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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgtgcgcctccttccactgatttatcgatttgcctaccctgttttccccgttgggcgttctcatcgaattcccgagtttggctccgtgcatgtgcagACAGGAAGTTTGGTAAAGGGAAGGATAAGATCGACGATGAGGACATCACCTTCCAGCGCATGGTTGCAAAG

Basic information

species Zea mays
transcript GRMZM2G146786_T01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G146786_T01 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os02g42540.1 (Oryza sativa), 3'ss of exon 1
gtgtgcgcctccttccactgatttatcgatttgcctaccctgttttccccgttgggcgttct------catcgaattcccgagtttggctccgtgcatgtgcagACAGGAAGTTTGGTAAAGGGAAGGATAAGATCGACGATGAGGACATCACCTTCCAGCGCATGGTTGCAAAG
|| ||||  |||  |   |  ||  |   |     |    | || |||||  | |  |||||        |||  |   | |  |||  |  | |  | |||||| |||||||  || || |||||||| ||||| || ||||||||||||||||||||||||||||| ||||||
gtttgcgattccggcgcatccttccttcttcccggtttattattctcccccattgatgttctgtgcgctttcggttgttcaatattgattttgggt-tctgcagATAGGAAGTGGGGGAAGGGGAAGGACAAGATTGATGATGAGGACATCACCTTCCAGCGCATGGTCGCAAAG

upper sequence: GRMZM2G146786_T01 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA09G28980.2 (Glycine max), 3'ss of exon 1
-----------------gtgtgcgcctccttccactgatttatcgatttgcctaccctgtt-ttccccgttgggcgttctcatcgaattcccgagtttggctccgtgca--tgtgcagACAGGAAGTTTGGTAAAGGGAAGGATAAGATCGACGATGAGGACATCACCTTCCAGCGCATGGTTGCAAAG
                  | |     |  || | |   ||| || ||| |       |||| ||    |||  |  || || | || ||       | ||     | ||  |  ||||| | ||| |  || || ||||| |||||||| |||||||| ||||| || ||||| |||||||||||||||
gtattattcattccattcttttttttttttttctcaagtttttcaattggttgttgttgttgtttaaagttttgatttttcgtggattttgattactgggtatgtttcaatttcgcagATAAGAAATGGGGCAAGGGGAAAGATAAGATTGACGATGAAGACATTACTTTCCAACGCATGGTTGCAAAG

upper sequence: GRMZM2G146786_T01 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA16G33570.2 (Glycine max), 3'ss of exon 1
------------gtgtgcgcctccttccactgatttatcgatttgcctaccctgttttccccgttgggcgttctcatcgaattcccgagtttggctccgtgcatgt---gcagACAGGAAGTTTGGTAAAGGGAAGGATAAGATCGACGATGAGGACATCACCTTCCAGCGCATGGTTGCAAAG
             |       |  |||  |   ||| || ||| | |  |  |||| |      |     || ||   | |||        ||| |  |||    |   ||||| | ||| |  ||||| || || |||||||| |||||||| ||||| || ||||| |||||||||||||||
gtattcattccattcctaatttttttcttcaagtttttcaattggtcgtcgttgttgtttaaagttttgattttccgtggattttgattactgggtatgtgtcaatttcgcagATAAGAAATGGGGTAAGGGAAAAGATAAGATTGACGATGAAGACATTACTTTCCAACGCATGGTTGCAAAG

upper sequence: GRMZM2G146786_T01 (Zea mays), 3'ss of exon 1
lower sequence: Vv16s0039g00280.t01 (Vitis vinifera), 3'ss of exon 1
gtgtgcgcctccttccactgatttatcgatttgcctaccctgttttccccgttgggcgttctcatcgaattcccgagtttggctccgtgcatgtgcagACAGGAAGTTTGGTAAAGGGAAGGATAAGATCGACGATGAGGACATCACCTTCCAGCGCATGGTTGCAAAG
  ||     || || || ||| |  | |||||          | | |  |  |||| |      ||   ||  |   ||||  |   ||    |||||| | ||| |  || ||||||||||| || || || ||||| || ||||| ||||||||||||||||| |||
--gtat-tttcttttcattgaatgttagatttcatgtatgcatatacaactatgggagaaaatttc---ttatctgatttgaattgttgt---tgcagATAAGAAATGGGGAAAAGGGAAGGACAAAATTGATGATGAAGATATCACTTTCCAGCGCATGGTTGCCAAG

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|211273251|gb|FL384319.1|FL384319
EST:     CATGTCCGGGCGCGAGGTCCGCGAGTACACCAATCTCAGCGACCCCAAAG                         ACAGGAAGTTTGGTAAAGGGAAGGATAAGATCGACGATGAGGACATCACCT
genomic: CATGTCCGGGCGCGAGGTCCGCGAGTACACCAATCTCAGCGACCCCAAAGgtgtgcgcct ... gcatgtgcagACAGGAAGTTTGGTAAAGGGAAGGATAAGATCGACGATGAGGACATCACCT
EST: gi|211532797|gb|FL373547.1|FL373547
EST:     CATGTCCGGGCGCGAGGTCCGCGAGTACACCAATCTCAGCGACCCCAAAG                         ACAGGAAGTTTGGTAAAGGGAAGGATAAGATCGACGATGAGGACATCACCT
genomic: CATGTCCGGGCGCGAGGTCCGCGAGTACACCAATCTCAGCGACCCCAAAGgtgtgcgcct ... gcatgtgcagACAGGAAGTTTGGTAAAGGGAAGGATAAGATCGACGATGAGGACATCACCT
EST: gi|211082871|gb|FL417813.1|FL417813
EST:     CATGTCCGGGCGCGAGGTCCGCGAGTACACCAATCTCAGCGACCCCAAAG                         ACAGGAAGTTTGGTAAAGGGAAGGATAAGATCGACGATGAGGACATCACCT
genomic: CATGTCCGGGCGCGAGGTCCGCGAGTACACCAATCTCAGCGACCCCAAAGgtgtgcgcct ... gcatgtgcagACAGGAAGTTTGGTAAAGGGAAGGATAAGATCGACGATGAGGACATCACCT
EST: gi|211536312|gb|FL400261.1|FL400261
EST:     CATGTCCGGGCGCGAGGTCCGCGAGTACACCAATCTCAGCGACCCCAAAG                         ACAGGAAGTTTGGTAAAGGGAAGGATAAGATCGACGATGAGGACATCACCT
genomic: CATGTCCGGGCGCGAGGTCCGCGAGTACACCAATCTCAGCGACCCCAAAGgtgtgcgcct ... gcatgtgcagACAGGAAGTTTGGTAAAGGGAAGGATAAGATCGACGATGAGGACATCACCT
EST: gi|211413441|gb|FL400135.1|FL400135
EST:     CATGTCCGGGCGCGAKGTCCGCGAGTACACCAATCTCAGCGACCCCAAAG                         ACAGGAAGTTTGGTAAAKGGAAGGATAAGATCGACGATGAGGACATCACCT
genomic: CATGTCCGGGCGCGAGGTCCGCGAGTACACCAATCTCAGCGACCCCAAAGgtgtgcgcct ... gcatgtgcagACAGGAAGTTTGGTAAAGGGAAGGATAAGATCGACGATGAGGACATCACCT
EST: gi|211334889|gb|FL419773.1|FL419773
EST:     CATGTCCGGGCGCGAGGTCCGCGAGTACACCAATCTCAGCGACCCCAAAG                         ACAGGAAGTTTGGTAAAGGGAAGGATAAGATCGACGATGAGGACATCACCT
genomic: CATGTCCGGGCGCGAGGTCCGCGAGTACACCAATCTCAGCGACCCCAAAGgtgtgcgcct ... gcatgtgcagACAGGAAGTTTGGTAAAGGGAAGGATAAGATCGACGATGAGGACATCACCT
EST: gi|211385044|gb|FL404090.1|FL404090
EST:     CATGTCCGGGCGCGAGGTCCGCGAGTACACCAATCTCAGCGACCCCAAAG                         ACAGGAAGTTTGGTAAAGGGAAGGATAAGATCGACGATGAGGACATCACCT
genomic: CATGTCCGGGCGCGAGGTCCGCGAGTACACCAATCTCAGCGACCCCAAAGgtgtgcgcct ... gcatgtgcagACAGGAAGTTTGGTAAAGGGAAGGATAAGATCGACGATGAGGACATCACCT
EST: gi|211421419|gb|FL412843.1|FL412843
EST:     CATGTCCGGGCGCGAGGTCCGCGAGTACACCAATCTCAGCGACCCCAAAG                         ACAGGAAGTTTGGTAAAGGGAAGGATAAGATCGACGATGAGGACATCACCT
genomic: CATGTCCGGGCGCGAGGTCCGCGAGTACACCAATCTCAGCGACCCCAAAGgtgtgcgcct ... gcatgtgcagACAGGAAGTTTGGTAAAGGGAAGGATAAGATCGACGATGAGGACATCACCT
EST: gi|32943201|gb|CF048020.1|CF048020
EST:     TACACCAATCTCAGCGACCCCAAAG                         ACAGGAAGTTTGGTAAAGGGAAGGATAAGATCGACGATGGGGACCATCACC
genomic: TACACCAATCTCAGCGACCCCAAAGgtgtgcgcct ... gcatgtgcagACAGGAAGTTTGGTAAAGGGAAGGATAAGATCGACGATGAGGA-CATCACC
EST: gi|211024425|gb|FL373964.1|FL373964
EST:     CATGTCCGGGCGCGAGGTCCGCGAGTACACCAATCTCAGCGACCCCAAAG                         ACAGGAAGTTTGGTAAAGGGAAGGATAAGATNCGACGATGAGGACATCACC
genomic: CATGTCCGGGCGCGAGGTCCGCGAGTACACCAATCTCAGCGACCCCAAAGgtgtgcgcct ... gcatgtgcagACAGGAAGTTTGGTAAAGGGAAGGATAAGAT-CGACGATGAGGACATCACC
EST: gi|211527056|gb|FL387984.1|FL387984
EST:     CATGTCCGGGCGCGAGGTCCGCGAGTACACCAATCTCAGCGACCCCAAAG                         ACAGGAAGTTTGGTAAAGGGAAGGATAAGATCGACGATGAGGACATCACCT
genomic: CATGTCCGGGCGCGAGGTCCGCGAGTACACCAATCTCAGCGACCCCAAAGgtgtgcgcct ... gcatgtgcagACAGGAAGTTTGGTAAAGGGAAGGATAAGATCGACGATGAGGACATCACCT
EST: gi|211500127|gb|FL425199.1|FL425199
EST:     CATGTCCGGGCGCGAGGTCCGCGAGTACACCAATCTCAGCGACCCCAAAG                         ACAGGAAGTTTGGTAAAGGGAAGGATAAGATCGACGATGAGGACATCACCT
genomic: CATGTCCGGGCGCGAGGTCCGCGAGTACACCAATCTCAGCGACCCCAAAGgtgtgcgcct ... gcatgtgcagACAGGAAGTTTGGTAAAGGGAAGGATAAGATCGACGATGAGGACATCACCT
EST: gi|211494457|gb|FL428223.1|FL428223
EST:     CATGTCCGGGCGCGAGGTCCGCGAGTACACCAATCTCAGCGACCCCAAAG                         ACAGGAAGTTTGGTNAAGGGAWGGATAAGATCGACGATGAGGACATCACCT
genomic: CATGTCCGGGCGCGAGGTCCGCGAGTACACCAATCTCAGCGACCCCAAAGgtgtgcgcct ... gcatgtgcagACAGGAAGTTTGGTAAAGGGAAGGATAAGATCGACGATGAGGACATCACCT
EST: gi|211346219|gb|FL403635.1|FL403635
EST:     CATGTCCGGGCGCGAGGTCCGCGAGTACACCAATCTCAGCGACCCCAAAG                         ACAGGAAGTTTGGTAAAGGGAAGGATAAGATCGACGATGAGGACATCACCT
genomic: CATGTCCGGGCGCGAGGTCCGCGAGTACACCAATCTCAGCGACCCCAAAGgtgtgcgcct ... gcatgtgcagACAGGAAGTTTGGTAAAGGGAAGGATAAGATCGACGATGAGGACATCACCT
EST: gi|93016518|gb|EB642038.1|EB642038
EST:     CGAGTACACCAATCTCAGCGACCCCAAAG                         ACAGGAAGTTTGGTAAAGGGAAGGATAAGATCGACGATGAGGACATCACCT
genomic: CGAGTACACCAATCTCAGCGACCCCAAAGgtgtgcgcct ... gcatgtgcagACAGGAAGTTTGGTAAAGGGAAGGATAAGATCGACGATGAGGACATCACCT
EST: gi|211271661|gb|FL410597.1|FL410597
EST:     CATGTCCGGGCGCGAGGTCCGCGAGTACACCAATCTCAGCGACCCCAAAG                         ACAGGAAGTTTGGTAAAGGGAAGGATAAGATCGACGATGAGGACATCACCT
genomic: CATGTCCGGGCGCGAGGTCCGCGAGTACACCAATCTCAGCGACCCCAAAGgtgtgcgcct ... gcatgtgcagACAGGAAGTTTGGTAAAGGGAAGGATAAGATCGACGATGAGGACATCACCT
EST: gi|211039375|gb|FL382073.1|FL382073
EST:     CATGTCCGGGCGCGAGGTCCGCGAGTACACCAATCTCAGCGACCCCAAAG                         ACAGGAAGTTTGGTAAAGGGAAGGATAAGATCGACGATGAGGACATCACCT
genomic: CATGTCCGGGCGCGAGGTCCGCGAGTACACCAATCTCAGCGACCCCAAAGgtgtgcgcct ... gcatgtgcagACAGGAAGTTTGGTAAAGGGAAGGATAAGATCGACGATGAGGACATCACCT
EST: gi|89758028|gb|DY687371.1|DY687371
EST:     CATGGCCGGGCGCGAGGGCCGCGAGTACACCAATCTCAGCGACCCCAAAG                         ACAGGAAGTTTGGTAAAGGGAAGGATAAGATCGACGATGAGGACATCACCT
genomic: CATGTCCGGGCGCGAGGTCCGCGAGTACACCAATCTCAGCGACCCCAAAGgtgtgcgcct ... gcatgtgcagACAGGAAGTTTGGTAAAGGGAAGGATAAGATCGACGATGAGGACATCACCT
EST: gi|58029564|gb|CX724991.1|CX724991
EST:     CATGTCCGGGCGCGAGGTCCGCGAGTACACCAATCTCAGCGACCCCAAAG                         ACAGGAAGTTTGGTAAAGGGAAGGATAAGATCGACGATGAGGACATCACCT
genomic: CATGTCCGGGCGCGAGGTCCGCGAGTACACCAATCTCAGCGACCCCAAAGgtgtgcgcct ... gcatgtgcagACAGGAAGTTTGGTAAAGGGAAGGATAAGATCGACGATGAGGACATCACCT
EST: gi|33771049|gb|CF273343.1|CF273343
EST:     CATGTCCGGGCGCGAGGTCCGCGAGTACACCAATCTCAGCGACCCCAAAG                         ACAGGAAGTTTGGTAAAGGGAAGGATAAGATCGACGATGAGGACATCACCT
genomic: CATGTCCGGGCGCGAGGTCCGCGAGTACACCAATCTCAGCGACCCCAAAGgtgtgcgcct ... gcatgtgcagACAGGAAGTTTGGTAAAGGGAAGGATAAGATCGACGATGAGGACATCACCT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgtgcgcctccttccactgatttatcgatttgcctaccctgttttccccgttgggcgttctcatcgaattcccgagtttggctccgtgcatgtgcagACAGGAAGTTTGGTAAAGGGAAGGATAAGATCGACGATGAGGACATCACCTTCCAGCGCATGGTTGCAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAAG