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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...actgatgttcagtaacatgtcataactagtgacgtgaacatatcagattccatttcctttgttttgtcctgttgacatatttctttcctttttatgccagAGAAAGAGAACTTGTGCCTTTATGGTTTGCCAAATGAGACTTGGGAGGTTACTCTTCCAGCTGAGGAAGTACCTCCTGAGCTTCCAGAACCAGCACTGGG

Basic information

species Zea mays
transcript GRMZM2G107807_T02
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G107807_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os02g35600.1 (Oryza sativa), 3'ss of exon 2
actgatgttcagtaacatgtcataactagtgacgtgaacatatcagattccatttcctttgttttgtcctgtt---gacatatttctttcctttttatgccagAGAAAGAGAACTTGTGCCTTTATGGTTTGCCAAATGAGACTTGGGAGGTTACTCTTCCAGCTGAGGAAGTACCTCCTGAGCTTCCAGAACCAGCACTGGG
| |||||    ||| |||  ||| || |||    ||   | || |  ||   || ||||  || |||| |  |   |||||| |  | |||| ||| |  |||||||||||||| ||||||||||||| ||||| |||||||| ||||| || || |||||||||||||||||||||||||| ||||||||||||||||||||
aatgatgaatggta-cattacatcacaagtagtctgttga-atgaagttatcttcccttgtttatgtcatagtaatgacatagtgatctcctattttt-tcagAGAAAGAGAACCTGTGCCTTTATGGATTGCCCAATGAGACCTGGGACGTGACCCTTCCAGCTGAGGAAGTACCTCCTGAACTTCCAGAACCAGCACTGGG

upper sequence: GRMZM2G107807_T01 (Zea mays), 3'ss of exon 2
lower sequence: AT2G02470.1 (Arabidopsis thaliana), 3'ss of exon 2
--------------------------------------------------------------------------actgatgttcag-taacatgtcat-aactagtgacgtgaacatatcagatt------ccatttcctttgttttgtcctgttgacatatttctttcctttttatgccagAGAAAGAGAACTTGTGCCTTTATGGTTTGCCAAATGAGACTTGGGAGGTTACTCTTCCAGCTGAGGAAGTACCTCCTGAGCTTCCAGAACCAGCACTGGG
                                                                             | |||| || |   ||||  |  | | |||  |   | | ||    ||       | |   || |||  | |    || |  | |||| ||| | ||||||  |||||| ||||| ||||| || |||||  | ||||||||||| |||||||||| ||| || | ||||||||| |||||||||||||| ||||||||  | ||
gtgagttatttcttcacaacttttaaaaaattagtcttgcttagcttctatagtttctagtgaaatgttttgttgaagttgttgagcttgtatgttgttgaattgtgttggttaaagattgagttagttagtcctcctctgtgtggtttttctttaaggtgtttcattcttgtttatgt-agAGAAGGAGAATTTGTGTCTCTATGGACTTCCAAATGAGACATGGGAGGTTAATCTACCCGTTGAGGAAGTTCCTCCTGAGCTTCCTGAACCAGCTTTAGG

upper sequence: GRMZM2G107807_T01 (Zea mays), 3'ss of exon 2
lower sequence: AT1G14510.1 (Arabidopsis thaliana), 3'ss of exon 2
---actgatgttcagtaacatgtcataactagtgacgtgaacatatcagattccatttcctttgttttgtcctgttgacatatttctttcctttttatgccagAGAAAGAGAACTTGTGCCTTTATGGTTTGCCAAATGAGACTTGGGAGGTTACTCTTCCAGCTGAGGAAGTACCTCCTGAGCTTCCAGAACCAGCACTGGG
     | |   |  || | || |  || |||  || |     |  ||   ||    || || | | ||| | | ||     ||| | ||  ||  ||   ||||||| || |||||||| ||||||||  | ||||||||||| |||||||||| |||||| | |||||| || |||||||||||||| ||||||||  | ||
ctttttaagtgtttgtgagat-ttgtacctaa-gatgaagttagttctctttgtggtttctct-tcttgacttcttagtgaattacgttttttgctaatgcagAGAAGGAAAACTTGTGTCTTTATGGACTTCCAAATGAGACATGGGAGGTTAATCTTCCCGTTGAGGAGGTCCCTCCTGAGCTTCCTGAACCAGCGTTAGG

upper sequence: GRMZM2G107807_T01 (Zea mays), 3'ss of exon 2
lower sequence: Vv12s0035g01980.t01 (Vitis vinifera), 3'ss of exon 2
---------actgatgttcagtaacatgtcataactag-tgacgtgaacatatcagattccatttcctttgttttgtcctgttgacatatttctttcctttttatgccagAGAAAGAGAACTTGTGCCTTTATGGTTTGCCAAATGAGACTTGGGAGGTTACTCTTCCAGCTGAGGAAGTACCTCCTGAGCTTCCAGAACCAGCACTGGG
         | | |  ||    |  ||  ||||  ||  | | ||   ||||   || | ||  |   || |||||   ||||   | ||||      || ||||   |||||| ||||||||||| || |||||  | ||||||||||| ||||| ||||  || || | |||||| ||||||||||||||||||||||||||| | ||
ttattttatattcactttttacattat-ccatatatatcttatgttggcataaatgagtgcaacttgcttattttgga-tgtttgtaaattt-----gttcttat---agAGAAGGAGAACTTGTGTCTGTATGGACTTCCAAATGAGACATGGGAAGTTAACCTGCCTGTTGAGGAGGTACCTCCTGAGCTTCCAGAACCAGCATTAGG

upper sequence: GRMZM2G107807_T01 (Zea mays), 3'ss of exon 2
lower sequence: EFJ23237 (Selaginella moellendorffii), 3'ss of exon 2
----------------------------actgatgttcagtaacatgtcataactagtgacgtgaacatatcagattccatttcctttgttttgtcctgttgacatatttctttccttttt-atgccagAGAAAGAGAACTTGTGCCTTTATGGTTTGCCAAATGAGACTTGGGAGGTTACTCTTCCAGCTGAGGAAGTACCTCCTGAGCTTCCAGAACCAGCACTGGG
                            | ||  || |    |||||| |||  || ||    |  | | |         |    ||   ||||   | | |    | || ||  ||| || |  |||||||| || || ||||||||||||||| | ||  | |||||||||||||| | ||||||||| |||||||| || || ||||| || || ||||| || ||
gtttgtactctttcttatcctttagtctagtgtggtgctactacatgt-atatataatggtcgggtcttttgtttaagtgtgatattgactttggtgtatggtgtcactttttctcttattgactccagAGAAGGAAAATTTGTGCCTTTATGGTCTCCCCGACGAGACTTGGGAGGTGAATCTTCCAGCCGAGGAAGTGCCGCCGGAGCTCCCTGAGCCAGCGCTCGG

upper sequence: GRMZM2G107807_T01 (Zea mays), 3'ss of exon 2
lower sequence: EFJ25244 (Selaginella moellendorffii), 3'ss of exon 2
----------------------------actgatgttcagtaacatgtcataactagtgacgtgaacatatcagattccatttcctttgttttgtcctgttgacatatttctttcctttttatgccagAGAAAGAGAACTTGTGCCTTTATGGTTTGCCAAATGAGACTTGGGAGGTTACTCTTCCAGCTGAGGAAGTACCTCCTGAGCTTCCAGAACCAGCACTGGG
                            | ||  || |    |||||| |||  || ||    |  | | |         |    ||   |||| | | | |    | || || | | || |  |||||||| ||||| ||||||||||||||| | ||  | |||||||||||||| | ||||||||| |||||||| || || ||||| || || ||||| || ||
gtttgtcctctttcttatcctttagtctagtgtggtgctactacatgt-atatataatggtcgggtcttttgtttaagtgtgatattgactttggcgtatggtgtcactttttccttattgactccagAGAAGGAGAATTTGTGCCTTTATGGTCTCCCCGACGAGACTTGGGAGGTGAATCTTCCAGCCGAGGAAGTGCCGCCGGAGCTCCCTGAGCCAGCGCTCGG

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|76285557|gb|DV025125.1|DV025125
EST:     TTCTATCAGCAGTGCGATCCAG                         AGAAAGAGAACTTGTGCCTTTATGGTTTGCCAAATGAGACTTGGGAGGTTA
genomic: TTCTATCAGCAGTGCGATCCAGgtgacgcgcc ... tttatgccagAGAAAGAGAACTTGTGCCTTTATGGTTTGCCAAATGAGACTTGGGAGGTTA
EST: gi|211290732|gb|FK964129.1|FK964129
EST:     TTCCGTGGTGCGCGCAGATGTGGAGAAGTTCTATCAGCAGTGCGATCCAG                         AGAAAGAGAACTTGTGCCTTTATGGTTTGCCAAATGAGACTTGGGAGGTTA
genomic: TTCCGTGGTGCGCGCAGATGTGGAGAAGTTCTATCAGCAGTGCGATCCAGgtgacgcgcc ... tttatgccagAGAAAGAGAACTTGTGCCTTTATGGTTTGCCAAATGAGACTTGGGAGGTTA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gattccatttcctttgttttgtcctgttgacatatttctttcctttttatgccagAGAAAGAGAACTTGTGCCTTTATGGTTTGCCAAATGAGACTTGGGAGGTTACTCTTCCAGCTGAGGAAGTACCTCCTGAGCTTCCAGAACCAGCACTGGG
                        tgttgac  putative branch site (score: 3)
                                tatttctttccttttt  CT-rich tract
                               atatttcttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
actgatgttcagtaacatgtcataactagtgacgtgaacatatcagattccatttcctttgttttgtcctgttgacatatttctttcctttttatgccagAGAAAGAGAACTTGTGCCTTTATGGTTTGCCAAATGAGACTTGGGAGGTTACTCTTCCAGCTGAGGAAGTACCTCCTGAGCTTCCAGAACCAGCACTGGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCTT
- tgatgtt
- - - - - - - -catgtca
- - - - - - - - - - - - - - - - - -gaacata