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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgcaaccttcaggaatcaacatacttgtgttaagttcatagcccaaggttcattcttgtatctggtatggtatttaaaaaagtttgccatttttctgtgatctgcagTCTGATGATGAACGGGAAATGTGTGCGAGGACTATTTACTGCACAAACATTGACAAGAAGGTTCCCTACCTACACTCATGCTATACCACTAGGTGTTCAT

Basic information

species Zea mays
transcript GRMZM2G173428_T04
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G173428_T04 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os08g02330.1 (Oryza sativa), 3'ss of exon 5
---------gtatgcaaccttcaggaatcaacata---cttgtgttaagttcatagcccaagg---ttcattcttgtatctg-gtatggtatttaaaaaagtttgccatt-tttctgtgatctgcagTCTGATGATGAACGGGAAATGTGTGCGAGGACTATTTACTGCACAAACATTGACAAGAAGGTTCCCTACCTACACTCATGCTATACCACTAGGTGTTCAT
          | ||||   |||| | ||   ||||    |  |  | | ||| ||   ||| |   || || |   ||  ||   |    || |  ||||| | |||    ||  |||   |||||||| |||||||| || || |||||||| |||||||||||||||||||||||||||||||||                                        
gtaagctgaatctgcacaattcatgtatttgcataaatttcattattaattcttatttcaatgaaatttatgcaaatacgtgtacacctgatgtctaaaagctggcccccattcttgttgcctgcagTCCGATGATGAGCGTGAGATGTGTGCAAGGACTATTTACTGCACAAACATTGACAAGAAG----------------------------------------

upper sequence: GRMZM2G173428_T04 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA04G40760.1 (Glycine max), 3'ss of exon 7
gtatgcaaccttcaggaatcaacatacttgtgttaagttcatagcccaaggttcattcttgtatctggtatggtatttaaaaaagtttgcc------atttttctgtgatctgcagTCTGATGATGAACGGGAAATGTGTGCGAGGACTATTTACTGCACAAACATTGACAAGAAGGTTCCCTACCTACACTCATGCTATACCACTAGGTGTTCAT
    | ||  ||      |    | | |||  |        |||   ||| || |     ||| ||| ||  | || ||       |  ||      ||  | || |  |   |||||||| |||||| |||| |||||| | || || ||||| |||||||| ||||||||||||                                        
----gtaatgtttcttctttgttagagttgcctattacatttag---aagattgaccagagtagctgataatgcatctattttgtctgacctatctaatggtgctatatttctcagTCTGAAGATGAAAGGGAGATGTGTTCAAGAACAATTTATTGCACAAATATTGACAAGAAG----------------------------------------

upper sequence: GRMZM2G173428_T04 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA06G14030.2 (Glycine max), 3'ss of exon 7
gtatgcaaccttcaggaatcaacatacttgtgttaagttcatagcccaaggttcattcttgtatctggtatggtatttaaaaaagtttgcc-attt-----ttctgtgatctgcagTCTGATGATGAACGGGAAATGTGTGCGAGGACTATTTACTGCACAAACATTGACAAGAAGGTTCCCTACCTACACTCATGCTATACCACTAGGTGTTCAT
    | ||  ||      |    | | |||  |        ||    | | || |     ||| ||| ||  | || |        |  || || |     | || |  |   |||||||| |||||| |||| |||||| | || || ||||| |||||||| ||||||||||||                                        
----gtaatgtttcttctttgttagagttgcctattacatttaaaagatgattgaccagagtagctgataatgcatctctttggtctgacctatctaacggtgctatatttctcagTCTGAAGATGAAAGGGAGATGTGTTCAAGAACAATTTATTGCACAAATATTGACAAGAAG----------------------------------------

upper sequence: GRMZM2G173428_T04 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA02G35640.1 (Glycine max), 3'ss of exon 6
gtatgcaaccttcaggaatcaacatacttgtgttaagttcatagcccaaggttcattcttgtatctggtatggtatttaaaaaagtttgcc------atttttctgtgatctgcagTCTGATGATGAACGGGAAATGTGTGCGAGGACTATTTACTGCACAAACATTGACAAGAAGGTTCCCTACCTACACTCATGCTATACCACTAGGTGTTCAT
         ||||     |  |  | | |   |||  || | |    | | || | |   ||| ||| ||  | || |        |  ||      ||  | || |  |   |||||||| |||||| |||| |||||| | || || ||||| |||||||| ||||||||||||                                        
-----gtttcttctttgttagagttgccta--ttacatttaaaag--atgattgactagagtagctgataatgcatctctttggtctgacctatctaatggtgctatatttctcagTCTGAAGATGAAAGGGAGATGTGTTCAAGAACAATTTATTGCACAAATATTGACAAGAAG----------------------------------------

upper sequence: GRMZM2G173428_T04 (Zea mays), 3'ss of exon 5
lower sequence: AT4G10610.2 (Arabidopsis thaliana), 3'ss of exon 5
gtatgcaaccttcaggaatcaacatacttgtgttaagttcatagcccaaggttcattcttgtatctggtatggtatttaaaaaagtttgccatttttctgtg---atctgcagTCTGATGATGAACGGGAAATGTGTGCGAGGACTATTTACTGCACAAACATTGACAAGAAGGTTCCCTACCTACACTCATGCTATACCACTAGGTGTTCAT
              | ||      | ||||||||   | || |  |  |  | ||   || |   |  | |   | | || |   ||     |  | ||||     |    || |||| ||||| || || |||||||| || ||||| |||||||| |||||||||||||||                                        
--------------gtaaggttttttcttgtgtttcat-cacattctgac-tgcaaagttatggtt--ttttagactcaagaggtttgattttagtcctgtctttgttcttagACTGAAGATGAGCGTGAGATGTGTGCAAGAACTATCTACTGCACTAACATTGACAAGAAG----------------------------------------

upper sequence: GRMZM2G173428_T04 (Zea mays), 3'ss of exon 5
lower sequence: Vv16s0098g01040.t01 (Vitis vinifera), 3'ss of exon 6
gtatgcaaccttcaggaatcaacatacttgtgttaagttcatagcccaaggttcattcttgtatctggtatggtatttaaaaaagtttgccatttttctgtgatctgcagTCTGATGATGAACGGGAAATGTGTGCGAGGACTATTTACTGCACAAACATTGACAAGAAGGTTCCCTACCTACACTCATGCTATACCACTAGGTGTTCAT
  |||        || |||    |||  |  |  | || |     | ||  ||  ||  | | |||  | || |  ||||  || |      || |  ||| |||  |||||||| |||||||| |||||||| || |||||||||||||| ||||| ||||| ||||||                                        
acatgttggtgctagaaatgggtatagcttagaaacgtgc-cgatcaaacattgtttactatttct--tgtgcttgttaattaaat-----gttatcgtgtcatc--cagTCTGAAGATGAACGTGAAATGTGCGCCAGGACTATTTACTGTACAAATATTGATAAGAAG----------------------------------------

upper sequence: GRMZM2G173428_T04 (Zea mays), 3'ss of exon 5
lower sequence: PP1S62_224V6.1 (Physcomitrella patens), 3'ss of exon 5
gtatgcaaccttcaggaatcaacatacttgtgttaagttcatagcccaaggttcattcttgtatctggtatggtatttaaaa--aagtttgccatttttctgtgatctgcagTCTGATGATGAACGGGAAATGTGTGCGAGGACTATTTACTGCACAAACATTGACAAGAAGGTTCCCTACCTACACTCATGCTATACCACTAGGTGTTCAT
    | ||   |     |    || ||   |||||   | |||  |||  |||| |   |    || | |||   | |      || || |  | | | |       | |||||||| ||||| || |||||||||||  |||| || ||||| ||||| ||||||||||||                                        
----ggaattgtttcatacttgca-acgattgttag--tgatatgccatagttcttgaatacggctcggatgaattctggctctaacttagttactctcca-----ttacagTCTGAAGATGAGCGTGAAATGTGTGCACGGACCATCTACTGTACAAATATTGACAAGAAG----------------------------------------

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|26558720|gb|CA830955.1|CA830955
EST:     ACATTCCTACCCAGG                         TCTGATGATGAACGGGAAATGTGTGCGAGGACTATTTACTGCACAAACATT
genomic: ACATTCCTACCCAGGgtatgcaacc ... tgatctgcagTCTGATGATGAACGGGAAATGTGTGCGAGGACTATTTACTGCACAAACATT
EST: gi|87156308|gb|DY401097.1|DY401097
EST:     ACATTCCTACCCAGG                         TCTGATGATGAACGGGAAATGTGTGCGAGGACTATTTACTGCACAAACATT
genomic: ACATTCCTACCCAGGgtatgcaacc ... tgatctgcagTCTGATGATGAACGGGAAATGTGTGCGAGGACTATTTACTGCACAAACATT
EST: gi|23199581|gb|BU582146.1|BU582146
EST:     ACATTCCTACCCAGG                         TCTGATGATGAACGGGAAATGTG-GCGAGGACTATTTACTGCACAAACATT
genomic: ACATTCCTACCCAGGgtatgcaacc ... tgatctgcagTCTGATGATGAACGGGAAATGTGTGCGAGGACTATTTACTGCACAAACATT
EST: gi|78116430|gb|DV534817.1|DV534817
EST:     TGCCATCGAAAACTGCCATTGCACCAGTCAATCCAACATTCCTACCCAGG                         TCTGATGATGAACGGGAAATGTGTGCGAGGACTATTTACTGCACAAACATT
genomic: TGCCATCGAAAACTGCCATTGCACCAGTCAATCCAACATTCCTACCCAGGgtatgcaacc ... tgatctgcagTCTGATGATGAACGGGAAATGTGTGCGAGGACTATTTACTGCACAAACATT
EST: gi|22545785|gb|BU098159.1|BU098159
EST:     TTCCTACCCAGG                         TCTGATGATGAACGGGAAATGTG-GCGAGGACTATTTACTGCACAAACATT
genomic: TTCCTACCCAGGgtatgcaacc ... tgatctgcagTCTGATGATGAACGGGAAATGTGTGCGAGGACTATTTACTGCACAAACATT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcttgtatctggtatggtatttaaaaaagtttgccatttttctgtgatctgcagTCTGATGATGAACGGGAAATGTGTGCGAGGACTATTTACTGCACAAACATTGACAAGAAGGTTCCCTACCTACACTCATGCTATACCACTAGGTGTTCAT
                                     tttttctgt  CT-rich tract
                  tatttaaaaaagttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgcaaccttcaggaatcaacatacttgtgttaagttcatagcccaaggttcattcttgtatctggtatggtatttaaaaaagtttgccatttttctgtgatctgcagTCTGATGATGAACGGGAAATGTGTGCGAGGACTATTTACTGCACAAACATTGACAAGAAGGTTCCCTACCTACACTCATGCTATACCACTAGGTGTTCAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG