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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttattaaaaaaatacataataatataataagtacctgtttgttctaaaaataatacttctgtaaatgagaatattatttttccttttggtaataatgcagGTTGATGATACTGAAGTCATCAGTTTTTTGCTGCAAACTGAAATAATTCCTCTGTGCTTGCGAACCATGGAGATGGGTAGTGAGCTATCCAAAACT

Basic information

species Zea mays
transcript GRMZM2G045331_T01
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G045331_T01 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os04g52340.1 (Oryza sativa), 3'ss of exon 7
ttattaaaaaaatacataataatataataagtacctgtttgttctaaaaataatacttctgtaaatgagaatattatttttccttttggtaata-atgcagGTTGATGATACTGAAGTCATCAGTTTTTTGCTGCAAACTGAAATAATTCCTCTGTGCTTGCGAACCATGGAGATGGGTAGTGAGCTATCCAAAACT
 | ||  |    | |    |  | |  |  ||       || | | | | || |  | ||  |||||  | ||    || |       |||||| | ||||||||||||||||||||| ||||||||| |||||||||||||||||||||||||||| ||||| |||||||| ||||| |||||||| || ||||||
ctctttgatgttttctaccttctttttttcgtgttgaactggttttaga-tatttttccttcaaatggaattaaagcttctttcacatgtaatacacgcagGTTGATGATACTGAAGTTATCAGTTTTCTGCTGCAAACTGAAATAATTCCTCTGTGTTTGCGTACCATGGAAATGGGAAGTGAGCTGTCAAAAACT

upper sequence: GRMZM2G045331_T01 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os07g37790.1 (Oryza sativa), 3'ss of exon 7
ttattaaaaaaatacataataatataataagtacctgtttgttctaaaaataatacttctgtaaatgagaatattatttttccttttggtaata-atgcagGTTGATGATACTGAAGTCATCAGTTTTTTGCTGCAAACTGAAATAATTCCTCTGTGCTTGCGAACCATGGAGATGGGTAGTGAGCTATCCAAAACT
 | ||  |    | |    |  | |  |  ||       || | | | | |  |  | ||  |||||  | ||    || |       |||||| | ||||||||||||||||||||| ||||||||| |||||||||||||||||||||||||||| ||||| |||||||| ||||| |||||||| || ||||||
-tctttgatgttttctaccttctttttttcgtgttgaactggttttagattttttttccttcaaatggaattaaagcttctttcacatgtaatacacgcagGTTGATGATACTGAAGTTATCAGTTTTCTGCTGCAAACTGAAATAATTCCTCTGTGTTTGCGTACCATGGAAATGGGAAGTGAGCTGTCAAAAACT

upper sequence: GRMZM2G045331_T01 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA08G43220.1 (Glycine max), 3'ss of exon 5
-ttattaaaaaaatacataataatataataagtacctgtttgttctaaaaataatacttctgtaaatgagaatattatttttccttttggtaataatgca---gGTTGATGATACTGAAGTCATCAGTTTTTTGCTGCAAACTGAAATAATTCCTCTGTGCTTGCGAACCATGGAGATGGGTAGTGAGCTATCCAAAACT
 || ||     |||   |  |  | |  ||| | | | |||  ||||    |  |  || | | |||    | ||| ||||||  | || |  | || ||   |||||||||||| ||||| || |||||  | ||   ||| || |||||||| |||||| |||| |||||||| ||||| ||||| ||||||||||| 
attgtttcttgaatttttttt--ttttgtaa-ttcatatttcatctattcttg-tttttttatcaattgtgacattttttttctgtctgatttttattcactagGTTGATGATACAGAAGTTATAAGTTTCCTTCTTTCAACAGAGATAATTCCCCTGTGCCTGCGCACCATGGAAATGGGCAGTGAACTATCCAAAACA

upper sequence: GRMZM2G045331_T01 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA18G10400.1 (Glycine max), 3'ss of exon 5
-ttattaaaaaaatacataataatataataagtacctgtttgttctaaaaataatacttctgtaaatgagaatattatttttc-cttttggtaataatgcagGTTGATGATACTGAAGTCATCAGTTTTTTGCTGCAAACTGAAATAATTCCTCTGTGCTTGCGAACCATGGAGATGGGTAGTGAGCTATCCAAAACT
 |||| |      |  |   |  | |  ||| | ||| |||  ||||    |  |  || ||| |||    | ||| ||  |  ||  |  | ||    |||||||||||||| ||||| || |||||  | ||   ||| || ||||||||||| ||||||||||||||||| ||||| ||||||||||||||||| 
attatcattgtttttaaatttttttttgtaa-tccctatttcatctattcttt-tgtttttgttaattctgacatttttcctggctgatttttattcaccagGTTGATGATACAGAAGTTATAAGTTTCCTTCTTTCAACAGAGATAATTCCTCTATGCTTGCGAACCATGGAAATGGGCAGTGAGCTATCCAAAACA

upper sequence: GRMZM2G045331_T01 (Zea mays), 3'ss of exon 6
lower sequence: AT3G20800.1 (Arabidopsis thaliana), 3'ss of exon 5
-----------------------------------------------------------------------------------------ttattaaaaaaatacataataatataata-agtacctgtttgttctaaaaataatacttctgt-aaatgagaatatt-------atttttccttttggtaataatgcagGTTGATGATACTGAAGTCATCAGTTTTTTGCTGCAAACTGAAATAATTCCTCTGTGCTTGCGAACCATGGAGATGGGTAGTGAGCTATCCAAAACT
                                                                                         || |   |    |      |  || | || || |  | | |  | |     |  |   | | | |||| ||||   |       ||  ||  ||    |  |  | |||||||||||||| || ||||| || ||  | ||   ||||||||| |||||||||||| | || |||||||| ||||| |||||||| || ||||| 
gtacaccatcccgtcccttttctgttccttgtttctctttggttttgatgttccccacctactttttgctgaaagcaaaggactaaaaattgtgttagtggtcttggtttctaaagtagagaatttatattcttttttggtggttagtgtatgaaataagaaaggttcatcggatccttatttcactttgttttccagGTTGATGATACAGAGGTCATTAGCTTCCTTCTTTCAACTGAAATTATTCCTCTGTGCCTCCGTACCATGGAAATGGGGAGTGAGCTGTCAAAAACA

upper sequence: GRMZM2G045331_T01 (Zea mays), 3'ss of exon 6
lower sequence: Vv19s0090g00930.t01 (Vitis vinifera), 3'ss of exon 7
-ttattaaaaaaatacataataatataataagtacctgtttgttctaaaaataatacttctgtaaatgagaatattatttttccttttggtaataatgcagGTTGATGATACTGAAGTCATCAGTTTTTTGCTGCAAACTGAAATAATTCCTCTGTGCTTGCGAACCATGGAGATGGGTAGTGAGCTATCCAAAACT
 ||| |    | ||   |  || | |    |     ||||  |  |   | |   | |  ||    | |  |  || ||||   ||||        | |||||||||||||| ||||| || |||||  | ||   ||| ||||||||||| |||||| | || |||||||||||||| |||||  | || ||||| 
attaattgctatattgtttgtattgtttgtaaggtttgttactcttgtgattccaagtattgctggttattacctt-ttttattttttcccctctttccagGTTGATGATACAGAAGTTATTAGTTTCCTTCTCTCAACAGAAATAATTCCGCTGTGCCTACGCACCATGGAGATGGGGAGTGAATTGTCAAAAACA

upper sequence: GRMZM2G045331_T01 (Zea mays), 3'ss of exon 6
lower sequence: PP1S276_27V6.1 (Physcomitrella patens), 3'ss of exon 5
---ttattaaaaaaatacataataatataataagta-cctgtttgttctaaaaataatacttctgtaaatgagaatattatttttccttttggtaataatgcagGTTGATGATACTGAAGTCATCAGTTTTTTGCTGCAAACTGAAATAATTCCTCTGTGCTTGCGAACCATGGAGATGGGTAGTGAGCTATCCAAAACT
      |  | ||| |||||| |   ||  ||  || |||||    |       |     | || |  ||   ||||  || ||  |||  ||||    ||||||| ||||| |||||||| || | |||  | |||  ||| || || |||||||||||| | ||||| ||||||||||| ||||| |||||||| || 
taaccttctagaaactacata-tcccatcttacatagcctgtaatgtgggtttttgtcggtcctttggatttaaatac-atgttagctt--ggtatatctgcagGTGGATGACACTGAAGTTATTAATTTCCTACTGTCAACCGAGATTATTCCTCTGTGCCTACGAACGATGGAGATGGGAAGTGAACTATCCAAGACA

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|211200410|gb|FL096663.1|FL096663
EST:     TTGAGTACCTAAGGCTTACTAGCTTGGGGGTCATTGGTGCTCTTGTCAAG                         GTTGATGATACTGAAGTCATCAGTTTTCTGCTGCAAACTGAAATAATTCCT
genomic: TTGAGTACCTAAGGCTTACTAGCTTGGGGGTCATTGGTGCTCTTGTCAAGgtaatttgtg ... aataatgcagGTTGATGATACTGAAGTCATCAGTTTTTTGCTGCAAACTGAAATAATTCCT
EST: gi|78088708|gb|DV517101.1|DV517101
EST:     TTGAGTACCTAAGGCTTACTAGCTTGGGGGTCATTGGTGCTCTTGTCAAG                         GTTGATGATACTGAAGTCATCAGTTTTTTGCTGCAAACTGAAATAATTCCT
genomic: TTGAGTACCTAAGGCTTACTAGCTTGGGGGTCATTGGTGCTCTTGTCAAGgtaatttgtg ... aataatgcagGTTGATGATACTGAAGTCATCAGTTTTTTGCTGCAAACTGAAATAATTCCT
EST: gi|149048884|gb|EE048384.2|EE048384
EST:     TTGAGTACCTAAGGCTTACTAGCTTGGGGGTCATTGGTGCTCTTGTCAAG                         GTTGATGATACTGAAGTCATCAGTTTTTTGCTGCAAACTGAAATAATTCCT
genomic: TTGAGTACCTAAGGCTTACTAGCTTGGGGGTCATTGGTGCTCTTGTCAAGgtaatttgtg ... aataatgcagGTTGATGATACTGAAGTCATCAGTTTTTTGCTGCAAACTGAAATAATTCCT
EST: gi|31351237|gb|CD435594.1|CD435594
EST:     TTGAGTACCTAAGGCTTACTAGCTTGGGGGTCATTGGTGCTCTTGTCAAG                         GTTGATGATACTGAAGTCATCAGTTTTCTGGCTGCAA-CTGAAATAATTCC
genomic: TTGAGTACCTAAGGCTTACTAGCTTGGGGGTCATTGGTGCTCTTGTCAAGgtaatttgtg ... aataatgcagGTTGATGATACTGAAGTCATCAGTTTTTTG-CTGCAAACTGAAATAATTCC
EST: gi|78091209|gb|DV519583.1|DV519583
EST:     TTGAGTACCTAAGGCTTACTAGCTTGGGGGTCATTGGTGCTCTTGTCAAG                         GTTGATGATACTGAAGTCATCAGTTTTTTGCTGCAAACTGAAATAATTCCT
genomic: TTGAGTACCTAAGGCTTACTAGCTTGGGGGTCATTGGTGCTCTTGTCAAGgtaatttgtg ... aataatgcagGTTGATGATACTGAAGTCATCAGTTTTTTGCTGCAAACTGAAATAATTCCT
EST: gi|71445883|gb|DR826933.1|DR826933
EST:     TTGAGTACCTAAGGCTTACTAGCTTGGGGGTCATTGGTGCTCTTGTCAAG                         GTTGATGATACTGAAGTCATCAGTTTTTTGCTGCAAACTGAAATAATTCCT
genomic: TTGAGTACCTAAGGCTTACTAGCTTGGGGGTCATTGGTGCTCTTGTCAAGgtaatttgtg ... aataatgcagGTTGATGATACTGAAGTCATCAGTTTTTTGCTGCAAACTGAAATAATTCCT
EST: gi|31356490|gb|CD440847.1|CD440847
EST:     TTGAGTACCTAAGGCTTACTAGCTTGGGGGTCATTGGTGCTCTTGTCAAG                         GTTGATGATACTGAAGTCATCAGTTTTCTGCTGCAAACTGAAATAATTCCT
genomic: TTGAGTACCTAAGGCTTACTAGCTTGGGGGTCATTGGTGCTCTTGTCAAGgtaatttgtg ... aataatgcagGTTGATGATACTGAAGTCATCAGTTTTTTGCTGCAAACTGAAATAATTCCT
EST: gi|76936740|gb|DV174858.1|DV174858
EST:     TTGAGTACCTAAGGCTTACTAGCTTGGGGGTCATTGGTGCTCTTGTCAAG                         GTTGATGATACTGAAGTCATCAGTTTTTTGCTGCAAACTGAAATAATTCCT
genomic: TTGAGTACCTAAGGCTTACTAGCTTGGGGGTCATTGGTGCTCTTGTCAAGgtaatttgtg ... aataatgcagGTTGATGATACTGAAGTCATCAGTTTTTTGCTGCAAACTGAAATAATTCCT
EST: gi|31354815|gb|CD439172.1|CD439172
EST:     TTGAGTACCTAAGGCTTACTAGCTTGGGGGTCATTGGTGCTCTTGTCAAG                         GTTGATGATACTGAAGTCATCAGTTTTCTGCTGCAAACTGAAATAATTCCT
genomic: TTGAGTACCTAAGGCTTACTAGCTTGGGGGTCATTGGTGCTCTTGTCAAGgtaatttgtg ... aataatgcagGTTGATGATACTGAAGTCATCAGTTTTTTGCTGCAAACTGAAATAATTCCT
EST: gi|74233595|gb|DT641509.1|DT641509
EST:     TTGAGTACCTAAGGCTTACTAGCTTGGGGGTCATTGGTGCTCTTGTCAAG                         GTTGATGATACTGAAGTCATCAGTTTTTTGCTGCAAACTGAAATAATTCCT
genomic: TTGAGTACCTAAGGCTTACTAGCTTGGGGGTCATTGGTGCTCTTGTCAAGgtaatttgtg ... aataatgcagGTTGATGATACTGAAGTCATCAGTTTTTTGCTGCAAACTGAAATAATTCCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaaaataatacttctgtaaatgagaatattatttttccttttggtaataatgcagGTTGATGATACTGAAGTCATCAGTTTTTTGCTGCAAACTGAAATAATTCCTCTGTGCTTGCGAACCATGGAGATGGGTAGTGAGCTATCCAAAACT
 ttctaaa  putative branch site (score: 2)
                        aatattatttttcctt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttattaaaaaaatacataataatataataagtacctgtttgttctaaaaataatacttctgtaaatgagaatattatttttccttttggtaataatgcagGTTGATGATACTGAAGTCATCAGTTTTTTGCTGCAAACTGAAATAATTCCTCTGTGCTTGCGAACCATGGAGATGGGTAGTGAGCTATCCAAAACT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATG