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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCGCACAACAAATTTTGGAGGAGAGGAAGCTTAATCAAACATTACTAGCCAACCACACTACATTGCTTGACTTGCTTGAAATTCCACAATTGATGGACACgtatgcaacttttatcttaccatcccctcgtctcgttactttatgtttgagtcatttgttattgacaatgccatttgtttttcataatgcataattttaactgttgtataattgtattgtcgctgaattatgcatgacaatcagtaaacttatgcttgtag

Basic information

species Zea mays
transcript GRMZM2G006781_T03
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G006781_T03 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os12g35290.1 (Oryza sativa), 5'ss of exon 3
CCGCACAACAAATTTTGGAGGAGAGGAAGCTTAATCAAACATTACTAGCCAACCACACTACATTGCTTGACTTGCTTGAAATTCCACAATTGATGGACACgtatgcaac-ttttatcttaccatcccctcgtctcgttactttatgtttgagtcatttgttattgacaat--gccattt-gtttttcataatgcataattttaactgttgtataattgtattgtcgctgaattatgcatgac--aatcagta-aacttatg---cttgtag------------------------------
| ||||| |||||||| || ||||||||||| ||||| |||||||||||||| ||||  ||| |||||||  |||||||||| |||||| |||||||||||||||   | |||| | |||  ||  | |     | ||   | ||  ||| ||  |||| | |||   ||  ||  ||| ||| |  ||  | |   | |||   | |  || |  |  ||| | | | | | |  ||||     ||  ||| || | | |   | || ||                              
CAGCACAGCAAATTTTAGAAGAGAGGAAGCTCAATCAGACATTACTAGCCAATCACAGCACACTGCTTGATCTGCTTGAAATCCCACAACTGATGGACACgtatgtgccatttttttttataatttcttaaagaccttcagtcat-cttgtgttgtttgatgttgttgatatgctgtttagttctcgattcttctctaatttctgtatgctacagatccatt-ttgttcagtaaaacatggtttgatttgtacaattgacgaatcatgaagaattacatttaacaatctacatgctcacag

upper sequence: GRMZM2G006781_T03 (Zea mays), 5'ss of exon 3
lower sequence: GLYMA16G22880.1 (Glycine max), 5'ss of exon 2
CCGCACAACAAATTTTGGAGGAGAGGAAGCTTAATCAAACATTACTAGCCAACCACACTACATTGCTTGACTTGCTTGAAATTCCACAATTGATGGACACgtatgc-----aacttttatcttaccatccc-ctcgtctcgttactttatgtttgagtcatttgttattgacaatgccatttgtttttcataatgcataattttaactgttgtataattgtattgtcgctgaattatgcatgacaatcagtaaacttatgcttgtag
| ||  | || ||||||||| |||||||| | || |||||| | ||| | || |||| ||| |||||||||||||| |||||||| ||| | |||||||||||||      ||  |  | | |   ||  | ||| |    || |   ||  |   ||  |    ||||   |    || ||  | |     | || |  | | || |  | |||  ||| |                                             
CTGCTGAGCAGATTTTGGAGAAGAGGAAGATGAACCAAACAATGCTAACTAATCACAGTACTTTGCTTGACTTGCTAGAAATTCCTCAACTCATGGACACgtatgttaaaaaagatagaccatttaattacactcctggaatttccacatactaatgttctcacatattatgacaatcacttcctctgtgagaagcct--tgtaaattcctatatttttgcag--------------------------------------------

upper sequence: GRMZM2G006781_T03 (Zea mays), 5'ss of exon 3
lower sequence: GLYMA02G04920.1 (Glycine max), 5'ss of exon 2
CCGCACAACAAATTTTGGAGGAGAGGAAGCTTAATCAAACATTACTAGCCAACCACACTACATTGCTTGACTTGCTTGAAATTCCACAATTGATGGACACgtatgc----aacttt----tatcttaccatcccctcgtctcgttactttatgtttgagtcatttgttattgacaatgccatttgtttttcataatgcataattttaactgttgtataattgtattgtcgctgaattatgcatgacaatcagtaaacttatgcttgtag
| ||  | |  ||||||||| |||||||| | || |||||| | ||| | || |||| ||| |||||||||||||| |||||||| ||| | |||||||||||||     || | |    ||| | |  |  | |  |    ||  |  | |  |   || |||   ||||   |    || ||  | |     | || |  | | || |  | |||  ||| |                                             
CTGCTGAGCGGATTTTGGAGAAGAGGAAGATGAACCAAACAATGCTAACTAATCACAGTACTTTGCTTGACTTGCTAGAAATTCCTCAACTCATGGACACgtatgttaaaaaatatagactatttaattacactcctggaatgt--ccatgtactaatgttattgcatattatgatgatcacttcctctgtgagaagcgt--tgtaaattcctatatttttgcag--------------------------------------------

upper sequence: GRMZM2G006781_T03 (Zea mays), 5'ss of exon 3
lower sequence: Vv04s0008g01350.t01 (Vitis vinifera), 5'ss of exon 3
CCGCACAACAAATTTTGGAGGAGAGGAAGCTTAATCAAACATTACTAGCCAACCACACTACATTGCTTGACTTGCTTGAAATTCCACAATTGATGGACACgtatgcaacttttatcttaccatcccctcgtctcgttactttatgtttgagtcatttgttattgacaatgccatttgtttttcataatgcataattttaactgt-tgtataattgtattgtcgctgaattatgcatgacaatcagtaaacttatgcttgtag
| ||| |||| |||||||||||||| ||| | || |||||||| |||||||| || | ||| ||||||||||||||||||||||| ||  | |||||||||||||       | | | |  |        | |    |    |||||  | | |          |  |||| |   || ||  ||     || || ||  ||     |||||                                                  
CTGCAGAACAGATTTTGGAGGAGAGAAAGATGAACCAAACATTGCTAGCCAATCATAGTACTTTGCTTGACTTGCTTGAAATTCCTCAGCTCATGGACACgtatg-------tgtttgaaaaagt-----tgtaaagatcacatgttaaattaaaagaagggaaaacatgctagaggtcttaaatggcctatgatatttgctaagcatataa--------------------------------------------------

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|149008084|gb|EE040323.2|EE040323
EST:     AACCACACTACATTGCTTGACTTGCTTGAAATTCCACAATTGATGGACAC                         GTGTATACGGAATGGGAACTATGATGAAGCACTTGACCTAGAAGCTTTTGT
genomic: AACCACACTACATTGCTTGACTTGCTTGAAATTCCACAATTGATGGACACgtatgcaact ... atgcttgtagGTGTATACGGAATGGGAACTATGATGAAGCACTTGACCTAGAAGCTTTTGT
EST: gi|148939698|gb|EC884368.2|EC884368
EST:     AACCACACTACATTGCTTGACTTGCTTGAAATTCCACAATTGATGGACAC                         GTGTATACGGAATGGGAACTATGATGAAGCACTTGACCTAGAAGCTTTTGT
genomic: AACCACACTACATTGCTTGACTTGCTTGAAATTCCACAATTGATGGACACgtatgcaact ... atgcttgtagGTGTATACGGAATGGGAACTATGATGAAGCACTTGACCTAGAAGCTTTTGT
EST: gi|148963434|gb|EE014450.2|EE014450
EST:     AACCACACTACATTGCTTGACTTGCTTGAAATTCCACAATTGATGGACAC                         GTGTATACGGAATGGGAACTATGATGAAGCACTTGACCTAGAAGCTTTTGT
genomic: AACCACACTACATTGCTTGACTTGCTTGAAATTCCACAATTGATGGACACgtatgcaact ... atgcttgtagGTGTATACGGAATGGGAACTATGATGAAGCACTTGACCTAGAAGCTTTTGT
EST: gi|4730483|gb|AI649649.1|AI649649
EST:     AACCACACTACATTGCTTGACTTGCTTGAAATTCCACAATTGATGGACAC                         GTGTATACGGAATGGGAACTATGATGAAGCACTTGACCTAGAAGCTTTTGT
genomic: AACCACACTACATTGCTTGACTTGCTTGAAATTCCACAATTGATGGACACgtatgcaact ... atgcttgtagGTGTATACGGAATGGGAACTATGATGAAGCACTTGACCTAGAAGCTTTTGT
EST: gi|211334830|gb|FL416303.1|FL416303
EST:     AACCACACTACATTGCTTGACTTGCTTGAAATTCCACAATTGATGGACAC                         GTGTATACGGAATGGGAACTATGATGAAGCACTTGACCTAGAAGCTTTTGT
genomic: AACCACACTACATTGCTTGACTTGCTTGAAATTCCACAATTGATGGACACgtatgcaact ... atgcttgtagGTGTATACGGAATGGGAACTATGATGAAGCACTTGACCTAGAAGCTTTTGT
EST: gi|71316958|gb|DR795163.1|DR795163
EST:     AACCACACTACATTGCTTGACTTGCTTGAAATTCCACAATTGATGGACAC                         GTGTATACGGAATGGGAACTATGATGAAGCACTTGAC
genomic: AACCACACTACATTGCTTGACTTGCTTGAAATTCCACAATTGATGGACACgtatgcaact ... atgcttgtagGTGTATACGGAATGGGAACTATGATGAAGCACTTGAC
EST: gi|71305530|gb|DR788908.1|DR788908
EST:     AACCACACTACATTGCTTGACTTGCTTGAAATTCCACAATTGATGGACAC                         GTGTATACGGAATGGGAACTATGATGAAGCACTTGACCTAGAAGCTTTTGT
genomic: AACCACACTACATTGCTTGACTTGCTTGAAATTCCACAATTGATGGACACgtatgcaact ... atgcttgtagGTGTATACGGAATGGGAACTATGATGAAGCACTTGACCTAGAAGCTTTTGT
EST: gi|86469576|gb|DY235946.1|DY235946
EST:     AACCACACTACATTGCTTGACTTGCTTGAAATTCCACAATTGATGGACAC                         GTGTATACGGAATGGGAACTATGATGAAGCACTTGACCTAAAAGCTTTTGT
genomic: AACCACACTACATTGCTTGACTTGCTTGAAATTCCACAATTGATGGACACgtatgcaact ... atgcttgtagGTGTATACGGAATGGGAACTATGATGAAGCACTTGACCTAGAAGCTTTTGT
EST: gi|211082178|gb|FL396889.1|FL396889
EST:     AACCACACTACATTGCTTGACTTGCTTGAAATTCCACAATTGATGGACAC                         GTGTATACGGAATGGGAACTATGATGAAGCACTTGACCTAGAAGCTTTTGT
genomic: AACCACACTACATTGCTTGACTTGCTTGAAATTCCACAATTGATGGACACgtatgcaact ... atgcttgtagGTGTATACGGAATGGGAACTATGATGAAGCACTTGACCTAGAAGCTTTTGT
EST: gi|71449856|gb|DR830906.1|DR830906
EST:     AACCACACTACATTGCTTGACTTGCTTGAAATTCCACAATTGATGGACAC                         GTGTATACGGAATGGGAACTATGATGAAGCACTTGACCTAGAAGCTTTTGT
genomic: AACCACACTACATTGCTTGACTTGCTTGAAATTCCACAATTGATGGACACgtatgcaact ... atgcttgtagGTGTATACGGAATGGGAACTATGATGAAGCACTTGACCTAGAAGCTTTTGT
EST: gi|148999331|gb|EE036267.2|EE036267
EST:     AACCACACTACATTGCTTGACTTGCTTGAAATTCCACAATTGATGGACAC                         GTGTATACGGAATGGGAACTATGATGAAGCACTTGACCTAGAAGCTTTTGT
genomic: AACCACACTACATTGCTTGACTTGCTTGAAATTCCACAATTGATGGACACgtatgcaact ... atgcttgtagGTGTATACGGAATGGGAACTATGATGAAGCACTTGACCTAGAAGCTTTTGT
EST: gi|148979834|gb|EE026851.2|EE026851
EST:     AACCACACTACATTGCTTGACTTGCTTGAAATTCCACAATTGATGGACAC                         GTGTATACGGAATGGGAACTATGATGAAGCACTTGACCTAGAAGCTTTTGT
genomic: AACCACACTACATTGCTTGACTTGCTTGAAATTCCACAATTGATGGACACgtatgcaact ... atgcttgtagGTGTATACGGAATGGGAACTATGATGAAGCACTTGACCTAGAAGCTTTTGT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CCGCACAACAAATTTTGGAGGAGAGGAAGCTTAATCAAACATTACTAGCCAACCACACTACATTGCTTGACTTGCTTGAAATTCCACAATTGATGGACACgtatgcaacttttatcttaccatcccctcgtctcgttactttatgtttgagtcatttgttattgacaatgccatttgtttttcataatgcataattttaactgttgtataattgtattgtcgctgaattatgcatgacaatcagtaaacttatgcttgtag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA