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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tttgcattacgtacggcaactaatataattattatgataactagctagcacaagtagtcaaaattaaggggctaaatttcttgagcaggagttactacagGTGCACCAACAGCAAATGCACAGTGAAGAAGCGCGTGGAGAGGTCCTCCGACGACCCCTCCGTGGTCATCACCACCTACGAGGGCCAGCACTGCCACAGC

Basic information

species Zea mays
transcript GRMZM2G143204_T02
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G143204_T02 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os03g55080.1 (Oryza sativa), 3'ss of exon 2
--tttgcattacgtacggcaactaatataattatt--atgataactagct---agcacaagtagtca----aaattaaggggctaaatttcttgag-caggagttactacagGTGCACCAACAGCAAATGCACAGTGAAGAAGCGCGTGGAGAGGTCCTCCGACGACCCCTCCGTGGTCATCACCACCTACGAGGGCCAGCACTGCCACAGC
      ||  ||   |   || |   || ||||||  |     | | | |    || ||| || |||    | |  ||         || |||||  |||||| ||||||||||||||||||||||| ||||| |||||||||||||||||| |||| ||||||||||| ||||| || |||||||||||||||||||||            
aagacacaccaccatccataattgccatcattattaaacatggatttgttcaaggctcaactaatcatcacataacaaaaaatggttttgcttgactcagGAGCTACTACAGGTGCACCAACAGCAAGTGCACTGTGAAGAAGCGCGTGGAGCGGTCTTCCGACGACCCTTCCGTCGTGATCACCACCTACGAGGGCCAG------------

upper sequence: GRMZM2G143204_T02 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA01G06870.4 (Glycine max), 3'ss of exon 2
-------tttgcattacgtacggcaactaa--tataattattatgataactagctagcacaagtagtcaaa-attaaggggcta--aatttcttgagcaggagttactacagGTGCACCAACAGCAAATGCACAGTGAAGAAGCGCGTGGAGAGGTCCTCCGACGACCCCTCCGTGGTCATCACCACCTACGAGGGCCAGCACTGCCACAGC
        |  | | |   |    |   ||  | | |  ||||   | |||    | ||    || | ||  |||  |  || |  |  |  ||  ||||||| |||||| ||||||| |||||||||||||| ||||||||| | || ||  | || ||||| |||||  |  | || || || || || || || ||             
agaacttatgacttcatacatattattcaaactctcaccattaaattgacttcacaacattgataattaattattctgatgcaattatgtctttttgcagGAGCTACTACCGGTGCACAAACAGCAAATGCACGGTGAAGAAGAGGGTTGAACGCTCTTCCGAGGACCCAACGATTGTGATTACTACATATGAAGGGCAA------------

upper sequence: GRMZM2G143204_T02 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA02G12830.1 (Glycine max), 3'ss of exon 2
-------------tttgcattacgtacggcaactaatataattattatgataactagctagcacaagtagtcaaaattaaggggctaaatttcttgagcaggagttactacagGTGCACCAACAGCAAATGCACAGTGAAGAAGCGCGTGGAGAGGTCCTCCGACGACCCCTCCGTGGTCATCACCACCTACGAGGGCCAGCACTGCCACAGC
              |   |||| | || |  |   | |   | |  |  | |   |  |  ||  | |    | ||||||        ||   ||  ||||||| |||||| ||||||| |||||||||||||| ||||||||| | || ||  |||| ||||| |||||  |  | || || ||||| || || || ||             
tataatgaccacactaatatta-gaactgttatccaaaccctcaccactaaattgacttcacaacattgcagataattaattattctgatacattttgcagGAGCTACTACCGGTGCACAAACAGCAAATGCACGGTGAAGAAGAGGGTTGAACGGTCTTCCGAGGACCCAACAATTGTGATTACCACATATGAAGGGCAA------------

upper sequence: GRMZM2G143204_T02 (Zea mays), 3'ss of exon 2
lower sequence: Vv01s0011g00720.t01 (Vitis vinifera), 3'ss of exon 2
-------tttgcattacgtacggcaactaata--taattattatgataactagctagcacaagtagtcaaaattaaggggctaaatttc----ttgagcaggagttactacagGTGCACCAACAGCAAATGCACAGTGAAGAAGCGCGTGGAGAGGTCCTCCGACGACCCCTCCGTGGTCATCACCACCTACGAGGGCCAGCACTGCCACAGC
        |||  ||    |       |  ||  || |||| ||   |  ||  | | |   ||| | ||||   |     |  |||      ||  ||||||| || ||| ||||||| |||||||||||||| ||||||||  | || ||  | ||||| || || |||  | | || ||||| || || || |||||             
gggatctcttgggttggaaaaaaatcttgttagctagttat-atagcagataaattggatttgtattgaaaaaagattaattttattcacacattttgcagGAGCTATTACCGGTGCACAAACAGCAAATGCACGGTGAAGAAAAGAGTTGAACGCTCCTCGGAGGATCCCAGCATCGTAATCACTACATATGAAGGCCAA------------

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|71442802|gb|DR823852.1|DR823852
EST:     AGATGGAGGAAGTATGGCCAGAAAGCTGTCAAGAACAGCCCTTTCCCAAG                         GAGTTACTACAGGTGCACCAACAGCAAATGCACAGTGAAGAAGCGCGTGGA
genomic: AGATGGAGGAAGTATGGCCAGAAAGCTGTCAAGAACAGCCCTTTCCCAAGgttggttcca ... gttactacagG--T-------G---CACCAACAGCAAATGCACAGTGAAGAAGCGCGTGGA
EST: gi|101386129|gb|EB815105.1|EB815105
EST:     AGATGGAGGAAGTATGGCCAGAAAGCTGTCAAGAACAGCCCTTTCCCAAG                         GTGCACCAACAGCAAATGCACAGTGAAGAAGCGCGTGGAGAGGTCCTCCGA
genomic: AGATGGAGGAAGTATGGCCAGAAAGCTGTCAAGAACAGCCCTTTCCCAAGgttggttcca ... gttactacagGTGCACCAACAGCAAATGCACAGTGAAGAAGCGCGTGGAGAGGTCCTCCGA
EST: gi|76913751|gb|DV165250.1|DV165250
EST:     AGATGGAGGAAGTATGGCCAGAAAGCTGTCAAGAACAGCCCTTTCCCAAG                         GAGTTACTACAGGTGCACCAACAGCAAATGCACAGTGAAGAAGCGCGTGGA
genomic: AGATGGAGGAAGTATGGCCAGAAAGCTGTCAAGAACAGCCCTTTCCCAAGgttggttcca ... gttactacagG--T-------G---CACCAACAGCAAATGCACAGTGAAGAAGCGCGTGGA
EST: gi|71441953|gb|DR823003.1|DR823003
EST:     AGATGGAGGAAGTATGGCCAGAAAGCTGTCAAGAACAGCCCTTTCCCAAG                         GAGTTACTACAGGTGCACCAACAGCAAATGCACAGTGAAAAAGCGCGTGGA
genomic: AGATGGAGGAAGTATGGCCAGAAAGCTGTCAAGAACAGCCCTTTCCCAAGgttggttcca ... gttactacagG--T-------G---CACCAACAGCAAATGCACAGTGAAGAAGCGCGTGGA
EST: gi|71428707|gb|DR809757.1|DR809757
EST:     AGATGGAGGAAGTATGGCCAGAAAGCTGTCAAGAACAGCCCTTTCCCAAG                         GAGTTACTACAGGTGCACCAACAGCAAATGCACAGTGAAGAAGCGCGTGGA
genomic: AGATGGAGGAAGTATGGCCAGAAAGCTGTCAAGAACAGCCCTTTCCCAAGgttggttcca ... gttactacagG--T-------G---CACCAACAGCAAATGCACAGTGAAGAAGCGCGTGGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tagcacaagtagtcaaaattaaggggctaaatttcttgagcaggagttactacagGTGCACCAACAGCAAATGCACAGTGAAGAAGCGCGTGGAGAGGTCCTCCGACGACCCCTCCGTGGTCATCACCACCTACGAGGGCCAGCACTGCCACAGC
                        ggctaaa  putative branch site (score: 3)
            tcaaaattaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tttgcattacgtacggcaactaatataattattatgataactagctagcacaagtagtcaaaattaaggggctaaatttcttgagcaggagttactacagGTGCACCAACAGCAAATGCACAGTGAAGAAGCGCGTGGAGAGGTCCTCCGACGACCCCTCCGTGGTCATCACCACCTACGAGGGCCAGCACTGCCACAGC

-ttgcatt
- - - - - - - - caactaa
- - - - - - - - - - - - - - - - - - - - - - - -gcacaag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -agcagga