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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTGTGCAGCTGTCTGCAGAACATGGAGAGAGATGTGTAGAGAGATTGTCAAGAGCCCAGAGTTTTCTGGAAAAATCACTTTTCCTGTTTCCTTGAAGCAGgtaatcatgcagctatgttataccttattatccatatatactgattccgttaccgttgtcaatactccatgtacagtattggtatgccaatcatatttggataatctaataagctcatgctgttcctcttctgtctacag

Basic information

species Zea mays
transcript GRMZM2G046816_T04
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G046816_T04 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os11g06420.2 (Oryza sativa), 5'ss of exon 2
----TTGTGCAGCTGTCTGCAGAACATGGAGAGAGATGTGTAGAGAGATTGTCAAGAGCCCAGAGTTTTCTGGAAAAATCACTTTTCCTGTTTCCTTGAAGCAGgtaatcatgcag-ctatgtt--------------atacctta--------------ttatccatat---atactgattccgttac-cgttgtcaatactcc-atgtacagtattggtatgc-caatcatatttgg------------------ataatctaataagctcatgctgttcctcttctgtctacag
    |||||| | |||||||||||||||||| |||||||||| |||||| |||||||  |||||||| | ||| || ||||| || ||| ||||  ||| |||||| ||||||||   | ||||              || | |||              |  ||||| |    | ||  | |    ||   ||||    | | | |   |||  | | | | |  ||  || || | |                  |||  |||||||| ||||| | |||| ||||| | |||||
TTGCTTGTGCGGGTGTCTGCAGAACATGGAGGGAGATGTGTAAAGAGATCGTCAAGAATCCAGAGTTGTGTGGGAAGATCACCTTCCCTATTTCTCTGAGgcaggtgatcatgcaaattgtgttgtttttagttttatatcctttacaagcaatatcagttcgtccatgttaggtgcttgtccttcaacatattgttggaatttcgaaacacaaaaatagaaagaacacccacatattgcaggattaccgtttgcttatatgctaataagttcatgttattccgcttctatgtacag

upper sequence: GRMZM2G046816_T04 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os11g06420.1 (Oryza sativa), 5'ss of exon 2
TTGTGCAGCTGTCTGCAGAACATGGAGAGAGATGTGTAGAGAGATTGTCAAGAGCCCAGAGTTTTCTGGAAAAATCACTTTTCCTGTTTCCTTGAAGCAGgtaatcatgcag-ctatgtt--------------atacctta--------------ttatccatat---atactgattccgttac-cgttgtcaatactcc-atgtacagtattggtatgc-caatcatatttgg------------------ataatctaataagctcatgctgttcctcttctgtctacag
|||||| | |||||||||||||||||| |||||||||| |||||| |||||||  |||||||| | ||| || ||||| || ||| ||||  ||| |||||| ||||||||   | ||||              || | |||              |  ||||| |    | ||  | |    ||   ||||    | | | |   |||  | | | | |  ||  || || | |                  |||  |||||||| ||||| | |||| ||||| | |||||
TTGTGCGGGTGTCTGCAGAACATGGAGGGAGATGTGTAAAGAGATCGTCAAGAATCCAGAGTTGTGTGGGAAGATCACCTTCCCTATTTCTCTGAGGCAGgtgatcatgcaaattgtgttgtttttagttttatatcctttacaagcaatatcagttcgtccatgttaggtgcttgtccttcaacatattgttggaatttcgaaacacaaaaatagaaagaacacccacatattgcaggattaccgtttgcttatatgctaataagttcatgttattccgcttctatgtacag

upper sequence: GRMZM2G046816_T04 (Zea mays), 5'ss of exon 2
lower sequence: GLYMA15G05490.1 (Glycine max), 5'ss of exon 3
TTGTGCAGCTGTCTGCAGAACATGGAGAGAGATGTGTAGAGAGATTGTCAAGAGCCCAGAGTTTTCTGGAAAAATCACTTTTCCTGTTTCCTTGAAGCAGgtaatcatgcagctatgttataccttattatc-catatatactgattccgttaccgttgtcaatactccatgtacagtattggtatgccaatcatatttggataatctaataagctcatgctgttcctcttctg-tctacag
 ||||| || || |||    | |||||  | ||||| |  || || || |||||||||||||||| ||| ||| | || || ||||| |||||||||||||| |   |     | | | ||| |  | | |  ||  | || | |       ||  ||     ||     || | |  | || || |   ||  |||  || | |   |  |  || ||  | | |  |||    | | |||
ATGTGCTGCAGTTTGCCAGTCTTGGAGGAATATGTGCAAGGACATCGTTAAGAGCCCAGAGTTTTGTGGCAAACTTACATTCCCTGTGTCCTTGAAGCAGgttaggttcattatttttcatagcagactgtttcacttttattaacca---aactattacatttatgtggtg-ataacaatgata-gttgatgttatg-ggttgaagcagcaccctgattgtttgctcctttcacttttcag

upper sequence: GRMZM2G046816_T04 (Zea mays), 5'ss of exon 2
lower sequence: GLYMA08G19520.4 (Glycine max), 5'ss of exon 4
TTGTGCAGCTGTCTGCAGAACATGGAGAGAGATGTGTAGAGAGATTGTCAAGAGCCCAGAGTTTTCTGGAAAAATCACTTTTCCTGTTTCCTTGAAGCAGgt-aatcatgcagctatgttataccttatta-tccatatatactgattccgttaccgttgtcaatactccatgtacagtattggtatgccaatcatatttggataatctaataagctcatgctgttcctcttctg-tctacag
 ||||| || || |||    | |||||  | ||||| |  || || || |||||||||||||||| ||| ||| | || || ||||| |||||||||||||| |         || | | ||| |  |||  | ||  | || | |       ||  ||     ||     || | |  | || || |   ||  |||  || | |   || |  || ||  | | |  |||  | | | |||
ATGTGCTGCAGTTTGCCAGTCTTGGAGGAATATGTGCAAGGACATCGTTAAGAGCCCAGAGTTTTGTGGCAAACTTACATTCCCTGTGTCCTTGAAGCAGgttaggttcattactttttcatagcagattgcttcacttttattaacca---aactattacatttatgtggtg-ataacaatgata-gttgatgttatg-ggttgaagcaacaccctgattgtttgctcctttcgcttttcag

upper sequence: GRMZM2G046816_T04 (Zea mays), 5'ss of exon 2
lower sequence: GLYMA12G13060.1 (Glycine max), 5'ss of exon 1
TTGTGCAGCTGTCTGCAGAACATGGAGAGAGATGTGTAGAGAGATTGTCAAGAGCCCAGAGTTTTCTGGAAAAATCACTTTTCCTGTTTCCTTGAAGCAGgtaatcatgcagctatgttatacct-tattatccatatatactgattccgttaccgttgtcaatactccatgtacagtattggtatgccaatcatatttggataatctaataagctcatgctgttcctcttctgtctacag
 ||||  ||  | ||||   | |||||||| ||||| | ||| |||||||  || || || |||| ||| || || ||||| ||||||||||||||||||||||         | | || | | | |||| |     || | |   ||    |    |   ||||    || |  |  ||  |  ||    | | ||||  ||    |  |    ||    ||||      |||   | ||
ATGTGTTGCCATGTGCAAGTCCTGGAGAGAAATGTGCAAAGAAATTGTCAGCAGTCCTGAATTTTGTGGGAAGATTACTTTCCCTGTTTCCTTGAAGCAGgtaa------gattttcttgttcttctattctatgcctaaaatatgtctaaaataagtaa-aatatgaaatttgtaccat--gactgaagtttaaatttttatg-cttggttgattc---ttgtttacagcctgggcatag

upper sequence: GRMZM2G046816_T04 (Zea mays), 5'ss of exon 2
lower sequence: AT1G76900.1 (Arabidopsis thaliana), 5'ss of exon 2
TTGTGCAGCTGTCTGCAGAACATGGAGAGAGATGTGTAGAGAGATTGTCAAGAGCCCAGAGTTTTCTGGAAAAATCACTTTTCCTGTTTCCTTGAAGCAGgtaatcatgcagctatgttataccttattatccatatatactgattccgttaccgttgtcaatactccatgtacagtattggtatgccaatcatatttggataatctaataagctcatgctgttcctcttctgtctacag
||||||  |||| |||||  |||||||||| ||||||| |||||||||  | || || ||| | || || |||||||| ||||||||||| ||||| ||||| |   | ||  | | |  ||   | | |||   | ||| || ||  ||||   || | | |  |  || |  |||| |    |        | | | |                                        
TTGTGCTTCTGTTTGCAGGTCATGGAGAGATATGTGTAAAGAGATTGTTCAAAGTCCGGAGCTCTCAGGCAAAATCACATTTCCTGTTTCGTTGAAACAGgttagatttcaattctttactaa--tgtcatcatcacata-tgttttggttagtcttatgattggtt-atttcaagtaatttcttcttcggtgtttatag----------------------------------------

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|31360425|gb|CD444782.1|CD444782
EST:     AGAGCCCAGAGTTTTCTGGAAAAATCACTTTTCCTGTTTCCTTGAAGCAG                         CCTGGGCCTCGAGATGGAACTATTCAGTGTTTTATTAAGAGGGATAAATCT
genomic: AGAGCCCAGAGTTTTCTGGAAAAATCACTTTTCCTGTTTCCTTGAAGCAGgtaatcatgc ... ctgtctacagCCTGGGCCTCGAGATGGAACTATTCAGTGTTTTATTAAGAGGGATACATCT
EST: gi|67042292|gb|CO468547.1|CO468547
EST:     CTGTTT-CTTGCAA-CAG                         ACTGGGCCTCGAGATGGAACTATTCAGTGTTTTATTAAGAGGGATATTTC
genomic: CTGTTTCCTTG-AAGCAGgtaatcatgc ... ctgtctacagCCTGGGCCTCGAGATGGAACTATTCAGTGTTTTATTAAGAGGGATACATC
EST: gi|211214115|gb|FL021289.1|FL021289
EST:     GAGCCCAGAGTTTTCTGGAAAAATCACTTTTTCCTGTTTCCTTGAAACAG                         CCCTGGGCCTCCAGATGGAACTATTCAGTGGTTTA
genomic: GAGCCCAGAGTTTTCTGGAAAAATCACTTTT-CCTGTTTCCTTGAAGCAGgtaatcatgc ... ctgtctacagCC-TGGGCCTCGAGATGGAACTATTCAGTGTTTTA
EST: gi|22819363|gb|BU499453.1|BU499453
EST:     AGAGCCCAGAGTTTTCTGGAAAAATCACTTTTCCTGTTTCCTTGAAGCAG                         CCTGGGCCTCGAGATGGAACTATTCAG-GTTTTATTAAGAGGGATACATCT
genomic: AGAGCCCAGAGTTTTCTGGAAAAATCACTTTTCCTGTTTCCTTGAAGCAGgtaatcatgc ... ctgtctacagCCTGGGCCTCGAGATGGAACTATTCAGTGTTTTATTAAGAGGGATACATCT
EST: gi|26559903|gb|CA832138.1|CA832138
EST:     AGAGCCCAGAGTTTTCTGGAAAAATCACTTTTCCTGTTTCCTTGAAGCAG                         CCTGGGCCTCGAGATGGAACTATTCAGTGTTTTATTAAGAGGGATACATCT
genomic: AGAGCCCAGAGTTTTCTGGAAAAATCACTTTTCCTGTTTCCTTGAAGCAGgtaatcatgc ... ctgtctacagCCTGGGCCTCGAGATGGAACTATTCAGTGTTTTATTAAGAGGGATACATCT
EST: gi|29130559|gb|CB381263.1|CB381263
EST:     AGAGCCCAGAGTTTTCTGGAAAAATCACTTTTCCTGTTTCCTTGAAGCAG                         CCTGGGCCTCGAGATGGAACTATTCA
genomic: AGAGCCCAGAGTTTTCTGGAAAAATCACTTTTCCTGTTTCCTTGAAGCAGgtaatcatgc ... ctgtctacagCCTGGGCCTCGAGATGGAACTATTCA
EST: gi|87156288|gb|DY401077.1|DY401077
EST:     AGAGCCCAGAGTTTTCTGGAAAAATCACTTTTCCTGTTTCCTTGAAGCAG                         CCTGGGCCTCGAGATGGAACTATTCAGTGTTTTATTAAGAGGGATACATCT
genomic: AGAGCCCAGAGTTTTCTGGAAAAATCACTTTTCCTGTTTCCTTGAAGCAGgtaatcatgc ... ctgtctacagCCTGGGCCTCGAGATGGAACTATTCAGTGTTTTATTAAGAGGGATACATCT
EST: gi|74238493|gb|DT646407.1|DT646407
EST:     AGAGCCCAGAGTTTTCTGGAAAAATCACTTTTCCTGTTTCCTTGAAGCAG                         CCTGGGCCTCGAGATGGAACTATTCAGTGTTTTATTAAGAGGGATACATCT
genomic: AGAGCCCAGAGTTTTCTGGAAAAATCACTTTTCCTGTTTCCTTGAAGCAGgtaatcatgc ... ctgtctacagCCTGGGCCTCGAGATGGAACTATTCAGTGTTTTATTAAGAGGGATACATCT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTGTGCAGCTGTCTGCAGAACATGGAGAGAGATGTGTAGAGAGATTGTCAAGAGCCCAGAGTTTTCTGGAAAAATCACTTTTCCTGTTTCCTTGAAGCAGgtaatcatgcagctatgttataccttattatccatatatactgattccgttaccgttgtcaatactccatgtacagtattggtatgccaatcatatttggataatctaataagctcatgctgttcctcttctgtctacag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC