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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgaattgatagaacctgtgttaactattaccctttcttctgtagtagatgttctggcacatgatttggtattctataaactgttttgctcacttttgcagGTTATTGGCTGGTCAATGTGGTTTGCAGAGTACCTCTTTTTGGAAAGGAGCTGGGCCAAGGATGAAAAGACACTAAAG

Basic information

species Zea mays
transcript GRMZM2G037104_T02
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G037104_T02 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os11g41900.1 (Oryza sativa), 3'ss of exon 5
tgaattgatagaacctgtgttaactattaccctttcttctgtagtagatgttctggcacatgatttggtattctataaactgttttgctcac-ttttgcagGTTATTGGCTGGTCAATGTGGTTTGCAGAGTACCTCTTTTTGGAAAGGAGCTGGGCCAAGGATGAAAAGACACTAAAG
   |  || |      |  || | |  |     ||||  | |||||  |          ||    ||      |    | |||| || |  | |||||||||||||||||||||| |||||||||||||| |||||||||||||||||||||||||| ||||||||||||||| | || 
-acacagacatgcgaagcattcagttatctatcttctgatatagtacttagcggttttgattgcatgcagacatgctcaatgttgtgattgcattttgcagGTTATTGGCTGGTCCATGTGGTTTGCAGAATACCTCTTTTTGGAAAGGAGCTGGGCAAAGGATGAAAAGACATTGAAA

upper sequence: GRMZM2G037104_T02 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA19G32420.1 (Glycine max), 3'ss of exon 5
tgaattgatagaacctgtgt----taactattacccttt-cttctgtagtagatgttctggcacatgatttggtattctataaactgttttgctcacttttgcagGTTATTGGCTGGTCAATGTGGTTTGCAGAGTACCTCTTTTTGGAAAGGAGCTGGGCCAAGGATGAAAAGACACTAAAG
|   ||   |  |  ||        || ||| |   | | ||| |       ||  | |  |     | || | ||   | |  ||   ||    || ||||||||| ||||||||||||||||||||| | ||||| || ||| |||| || || ||||||||||||||||  ||| |||||
tatcttatcatgagttgaacattacaagtataattttctacttataatcccaattattttaccttcaaattaggat---agaggctaagtt--ctacatttgcagGTCATTGGCTGGTCAATGTGGTTTTCTGAGTATCTTTTTCTGGAGAGAAGTTGGGCCAAGGATGAAAGCACATTAAAG

upper sequence: GRMZM2G037104_T02 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA03G29600.1 (Glycine max), 3'ss of exon 5
tgaattgatagaacctgtgttaactattac---cctttcttctgtagtagatgttctggcacatgat-ttggtattctataaactgttttgctc-acttttgcagGTTATTGGCTGGTCAATGTGGTTTGCAGAGTACCTCTTTTTGGAAAGGAGCTGGGCCAAGGATGAAAAGACACTAAAG
     ||    | |||| ||  |  |||||   | |   || | || |     | |   |   | |  ||   |||     |   | |  | || || ||||||||| ||||||||||||||||||||| | ||||| || ||| |||| || || ||||||||||||||||  ||| |||||
-----tgtcttatcctgagtagaacattacaagcatgatttttctacttatgatcccaactagttaccttcaaattgggatagaggctaagttctacatttgcagGTCATTGGCTGGTCAATGTGGTTTTCTGAGTATCTTTTTCTGGAGAGAAGTTGGGCCAAGGATGAAAGCACATTAAAG

upper sequence: GRMZM2G037104_T02 (Zea mays), 3'ss of exon 4
lower sequence: AT3G57650.1 (Arabidopsis thaliana), 3'ss of exon 5
--tgaattgatagaacctgtgttaactattaccctttcttctgtagtagatgttctggcacatgatt-tggtattctataaactgt-tttgctcacttttgcagGTTATTGGCTGGTCAATGTGGTTTGCAGAGTACCTCTTTTTGGAAAGGAGCTGGGCCAAGGATGAAAAGACACTAAAG
  |||    | |  |    | |    || ||| |||       |  |  ||   |||  ||||  |  | ||| || |||||| |  ||| | |||   | ||||| || |||||||||||||||||  | ||||| |||||| ||||||| |  ||||||||||||||||  || ||||||
tttgagaaaaaatcattgttttaggttaatacacttctccgccttttttat---ctgttacatattcatagtactc-ataaacagaattttcacacacatacagGTCATAGGCTGGTCAATGTGGTTCTCGGAGTATCTCTTTCTGGAAAGAAATTGGGCCAAGGATGAAAGCACTCTAAAG

upper sequence: GRMZM2G037104_T02 (Zea mays), 3'ss of exon 4
lower sequence: Vv08s0007g08110.t01 (Vitis vinifera), 3'ss of exon 5
tgaattgatagaacctgtgttaactattaccctttcttctgtagtagatgttctggcacatgatttggtattctata-aactgttttg---ctcacttttgcagGTTATTGGCTGGTCAATGTGGTTTGCAGAGTACCTCTTTTTGGAAAGGAGCTGGGCCAAGGATGAAAAGACACTAAAG
    | |||     |||  |  | | ||        ||    | |  |   | || ||| |   |   ||| |   | || |||| ||   |  | || | ||||| || || ||||||||||||||| | |||||  | ||| ||||||| | |||||||||||||||||  | | |||||
----tagatgtcgtctgcatacatttttctttgcaattgctcattgaacactttgacacctctatatatatacaggataaatgttatgtgtccaatttattcagGTGATAGGTTGGTCAATGTGGTTTTCTGAGTATTTATTTCTGGAAAGAAACTGGGCCAAGGATGAAAGCATAATAAAG

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|67020755|gb|CO449504.1|CO449504
EST:     GCCTTGGAAGTACACTTGCTGTCATGAAGAAGTCATCCAAGTTCCTTCCA                         GTTATTGGCTGGTCAATGTGGTTTGCAGAGTACCTCTTTTTGGAAAGGAGC
genomic: GCCTTGGAAGTACACTTGCTGTCATGAAGAAGTCATCCAAGTTCCTTCCAgtgagttagt ... acttttgcagGTTATTGGCTGGTCAATGTGGTTTGCAGAGTACCTCTTTTTGGAAAGGAGC
EST: gi|31358977|gb|CD443334.1|CD443334
EST:     GGAAGTACACTTGCTGTCATGAAGAAGTCATCCAAGTTCCTTCCA                         GTTATTGGCTGGTCAATGTGGTTTGCAGAGTACCTCTTTTTGGAAAGGAGC
genomic: GGAAGTACACTTGCTGTCATGAAGAAGTCATCCAAGTTCCTTCCAgtgagttagt ... acttttgcagGTTATTGGCTGGTCAATGTGGTTTGCAGAGTACCTCTTTTTGGAAAGGAGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agatgttctggcacatgatttggtattctataaactgttttgctcacttttgcagGTTATTGGCTGGTCAATGTGGTTTGCAGAGTACCTCTTTTTGGAAAGGAGCTGGGCCAAGGATGAAAAGACACTAAAG
                                        tgctcac  putative branch site (score: 2)
                                     ttttgctcactttt  CT-rich tract
                       tattctataaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgaattgatagaacctgtgttaactattaccctttcttctgtagtagatgttctggcacatgatttggtattctataaactgttttgctcacttttgcagGTTATTGGCTGGTCAATGTGGTTTGCAGAGTACCTCTTTTTGGAAAGGAGCTGGGCCAAGGATGAAAAGACACTAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG
tgaattg
- - - - - gaacctg
- - - - - - - - - - - - - - - - - tcttctg
- - - - - - - - - - - - - - - - - - - - - - - - tgttctg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - catgatt