGCGCCCAAGCATTGGATGCTCGACAAGCTTGGCGGAGCTTTT

Basic information

species Zea mays
transcript GRMZM2G158584_T04
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G158584_T04 (Zea mays), 3'ss of exon 5
lower sequence: PP1S461_1V6.1 (Physcomitrella patens), 3'ss of exon 1
-ctgttacttttaacagctaatgcaatctggatgagtcacctatgaattccatactggaatctgttgcgcttttgttgatc-attattattttgcaatccagGCTAGGGGATTGAAGAAGCACTTGAAGAGGCTCAATGCGCCCAAGCATTGGATGCTCGACAAGCTTGGCGGAGCTTTT
 |||  |  || ||  |    ||   |  || |  |       |  ||   ||   | | | ||   ||  ||    | ||  ||  | || |||  |  ||||| | || |||||||||||  |||||||||||||||||||||||||||||||||| |||||| | || || || || 
cctgcaagcttaaaatgggggtggtttagggttttgaagttggttgat--gatgaggaagtttgagtcgtgttctgagttctgtttctcttgtgcgttttagGCTCGTGGTTTGAAGAAGCATCTGAAGAGGCTCAATGCGCCCAAGCATTGGATGCTTGACAAGTTGGGTGGTGCCTTC

upper sequence: GRMZM2G158584_T04 (Zea mays), 3'ss of exon 5
lower sequence: PP1S2_16V6.1 (Physcomitrella patens), 3'ss of exon 1
ctgttacttttaaca--gctaatgcaatctggatgagtcacctatgaattccatactggaatctgttgcgcttttgttgatcattattattttgcaatccagGCTAGGGGATTGAAGAAGCACTTGAAGAGGCTCAATGCGCCCAAGCATTGGATGCTCGACAAGCTTGGCGGAGCTTTT
 | |   ||    ||  | |      || |   ||       |||  | |  ||  |||  | |  ||  ||  |||   ||||  ||    |      |||||| | || ||||||||||| |||||||||||||||||||||| ||| |||||||| |||||| | || || || |||
-tttcgtttacgtcattgttcgcttcatttttgtggtcggtttatcgactggattttggcctgtcatggtctcctgt-attcatctttccaatctctggcagGCTCGCGGTTTGAAGAAGCATTTGAAGAGGCTCAATGCGCCCAGGCACTGGATGCTTGACAAGTTGGGTGGTGCCTTT

upper sequence: GRMZM2G158584_T04 (Zea mays), 3'ss of exon 5
lower sequence: PP1S38_194V6.1 (Physcomitrella patens), 3'ss of exon 1
ctgttacttttaacag-ctaatgcaatctggatgagtcacctatgaattccatactggaatctgttgcgcttttgttgatcattattattttgcaa-tccagGCTAGGGGATTGAAGAAGCACTTGAAGAGGCTCAATGCGCCCAAGCATTGGATGCTCGACAAGCTTGGCGGAGCTTTT
 | |   |||    |  ||      |  || | ||        |   ||||  | ||  |  ||| ||   ||      | ||| || | |||    || ||||| | || ||||||||||| ||||||||||||||||| ||||  ||||||||||| |||||| | || || || || 
ttatcggtttacgtaaacttgctttacttgtacgaagagtgcgtttgttcctgagtg--acgtgtggcttgttacgaactaattgttttcttgtgtctctagGCTCGCGGTTTGAAGAAGCATTTGAAGAGGCTCAATGCTCCCAGACATTGGATGCTTGACAAGTTGGGTGGTGCCTTC

upper sequence: GRMZM2G158584_T04 (Zea mays), 3'ss of exon 5
lower sequence: PP1S81_172V6.1 (Physcomitrella patens), 3'ss of exon 1
-ctgttacttttaacagctaatgcaatctggatgagtcacctatgaattccatactggaatctgttgcgcttttgttgatcatt--attattttgcaatccagGCTAGGGGATTGAAGAAGCACTTGAAGAGGCTCAATGCGCCCAAGCATTGGATGCTCGACAAGCTTGGCGGAGCTTTT
   |||  |||    |||  ||    |    ||| |       |   |||  |  |  | | | || || | || ||| |  ||   |||||||    | |||||| | || ||||||||||| |||||||||||||||||||||||||||||||||||||||||  | || || || |||
gaggttggtttcg-tagc--atatttttgaaatgtgcgctgatttttttcttttttttatttttttacgttgtttttgttttttttgttatttttttcttcagGCTCGTGGTTTGAAGAAGCATTTGAAGAGGCTCAATGCGCCCAAGCATTGGATGCTCGACAAATTGGGTGGCGCCTTT

upper sequence: GRMZM2G158584_T04 (Zea mays), 3'ss of exon 5
lower sequence: PP1S282_25V6.1 (Physcomitrella patens), 3'ss of exon 1
ctgttacttttaacagctaatgcaatctggatgagtcaccta--tgaattccatactggaatctgttgcgcttttgttgatcattattattttgcaatccagGCTAGGGGATTGAAGAAGCACTTGAAGAGGCTCAATGCGCCCAAGCATTGGATGCTCGACAAGCTTGGCGGAGCTTTT
 || |    |  | |   |  |   || | ||       ||   |||   || |  |  | |     | |   |         ||    | ||| | |||||||| | || ||||||||||| |||||||||||||||||||| |||||||||||||| |||||||| || || || || 
atgctggagt-gagaatcagggtcttcggtattttgggactggctgatcaccctgttcaattggtacgtgtgctaaacatgtgttgcggtgttg-attccagGCTCGCGGTTTGAAGAAGCATTTGAAGAGGCTCAATGCGCCTAAGCATTGGATGCTTGACAAGCTGGGTGGCGCCTTC

upper sequence: GRMZM2G158584_T04 (Zea mays), 3'ss of exon 5
lower sequence: EFJ26570 (Selaginella moellendorffii), 3'ss of exon 1
ctgttacttttaacagctaatgcaatctggatgagtcacctatgaattccatactggaatctgttgcgcttttgttga-tcattattattttgcaatccagGCTAGGGGATTGAAGAAGCACTTGAAGAGGCTCAATGCGCCCAAGCATTGGATGCTCGACAAGCTTGGCGGAGCTTTT
                                                        ||    |  ||  |   |     | |  ||| || ||   | ||||   | ||   |||||||||  |||||  ||||||||| |||||||||||||||||   |||||| ||||| || || 
----------------------------------------------------gtgagagcgcgcggctatcgcgggatcttacgattcttgtgttgtgcagGTGCGCGGGCCGAAGAAGCATCTGAAGGTGCTCAATGCCCCCAAGCATTGGATGCTGAGCAAGCTCGGCGGTGCCTTC

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|149103360|gb|EE288742.2|EE288742
EST:     CCAAGATGCCCATGCGTCCCCGCGCCCCTCGCCAGCTGATGTCGTACTAG                         GCTAGGGGATTGAAGAAGCACTTGAAGAGGCTCAATGCGCCCAAGCATTGG
genomic: CCAAGATGCCCATGCGTCCCCGCGCCCCTCGCCAGCTGATGTCGTACTAGgtatacatac ... tgcaatccagGCTAGGGGATTGAAGAAGCACTTGAAGAGGCTCAATGCGCCCAAGCATTGG
EST: gi|71431329|gb|DR812379.1|DR812379
EST:     CCAAGATGCCCATGCGTCCCCGCGCCCCTCGCCAGCTGATGTCGTACTAG                         GCTAGGGGATTGAAGAAGCACTTGAAGAGGCTCAATGCGCCCAAGCATTGG
genomic: CCAAGATGCCCATGCGTCCCCGCGCCCCTCGCCAGCTGATGTCGTACTAGgtatacatac ... tgcaatccagGCTAGGGGATTGAAGAAGCACTTGAAGAGGCTCAATGCGCCCAAGCATTGG
EST: gi|30032065|gb|CB833916.1|CB833916
EST:     GATGCCCATGCGTCCCCGCGCCCCTCGCCAGCTGATGTCGTACTAG                         GCTAGGGGATTGAAGAAGCACTTGAAGAGGCTCAATGCGCCCAAGCATTGG
genomic: GATGCCCATGCGTCCCCGCGCCCCTCGCCAGCTGATGTCGTACTAGgtatacatac ... tgcaatccagGCTAGGGGATTGAAGAAGCACTTGAAGAGGCTCAATGCGCCCAAGCATTGG
EST: gi|29544094|gb|CB604474.1|CB604474
EST:     ATGCCCATGCGTCCCCGCGCCCCTCGCCAGCTGATGTCGTACTAG                         GCTAGGGGATTGAAGAAGCNCTTGAAGAGGCTCAATGCGCCCAAGCATTGG
genomic: ATGCCCATGCGTCCCCGCGCCCCTCGCCAGCTGATGTCGTACTAGgtatacatac ... tgcaatccagGCTAGGGGATTGAAGAAGCACTTGAAGAGGCTCAATGCGCCCAAGCATTGG
EST: gi|149028385|gb|EE154636.2|EE154636
EST:     CCAAGATGCCCATGCGTCCCCGCGCCCCTCGCCAGCTGATGTCGTACTAG                         GCTAGGGGATTGAAGAAGCACTTGAAGAGGCTCAATGCGCCCAAGCATTGG
genomic: CCAAGATGCCCATGCGTCCCCGCGCCCCTCGCCAGCTGATGTCGTACTAGgtatacatac ... tgcaatccagGCTAGGGGATTGAAGAAGCACTTGAAGAGGCTCAATGCGCCCAAGCATTGG
EST: gi|29544577|gb|CB604957.1|CB604957
EST:     CCAAGATGCCCATGCGTCCCCGCGCCCCTCGCCAGCTGATGTCGTACTAG                         GCTAGGGGATTGAAGAAGCACTTGAAGAGGCTCAATGCGCCCAAGCATTGG
genomic: CCAAGATGCCCATGCGTCCCCGCGCCCCTCGCCAGCTGATGTCGTACTAGgtatacatac ... tgcaatccagGCTAGGGGATTGAAGAAGCACTTGAAGAGGCTCAATGCGCCCAAGCATTGG
EST: gi|71419899|gb|DR804931.1|DR804931
EST:     CCAAGATGCCCATGCGTCCCCGCGCCCCTCGCCAGCTGATGTCGTACTAG                         GCTAGGGGATTGAAGAAGCACTTGAAGAGGCTCAATGCGCCCAAGCATTGG
genomic: CCAAGATGCCCATGCGTCCCCGCGCCCCTCGCCAGCTGATGTCGTACTAGgtatacatac ... tgcaatccagGCTAGGGGATTGAAGAAGCACTTGAAGAGGCTCAATGCGCCCAAGCATTGG
EST: gi|211145652|gb|FL480707.1|FL480707
EST:     CCAAGATGCCCATGCGTCCCCGCGCCCYTCGCCAGCTGATGTCGTACTAG                         GCTAGGGGATTGAAGAAGCACTTGAAGAGGCTCAATGCGCCCAAGCATTGG
genomic: CCAAGATGCCCATGCGTCCCCGCGCCCCTCGCCAGCTGATGTCGTACTAGgtatacatac ... tgcaatccagGCTAGGGGATTGAAGAAGCACTTGAAGAGGCTCAATGCGCCCAAGCATTGG
EST: gi|30087079|gb|CB885287.1|CB885287
EST:     CCAAGATGCCCATGCGTCCCCGCGCCCCTCGCCAGCTGATGTCGTACTAG                         GCTAGGGGATTGAAGAAGCACTTGAAGAGGCTCAATGCGCCCAAGCATTGG
genomic: CCAAGATGCCCATGCGTCCCCGCGCCCCTCGCCAGCTGATGTCGTACTAGgtatacatac ... tgcaatccagGCTAGGGGATTGAAGAAGCACTTGAAGAGGCTCAATGCGCCCAAGCATTGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attccatactggaatctgttgcgcttttgttgatcattattattttgcaatccagGCTAGGGGATTGAAGAAGCACTTGAAGAGGCTCAATGCGCCCAAGCATTGGATGCTCGACAAGCTTGGCGGAGCTTTT
                           tgttgat  putative branch site (score: 4)
                                       ttatttt  putative PPT
                        ttttgttgatcattat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ctgttacttttaacagctaatgcaatctggatgagtcacctatgaattccatactggaatctgttgcgcttttgttgatcattattattttgcaatccagGCTAGGGGATTGAAGAAGCACTTGAAGAGGCTCAATGCGCCCAAGCATTGGATGCTCGACAAGCTTGGCGGAGCTTTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT