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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgggtgcaaagcaattattcgttttgttgctattttttttctgagtgaattaactagttcatgctaattgcatttatagGAATTGTCATCAGATTCATCCCAGCATGTTCGTTCAGCTTTAGCCTCAGTCATTATGGGAATGGCTCCTGTACTGGGAAAG

Basic information

species Zea mays
transcript GRMZM2G122135_T04
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G122135_T01 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA20G24790.1 (Glycine max), 3'ss of exon 6
---------------------------------------------gtgggtgcaaag-caattattcgttttg--ttgctattttttt----tctgagtgaattaactagttcatgctaattgca------tttatagGAATTGTCATCAGATTCATCCCAGCATGTTCGTTCAGCTTTAGCCTCAGTCATTATGGGAATGGCTCCTGTACTGGGAAAG
                                              |   | || || |  |  || ||||||  |||  | ||   |    |     |  ||| ||  ||| | | |  ||| |      |||  ||||||||||||||||||| || |||||||| || || ||||| || ||||| || |||||||||||||| ||  ||||||||
gtatacatctttggaaaagaaattataacacattaatattactgattatatacagaggctttccttggttttggtttgtcaattcagtaggataaatttatatttacaggtttaagttctttgaaacaacttttgcagGAATTGTCATCAGATTCTTCACAGCATGTCCGGTCTGCTTTGGCTTCAGTAATAATGGGAATGGCTCCAGTGTTGGGAAAG

upper sequence: GRMZM2G122135_T01 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA10G42250.1 (Glycine max), 3'ss of exon 6
---------------------------------------------gtgggtgcaaag-caattattcgttttgtt--gctatttt--ttttctgagt--gaattaactagttcatgctaattgca------tttatagGAATTGTCATCAGATTCATCCCAGCATGTTCGTTCAGCTTTAGCCTCAGTCATTATGGGAATGGCTCCTGTACTGGGAAAG
                                              |   | || || |  || || |||||| |  |  | ||   | | || | |    ||| ||  ||| | | |  ||| |      |||  ||||||||||||||||||| || |||||||| || || ||||| || ||||| || |||||||||||||| ||  ||||||||
gtatacatctttggaaaagaaattataacacattagtattactgattatatacagaggcttttcttggttttggttggtcaattcagtatgctaaatttatatttacaggtttaagttctttgaaacaacttttgcagGAATTGTCATCAGATTCTTCTCAGCATGTCCGGTCTGCTTTGGCTTCAGTAATAATGGGAATGGCTCCAGTGTTGGGAAAG

upper sequence: GRMZM2G122135_T01 (Zea mays), 3'ss of exon 6
lower sequence: Vv17s0000g03870.t01 (Vitis vinifera), 3'ss of exon 7
-----------------------------------------------------------gtgggtgcaaagcaattattcgttttgttgctattttttttctgagtgaat-taactagttcatgctaattgcatttatagGAATTGTCATCAGATTCATCCCAGCATGTTCGTTCAGCTTTAGCCTCAGTCATTATGGGAATGGCTCCTGTACTGGGAAAG
                                                              ||||     | |||   |  |   |  || |  | | ||| |     | | ||||| | |    |  | | | |  ||||||| ||||||||||| ||||||||||||||||| ||||| || ||||| |||||||||||||| |||||  | ||||||
gtatacatgcttgcaaaagttttaagtttcattatgctatgaagtttcttatgggcttacatggtggggttctatttaccactgcttatctgtcatctgtcttaaaatttgtgactagattagaaaatgtccttctgcagGAATTATCATCAGATTCTTCCCAGCATGTTCGTTCTGCTTTGGCTTCAGTTATTATGGGAATGGCACCTGTTTTAGGAAAG

upper sequence: GRMZM2G122135_T01 (Zea mays), 3'ss of exon 6
lower sequence: Vv01s0011g03280.t01 (Vitis vinifera), 3'ss of exon 5
---------------------------gtgggtgcaaagcaattattcgttttgtt-gctattttttttctgagtgaatt-----------aactagttca-----tgctaattgcattt-atagGAATTGTCATCAGATTCATCCCAGCATGTTCGTTCAGCTTTAGCCTCAGTCATTATGGGAATGGCTCCTGTACTGGGAAAG
                            |  ||   |   |||   || |||||||  | |  ||  |  ||||  |||            | ||   |||     || | ||  |||||  ||||||||||||| |||||| ||||||||||| || || || || || |||||  | |||||||||||||| ||  | ||||||
gtgctcacgtttattaaaagagtgtttctctgtattatataatgtctccttttgttcacgaacttactattgagctaatgtgcacctgttgagctttctcaatatttggtgatgtcattttgtagGAATTGTCATTAGATTCGTCCCAGCATGTCCGCTCTGCCTTGGCTTCAGTTTTAATGGGAATGGCTCCCGTCTTAGGAAAG

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|32929087|gb|CF033899.1|CF033899
EST:     GCATATTAAATCCACAGCTTTCAATCCAACATATTCTTCCGTGCGTTAAG                         GAATTGTCATCAGATTCATCCCAGCATGTTCGTTCAGCTTTAGCCTCAGTC
genomic: GCATATTAAATCCACAGCTTTCAATCCAACATATTCTTCCGTGCGTTAAGgtgggtgcaa ... gcatttatagGAATTGTCATCAGATTCATCCCAGCATGTTCGTTCAGCTTTAGCCTCAGTC
EST: gi|6564198|gb|AW231820.1|AW231820
EST:     GCATATTAAATCCACAGCTTTCAATCCAACATATTCTTCCGTGCGTTAAG                         GAATTGTCATCAGATTCATCCCAGCATGTTCG
genomic: GCATATTAAATCCACAGCTTTCAATCCAACATATTCTTCCGTGCGTTAAGgtgggtgcaa ... gcatttatagGAATTGTCATCAGATTCATCCCAGCATGTTCG
EST: gi|31356310|gb|CD440667.1|CD440667
EST:     GCATATTAAATCCACAGCTTTCAATCCAACATATTCTTCCGTGCGTTAAG                         GAATTGTCATCAGATTCATCCCAGCATGTTCGTTCAGCTTTAGCCTCAGTC
genomic: GCATATTAAATCCACAGCTTTCAATCCAACATATTCTTCCGTGCGTTAAGgtgggtgcaa ... gcatttatagGAATTGTCATCAGATTCATCCCAGCATGTTCGTTCAGCTTTAGCCTCAGTC
EST: gi|211334572|gb|FL404959.1|FL404959
EST:     GCATATTAAATCCACAGCTTTCAATCCAACATATTCTTCCGTGCGTTAAG                         GAATTGTCATCAKATTCATCCCASCATGTTCGTTCAGCTTTAGCCTCAGTC
genomic: GCATATTAAATCCACAGCTTTCAATCCAACATATTCTTCCGTGCGTTAAGgtgggtgcaa ... gcatttatagGAATTGTCATCAGATTCATCCCAGCATGTTCGTTCAGCTTTAGCCTCAGTC
EST: gi|5566949|gb|AI881860.1|AI881860
EST:     GCATATTAAATCCACAGCTTTCAATCCAACATATTCTTCCGTGCGTTAAG                         GAATTGTCATCAGATTCATCCCAGCATGTTCGTTCAGCTTTAGCCTCAGTC
genomic: GCATATTAAATCCACAGCTTTCAATCCAACATATTCTTCCGTGCGTTAAGgtgggtgcaa ... gcatttatagGAATTGTCATCAGATTCATCCCAGCATGTTCGTTCAGCTTTAGCCTCAGTC
EST: gi|40336631|gb|CK370701.1|CK370701
EST:     ATATTCTTCCGTGCGTTAAG                         GAATTGTCATCAGATTCATCCCAGCATGTTCGTTCAGCTTTAGCCTCAGTC
genomic: ATATTCTTCCGTGCGTTAAGgtgggtgcaa ... gcatttatagGAATTGTCATCAGATTCATCCCAGCATGTTCGTTCAGCTTTAGCCTCAGTC
EST: gi|67034361|gb|CO462911.1|CO462911
EST:     GCATATTANATCCACAGCTTTCAATCCAACATATTCTTCCGTGCGTTAAG                         GAATTGTCATCAGATTCATCCCAGCATGTTCGTTCAGCTTTAGCCTCAGTC
genomic: GCATATTAAATCCACAGCTTTCAATCCAACATATTCTTCCGTGCGTTAAGgtgggtgcaa ... gcatttatagGAATTGTCATCAGATTCATCCCAGCATGTTCGTTCAGCTTTAGCCTCAGTC
EST: gi|32914759|gb|CF019571.1|CF019571
EST:     ACATATTCTTCCGTGCGTTAAG                         GAATTGTCATCAGATTCATCCCAGCATGGTTCGTTCAGCTTTAGCCTCAGT
genomic: ACATATTCTTCCGTGCGTTAAGgtgggtgcaa ... gcatttatagGAATTGTCATCAGATTCATCCCAGCAT-GTTCGTTCAGCTTTAGCCTCAGT
EST: gi|24763712|gb|CA398883.1|CA398883
EST:     GCATATTAAATCCACAGCTTTCAATCCAACATATTCTTCCGTGCGTTAAG                         GAATTGTCATCAGATTCATCCCAGCATGTTCGTTCAGCTTTAGCCTCAGTC
genomic: GCATATTAAATCCACAGCTTTCAATCCAACATATTCTTCCGTGCGTTAAGgtgggtgcaa ... gcatttatagGAATTGTCATCAGATTCATCCCAGCATGTTCGTTCAGCTTTAGCCTCAGTC
EST: gi|32941448|gb|CF046267.1|CF046267
EST:     GCATATTAAATCCACAGCTTTCAATCCAACATATTCTTCCGTGCGTTAAG                         GAATTGTCATCAGATTCATCCCAGCATGTTCGTTCAGCTTTAGCCTCAGTC
genomic: GCATATTAAATCCACAGCTTTCAATCCAACATATTCTTCCGTGCGTTAAGgtgggtgcaa ... gcatttatagGAATTGTCATCAGATTCATCCCAGCATGTTCGTTCAGCTTTAGCCTCAGTC
EST: gi|211221964|gb|FL414368.1|FL414368
EST:     GCATATTAAATCCACAGCTTTCAATCCAACATATTCTTCCGTGCGTTAAG                         GAATTGTCATCATATTCATCCCAGCATGTTCGTTCAGCTTTAGCCTCAGTC
genomic: GCATATTAAATCCACAGCTTTCAATCCAACATATTCTTCCGTGCGTTAAGgtgggtgcaa ... gcatttatagGAATTGTCATCAGATTCATCCCAGCATGTTCGTTCAGCTTTAGCCTCAGTC
EST: gi|32919959|gb|CF024771.1|CF024771
EST:     GCATATTAAATCCACAGCTTTCAATCCAACATATTCTTCCGTGCGTTAAG                         GAATTGTCATCAGATTCATCCCAGCATGGTTCGTTCAGCTTTAGCCTCAGT
genomic: GCATATTAAATCCACAGCTTTCAATCCAACATATTCTTCCGTGCGTTAAGgtgggtgcaa ... gcatttatagGAATTGTCATCAGATTCATCCCAGCAT-GTTCGTTCAGCTTTAGCCTCAGT
EST: gi|32928593|gb|CF033405.1|CF033405
EST:     GCATATTAAATCCACAGCTTTCAATCCAACATATTCTTCCGTGCGTTAAG                         GAATTGTCATCAGATTCATCCCAGCATGTTCGTTCAGCTTTAGCCTCAGTC
genomic: GCATATTAAATCCACAGCTTTCAATCCAACATATTCTTCCGTGCGTTAAGgtgggtgcaa ... gcatttatagGAATTGTCATCAGATTCATCCCAGCATGTTCGTTCAGCTTTAGCCTCAGTC
EST: gi|31361222|gb|CD445579.1|CD445579
EST:     GCATATTAAATCCACAGCTTTCAATCCAACATATTCTTCCGTGCGTTAAG                         GAATTGTCATCAGATTCATCCCAGCATGTTCGTTCAGCTTTAGCCTCAGTC
genomic: GCATATTAAATCCACAGCTTTCAATCCAACATATTCTTCCGTGCGTTAAGgtgggtgcaa ... gcatttatagGAATTGTCATCAGATTCATCCCAGCATGTTCGTTCAGCTTTAGCCTCAGTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgttgctattttttttctgagtgaattaactagttcatgctaattgcatttatagGAATTGTCATCAGATTCATCCCAGCATGTTCGTTCAGCTTTAGCCTCAGTCATTATGGGAATGGCTCCTGTACTGGGAAAG
                                     tgctaat  putative branch site (score: 2)
      tattttttttctga  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgggtgcaaagcaattattcgttttgttgctattttttttctgagtgaattaactagttcatgctaattgcatttatagGAATTGTCATCAGATTCATCCCAGCATGTTCGTTCAGCTTTAGCCTCAGTCATTATGGGAATGGCTCCTGTACTGGGAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TCAGCT