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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aagagtctaacagatcactgctgctccttttttaatcagtgtatgtgtgcttcctcatgagttaagcacttatcttgtaaatcctttctatctgttttagATGTCACCGAGCCACTTCTTGTGGAGGTTGACCAGATCTATCACCTTGCTTGCCCTGCTTCACCAATCTTCTACAAGCACAATCCTGTTAAG

Basic information

species Zea mays
transcript GRMZM2G044027_T02
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G044027_T02 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os03g16980.4 (Oryza sativa), 3'ss of exon 4
---aagagtctaacagatcactgctgctccttttttaatcagtgtatgtgtgcttcctcatgagttaagcacttatcttgtaaatcctttctatctgttttagATGTCACCGAGCCACTTCTTGTGGAGGTTGACCAGATCTATCACCTTGCTTGCCCTGCTTCACCAATCTTCTACAAGCACAATCCTGTTAAG
   ||||  ||||    |   |||      || | |  |   |  |   ||   |  |  |||| ||   |   || ||| |  |  ||| |||   ||| |||||||||| |||| || ||||||||||||||||| ||||||||||||||||||||||||||||||||||||||||||||||| ||||| |||
cttaagacactaaactttttttgcgatcagttctatcgtatcttcaaaagtatattattgtgagatattaaa--attttg-accttttttttattcatttcagATGTCACCCAGCCCCTGCTTGTGGAGGTTGACCAAATCTATCACCTTGCTTGCCCTGCTTCACCAATCTTCTACAAGCACAACCCTGTCAAG

upper sequence: GRMZM2G044027_T02 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA11G15010.1 (Glycine max), 3'ss of exon 4
aagagtctaacagatcactgctgctccttttttaatcagtgtatgtgtgcttcctca--tgagtt---aagcacttatcttgtaaatcctttctatctgttt---tagATGTCACCGAGCCACTTCTTGTGGAGGTTGACCAGATCTATCACCTTGCTTGCCCTGCTTCACCAATCTTCTACAAGCACAATCCTGTTAAG
        |||| | ||    || | || |      ||| || | | ||| |  | |  || |||   |   | |||   || |  | ||||   | |   |    ||||||||| |||| | |  |  | |||||||| || |||||||| ||||| ||||||||||| ||||||||||||||  |||| ||||| |||
--------aacataacatgaatgattctatcaggtgcagagtttctctgcgtttttagatgtgttttaatttaattaaaatgcatgtacttttcttttccctgaacagATGTCACAGAGCAATTGTTGATTGAGGTTGATCAAATCTATCATCTTGCATGCCCTGCTTCTCCAATCTTCTACAAATACAACCCTGTAAAG

upper sequence: GRMZM2G044027_T02 (Zea mays), 3'ss of exon 4
lower sequence: AT3G46440.1 (Arabidopsis thaliana), 3'ss of exon 4
-aagagtctaacagatcactg--ctgctccttttttaatcagtgtatgtgtgcttcctcatgagttaagcacttatcttgtaaatcctttctatctgttttagATGTCACCGAGCCACTTCTTGTGGAGGTTGACCAGATCTATCACCTTGCTTGCCCTGCTTCACCAATCTTCTACAAGCACAATCCTGTTAAG--------
  |  || |   |  || |||   || | ||  | |    | || |    | ||  ||  ||   ||  || |||| || |       || |   | |   ||||||||| ||||||||| |  | |||||||| ||||| || || ||||| || |||||||| || |||||||||||| |||| ||||| |||        
gtatggttttgaaattctctggcttgttgctgctattgagaatggaatattcctgtcttttgttctatccatttatattttgg-----ttttgggtttaacagATGTCACGGAGCCACTTTTGATCGAGGTTGATCAGATTTACCATCTTGCATGTCCTGCTTCTCCTATCTTCTACAAGTACAACCCTGTGAAGACAATCAA

upper sequence: GRMZM2G044027_T02 (Zea mays), 3'ss of exon 4
lower sequence: PP1S189_118V6.1 (Physcomitrella patens), 3'ss of exon 4
---aagagtctaa----cagatcactgctgctcctttttta-atcagtgt-atgtgtgcttcctcatgagttaagcacttatcttgtaaatcctttctatctgttttagATGTCACCGAGCCACTTCTTGTGGAGGTTGACCAGATCTATCACCTTGCTTGCCCTGCTTCACCAATCTTCTACAAGCACAATCCTGTTAAG
    | |||  ||    |||   | ||    | || |||||  |  |||  | ||   | || |    || | |     | | || |  |||| |  ||||||    |||||| || ||| || |  |||| || || |||||||| ||||| || ||||| ||||||||||| || ||||||||| ||||| | || |||
aattaaagttaaatctgcagtgtattgaacatgctattttatgttggtgggaagtaaacatctt----agctgattttgtgtatttt--atccctcatatctgc---agATGTGACAGAGACATTATTTGTTGAAGTAGACCAGATTTATCATCTGGCTTGTCCTGCTTCACCCATTTTCTACAAGTACAATGCCGTGAAG

upper sequence: GRMZM2G044027_T02 (Zea mays), 3'ss of exon 4
lower sequence: EFJ17446 (Selaginella moellendorffii), 3'ss of exon 3
aagagtctaacagatcactgctgctccttttttaatcagtgtatgtgtgcttcctcatgagttaagcacttatcttgtaaatcctttctatctgttttagATGTCACCGAGCCACTTCTTGTGGAGGTTGACCAGATCTATCACCTTGCTTGCCCTGCTTCACCAATCTTCTACAAGCACAATCCTGTTAAG
                                            || || | |  ||  |||   |||  ||   ||   || ||  ||  |||||| ||| ||||| |||||  | |||||||| ||||||||||| || || || || || || ||||| || |||||||||||| ||||||| || || 
--------------------------------------------gtatggtgcg-cacaagtgttgcaacta---tgatcatgctg-ctccctgtttcagACGTCACGGAGCCTTTGCTTGTGGAAGTTGACCAGATTTACCATCTGGCATGTCCCGCTTCTCCCATCTTCTACAAGTACAATCCCGTGAAA

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|6637013|gb|AW261285.1|AW261285
EST:     TAACCTGAAGAAGTGGATCGGACACCCAAGATTTGAGCTCATCCGCCATG                         ATGTCACCGAGCCACTTCTTGTGGAGGTTGACCAGATCTATCACCTTGCTT
genomic: TAACCTGAAGAAGTGGATCGGACACCCAAGATTTGAGCTCATCCGCCATGgtaaataact ... tctgttttagATGTCACCGAGCCACTTCTTGTGGAGGTTGACCAGATCTATCACCTTGCTT
EST: gi|149097834|gb|EE183762.2|EE183762
EST:     TAACCTGAAGAAGTGGATCGGACACCCAAGATTTGAGCTCATCCGCCATG                         ATGTCACCGAGCCACTTCTTGTGGAGGTTGACCAGATCTATCACCTTGCTT
genomic: TAACCTGAAGAAGTGGATCGGACACCCAAGATTTGAGCTCATCCGCCATGgtaaataact ... tctgttttagATGTCACCGAGCCACTTCTTGTGGAGGTTGACCAGATCTATCACCTTGCTT
EST: gi|14206834|gb|BG840512.1|BG840512
EST:     CGGACACCCAAGATTTGAGCTCATCCGCCATG                         ATGTCACCGAGCCACTTCTTGTGGAGGTTGACCAGATCTATCACCTTGCTT
genomic: CGGACACCCAAGATTTGAGCTCATCCGCCATGgtaaataact ... tctgttttagATGTCACCGAGCCACTTCTTGTGGAGGTTGACCAGATCTATCACCTTGCTT
EST: gi|6194647|gb|AW146751.1|AW146751
EST:     TAACCTGAAGAAGTGGATCGGACACCCAAGATTTGAGCTCATCCGCCATG                         ATGTCACTGAGCCACTTCTTGTGGAGGTTGACCAGATCTATCACCTTGCTT
genomic: TAACCTGAAGAAGTGGATCGGACACCCAAGATTTGAGCTCATCCGCCATGgtaaataact ... tctgttttagATGTCACCGAGCCACTTCTTGTGGAGGTTGACCAGATCTATCACCTTGCTT
EST: gi|6020952|gb|AW065880.1|AW065880
EST:     TAACCTGAAGAAGTGGATCGGACACCCAAGATTTGAGCTCATCCGCCATG                         ATGTCACTGAGCCACTTCTTGTGGAGGTTGACCAGATCTATCACCTTGCTT
genomic: TAACCTGAAGAAGTGGATCGGACACCCAAGATTTGAGCTCATCCGCCATGgtaaataact ... tctgttttagATGTCACCGAGCCACTTCTTGTGGAGGTTGACCAGATCTATCACCTTGCTT
EST: gi|211032180|gb|FL277400.1|FL277400
EST:     TCATCCGCCATG                         ATGTCACTGAGCCACTTCTTGTGGAGGTTGACCAGATCTATCACCTTGCTT
genomic: TCATCCGCCATGgtaaataact ... tctgttttagATGTCACCGAGCCACTTCTTGTGGAGGTTGACCAGATCTATCACCTTGCTT
EST: gi|60672298|gb|DN475062.1|DN475062
EST:     TAACCTGAAGAAGTGGATCGGACACCCAAGATTTGAGCTCATCCGCCATG                         ATGTCACCGAGCCACTTCTTGTGGAGGTTGACCAGGTCTATCACCTTGCTT
genomic: TAACCTGAAGAAGTGGATCGGACACCCAAGATTTGAGCTCATCCGCCATGgtaaataact ... tctgttttagATGTCACCGAGCCACTTCTTGTGGAGGTTGACCAGATCTATCACCTTGCTT
EST: gi|32788262|gb|CD940498.1|CD940498
EST:     TAACCTGAAGAAGTGGATCGGACACCCAAGATTTGAGCTCATCCGCCATG                         ATGTCACCGAGCCACTTCTTGTGGAGGTTGACCAGATC
genomic: TAACCTGAAGAAGTGGATCGGACACCCAAGATTTGAGCTCATCCGCCATGgtaaataact ... tctgttttagATGTCACCGAGCCACTTCTTGTGGAGGTTGACCAGATC
EST: gi|40334152|gb|CK368222.1|CK368222
EST:     TAACCTGAAGAAGTGGATCGGACACCCAAGATTTGAGCTCATCCGCCATG                         ATGTCACCGAGCCACTTCTTGTGGAGTTTGACCAGATCTATCACCTTGCTT
genomic: TAACCTGAAGAAGTGGATCGGACACCCAAGATTTGAGCTCATCCGCCATGgtaaataact ... tctgttttagATGTCACCGAGCCACTTCTTGTGGAGGTTGACCAGATCTATCACCTTGCTT
EST: gi|22473192|gb|BU037672.1|BU037672
EST:     TAACCTGAAGAAGTGGATCGGACACCCAAGATTTGAGCTCATCCGCCATG                         ATGTCACTGAGCCACTTCTTGTGGAGGTTGACCAGATCTATCACCTTGCTT
genomic: TAACCTGAAGAAGTGGATCGGACACCCAAGATTTGAGCTCATCCGCCATGgtaaataact ... tctgttttagATGTCACCGAGCCACTTCTTGTGGAGGTTGACCAGATCTATCACCTTGCTT
EST: gi|213173372|gb|FM186537.1|FM186537
EST:     TAACCTGAAGAAGTGGATCGGACACCCAAGATTTGAGCTCATCCGCCATG                         ATGTCACCGAGCCACTTCTTGTGGAGGTTGACCAGATCTATCACCTTGCTT
genomic: TAACCTGAAGAAGTGGATCGGACACCCAAGATTTGAGCTCATCCGCCATGgtaaataact ... tctgttttagATGTCACCGAGCCACTTCTTGTGGAGGTTGACCAGATCTATCACCTTGCTT
EST: gi|26558105|gb|CA830340.1|CA830340
EST:     TAACCTGAAGAAGTGGATCGGACACCCAAGATTTGAGCTCATCCGCCATG                         ATGTCACTGAGCCACTTCTTGTGGAGGTTGACCAGATCTATCACCTTGCTT
genomic: TAACCTGAAGAAGTGGATCGGACACCCAAGATTTGAGCTCATCCGCCATGgtaaataact ... tctgttttagATGTCACCGAGCCACTTCTTGTGGAGGTTGACCAGATCTATCACCTTGCTT
EST: gi|148945878|gb|EC891170.2|EC891170
EST:     TAACCTGAAGAAGTGGATCGGACACCCAAGATTTGAGCTCATCCGCCATG                         ATGTCACCGAGCCACTTCTTGTGGAGGTTGACCAGATCTATCACCTTGCTT
genomic: TAACCTGAAGAAGTGGATCGGACACCCAAGATTTGAGCTCATCCGCCATGgtaaataact ... tctgttttagATGTCACCGAGCCACTTCTTGTGGAGGTTGACCAGATCTATCACCTTGCTT
EST: gi|67016223|gb|CO444972.1|CO444972
EST:     TAACCTGAAGAAGTGGATCGGACACCCAAGATTTGAGCTCATCCGCCATG                         ATGTCACTGAGCCACTTCTTGTGGAGGTTGACCAGATCTATCACCTTGCTT
genomic: TAACCTGAAGAAGTGGATCGGACACCCAAGATTTGAGCTCATCCGCCATGgtaaataact ... tctgttttagATGTCACCGAGCCACTTCTTGTGGAGGTTGACCAGATCTATCACCTTGCTT
EST: gi|67013235|gb|CO441984.1|CO441984
EST:     TAACCTGAAGAAGTGGATCGGACACCCAAGATTTGAGCTCATCCGCCATG                         ATGTCACTGAGCCACTTCTTGTGGAGGTTGACCAGATCTATCACCTTGCTT
genomic: TAACCTGAAGAAGTGGATCGGACACCCAAGATTTGAGCTCATCCGCCATGgtaaataact ... tctgttttagATGTCACCGAGCCACTTCTTGTGGAGGTTGACCAGATCTATCACCTTGCTT
EST: gi|21987903|gb|BQ779431.1|BQ779431
EST:     TAACCTGAAGAAGTGGATCGGACACCCAAGATTTGAGCTCATCCGCCATG                         ATGTCACTGAGCCACTTCTTGTGGAGGTTGACCAGATCTATCACCTTGCTT
genomic: TAACCTGAAGAAGTGGATCGGACACCCAAGATTTGAGCTCATCCGCCATGgtaaataact ... tctgttttagATGTCACCGAGCCACTTCTTGTGGAGGTTGACCAGATCTATCACCTTGCTT
EST: gi|32165003|gb|CD670321.1|CD670321
EST:     TAACCTGAAGAAG-GGATCGGACACCCAAGATTTGAGCTCATCCGCCATG                         ATGTCACCGAGCCACTTCTTGTGGAGGTTGACCAGATCTATCACCTTGCTT
genomic: TAACCTGAAGAAGTGGATCGGACACCCAAGATTTGAGCTCATCCGCCATGgtaaataact ... tctgttttagATGTCACCGAGCCACTTCTTGTGGAGGTTGACCAGATCTATCACCTTGCTT
EST: gi|148951041|gb|EC896695.2|EC896695
EST:     TAACCTGAAGAAGTGGATCGGACACCCAAGATTTGAGCTCATCCGCCATG                         ATGTCACCGAGCCACTTCTTGTGGAGGTTGACCAGATCTATCACCTTGCTT
genomic: TAACCTGAAGAAGTGGATCGGACACCCAAGATTTGAGCTCATCCGCCATGgtaaataact ... tctgttttagATGTCACCGAGCCACTTCTTGTGGAGGTTGACCAGATCTATCACCTTGCTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtgcttcctcatgagttaagcacttatcttgtaaatcctttctatctgttttagATGTCACCGAGCCACTTCTTGTGGAGGTTGACCAGATCTATCACCTTGCTTGCCCTGCTTCACCAATCTTCTACAAGCACAATCCTGTTAAG
                                    tcctttctatctgttt  CT-rich tract
                             ttgtaaat  TA-rich tract