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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cgatgcaataggtggaacccactaaaacagtggtttgcagcttcttgttctattataatgcttgtgcaatactaatggaaggtggtgctgtgtatggcagGTGAAAGTGTGGTGCACAAAACAAGAAGCAAGCGTGATCAATATTGATATGAAAGCAAATATTTGTTCGGTTAAATATAATCCTGGGTCAAGCTTCTATG

Basic information

species Zea mays
transcript GRMZM2G126795_T02
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G126795_T02 (Zea mays), 3'ss of exon 11
lower sequence: LOC_Os02g53140.1 (Oryza sativa), 3'ss of exon 9
---cgatgcaataggtggaacccactaaaacagtggtttgcagcttcttgttctattataatgcttgtgcaatactaatggaaggtggtgctgtgtatggcagGTGAAAGTGTGGTGCACAAAACAAGAAGCAAGCGTGATCAATATTGATATGAAAGCAAATATTTGTTCGGTTAAATATAATCCTGGGTCAAGCTTCTATG
   |  |    ||  | |      | ||     | |  ||||              | || |||    | |   || ||||||  |  |||||| | ||  |||| ||||||||||||||||| ||||||||||| |  ||||||||||||||||| || |||||||| || || ||||||||||||||||| |||  |||||
gtgcatttttctacctaggctatcccaacctcattgaatgcatagatggaagtatctgtattgca---gtataccttatggaacctactgctgtttgtgctagGTCAAAGTGTGGTGCACAAAGCAAGAAGCAAGTGCCATCAATATTGATATGAAGGCCAATATTTGCTCTGTCAAATATAATCCTGGGTCGAGCCACTATG

upper sequence: GRMZM2G126795_T02 (Zea mays), 3'ss of exon 11
lower sequence: AT2G32950.1 (Arabidopsis thaliana), 3'ss of exon 9
--cgatgcaataggtggaacccactaaaacagtggtttgcagcttcttgt-tctattataatgcttgtgcaatactaatggaaggtggtgctgtgtatgg--cagGTGAAAGTGTGGTGCACAAAACAAGAAGCAAGCGTGATCAATATTGATATGAAAGCAAATATTTGTTCGGTTAAATATAATCCTGGGTCAAGCTTCTATG
    |  ||||       ||    |||  |       ||||  || |||  ||| ||| |     | |   | | |||   |  ||| || ||||| ||   ||||| ||||| |||||||| |  || |||||||| ||||| |||||||||||||||||||| || ||||  || || || |||||||| ||||||  |||  
tttaagtcaatt--cactactagttaatcctcaaccatgca--ttattgcatctgttaaatcatgtctcatagattaaccaattgtgctg-tgtgtttgatccagGTTAAAGTTTGGTGCACGAGGCAGGAAGCAAGTGTGATTAATATTGATATGAAAGCAAACATATGTTGTGTCAAGTACAATCCTGGCTCAAGCAACTACA

upper sequence: GRMZM2G126795_T02 (Zea mays), 3'ss of exon 11
lower sequence: Vv12s0059g01420.t01 (Vitis vinifera), 3'ss of exon 9
----cgatgcaat--aggtggaacccactaaaacagtggtttgcagcttcttgttctattataatgcttgtgcaatactaatggaaggtggtgctgtgtatggcagGTGAAAGTGTGGTGCACAAAACAAGAAGCAAGCGTGATCAATATTGATATGAAAGCAAATATTTGTTCGGTTAAATATAATCCTGGGTCAAGCTTCTATG
    |  |  |||   |||       |||  |  | ||||||| |  | ||      |  ||| |   | |    ||  ||   || ||     |||      ||||| ||||| ||||||||||| || || || |||||  | || ||||| |||||||||||||| ||||  || || ||||||||||| || ||| | ||| 
agttcattataatcagggtactggggactcca-tattggtttg-acatgctaaactaaccatagtttgtatctgttatgaacttaatgta----tgtaataaacagGTCAAAGTTTGGTGCACAAACCAGGAGGCTAGCGTTCTTAACATTGACATGAAAGCAAATATATGTTGTGTCAAGTATAATCCTGGATCTAGCATTTATA

upper sequence: GRMZM2G126795_T02 (Zea mays), 3'ss of exon 11
lower sequence: Vv10s0523g00030.t01 (Vitis vinifera), 3'ss of exon 9
cgatgcaataggtggaacccactaaaacagtggtttgcagcttcttgttctattataatgcttgtgcaatac-taatggaaggtggtgctgtgtat--ggcagGTGAAAGTGTGGTGCACAAAACAAGAAGCAAGCGTGATCAATATTGATATGAAAGCAAATATTTGTTCGGTTAAATATAATCCTGGGTCAAGCTTCTATG
   |  | || ||||||       |   ||     |     |  || |||  ||   |||  | | || |   |  || |     || || |||||    ||||| ||| | ||||||||||| || ||||| |||||  | || ||||| ||||||||||||||||||||||| || ||||||||||| || ||| | || |
--ttagagtatgtggaattttagcagtaagctaactctgattgatttttcattttagatgagttt-cagtgtgttgtgtatctctgttctatgtatcaaacagGTCAAAATTTGGTGCACAAAGCAGGAAGCTAGCGTTCTTAACATTGACATGAAAGCAAATATTTGTTCGGTCAAGTATAATCCTGGATCTAGCATTTACG

upper sequence: GRMZM2G126795_T02 (Zea mays), 3'ss of exon 11
lower sequence: PP1S86_153V6.2 (Physcomitrella patens), 3'ss of exon 9
----------------------------------------------cgatgcaataggtggaacccactaaa----acagtggtttgcagcttcttgttcta----ttataatgcttgtgcaatactaatggaaggtg---gtgctgtgtatggcagGTGAAAGTGTGGTGCACAAAACAAGAAGCAAGCGTGATCAATATTGATATGAAAGCAAATATTTGTTCGGTTAAATATAATCCTGGGTCAAGCTTCTATG
                                                 | |  | |      |||  ||||    |  || ||||   |  |  ||    |    |   |  |  |||| | |       |||| |    |   ||| | | |||||||||  | ||||| || |  |||||  |||||||||| ||||| |||||||||||||||||||| |  || || || || || || ||||||  |||||
gtgatttgttgaaatgttgtgattttatcactcaagtaactgatggaccttcgtttgacaaggccccttaaactggaaggtagtttttgggcttctgcatcaaggatcgaagcgaatgtgtagttgatcctgaagctttttgcattgtttcttgcagGTGAAGATATGGTGTACGAGGCAAGAGTCAAGCGTGATAAATATAGATATGAAAGCAAATATTTGCTGTGTGAAGTACAACCCAGGATCAAGCAACTATG

upper sequence: GRMZM2G126795_T02 (Zea mays), 3'ss of exon 11
lower sequence: PP1S135_17V6.1 (Physcomitrella patens), 3'ss of exon 9
----------------------------------------------cgatgcaataggtggaacccactaaaac---agtggtttgcagcttcttgttctat-tataatgcttgtgcaatactaatggaaggtggtgctgtgtatggcagGTGAAAGTGTGGTGCACAAAACAAGAAGCAAGCGTGATCAATATTGATATGAAAGCAAATATTTGTTCGGTTAAATATAATCCTGGGTCAAGCTTCTATG
                                              || | |  |   |  | |    | ||||    ||  |||| || ||   |    || | ||||    |    || | ||  |    |  || |     | |||||||||  | |||||||| |  |||||  |||||||||| ||||| || ||||| ||||||||||| |  || || ||||||||||| ||||||  |||||
gtaacctgttgaaatctggtgaacttaatcactcttgtacttgatgcggttctgtttttcaagctttttcaaactcaggttatttggagttttccgcatcatgtttaatatgcggttgatccgaaatgttttta-tgttactgtttgcagGTGAAGATATGGTGCACGAGGCAAGAGTCAAGCGTGATAAATATAGACATGAAGGCAAATATTTGCTGTGTGAAGTATAATCCTGGATCAAGCAGCTATG

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|71448214|gb|DR829264.1|DR829264
EST:     TAGTTTCAGATGGTCACAGTGATTCATGAATGCAACAACAGGTTTTTGGT                         GTGAAAGTGTGGTGCACAAAACAAGAAGCAAGCGTGATCAATATTGATATG
genomic: TAGTTTCAGATGGTCACAGTGATTCATGAATGCAACAACAGGTTTTTGGTgtatgcattt ... tgtatggcagGTGAAAGTGTGGTGCACAAAACAAGAAGCAAGCGTGATCAATATTGATATG






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgttctattataatgcttgtgcaatactaatggaaggtggtgctgtgtatggcagGTGAAAGTGTGGTGCACAAAACAAGAAGCAAGCGTGATCAATATTGATATGAAAGCAAATATTTGTTCGGTTAAATATAATCCTGGGTCAAGCTTCTATG
                        tactaat  putative branch site (score: 1)
     tattataat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cgatgcaataggtggaacccactaaaacagtggtttgcagcttcttgttctattataatgcttgtgcaatactaatggaaggtggtgctgtgtatggcagGTGAAAGTGTGGTGCACAAAACAAGAAGCAAGCGTGATCAATATTGATATGAAAGCAAATATTTGTTCGGTTAAATATAATCCTGGGTCAAGCTTCTATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
-gatgcaa
- - - - - - - - -cccacta
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgcttgt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ggtgctg