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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgcctgcttcagtagagatgctactcctttgccttgtgattcgatggttttgagactaattggttctatgttgtgcggtagCTCGTTGTGCTCTACGTGGATTTCAAGCTCGACGAGAGTTACACGCCGAGCAAGATCTCCATCCGGGCCGGGGATGGCTTCCACAACCTAAAG

Basic information

species Zea mays
transcript GRMZM2G054247_T02
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G054247_T03 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os05g50360.1 (Oryza sativa), 3'ss of exon 2
----------gtgcctgcttcagtagagatgctactcctttgcctt--gtgattcgatggttttgagactaattggttctatgttgtgcggtagCTCGTTGTGCTCTACGTGGATTTCAAGCTCGACGAGAGTTACACGCCGAGCAAGATCTCCATCCGGGCCGGGGATGGCTTCCACAACCTAAAG
            |  | | ||| | | | |     |  ||||  |   |||  |    |   ||     |   |   |   ||||| |  | |||| || ||| | || ||||||||||||||||||||||| || ||||| |||||||||||  |||||||||| |||||||||||||| || |||
gtgagtggagagggattcctcacttgggctcaattttgtttgattcgagtggataatcgtgcttagttgttcctcccttgctgttgcgtcgcagCTTGTCGTGGTGTATGTGGATTTCAAGCTCGACGAGAGCTATACGCCTAGCAAGATCTCTGTCCGGGCCGGCGATGGCTTCCACAATCTCAAG

upper sequence: GRMZM2G054247_T03 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA16G25220.1 (Glycine max), 3'ss of exon 2
gtgcctgcttc---agtagagatgctactcctt------------tgccttgtg---attcgatggttttgagactaattggttctatgttgt-gcggtagCTCGTTGTGCTCTACGTGGATTTCAAGCTCGACGAGAGTTACACGCCGAGCAAGATCTCCATCCGGGCCGGGGATGGCTTCCACAACCTAAAG
  ||||| ||    ||  |||||  || || ||            | | | ||    ||| |||   | |  ||  ||     |   | |||| | || || |  ||||||| ||||||||||||||||| |||||||||||||||||||||||  | |||||||| ||||| ||||| || |||||| | |||
-agcctggttttctagcggagatattagtcattggaaaacagtgatacttggtaccaatttgatttatatatgaaaaaaaaaatgatttttgttgtggcagTTAATTGTGCTGTACGTGGATTTCAAGCTTGACGAGAGTTACACGCCGAGCAAAGTTTCCATCCGTGCCGGTGATGGTTTTCACAACTTGAAG

upper sequence: GRMZM2G054247_T03 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA04G13520.1 (Glycine max), 3'ss of exon 1
----gtgcctgcttcagtagag----atgctactcctttgccttgtgattcgatggttttgagactaattg---------gttctatgttgt-gcggtagCTCGTTGTGCTCTACGTGGATTTCAAGCTCGACGAGAGTTACACGCCGAGCAAGATCTCCATCCGGGCCGGGGATGGCTTCCACAACCTAAAG
    || | |     | ||  |    ||  |   |  ||| ||    ||   |  || |  | |  |||||         |||  || |||| | || || |  ||||||| ||||| | ||||||||| |||||||||||||||| ||||||  | |||||||  ||||| ||||| || |||||| | |||
gaaggttcttatcaaattattgggtcattttgtccacttggctaaccatataaaagtatcaataagaattgtaatgtggggtttcattttgttgtggcagTTGATTGTGCTTTACGTCGTTTTCAAGCTTGACGAGAGTTACACGCTGAGCAAAGTTTCCATCCATGCCGGTGATGGTTTTCACAACTTGAAG

upper sequence: GRMZM2G054247_T03 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA20G20840.1 (Glycine max), 3'ss of exon 2
----------------------------------------------------------------------gtgcctgcttcagtagag----atgctactcctttgccttgtgattcga---tggttttgagact--aatt---ggttctatgttgt-gcggtagCTCGTTGTGCTCTACGTGGATTTCAAGCTCGACGAGAGTTACACGCCGAGCAAGATCTCCATCCGGGCCGGGGATGGCTTCCACAACCTAAAG-------
                                                                      || | |     | ||  |    ||  |   |  ||| ||    ||   |   || | |    | |  |||    ||||  || |||| | || || |  ||||||| || |||| ||||||||| |||||||||||||||||||||||  | |||||||  ||||| ||||| || |||||| | |||       
gtatgagctctaccttagtttgttgctcttcttattaagttcttaatcagtgcggtggcattgtccaaaggttcttatcaaattattgggtcattttgtccacttggctaaccatataaacatgatgtaagaattgtaatgtggggtttcattttgttgtggcagTTGATTGTGCTTTATGTGGTTTTCAAGCTTGACGAGAGTTACACGCCGAGCAAAGTTTCCATCCTTGCCGGTGATGGTTTTCACAACTTGAAGGTAAATT

upper sequence: GRMZM2G054247_T03 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA02G06190.3 (Glycine max), 3'ss of exon 3
gtgcctgcttcagtagagatgctactcctttgccttgtgattcgatggttttgagactaattggttctatgttgtgcggtagCTCGTTGTGCTCTACGTGGATTTCAAGCTCGACGAGAGTTACACGCCGAGCAAGATCTCCATCCGGGCCGGGGATGGCTTCCACAACCTAAAG
        | |  |  | ||   |     |    ||    ||      | || |   |  ||  ||    ||||||  | || |  ||||||| ||||||||||||||||| || ||||||||||||||||||||  | |||||||| ||||| ||||| || |||||| | |||
-------gtacgttgtaaataa-ataaaataaagttagagtttttaaatgttaatttttgtttttttggggttgtg--gcagTTGATTGTGCTGTACGTGGATTTCAAGCTTGATGAGAGTTACACGCCGAGCAAAGTTTCCATCCGTGCCGGTGATGGTTTTCACAACTTGAAG

upper sequence: GRMZM2G054247_T03 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA10G09250.1 (Glycine max), 3'ss of exon 1
----gtgcctgcttcagtagag----atgctactcctttgccttgtgattcgatggttttgagactaattg---------gttctatgttgt-gcggtagCTCGTTGTGCTCTACGTGGATTTCAAGCTCGACGAGAGTTACACGCCGAGCAAGATCTCCATCCGGGCCGGGGATGGCTTCCACAACCTAAAG
    || | |     | ||  |    ||  |   |  ||| ||    ||   |  || |  | |  |||||         |||  || |||| | ||||| |  ||||||| ||||||| ||||||||| ||||||||||||| |||||||||  | |||||||  ||| | ||||| || |||||| | |||
gaaggttcttatcaaattattgggtcattttgtccacttggctaaccatataaaagtatcaataagaattgtaatgtggggtttcattttgttgtggtagTTGATTGTGCTTTACGTGGTTTTCAAGCTTGACGAGAGTTACATGCCGAGCAAAGTTTCCATCCTTGCCCGTGATGGTTTTCACAACTTGAAG

upper sequence: GRMZM2G054247_T03 (Zea mays), 3'ss of exon 2
lower sequence: Vv04s0023g01940.t01 (Vitis vinifera), 3'ss of exon 2
--gtgcctgcttcagtagagatgctactcctttg---ccttgtgattcgatggttttga-gactaattggttctatg--ttgtgcggtagCTCGTTGTGCTCTACGTGGATTTCAAGCTCGACGAGAGTTACACGCCGAGCAAGATCTCCATCCGGGCCGGGGATGGCTTCCACAACCTAAAG
  |||  |||     | |   |   | |  |||    ||   | ||    ||||||||  |||| | ||||     |  || |     |||| |||||  | || |||||||||||||| |||||||| ||||||||||| |||||||| || || ||||| ||||||||||||||| | |||
gtgtgtatgcaattttgggtttctgatttttttctttcccccttatcgtttggttttggtgactgaatggtgaatagatttctcttaaagCTGGTTGTAATTTATGTGGATTTCAAGCTGGACGAGAGCTACACGCCGAGTAAGATCTCTATTCGAGCCGGAGATGGCTTCCACAACTTGAAG

upper sequence: GRMZM2G054247_T03 (Zea mays), 3'ss of exon 2
lower sequence: PP1S42_273V6.1 (Physcomitrella patens), 3'ss of exon 2
--------------------gtgcctgcttcagtagagatgctactcctttgccttgtgattcgatggttttgagactaattggttctatgttgtgcggtagCTCGTTGTGCTCTACGTGGATTTCAAGCTCGACGAGAGTTACACGCCGAGCAAGATCTCCATCCGGGCCGGGGATGGCTTCCACAACCTAAAG
                     |   ||   || | |    | ||||| |  |   |  |  | |   |   | |  ||   | || || ||  ||   | |||  |||| ||| | ||||||||||||| |||| ||||||||||| |||| |||||| || || || || ||  ||   || ||  | ||   |
gtttgatcagatgttaggttttagatggagcattgggagagttactcatg-gttgtaagtatagtcagccctcattctttctcgtcctctgacgt-ttgcagCAAGTTGCGCTTTTCGTGGATTTCAAGGTCGATGAGAGTTACACCCCGAACAAGATATCAATTCGAGCTGGCAATTCTTTTCATGATCTTCGG

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|148954203|gb|EC899610.2|EC899610
EST:     CGCAGCCGCACCTGGTGAACATCCAGTTCCAGAAGAAGGTGCAGCTGCAG                         CTCGTTGTGCTCTACGTGGATTTCAAGCTCGACGAGAGTTACACGCCGAGC
genomic: CGCAGCCGCACCTGGTGAACATCCAGTTCCAGAAGAAGGTGCAGCTGCAGgtgcctgctt ... tgtgcggtagCTCGTTGTGCTCTACGTGGATTTCAAGCTCGACGAGAGTTACACGCCGAGC
EST: gi|87153735|gb|DY398524.1|DY398524
EST:     CGCAGCCGCACNTGGTGAACATCCAGTTCCAGAAGAAGGTGCAGCTGCAG                         CTCGTTGTGCTCTACGTGGATTTCAAGCTCGACGAGAGTTACACGCCGAGC
genomic: CGCAGCCGCACCTGGTGAACATCCAGTTCCAGAAGAAGGTGCAGCTGCAGgtgcctgctt ... tgtgcggtagCTCGTTGTGCTCTACGTGGATTTCAAGCTCGACGAGAGTTACACGCCGAGC
EST: gi|22490544|gb|BU050467.1|BU050467
EST:     CGCAGCCGCACCTGGTGAACATCCAGTTCCAGAAGAAGGTGCAGCTGCAG                         CTCGTTGTGCTCTACGTGGATTTCAAGCTCGACGAGAGTTACACGCCGAGC
genomic: CGCAGCCGCACCTGGTGAACATCCAGTTCCAGAAGAAGGTGCAGCTGCAGgtgcctgctt ... tgtgcggtagCTCGTTGTGCTCTACGTGGATTTCAAGCTCGACGAGAGTTACACGCCGAGC
EST: gi|71427965|gb|DR809015.1|DR809015
EST:     CCTGGTGAACATCCATTTCCAGAAGAAGGTGCAGCTGCAG                         CTCGTTGTGCTTTACGTGGATTTCAAGCTCGACGAGAGTTACACGCCGAGC
genomic: CCTGGTGAACATCCAGTTCCAGAAGAAGGTGCAGCTGCAGgtgcctgctt ... tgtgcggtagCTCGTTGTGCTCTACGTGGATTTCAAGCTCGACGAGAGTTACACGCCGAGC
EST: gi|94476642|gb|EB705600.1|EB705600
EST:     CCAGTTCCAGAAGAAGGTGCAGCTGCAG                         CTCGTTGTGCTCTACGTGGATTTCAAGCTCGACGAGAGTTACACGCCGAGC
genomic: CCAGTTCCAGAAGAAGGTGCAGCTGCAGgtgcctgctt ... tgtgcggtagCTCGTTGTGCTCTACGTGGATTTCAAGCTCGACGAGAGTTACACGCCGAGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctttgccttgtgattcgatggttttgagactaattggttctatgttgtgcggtagCTCGTTGTGCTCTACGTGGATTTCAAGCTCGACGAGAGTTACACGCCGAGCAAGATCTCCATCCGGGCCGGGGATGGCTTCCACAACCTAAAG
                           gactaat  putative branch site (score: 2)
                            actaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgcctgcttcagtagagatgctactcctttgccttgtgattcgatggttttgagactaattggttctatgttgtgcggtagCTCGTTGTGCTCTACGTGGATTTCAAGCTCGACGAGAGTTACACGCCGAGCAAGATCTCCATCCGGGCCGGGGATGGCTTCCACAACCTAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAGA