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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacaacataaagaattccaaattcttacaccttaccagtttcttatacttcctgccttgttgaatgtcttaatgtaacaattgttctaattagGGGCCAAGAAGCTCGCTCAAATTCGAGAGAACAGCAATTTCTTCCGCTCGGAGCTTCAGAAAATGGGTTTTGAGGTTCTTGGAGATAATGATTCACCTGT

Basic information

species Zea mays
transcript GRMZM2G010202_T02
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G010202_T02 (Zea mays), 3'ss of exon 8
lower sequence: LOC_Os01g70380.1 (Oryza sativa), 3'ss of exon 9
gtacaacataaagaattccaaattcttacaccttaccagtttcttatacttcctgccttgttgaatgtcttaatgtaacaattgttctaattagGGGCCAAGAAGCTCGCTCAAATTCGAGAGAACAGCAATTTCTTCCGCTCGGAGCTTCAGAAAATGGGTTTTGAGGTTCTTGGAGATAATGATTCACCTGT
                       | | | | |||     ||||||||   | ||| |||   |||  || ||||||||  |||||||||| |||||||||||||||| ||||| |||||||||||||||||||||||||| || ||||||||||||||||||||||| ||||||||||| ||||| || || ||
--------------------gtatatcagaacttgttgatttcttatttcttctgtctttaggaaattcctaatgtaattattgttctaaatagGGGCCAAGAAGCTTGCTCAGATTCGAGAGAACAGCAATTTCTTCCGTTCAGAGCTTCAGAAAATGGGTTTTGAAGTTCTTGGAGACAATGACTCGCCGGT

upper sequence: GRMZM2G010202_T02 (Zea mays), 3'ss of exon 8
lower sequence: LOC_Os01g70370.1 (Oryza sativa), 3'ss of exon 9
------gtacaacataaagaattcca-aattcttacaccttaccagtttcttatacttcctgccttgttgaatgtcttaatgtaacaattgttctaattagGGGCCAAGAAGCTCGCTCAAATTCGAGAGAACAGCAATTTCTTCCGCTCGGAGCTTCAGAAAATGGGTTTTGAGGTTCTTGGAGATAATGATTCACCTGT
       ||     ||||| |    | || || | |   | |   ||| || ||||||       ||  ||   || ||||||||  |||||| |||  ||| ||||||||||| ||||| ||||| |||||||||||||||||||| || || ||| |||||||||||||||| ||||||||||| || || || |||||
gacaacatattttttaaagtacagaacaaatcatccgtttcaat-gttcctaatactttagataatgaggagattcctaatgtaattattgttataaacagGAGCCAAGAAGCTTGCTCAGATTCGGGAGAACAGCAATTTCTTCCGTTCAGAACTTGAGAAAATGGGTTTTGAAGTTCTTGGAGACAACGACTCGCCTGT

upper sequence: GRMZM2G010202_T02 (Zea mays), 3'ss of exon 8
lower sequence: GLYMA02G07250.1 (Glycine max), 3'ss of exon 9
-----------------------------gtacaacataaagaattccaaattcttacacct-taccagtttc--ttatactt-cctgccttgttga--atgtcttaatgtaacaattgttctaattagGGGCCAAGAAGCTCGCTCAAATTCGAGAGAACAGCAATTTCTTCCGCTCGGAGCTTCAGAAAATGGGTTTTGAGGTTCTTGGAGATAATGATTCACCTGT
                              |   |  |  |   ||  |   | ||  |  |  | || |     | ||| |   || | ||||| |   ||  || | ||||   || |||||  |||| ||| |||| || || |||||||||||||| ||||| || ||  | || || || ||||| ||||| |||||||||||||| ||||||||||| || ||
gtttggctggcactagttctgctctttgctttgcatttgtattgtttgatgattttttatgtgcatcaatccaaataatattcgtctactttgtttaccgtgcattgaagtaa-gttttttctatatagGTGCCCAGAAACTTGCACAAATTCGAGAGAATAGCAACTTTTTTAGGTCAGAACTGCAGAAGATGGGATTTGAGGTTCTTGGGGATAATGATTCTCCAGT

upper sequence: GRMZM2G010202_T02 (Zea mays), 3'ss of exon 8
lower sequence: GLYMA16G26210.1 (Glycine max), 3'ss of exon 9
---------------------------gtacaacataaagaattccaaattcttacaccttaccagtttc--ttatactt-cctgccttgttgaa--tgtcttaatgtaacaattgttctaattagGGGCCAAGAAGCTCGCTCAAATTCGAGAGAACAGCAATTTCTTCCGCTCGGAGCTTCAGAAAATGGGTTTTGAGGTTCTTGGAGATAATGATTCACCTGT
                           |     |||    | ||     || ||       | || |     | ||| |   || | ||||| |   ||  || | ||||   |  |||||  |||| ||| |||| || || ||||||||||| || ||||| || ||| | || ||  | ||||| ||||| |||||||||||||| ||||||||||| || ||
gtttggctggcactagttctgctctttgctttgcatttgtatttgatggttttttacgtgcatcaatccaaataatattcatctactttgtttaccttgcattgaagtaa-gttgtttctatatagGTGCCCAGAAACTTGCACAAATTCGAGAAAATAGCAACTTTTTCAGGTCAGAATTGCAGAAGATGGGATTTGAGGTTCTTGGGGATAATGATTCTCCAGT

upper sequence: GRMZM2G010202_T02 (Zea mays), 3'ss of exon 8
lower sequence: AT5G23670.1 (Arabidopsis thaliana), 3'ss of exon 9
-----------------gtacaacataaagaatt--ccaaattcttacaccttaccagtttcttat-acttcctgccttgt----tgaatgtcttaatgtaacaattgttctaattagGGGCCAAGAAGCTCGCTCAAATTCGAGAGAACAGCAATTTCTTCCGCTCGGAGCTTCAGAAAATGGGTTTTGAGGTTCTTGGAGATAATGATTCACCTGT
                   ||    | |  ||||  ||  |||       || | ||   ||| || |  || || ||  |    | ||       ||    |     | || |  ||||||  | ||||| ||   ||| || ||||||||||| || |||||  | ||||| ||||| ||||| |||||||| |||||||| |||||||| || ||
gtactcgattttttttctcaccgtgtcattaattggcctcatttgggtcactgagcacaatctaatcaggtcatgactcataacctaaaaactcccattcttctcaaatactgaacagGGGCACAAAAGCTAGCAAGAATACGTGAGAACAGCAACTTTTTCCGGGCTGAGCTGCAGAAGATGGGATTTGAGGTACTTGGAGACAATGATTCCCCAGT

upper sequence: GRMZM2G010202_T02 (Zea mays), 3'ss of exon 8
lower sequence: AT3G48780.1 (Arabidopsis thaliana), 3'ss of exon 9
gtacaacataaagaattccaaattcttacaccttaccagtttcttatacttcctgccttgttgaatgtcttaatgtaacaattgttctaattagGGGCCAAGAAGCTCGCTCAAATTCGAGAGAACAGCAATTTCTTCCGCTCGGAGCTTCAGAAAATGGGTTTTGAGGTTCTTGGAGATAATGATTCACCTGT
|||       |     |      |||| || ||    | | | ||   ||    || | ||  ||| ||  | | | | |||    ||    ||||||  | ||| | ||   |||  | ||||||||||| || ||| |  | ||| | ||||| ||||| ||||| ||||||||||| ||||||||||| ||
gtatcttgatagcttatttttgctctttcagct-gtaactcttttgctctatgagcttcgt--aatctcaaacttttataatcac-ctgggcagGGGCACAAAAGTTAGCAAGAATAAGGGAGAACAGCAACTTTTTCAGGGCTGAGTTGCAGAAGATGGGGTTTGAAGTTCTTGGAGACAATGATTCACCAGT

upper sequence: GRMZM2G010202_T02 (Zea mays), 3'ss of exon 8
lower sequence: Vv14s0068g01300.t01 (Vitis vinifera), 3'ss of exon 9
----------------gtacaacataaagaattccaaattcttacaccttaccagtt---tcttatacttcctgccttgttgaatgtctt--aatgtaacaattgt---tctaattagGGGCCAAGAAGCTCGCTCAAATTCGAGAGAACAGCAATTTCTTCCGCTCGGAGCTTCAGAAAATGGGTTTTGAGGTTCTTGGAGATAATGATTCACCTGT
                 |    |||      ||  || |||| |  | | |    ||   | | | |||  |       || | ||| ||  | | ||    |  |   || |  |||| ||| | || || || ||||| || ||||| ||||| || ||| | || || || ||||  |||||||||||||||||||| |||||||| || || ||
gtaggataaataaatcttctgtcatgcttggttttaacttct-attcttgaatctttaggtttcagactctccattgctttaattgtttttgattttagtgctcttgtgtccatgtagGAGCCCAAAAACTTGCACAAATACGTGAGAATAGCAACTTTTTCAGGTCAGAACTGCAGAGCATGGGTTTTGAGGTTCTTGGGGATAATGACTCTCCAGT

upper sequence: GRMZM2G010202_T02 (Zea mays), 3'ss of exon 8
lower sequence: Vv17s0000g00500.t01 (Vitis vinifera), 3'ss of exon 10
--------------gtacaacataaagaattccaaattcttacaccttaccagtttcttatacttc-ctgccttgttgaatgtcttaatgtaacaattgttctaat--tagGGGCCAAGAAGCTCGCTCAAATTCGAGAGAACAGCAATTTCTTCCGCTCGGAGCTTCAGAAAATGGGTTTTGAGGTTCTTGGAGATAATGATTCACCTGT
               ||   ||  |   ||       || | || ||   ||       ||  |   ||   ||| | | ||| || || |  |  |||||  |||  |||||||  ||||  | || | ||| || |||||||| || || ||| | || || || ||||| ||||| |||||||||||||||||||||||||| |||||
gttcaccctcttctatatttcaccatttatggtgg-ctcatgcagctctgcaaacctagatcttgagcttatttgcttattgt-ttgatctg-cttttgtttaaatattagGGGCTCAGAAATTGGCACGAATACGTGAGAACAGTAACTTTTTCAGATCAGAACTGCAGAAGATGGGCTTTGAGGTTCTTGGAGATAATGATTCTCCTGT

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|71445384|gb|DR826434.1|DR826434
EST:     GGTCATTTCAGCTATAAAGGTCATCCTTGGGGAAGATGGAACTAACAGAG                         GGGCCAAGAAGCTCGCTCAAATTCGAGAGAACAGCAATTTCTTCCGCTCGG
genomic: GGTCATTTCAGCTATAAAGGTCATCCTTGGGGAAGATGGAACTAACAGAGgtacaacata ... ttctaattagGGGCCAAGAAGCTCGCTCAAATTCGAGAGAACAGCAATTTCTTCCGCTCGG
EST: gi|148947745|gb|EC893228.2|EC893228
EST:     GTCATTTCAGCTATAAAGGTCATCCTTGGGGGAAGAAGGAACTAACAGAG                         GGGCCAAGAAGCTCGCTCAAATTCGAGAGAACAGCAATTTCTTCCGCTCGG
genomic: GTCATTTCAGCTATAAAGGTCATCCTT-GGGGAAGATGGAACTAACAGAGgtacaacata ... ttctaattagGGGCCAAGAAGCTCGCTCAAATTCGAGAGAACAGCAATTTCTTCCGCTCGG
EST: gi|211322418|gb|FL451106.1|FL451106
EST:     GGTCATTTCAGCTATAAAGGTCATCCTTGGGGAAGATGGAACTAACAGAG                         GGGCCAAGAAGCTCGCTCAAATTCGAGAGAACAGCAATTTCTTCCGCTCGG
genomic: GGTCATTTCAGCTATAAAGGTCATCCTTGGGGAAGATGGAACTAACAGAGgtacaacata ... ttctaattagGGGCCAAGAAGCTCGCTCAAATTCGAGAGAACAGCAATTTCTTCCGCTCGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttcttatacttcctgccttgttgaatgtcttaatgtaacaattgttctaattagGGGCCAAGAAGCTCGCTCAAATTCGAGAGAACAGCAATTTCTTCCGCTCGGAGCTTCAGAAAATGGGTTTTGAGGTTCTTGGAGATAATGATTCACCTGT
                                 atgtaac  putative branch site (score: 3)
                                          ttgttct  putative PPT
                              ttaatgtaacaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacaacataaagaattccaaattcttacaccttaccagtttcttatacttcctgccttgttgaatgtcttaatgtaacaattgttctaattagGGGCCAAGAAGCTCGCTCAAATTCGAGAGAACAGCAATTTCTTCCGCTCGGAGCTTCAGAAAATGGGTTTTGAGGTTCTTGGAGATAATGATTCACCTGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT