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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgctagatctctgttacatgagaggtggtatattttcatagtttttcctgatattggtgtttgtgattgtctgtaacagACCATCAAGACAAATGTTATTGGTACCCTGAACATGCTAGGACTTGCAAAGAGAGTTGGAGCTAG

Basic information

species Zea mays
transcript GRMZM2G165357_T02
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G165357_T02 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os03g16980.4 (Oryza sativa), 3'ss of exon 5
------------------------gtatgctagatctctgttacatgagaggtggtatattttcatagtttttcctgatattggtgtttgtg-attgtctgtaacagACCATCAAGACAAATGTTATTGGTACCCTGAACATGCTAGGACTTGCAAAGAGAGTTGGAGCTAG
                         | || ||  || |   ||    |       | | | |||||    | | ||||||||    |   || ||  ||    |||||||||||||||||| ||||| || |||||||||||||| |||||||| |||||||||||||||||
gtacagtctctattatatatataactctgttaagtc-caactattcaaatacaaatct-tgttcatgtcctgttctgatatttaaatggatgtataatcatgtacagACCATCAAGACAAACGTTATCGGAACCCTGAACATGCTTGGACTTGCCAAGAGAGTTGGAGCTAG

upper sequence: GRMZM2G165357_T02 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA11G15020.1 (Glycine max), 3'ss of exon 5
-------------gtatgctagatctctgttacatgagaggtggtatattttcatagtttttcctgatattg------gtgtttgtgat-tgtctgtaacagACCATCAAGACAAATGTTATTGGTACCCTGAACATGCTAGGACTTGCAAAGAGAGTTGGAGCTAG
              | ||  |  | | | || | ||| || |  | | |||     | |  |   || | |        |||| |  |  |   | | |||||| || ||||||||||| ||||| || ||||||||||| || ||||||||  ||||||| || ||
atattaattctacttctgtcatgtgt-tattgcttgaaagttc-tgtttttcagctgatccttgagacactatctaatatgttaggaaaataatttttacagACAATAAAGACAAATGTGATTGGCACACTGAACATGCTTGGGCTTGCAAAACGAGTTGGGGCAAG

upper sequence: GRMZM2G165357_T02 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA13G40960.1 (Glycine max), 3'ss of exon 6
gtatgctagatctctgtta--catgagaggtggtatattttcatagttt-----ttcctga-----tattggt---gtttgtgattgtctg------taacagACCATCAAGACAAATGTTATTGGTACCCTGAACATGCTAGGACTTGCAAAGAGAGTTGGAGCTAG
   ||        |||| |  ||| |  | | | |  || ||   | ||     | | |||     |||   |    ||||| || |  |       | |||||| || ||||||||||| ||||| || ||||||||||| || ||||||||| |||| ||||| ||
---tgtctacctcctgtcatgcatcattgatcgaaagttctctctgcttatctgtccttgaaagactatatatctaatttgtaatggagtaattactttacagACAATAAAGACAAATGTGATTGGCACACTGAACATGCTTGGGCTTGCAAAGCGAGTAGGAGCAAG

upper sequence: GRMZM2G165357_T02 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA12G06990.1 (Glycine max), 3'ss of exon 5
---gtatgctagatctctgttacatgagaggt------ggtatattttcatagtttttcct---gatattg------gtgtttgtgattgtctgtaacagACCATCAAGACAAATGTTATTGGTACCCTGAACATGCTAGGACTTGCAAAGAGAGTTGGAGCTAG
    | |  |  |  ||||| |  ||  |  |       ||    |||   || || ||||   || | |        |||| |  | |   | | |||||| || ||||||||||| |||||||| ||||||||||| || ||||| ||| ||||||| || ||
tatatttattctacttctgtcatgtgtcatatcttgaaagttctgtttttcagcttatccttgagacactatctaatatgttgggaaataatttttacagACAATAAAGACAAATGTGATTGGTACACTGAACATGCTTGGGCTTGCCAAGCGAGTTGGGGCAAG

upper sequence: GRMZM2G165357_T02 (Zea mays), 3'ss of exon 4
lower sequence: Vv13s0019g00840.t01 (Vitis vinifera), 3'ss of exon 5
gtatgctagatctctgttacatgagaggtggtatattttc--------atagttt-----ttcctgatattggtgtttgtgatt------gtctgtaacagACCATCAAGACAAATGTTATTGGTACCCTGAACATGCTAGGACTTGCAAAGAGAGTTGGAGCTAG
 | | |||  |   |  |   | |    |  ||| ||||         ||  |||     ||  ||||  |  |  |||| | |       |   |||||||| || ||||||||||| ||||| ||| |||||||| | || ||||| |||||||||||||| ||
-tcttctaatttcttaatgagtaatcaattatatgtttttccctgagtatgctttggacattaatgatggttttccttgtaaatcatgcaatacttaacagACAATAAAGACAAATGTGATTGGCACCTTGAACATGTTGGGGCTTGCCAAGAGAGTTGGAGCCAG

upper sequence: GRMZM2G165357_T02 (Zea mays), 3'ss of exon 4
lower sequence: PP1S189_118V6.1 (Physcomitrella patens), 3'ss of exon 5
-------------gtatgctagatc-tctgttacatgagaggtggtatat-tttca----tagtttttcctgatattggtgtttgtgattgtctgtaacagACCATCAAGACAAATGTTATTGGTACCCTGAACATGCTAGGACTTGCAAAGAGAGTTGGAGCTAG
             | || || || | | |||    |||   |   | |   |||||     || ||    ||| ||| | |||||  | |   | |  |||||||||||||||||||| |||||||| || |||||||| ||||| || ||  ||||||| || ||
tatatatatataagaatccttgagcgtttgtagagtgaagagatatgtgcgtttcagtttcagattggtttgaaatttg-gtttgaaacttcattttgcagACCATCAAGACAAATGTGATTGGTACGCTCAACATGCTTGGACTCGCTAAACGAGTTGGTGCAAG

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|32829264|gb|CD968942.1|CD968942
EST:     ACCTTGCTTGCCCTGCTTCACCAATCTTCTACAAGCACAACCCTGTTAAG                         ACCATCAAGACAAATGTTATTGGT
genomic: ACCTTGCTTGCCCTGCTTCACCAATCTTCTACAAGCACAACCCTGTTAAGgtatgctaga ... tctgtaacagACCATCAAGACAAATGTTATTGGT
EST: gi|149070503|gb|EE158907.2|EE158907
EST:     ACCTTGCTTGCCCTGCTTCACCAATCTTCTACAAGCACAACCCTGTTAAG                         ACCATCAAGACAAATGTTATTGGTACCCTGAACATGCTAGGACTTGCAAAG
genomic: ACCTTGCTTGCCCTGCTTCACCAATCTTCTACAAGCACAACCCTGTTAAGgtatgctaga ... tctgtaacagACCATCAAGACAAATGTTATTGGTACCCTGAACATGCTAGGACTTGCAAAG
EST: gi|211182716|gb|FL410032.1|FL410032
EST:     ACCTTGCTTGCCCTGCTTCACCAATCTTCTACAAGCACAACCCTGTTAAG                         ACCATCAAGACAAATGTTATTGGTACCCTGAACATGCTTGGACTTGCAAAG
genomic: ACCTTGCTTGCCCTGCTTCACCAATCTTCTACAAGCACAACCCTGTTAAGgtatgctaga ... tctgtaacagACCATCAAGACAAATGTTATTGGTACCCTGAACATGCTAGGACTTGCAAAG
EST: gi|32829447|gb|CD969125.1|CD969125
EST:     ACCTTGCTTGCCCTGCTTCACCAATCTTCTACAAGCACAACCCTGTTAAG                         ACCATCAAGACAAATGTTATTGGT
genomic: ACCTTGCTTGCCCTGCTTCACCAATCTTCTACAAGCACAACCCTGTTAAGgtatgctaga ... tctgtaacagACCATCAAGACAAATGTTATTGGT
EST: gi|149082965|gb|EE172201.2|EE172201
EST:     ACCTTGCTTGCCCTGCTTCACCAATCTTCTACAAGCACAACCCTGTTAAG                         ACCATCAAGACAAATGTTATTGGTACCCTGAACATGCTAGGACTTGCAAAG
genomic: ACCTTGCTTGCCCTGCTTCACCAATCTTCTACAAGCACAACCCTGTTAAGgtatgctaga ... tctgtaacagACCATCAAGACAAATGTTATTGGTACCCTGAACATGCTAGGACTTGCAAAG
EST: gi|60394382|gb|DN227252.1|DN227252
EST:     ACCTTGCTTGCCCTGCTTCACCAATCTTCTACAAGCACAACCCTGTTAAG                         ACCATCAAGACAAATGTTATTGGTACCCTGAACATGCTAGGACTTGCAAAG
genomic: ACCTTGCTTGCCCTGCTTCACCAATCTTCTACAAGCACAACCCTGTTAAGgtatgctaga ... tctgtaacagACCATCAAGACAAATGTTATTGGTACCCTGAACATGCTAGGACTTGCAAAG
EST: gi|149070980|gb|EE159385.2|EE159385
EST:     ACCTTGCTTGCCCTGCTTCACCAATCTTCTACAAGCACAACCCTGTTAAG                         ACCATCAAGACAAATGTTATTGGTACCCTGAACATGCTAGGACTTGCAAAG
genomic: ACCTTGCTTGCCCTGCTTCACCAATCTTCTACAAGCACAACCCTGTTAAGgtatgctaga ... tctgtaacagACCATCAAGACAAATGTTATTGGTACCCTGAACATGCTAGGACTTGCAAAG
EST: gi|32914071|gb|CF018883.1|CF018883
EST:     ACCTTGCTTGCCCTGCTTCACCAATCTTCTACAAGCACAACCCTGTTAAG                         ACCATCAAGACAAATGTTATTGGTACCCTGAACATGCTAGGACTTGCAAAG
genomic: ACCTTGCTTGCCCTGCTTCACCAATCTTCTACAAGCACAACCCTGTTAAGgtatgctaga ... tctgtaacagACCATCAAGACAAATGTTATTGGTACCCTGAACATGCTAGGACTTGCAAAG
EST: gi|71444250|gb|DR825300.1|DR825300
EST:     ACCTTGCTTGCCCTGCTTCACCAATCTTCTACAAGCACAACCCTGTTAAG                         ACCATCGAGACAAATGTTATTGGTACCCTGAACATGCTAGGACTTGCAAAG
genomic: ACCTTGCTTGCCCTGCTTCACCAATCTTCTACAAGCACAACCCTGTTAAGgtatgctaga ... tctgtaacagACCATCAAGACAAATGTTATTGGTACCCTGAACATGCTAGGACTTGCAAAG
EST: gi|60339871|gb|DN206844.1|DN206844
EST:     ACCTTGCTTGCCCTGCTTCACCAATCTTCTACAAGCACAACCCTGTTAAG                         ACCATCAAGACAAATGTTATTGGTACCCTGAACATGCTAGGACTTGCAAAG
genomic: ACCTTGCTTGCCCTGCTTCACCAATCTTCTACAAGCACAACCCTGTTAAGgtatgctaga ... tctgtaacagACCATCAAGACAAATGTTATTGGTACCCTGAACATGCTAGGACTTGCAAAG
EST: gi|15100352|gb|BI396143.1|BI396143
EST:     ACCTTGCTTGCCCTGCTTCACCAATCTTCTACAAGCACAACCCTGTTAAG                         ACCATCAAGACAAATGTTATTGGTACCCTGAACATGCTTGGACTTGCAAAG
genomic: ACCTTGCTTGCCCTGCTTCACCAATCTTCTACAAGCACAACCCTGTTAAGgtatgctaga ... tctgtaacagACCATCAAGACAAATGTTATTGGTACCCTGAACATGCTAGGACTTGCAAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtggtatattttcatagtttttcctgatattggtgtttgtgattgtctgtaacagACCATCAAGACAAATGTTATTGGTACCCTGAACATGCTAGGACTTGCAAAGAGAGTTGGAGCTAG
                     tcctgat  putative branch site (score: 3)
     atattttcatagtttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgctagatctctgttacatgagaggtggtatattttcatagtttttcctgatattggtgtttgtgattgtctgtaacagACCATCAAGACAAATGTTATTGGTACCCTGAACATGCTAGGACTTGCAAAGAGAGTTGGAGCTAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCT