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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgtcctatgcaatttccattttaagccccgtttgcatcgctcattaattatcatggtctgctatgatataatttggggtaatatattttcactactgcagGAACTCCTTACACACAGCAATCATACAAGGTTAGCGAATCGTTCCCTTACAAGTGGATCAATAAAAAGTGGAAAGAAGGGTTCCATGTAACATCTATGGC

Basic information

species Zea mays
transcript GRMZM2G164265_T01
intron # 14
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G164265_T02 (Zea mays), 3'ss of exon 14
lower sequence: LOC_Os07g07560.2 (Oryza sativa), 3'ss of exon 14
-------------------------------------------------------------tgtcc-tatgcaatttccattttaagccccgtttgcatcgctcattaattatcatggtctgctatgatataatttggggtaatatattttcactactgcagGAACTCCTTACACACAGCAATCATACAAGGTTAGCGAATCGTTCCCTTACAAGTGGATCAATAAAAAGTGGAAAGAAGGGTTCCATGTAACATCTATGGC
                                                             | ||| ||||     |      | |  |   ||       | ||| | ||| | |||  |  | ||  || |  |   ||   |||| | || || ||||||||| |||||| | || || |||||||||||||| || || ||||| | |||||||||||||||||||||||||||||| || ||||| |||||||||||
gtctgggatgtgtttcttattagtcattttatatcccgaccattcttctttgacgatgaattatccatatgtttcatatggacttaatcattttgttgctccccatgagttaacctggcttagt-tgtgatcacctatagtttgatatgtccattattgcagGAACACCTTACTCCCAACAGTCATACAAGGTTAGTGAGTCATTCCCCTTCAAGTGGATCAATAAAAAGTGGAAAGAAGGTTTTCATGTGACATCTATGGC

upper sequence: GRMZM2G164265_T02 (Zea mays), 3'ss of exon 14
lower sequence: GLYMA16G04580.1 (Glycine max), 3'ss of exon 14
-----tgtcctatgcaatttccattttaagccccgtttgcatcgctcattaattatcatggtctgctatgatataatttggggtaatatattttcactactgcagGAACTCCTTACACACAGCAATCATACAAGGTTAGCGAATCGTTCCCTTACAAGTGGATCAATAAAAAGTGGAAAGAAGGGTTCCATGTAACATCTATGGC
     |  |   |  || |||  |  | |        |  |  | || | |    | |||   |  |||    | || |   ||   |    || |||  |  ||||||||||||||| ||||| || ||||| || || ||||| || |||| ||| ||||| || || |||||||||||||| |||||||| || || ||| |
tattttagctcgtttaacttctgtgatgaaaggaacatcaactgttcttcagaatttatgactttatat----ttatctcatgtttgaatcctttact-ttatagGAACTCCTTACACGCAGCAGTCCTACAAAGTGAGTGAATCATTTCCTTTCAAATGGATAAACAAGAAGTGGAAAGAAGGATTCCATGTTACCTCAATGAC

upper sequence: GRMZM2G164265_T02 (Zea mays), 3'ss of exon 14
lower sequence: AT3G03940.1 (Arabidopsis thaliana), 3'ss of exon 14
tgtcc-tatgcaatttccattttaagccccgtttgcatcgctcattaattatcatggtctgcta-tgatataatttggggtaatatattttcactactgcagGAACTCCTTACACACAGCAATCATACAAGGTTAGCGAATCGTTCCCTTACAAGTGGATCAATAAAAAGTGGAAAGAAGGGTTCCATGTAACATCTATGGC
 |||  ||  ||  |  |||  ||| |   |         || ||| |||   |  |  ||  |    | | | ||     | |  || |  | | |   |||||||||||| || |||||||| ||||| || ||||| || || || | ||||||||| |||||||||||||||||||| || ||||||||||| ||| |
-gtcggtagtcacgtctcatgataa-ctttgccaatga-acttattgattcataaagcatgaaagccgttttacttattccacttcatgt--aatgcgatagGAACTCCTTATACCCAGCAATCTTACAAAGTCAGCGACTCATTTCCATTCAAGTGGATAAATAAAAAGTGGAAAGAAGGTTTTCATGTAACATCCATGAC

upper sequence: GRMZM2G164265_T02 (Zea mays), 3'ss of exon 14
lower sequence: AT5G18190.1 (Arabidopsis thaliana), 3'ss of exon 14
---------------------------tgtcctatgcaatttccat-tttaagccccgtttgcatcgctcattaattatcatggtctgctatgatataatttggggtaatat-attttcactact-----gcagGAACTCCTTACACACAGCAATCATACAAGGTTAGCGAATCGTTCCCTTACAAGTGGATCAATAAAAAGTGGAAAGAAGGGTTCCATGTAACATCTATGGC
                             |  ||||  |     |   || |     |      |||  | || ||||| |   | |   |||   |  | |    |||| |  |  |   |        | ||||||  |||| || |||||||| ||||| || ||||| || || |||| ||||||||| || || || ||||||||||  ||||||||||| || ||| |
gttggtgttaatggtagtaatctgcaaatttttatgtcacacaaacacttgactatagaaaatgtcgtactttcattataaccatataacatggagtcttctttactaattttgtgcttgttgtaaattggtagGAACGTCTTATACTCAGCAATCTTACAAAGTCAGCGACTCTTTTCCTTTCAAGTGGATAAACAAGAAATGGAAAGAAGATTTCCATGTAACCTCCATGAC

upper sequence: GRMZM2G164265_T02 (Zea mays), 3'ss of exon 14
lower sequence: Vv08s0007g07420.t01 (Vitis vinifera), 3'ss of exon 14
--tgtcctatgcaatttccattttaagccccgtttgcatcgctcattaattatcatggtctgctatgatataatttggggtaatatattttcactactgcagGAACTCCTTACACACAGCAATCATACAAGGTTAGCGAATCGTTCCCTTACAAGTGGATCAATAAAAAGTGGAAAGAAGGGTTCCATGTAACATCTATGGC
   |||  || ||| ||  ||  |         |    ||     ||   |||  |  |  | |     ||   ||    |  | | || |   ||    |||||||||||| || ||||| |||||||| || || ||||| || || |  || ||||| ||||| |||||||||||||| |||||||| ||||||||| |
tcagtctcatccaaatttgatcatggaatttaatcttgtcat--gttgcatattgttttgagttggcccatgtgtttatatggtgttttctgtttatgttagGAACTCCTTATACCCAGCAGTCATACAAAGTGAGTGAATCCTTTCCCTTTAAATGGATTAATAAGAAGTGGAAAGAAGGTTTCCATGTCACATCTATGAC

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|5915380|gb|AW053021.1|AW053021
EST:     AGCAATTGCTGGATCAACCAATGGGAGTTCATTGGTTGTCATGTCCAAAG                         GAACTCCTTACACACAGCAATCATACAAGGTTAGCGAATCGTTCCCTTACA
genomic: AGCAATTGCTGGATCAACCAATGGGAGTTCATTGGTTGTCATGTCCAAAGgtctgaattt ... actactgcagGAACTCCTTACACACAGCAATCATACAAGGTTAGCGAATCGTTCCCTTACA
EST: gi|149102515|gb|EE287878.2|EE287878
EST:     AGCAATTGCTGGATCAACCAATGGGAGTTCATTGGTTGTCATGTCCAAAG                         GAACTCCTTACACACAGCAATCATACAAGGTTAGCGAATCGTTCCCTTACA
genomic: AGCAATTGCTGGATCAACCAATGGGAGTTCATTGGTTGTCATGTCCAAAGgtctgaattt ... actactgcagGAACTCCTTACACACAGCAATCATACAAGGTTAGCGAATCGTTCCCTTACA
EST: gi|149097990|gb|EE183935.2|EE183935
EST:     AGCAATTGCTGGATCAACCAATGGGAGTTCATTGGTTGTCATGTCCAAAG                         GAACTCCTTACACACAGCAATCATACAAGGTTAGCGAATCGTTCCCTTACA
genomic: AGCAATTGCTGGATCAACCAATGGGAGTTCATTGGTTGTCATGTCCAAAGgtctgaattt ... actactgcagGAACTCCTTACACACAGCAATCATACAAGGTTAGCGAATCGTTCCCTTACA
EST: gi|148974692|gb|EE025499.2|EE025499
EST:     AGCAATTGCTGGATCAACCAATGGGAGTTCATTGGTTGTCATGTCCAAAG                         GAACTCCTTACACACAGCAATCATACAAGGTTAGCGAATCGTTCCCTTACA
genomic: AGCAATTGCTGGATCAACCAATGGGAGTTCATTGGTTGTCATGTCCAAAGgtctgaattt ... actactgcagGAACTCCTTACACACAGCAATCATACAAGGTTAGCGAATCGTTCCCTTACA
EST: gi|71430774|gb|DR811824.1|DR811824
EST:     AGCAATTGCTGGATCAACCAATGGGAGTTCATTGGTTGTCATGTCCAAAG                         GAACTCCTTACACACAGCAATCATACAAGGTTAGCGAATCGTTCCCTTACA
genomic: AGCAATTGCTGGATCAACCAATGGGAGTTCATTGGTTGTCATGTCCAAAGgtctgaattt ... actactgcagGAACTCCTTACACACAGCAATCATACAAGGTTAGCGAATCGTTCCCTTACA
EST: gi|149031683|gb|EE154868.2|EE154868
EST:     AGCAATTGCTGGATCAACCAATGGGAGTTCATTGGTTGTCATGTCCAAAG                         GAACTCCTTACACACAGCAATCATACAAGGTTAGCGAATCGTTCCCTTACA
genomic: AGCAATTGCTGGATCAACCAATGGGAGTTCATTGGTTGTCATGTCCAAAGgtctgaattt ... actactgcagGAACTCCTTACACACAGCAATCATACAAGGTTAGCGAATCGTTCCCTTACA
EST: gi|78113586|gb|DV531977.1|DV531977
EST:     AGCAATTGCTGGATCAACCAATGGGAGTTCATTGGTTGTCATGTCCAAAG                         GAACTCCTTACACACAGCAATCATACAAGGTTAGCGAATCGTTCCCTTACA
genomic: AGCAATTGCTGGATCAACCAATGGGAGTTCATTGGTTGTCATGTCCAAAGgtctgaattt ... actactgcagGAACTCCTTACACACAGCAATCATACAAGGTTAGCGAATCGTTCCCTTACA
EST: gi|149098314|gb|EE184284.2|EE184284
EST:     AGCAATTGCTGGATCAACCAATGGGAGTTCATTGGTTGTCATGTCCAAAG                         GAACTCCTTACACACAGCAATCATACAAGGTTAGCGAATCGTTCCCTTACA
genomic: AGCAATTGCTGGATCAACCAATGGGAGTTCATTGGTTGTCATGTCCAAAGgtctgaattt ... actactgcagGAACTCCTTACACACAGCAATCATACAAGGTTAGCGAATCGTTCCCTTACA
EST: gi|148937186|gb|EC881367.2|EC881367
EST:     AGCAATTGCTGGATCAACCAATGGGAGTTCATTGGTTGTCATGTCCAAAG                         GAACTCCTTACACACAGCAATCATACAAGGTTAGCGAATCGTTCCCTTACA
genomic: AGCAATTGCTGGATCAACCAATGGGAGTTCATTGGTTGTCATGTCCAAAGgtctgaattt ... actactgcagGAACTCCTTACACACAGCAATCATACAAGGTTAGCGAATCGTTCCCTTACA
EST: gi|71300241|gb|DR786191.1|DR786191
EST:     AGCAATTGCTGGATCAACCAATGGGAGTTCATTGGTTGTCATGTCCAAAG                         GAACTCCTTACACACAGCAATCATACAAGGTTAGCGAATCGTTCCCTTACA
genomic: AGCAATTGCTGGATCAACCAATGGGAGTTCATTGGTTGTCATGTCCAAAGgtctgaattt ... actactgcagGAACTCCTTACACACAGCAATCATACAAGGTTAGCGAATCGTTCCCTTACA
EST: gi|148999277|gb|EE036205.2|EE036205
EST:     AGCAATTGCTGGATCAACCAATGGGAGTTCATTGGTTGTCATGTCCAAAG                         GAACTCCTTACACACAGCAATCATACAAGGTTAGCGAATCGTTCCCTTACA
genomic: AGCAATTGCTGGATCAACCAATGGGAGTTCATTGGTTGTCATGTCCAAAGgtctgaattt ... actactgcagGAACTCCTTACACACAGCAATCATACAAGGTTAGCGAATCGTTCCCTTACA
EST: gi|148950556|gb|EC896133.2|EC896133
EST:     AGCAATTGCTGGATCAACCAATGGGAGTTCATTGGTTGTCATGTCCAAAG                         GAACTCCTTACACACAGCAATCATACAAGGTTAGCGAATCGTTCCCTTACA
genomic: AGCAATTGCTGGATCAACCAATGGGAGTTCATTGGTTGTCATGTCCAAAGgtctgaattt ... actactgcagGAACTCCTTACACACAGCAATCATACAAGGTTAGCGAATCGTTCCCTTACA
EST: gi|71764976|gb|DR962913.1|DR962913
EST:     AGCAATTGCTGGATCAACCAATGGGAGTTCATTGGTTGTCATGTCCAAAG                         GAACTCCTTACACACAGCAATCATACAAGGTTAGCGAATCGTTCCCTTACA
genomic: AGCAATTGCTGGATCAACCAATGGGAGTTCATTGGTTGTCATGTCCAAAGgtctgaattt ... actactgcagGAACTCCTTACACACAGCAATCATACAAGGTTAGCGAATCGTTCCCTTACA
EST: gi|32855731|gb|CD995412.1|CD995412
EST:     AGCAATTGCTGGATCAACCAATGGGAGTTCATTGGTTGTCATGTCCAAAG                         GAACTCCTTACACTCAGCAATCATACAAGGTTAGCGAATCGTTCCCTTACA
genomic: AGCAATTGCTGGATCAACCAATGGGAGTTCATTGGTTGTCATGTCCAAAGgtctgaattt ... actactgcagGAACTCCTTACACACAGCAATCATACAAGGTTAGCGAATCGTTCCCTTACA
EST: gi|5555573|gb|AI881524.1|AI881524
EST:     AGCAATTGCTGGATCAACCAATGGGAGTTCATTGGTTGTCATGTCCAAAG                         GAACTCCTTACACTCAGCAATCATACAAGGTTAGCGAATCGTTCCCTTACA
genomic: AGCAATTGCTGGATCAACCAATGGGAGTTCATTGGTTGTCATGTCCAAAGgtctgaattt ... actactgcagGAACTCCTTACACACAGCAATCATACAAGGTTAGCGAATCGTTCCCTTACA
EST: gi|71300237|gb|DR786190.1|DR786190
EST:     AGCAATTGCTGGATCAACCAATGGGAGTTCATTGGTTGTCATGTCCAAAG                         GAACTCCTTACACACAGCAATCATACAAGGTTAGCGAATCGTTCCCTTACA
genomic: AGCAATTGCTGGATCAACCAATGGGAGTTCATTGGTTGTCATGTCCAAAGgtctgaattt ... actactgcagGAACTCCTTACACACAGCAATCATACAAGGTTAGCGAATCGTTCCCTTACA
EST: gi|33093570|gb|CF053564.1|CF053564
EST:     AGCAATTGCTGGATCAACCAATGGGAGTTCATTGGTTGTCATGTCCAAAG                         GAACTCCTTACACTCAGCAATCATACGAGGTTAGCGAATCGTTCCCTTACA
genomic: AGCAATTGCTGGATCAACCAATGGGAGTTCATTGGTTGTCATGTCCAAAGgtctgaattt ... actactgcagGAACTCCTTACACACAGCAATCATACAAGGTTAGCGAATCGTTCCCTTACA
EST: gi|148950415|gb|EC895982.2|EC895982
EST:     AGCAATTGCTGGATCAACCAATGGGAGTTCATTGGTTGTCATGTCCAAAG                         GAACTCCTTACACACAGCAATCATACAAGGTTAGCGAATCGTTCCCTTACA
genomic: AGCAATTGCTGGATCAACCAATGGGAGTTCATTGGTTGTCATGTCCAAAGgtctgaattt ... actactgcagGAACTCCTTACACACAGCAATCATACAAGGTTAGCGAATCGTTCCCTTACA
EST: gi|33093597|gb|CF053591.1|CF053591
EST:     AGCAATTGCTGGATCAACCAATGGGAGTTCATTGGTTGTCATGTCCAAAG                         GAACTCCTTACACTCAGCAATCATACAAGGTTAGCGAATCGTTCCCTTACA
genomic: AGCAATTGCTGGATCAACCAATGGGAGTTCATTGGTTGTCATGTCCAAAGgtctgaattt ... actactgcagGAACTCCTTACACACAGCAATCATACAAGGTTAGCGAATCGTTCCCTTACA
EST: gi|148939598|gb|EC884226.2|EC884226
EST:     AGCAATTGCTGGATCAACCAATGGGAGTTCATTGGTTGTCATGTCCAAAG                         GAACTCCTTACACACAGCAATCATACAAGGTTAGCGAATCGTTCCCTTACA
genomic: AGCAATTGCTGGATCAACCAATGGGAGTTCATTGGTTGTCATGTCCAAAGgtctgaattt ... actactgcagGAACTCCTTACACACAGCAATCATACAAGGTTAGCGAATCGTTCCCTTACA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aattatcatggtctgctatgatataatttggggtaatatattttcactactgcagGAACTCCTTACACACAGCAATCATACAAGGTTAGCGAATCGTTCCCTTACAAGTGGATCAATAAAAAGTGGAAAGAAGGGTTCCATGTAACATCTATGGC
 cattaat  putative branch site (score: 3)
                                        ttttcact  putative PPT
                                 taatatattttcacta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgtcctatgcaatttccattttaagccccgtttgcatcgctcattaattatcatggtctgctatgatataatttggggtaatatattttcactactgcagGAACTCCTTACACACAGCAATCATACAAGGTTAGCGAATCGTTCCCTTACAAGTGGATCAATAAAAAGTGGAAAGAAGGGTTCCATGTAACATCTATGGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - ctatgca
- - - - - - - - - - - - - - - -ttgcatc
- - - - - - - - - - - - - - - - - - - - - - - - - - - -gtctgct