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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atatatataatgcctacattaatgcttagtttgtatcctgttgaccccatgcctggattcagtaactcacattagaaactatttgcacctttatccacagGCTATGGCCCAGGTTGGGGGTCTGGTGATGCTGCAACCTGAAGTTGGTGGATCTCGAGACAACTTCTTTTTCGCCGGGATTGACAAAGTTAGGTTCAGGA

Basic information

species Zea mays
transcript GRMZM2G024482_T01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G024482_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os08g12840.1 (Oryza sativa), 3'ss of exon 3
atatatata-atgcctacattaatgcttagtttgtatcctgttgaccccatgcctggattcagt--aactcacattagaaactatttgcacctttatccacagGCTATGGCCCAGGTTGGGGGTCTGGTGATGCTGCAACCTGAAGTTGGTGGATCTCGAGACAACTTCTTTTTCGCCGGGATTGACAAAGTTAGGTTCAGGA
| ||    | ||| ||  ||   |  | | |   |||  |  |  |  || |     |  ||    ||||  | | |        |   |||||||| ||||||||||||||||||||||||||||||||||| |||| |||||| |||| |||||||| ||||| ||||| || || || ||||| ||||| |||||| | |
agatgaggacatggctggatgttttttaattgcttattgttctatcatcaagtagacaaacatctgaacttccctcatgtgaggct---acctttatgcacagGCTATGGCCCAGGTTGGGGGTCTGGTGATGTTGCAGCCTGAAATTGGCGGATCTCGGGACAATTTCTTCTTTGCAGGAATTGATAAAGTGAGGTTCCGTA

upper sequence: GRMZM2G024482_T01 (Zea mays), 3'ss of exon 2
lower sequence: Vv12s0055g01100.t01 (Vitis vinifera), 3'ss of exon 3
-atatatataatgcctacattaatgcttagtttgtatcctgttgaccccatgcctggattcagtaactcacattagaaactatttgcacct-ttatccacagGCTATGGCCCAGGTTGGGGGTCTGGTGATGCTGCAACCTGAAGTTGGTGGATCTCGAGACAACTTCTTTTTCGCCGGGATTGACAAAGTTAGGTTCAGGA
   |    | |  | || ||  |   | ||  | ||| || |  ||    || ||    || | |        || |   | |||     | ||    |||||| ||||| |||||||| ||  |||| ||||| ||||||||||| || || ||||| || || ||||| || || || ||||||||||| || ||| |||
ggaaggccttacacataaatatactgtaaggctttatact-taaacatgctgtctttggtctg-atggagtggtaaattttttttctgtttgttggatacagGCAATGGCACAGGTTGGTGGCTTGGTAATGCTACAACCTGAAGTGGGAGGCTCTCGTGAAAATTTCTTCTTTGCTGGAATTGACAAAGTAAGATTCCGGA

upper sequence: GRMZM2G024482_T01 (Zea mays), 3'ss of exon 2
lower sequence: Vv00s0357g00070.t01 (Vitis vinifera), 3'ss of exon 3
-------atatatataatgcctacattaatgcttagtttgtatcctgttgaccccatgcctggattcagtaactcacattagaaactatttgcacctttatccacagGCTATGGCCCAGGTTGGGGGTCTGGTGATGCTGCAACCTGAAGTTGGTGGATCTCGAGACAACTTCTTTTTCGCCGGGATTGACAAAGTTAGGTTCAGGA
       ||   | | |   |    ||  |    |||||| ||   | | ||   |    ||  |  ||||| |     |  ||    || |    |       ||||| ||||| |||||||||||  |||| ||||| |||||||||||||| || ||||| || || ||||| || || || || |||||||| ||||||  ||
ttgttaaattctttttacaaccctgtttctatcaagtttggatttggat-acattacatgtgcctctagtaattgctgatgaaagtggttggtgggtc------cagGCAATGGCTCAGGTTGGGGGCTTGGTTATGCTTCAACCTGAAGTTGGAGGCTCTCGTGAGAATTTCTTCTTTGCAGGAATCGACAAAGTGAGGTTCCAGA

upper sequence: GRMZM2G024482_T01 (Zea mays), 3'ss of exon 2
lower sequence: Vv00s0357g00020.t01 (Vitis vinifera), 3'ss of exon 3
-------atatatataatgcctacattaatgcttagtttgtatcctgttgaccccatgcctggattcagtaactcacattagaaactatttgcacctttatccacagGCTATGGCCCAGGTTGGGGGTCTGGTGATGCTGCAACCTGAAGTTGGTGGATCTCGAGACAACTTCTTTTTCGCCGGGATTGACAAAGTTAGGTTCAGGA
       ||   | | |   |    ||  |    |||| | ||   | | ||   |    ||  |  ||||| |     |  ||    || |    |       ||||| ||||| |||||||||||  |||| ||||| |||||||||||||| || ||||| || || ||||| || || || || |||||||| |||||| |||
ttgttaaattctttttacaaccctgtttctatcaagttcgcatttggat-acattacatgtgcctctagtaattgctgatgaaagtggttggtgggtc------cagGCAATGGCTCAGGTTGGGGGCTTGGTTATGCTTCAACCTGAAGTTGGAGGCTCTCGTGAGAATTTCTTCTTTGCAGGAATCGACAAAGTGAGGTTCCGGA

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|18179048|gb|BM380258.1|BM380258
EST:     AGGACATTTTCCTGAACGCCCCATAATGCCCGGTGTCCTCATGGTCGAG                         GCTATGGCCCAGGTTGGGGGTCTGGTGATGCTGCAACCTGAAGTTGGTGGA
genomic: AGGACATTTTCCTGAACGCCCCATAATGCCCGGTGTCCTCATGGTCGAGgtatgcacca ... ttatccacagGCTATGGCCCAGGTTGGGGGTCTGGTGATGCTGCAACCTGAAGTTGGTGGA
EST: gi|211091572|gb|FL457274.1|FL457274
EST:     CAGGACATTTTCCTGAACGCCCCATAATGCCCGGTGTCCTCATGGTCGAG                         GCTATGGCCCAGGTTGGGGGTCTGGTGATGCTGCAACCTGAAGTTGGTGGA
genomic: CAGGACATTTTCCTGAACGCCCCATAATGCCCGGTGTCCTCATGGTCGAGgtatgcacca ... ttatccacagGCTATGGCCCAGGTTGGGGGTCTGGTGATGCTGCAACCTGAAGTTGGTGGA
EST: gi|33092892|gb|CF052886.1|CF052886
EST:     CAGGACATTTTCCTGAACGCCCCATAATGCCCGGTGTCCTCATGGTCGAG                         GCTATGGCCCAGGTTGGGGGTCTGGTGATGCTGCAACCTGAAGTTGGTGGA
genomic: CAGGACATTTTCCTGAACGCCCCATAATGCCCGGTGTCCTCATGGTCGAGgtatgcacca ... ttatccacagGCTATGGCCCAGGTTGGGGGTCTGGTGATGCTGCAACCTGAAGTTGGTGGA
EST: gi|166536311|gb|EG218725.1|EG218725
EST:     CAGGACATTTTCCTGAACGCCCCATAATGCCCGGTGTCCTCATGGTCGAG                         GCTATGGCCCAGGTTGGGGGTCTGGTGA
genomic: CAGGACATTTTCCTGAACGCCCCATAATGCCCGGTGTCCTCATGGTCGAGgtatgcacca ... ttatccacagGCTATGGCCCAGGTTGGGGGTCTGGTGA
EST: gi|37396344|gb|CF635461.1|CF635461
EST:     CAGGACATTTTCCTGAACGCCCCATAATGCCCGGTGTCCTCATGGTCGAG                         GCTATGGCCCAGGTTGGGGGTCTGGTGATGCTGCAACCTGAAGTTGGTGGA
genomic: CAGGACATTTTCCTGAACGCCCCATAATGCCCGGTGTCCTCATGGTCGAGgtatgcacca ... ttatccacagGCTATGGCCCAGGTTGGGGGTCTGGTGATGCTGCAACCTGAAGTTGGTGGA
EST: gi|71305724|gb|DR789001.1|DR789001
EST:     CAGGACATTTTCCTGAACGCCCCATAATGCCCGGTGTCCTCATGGTCGAG                         GCTATGGCCCAGGTTGGGGGTCTGGTGATGCTGCAACCTGAAGTTGGTGGA
genomic: CAGGACATTTTCCTGAACGCCCCATAATGCCCGGTGTCCTCATGGTCGAGgtatgcacca ... ttatccacagGCTATGGCCCAGGTTGGGGGTCTGGTGATGCTGCAACCTGAAGTTGGTGGA
EST: gi|50338308|gb|CO533434.1|CO533434
EST:     CAGGACATTTTCCTGAACGCCCCATAATGCCCGGTGTCCTCATGGTCGAG                         GCTATGGCCCAGGTTGGGGGTCTGGTGATGCTGCAACCTGAAGTTGGTGGA
genomic: CAGGACATTTTCCTGAACGCCCCATAATGCCCGGTGTCCTCATGGTCGAGgtatgcacca ... ttatccacagGCTATGGCCCAGGTTGGGGGTCTGGTGATGCTGCAACCTGAAGTTGGTGGA
EST: gi|211091571|gb|FL457273.1|FL457273
EST:     CAGGACATTTTCCTGAACGCCCCATAATGCCCGGTGTCCTCATGGTCGAG                         GCTATGGCCCAGGTTGGGGGTCTGGTGATGCTGCAACCTGAAGTTGGTGGA
genomic: CAGGACATTTTCCTGAACGCCCCATAATGCCCGGTGTCCTCATGGTCGAGgtatgcacca ... ttatccacagGCTATGGCCCAGGTTGGGGGTCTGGTGATGCTGCAACCTGAAGTTGGTGGA
EST: gi|113669978|gb|DW819268.1|DW819268
EST:     CAGGACATTTTCCTGAACGCCCCATAATGCCCGGTGTCCTCATGGTCGAG                         GCTATGGCCCAGGTTGGGGGTCTGGTGATGCTGCAAC-TGAAGTTGG
genomic: CAGGACATTTTCCTGAACGCCCCATAATGCCCGGTGTCCTCATGGTCGAGgtatgcacca ... ttatccacagGCTATGGCCCAGGTTGGGGGTCTGGTGATGCTGCAACCTGAAGTTGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cccatgcctggattcagtaactcacattagaaactatttgcacctttatccacagGCTATGGCCCAGGTTGGGGGTCTGGTGATGCTGCAACCTGAAGTTGGTGGATCTCGAGACAACTTCTTTTTCGCCGGGATTGACAAAGTTAGGTTCAGGA
                  aactcac  putative branch site (score: 2)
                                          cctttatcc  putative PPT
                         attagaaactattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atatatataatgcctacattaatgcttagtttgtatcctgttgaccccatgcctggattcagtaactcacattagaaactatttgcacctttatccacagGCTATGGCCCAGGTTGGGGGTCTGGTGATGCTGCAACCTGAAGTTGGTGGATCTCGAGACAACTTCTTTTTCGCCGGGATTGACAAAGTTAGGTTCAGGA

- - - - - -gcctaca
- - - - - - - - - - -atgctta
- - - - - - - - - - - - - - - - - - cctgttg
- - - - - - - - - - - - - - - - - - - - - - - - - gcctgga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ttgcacc