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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgttcctttttctctgaagatgttgcttatatttttaactcatttttcttgtttaactgttagttgttactgtaacaccgaatacttgagaatgtatatctatgtcaaagactaatgtgatactgttatacagCTTGATATGCTACAAGAGGAGAATGAAAGTGTTCTAGAAAAG

Basic information

species Zea mays
transcript GRMZM2G126266_T02
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G126266_T02 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os01g70320.1 (Oryza sativa), 3'ss of exon 3
gtgttcctttttctctgaagatgttgcttatatttttaactcattttt-cttgtttaactgttagttgttactgtaacaccgaatactt--gagaatgtatatc---tatgtcaaagactaatgtgatactgttatacagCTTGATATGCTACAAGAGGAGAATGAAAGTGTTCTAGAAAAG
|| |||||| ||||||  | |   |  |||||  | |||   |||||  ||  |    |||| |      ||| | ||   |||   ||    || ||| ||||   | | |  ||||||||||  || ||||  ||||||||||||| ||||||||||||||||| |||||||||||||||
gttttccttattctctataaac--tagttatacgtataatatattttagctcatggttctgtcacga---actttgacctagaactttttgaggagtgtttatcagatgtttttaagactaatgcaatgctgtcctacagCTTGATATACTACAAGAGGAGAATGAGAGTGTTCTAGAAAAG

upper sequence: GRMZM2G126266_T02 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA04G37710.1 (Glycine max), 3'ss of exon 3
-----gtgttcctttttctctgaagatgttgcttatatttttaactcatttttcttgt-ttaactgt--tagttgttactgtaacaccgaatacttgagaatgtatatctatgtcaaagactaatg-----tgatactgttat-acagCTTGATATGCTACAAGAGGAGAATGAAAGTGTTCTAGAAAAG
      | ||    ||   |       ||  |  | |  |  |  | ||  | ||| | ||  || |  || || |||   |   |     |  || |     | |||  | |   |    | | |     | |||||| |||  |||||||||||||||||||| ||||||||   | |  ||||||||
gtataatatttacattcaccaatttcagtctccaaaaactaaatatgatgatccttatattggctatgctaatttttaagctttaagtaggtttttaaagtaatttataaaggatgagttttgaagctgattcatactgatattgcagCTTGATATGCTACAAGAAGAGAATGAGGATTTATTAGAAAAG

upper sequence: GRMZM2G126266_T02 (Zea mays), 3'ss of exon 3
lower sequence: AT3G48860.2 (Arabidopsis thaliana), 3'ss of exon 3
--gtgttcctttttctctgaagatgttgcttatatttttaactcatttttcttgtt-taactgttagttgttactgtaacaccgaatacttgagaatgtatatctatgtcaaagactaatgtgatactgttatacagCTTGATATGCTACAAGAGGAGAATGAAAGTGTTCTAGAAAAG
   |||   | ||||| |  |    ||     ||| |     ||| |||  || || ||| | |||||    | |  ||       |   ||||    ||    |        | || || | ||  |  ||| ||||| ||||||||||||||||||||||| | ||| || || |||
gtatgtgattgtttcttttgaaccttttgcggtatctcg---tcaatttagttattgtaaattttagtcaa-attagaattt---gtgtatgagt-cataagagttgacttggggctgat-tcatttttatatgcagCTGGATATGCTACAAGAGGAGAATGAGAATGTACTGGAGAAG

upper sequence: GRMZM2G126266_T02 (Zea mays), 3'ss of exon 3
lower sequence: AT5G13260.1 (Arabidopsis thaliana), 3'ss of exon 3
gtgttcctttttctctgaagatgttgcttatatttttaactcatttttcttgtttaactgttagttgttactgtaacaccgaatacttgagaatgtatatctatgtcaaagactaatgtgatactgttatacagCTTGATATGCTACAAGAGGAGAATGAAAGTGTTCTAGAAAAG
                              |||  | || || ||||| ||       | |   ||  ||   |||            || |||||     ||  |  ||    |  ||  |  |     ||||||||||||||| |||||||||||||| ||| | || ||||||
-----------------------------gtatgct-aattcgtttttttttccg---tatctatttatatcttaatg----------gataatgt---catagatggaaactgagagttgttttacatcacagCTTGATATGCTGCAAGAGGAGAATGATAGTATACTTGAAAAG

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|86469940|gb|DY236310.1|DY236310
EST:     GCTCAAGAGAATCAGGACTGAAAAGAGAGGCATCTACACTTCACGATGAG                         CTTGATATGCTACAAGAGGAGAATGAAAGTGTTCTAGAAAAG
genomic: GCTCAAGAGAATCAGGACTGAAAAGAGAGGCATCTACACTTCACGATGAGgtgttccttt ... tgttatacagCTTGATATGCTACAAGAGGAGAATGAAAGTGTTCTAGAAAAG
EST: gi|211421443|gb|FL301679.1|FL301679
EST:     GCTCAAGAGAATCAGGACTGAAAAGAGAGGCATCTACACTTCACGATGAG                         CTTGATATGCTACAAGAGGAGAATGAAAGTGTTCTAGAAAAG
genomic: GCTCAAGAGAATCAGGACTGAAAAGAGAGGCATCTACACTTCACGATGAGgtgttccttt ... tgttatacagCTTGATATGCTACAAGAGGAGAATGAAAGTGTTCTAGAAAAG
EST: gi|211421445|gb|FL301681.1|FL301681
EST:     GCTCAAGAGAATCAGGACTGAAAAGAGAGGCATCTACACTTCACGATGAG                         CTTGATATGCTACAAGAGGAGAATGAAAGTGTTCTAGAAAAG
genomic: GCTCAAGAGAATCAGGACTGAAAAGAGAGGCATCTACACTTCACGATGAGgtgttccttt ... tgttatacagCTTGATATGCTACAAGAGGAGAATGAAAGTGTTCTAGAAAAG
EST: gi|211421444|gb|FL301680.1|FL301680
EST:     GCTCAAGAGAATCAGGACTGAAAAGAGAGGCATCTACACTTCACGATGAG                         CTTGATATGCTACAAGAGGAGAATGAAAGTGTTCTAGAAAAG
genomic: GCTCAAGAGAATCAGGACTGAAAAGAGAGGCATCTACACTTCACGATGAGgtgttccttt ... tgttatacagCTTGATATGCTACAAGAGGAGAATGAAAGTGTTCTAGAAAAG
EST: gi|211120827|gb|FL155530.1|FL155530
EST:     GCTCAAGAGAATCAGGACTGAAAAGAGAGGCATCTACACTTCACGATGAG                         CTTGATATGCTACAAGAGGAGAATGAAAGTGTTCTAGAAAAG
genomic: GCTCAAGAGAATCAGGACTGAAAAGAGAGGCATCTACACTTCACGATGAGgtgttccttt ... tgttatacagCTTGATATGCTACAAGAGGAGAATGAAAGTGTTCTAGAAAAG
EST: gi|211421446|gb|FL301682.1|FL301682
EST:     GCTCAAGAGAATCAGGACTGAAAAGAGAGGCATCTACACTTCACGATGAG                         CTTGATATGCTACAAGAGGAGAATGAAAGTGTTCTAGAAAAG
genomic: GCTCAAGAGAATCAGGACTGAAAAGAGAGGCATCTACACTTCACGATGAGgtgttccttt ... tgttatacagCTTGATATGCTACAAGAGGAGAATGAAAGTGTTCTAGAAAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cgaatacttgagaatgtatatctatgtcaaagactaatgtgatactgttatacagCTTGATATGCTACAAGAGGAGAATGAAAGTGTTCTAGAAAAG
                               gactaat  putative branch site (score: 2)
            aatgtatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgttcctttttctctgaagatgttgcttatatttttaactcatttttcttgtttaactgttagttgttactgtaacaccgaatacttgagaatgtatatctatgtcaaagactaatgtgatactgttatacagCTTGATATGCTACAAGAGGAGAATGAAAGTGTTCTAGAAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA