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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tttcaatgcttattaccaagcatttgtgatcgttatagttcctatagctttgtgtttgtgtttcagactttttcctttcatttttttggtgttggttcagGCCGTCTGCACAGAGGCTGGAATGTTTGCTCTTCGTGAGAGAAGGGTGCACGTTACCCAGGAGGACTTCGAGATGGCAGTGGCCAAGGTGATGAAGAAAG

Basic information

species Zea mays
transcript GRMZM2G107362_T04
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G107362_T04 (Zea mays), 3'ss of exon 8
lower sequence: LOC_Os02g11050.1 (Oryza sativa), 3'ss of exon 8
----tttcaatgcttat---taccaagcatttgtgatcgttatagttcctatagctttgtgtttgtgtttcagactttttcctttcatttttttggtgttggttcagGCCGTCTGCACAGAGGCTGGAATGTTTGCTCTTCGTGAGAGAAGGGTGCACGTTACCCAGGAGGACTTCGAGATGGCAGTGGCCAAGGTGATGAAGAAAG
||||| || ||| |||| | || ||| |||| ||||||| | ||||| | || ||||| | | | | ||| | ||||||| ||||||||||| ||||||||||||||||||||||||||||||||||| || || || |||||||| |||||||||||||| ||||||||||||||||
ttcaaaacaatgtgcatatatacacagcactatagaacgtcatagctcctata-ccttgtgatcatgc----aactttattcactttctctttcatcatc--ttcagGCGGTCTGCACAGAAGCTGGAATGTTTGCTCTTCGTGAGAGAAGGGTGCATGTAACACAAGAGGACTTTGAGATGGCAGTGGCGAAGGTGATGAAGAAAG

upper sequence: GRMZM2G107362_T04 (Zea mays), 3'ss of exon 8
lower sequence: GLYMA07G00420.1 (Glycine max), 3'ss of exon 8
tttcaatgcttattaccaagcatttgtgatcgttatagttcctatagctttgtgtttgtgtttcagactttttcc----tttcatttttttggtgttggttcagGCCGTCTGCACAGAGGCTGGAATGTTTGCTCTTCGTGAGAGAAGGGTGCACGTTACCCAGGAGGACTTCGAGATGGCAGTGGCCAAGGTGATGAAGAAAG
||||| | | | ||||| | ||| | | || || | | | || ||| | | | || | | |||| || | | ||||| || ||||| || ||||||||||||||| | | ||| | ||||| ||||| || |||||||| || |||||||| ||||| ||||||||||| || |
-gcaaatgcagagca--atttgtttgtcaatgttgttaa-cttaatgcaatatttaagtattttatagcctgaccaacgctcaaattttgtgccttgtatgcagGCTGTTTGCACTGAAGCTGGAATGTTTGCTTTGAGGGAGCGGAGGGTACACGTGACTCAGGAGGATTTTGAGATGGCCGTGGCGAAGGTGATGAAAAAGG

upper sequence: GRMZM2G107362_T04 (Zea mays), 3'ss of exon 8
lower sequence: GLYMA08G24000.1 (Glycine max), 3'ss of exon 8
tttcaatgcttattaccaagcatttgtgatcgttatagttcctatagctttgtgttt-gtgtttcagactttttcctttcatttt-tttggtgttggttcagGCCGTCTGCACAGAGGCTGGAATGTTTGCTCTTCGTGAGAGAAGGGTGCACGTTACCCAGGAGGACTTCGAGATGGCAGTGGCCAAGGTGATGAAGAAAG
| ||||| || | |||| || || | || | ||| || | | || || ||| | | | || | ||| ||| | ||||| || ||||| || |||||||||||||| | | ||| | ||||| ||||| || |||||||| || |||||||| ||||||||||||||||| || |
tactaatgcaaat-gcagagcaatt-tgtttgtcaatgttaacttaatgtgttattaagtattttatagcctgaccaacgctcaaattttgtgcctttgcagGCTGTTTGCACCGAAGCTGGAATGTTTGCATTGAGGGAGCGGAGGGTACACGTGACTCAGGAGGATTTTGAGATGGCTGTGGCCAAGGTGATGAAAAAGG

upper sequence: GRMZM2G107362_T04 (Zea mays), 3'ss of exon 8
lower sequence: AT5G20000.1 (Arabidopsis thaliana), 3'ss of exon 8
tttcaatgcttattaccaagcatttgtgatcgttatagttcctatagctttgtgtttgtgtttcagactttttcctttc--atttttttggt-gttg-gttcagGCCGTCTGCACAGAGGCTGGAATGTTTGCTCTTCGTGAGAGAAGGGTGCACGTTACCCAGGAGGACTTCGAGATGGCAGTGGCCAAGGTGATGAAGAAAG
|| | ||| | | | | ||| || | | || | | | || || || |||||||| || | |||||| || ||||| ||||| || |||||||| ||||||||||| || || || || || ||||| ||||| |||||||| ||||| ||||| ||||||||||
-------------------------gtaagtgtttctctgtccctgcttctgtcttgttctctccaatctgtctctctctaatgtttttggttattacggtcagGCTGTATGCACGGAGGCGGGCATGTTTGCACTTCGTGAGAGGAGAGTACATGTGACTCAGGAAGACTTTGAGATGGCTGTGGCGAAGGTAATGAAGAAAG

upper sequence: GRMZM2G107362_T04 (Zea mays), 3'ss of exon 8
lower sequence: AT5G19990.1 (Arabidopsis thaliana), 3'ss of exon 8
tttcaatgcttattaccaagcatttgtgatcgttatagttcctatagctttgtgtttgtgtttcagactttttcctttcatttttttggt--gttggttcagGCCGTCTGCACAGAGGCTGGAATGTTTGCTCTTCGTGAGAGAAGGGTGCACGTTACCCAGGAGGACTTCGAGATGGCAGTGGCCAAGGTGATGAAGAAAG
||| ||| || | || ||| ||| || | | | ||| | || | || |||||||| | | |||||| || ||||| ||||| |||||||||||||| |||||||| || || ||||| || || || ||||| |||||||| ||||||||||| ||||||||||
--------------gtaaagtgttttctatttctctacttc-tatcttgttctctctacattttg----cctctctcttatgtttttggttaatacggtcagGCTGTGTGCACGGAGGCGGGAATGTTTGCTCTGCGTGAGAGGAGAGTACACGTGACACAAGAAGACTTTGAGATGGCGGTGGCCAAGGTAATGAAGAAAG

upper sequence: GRMZM2G107362_T04 (Zea mays), 3'ss of exon 8
lower sequence: Vv04s0008g04690.t01 (Vitis vinifera), 3'ss of exon 8
tttcaatgcttattaccaagcatttgtgatcgttatagttcctatagctttgtgtttgtgtttcagactttttcctttcatttttttggtgttggtt--cagGCCGTCTGCACAGAGGCTGGAATGTTTGCTCTTCGTGAGAGAAGGGTGCACGTTACCCAGGAGGACTTCGAGATGGCAGTGGCCAAGGTGATGAAGAAAG
| | | |||||| | ||| | | | | | | | | | ||||| || ||| | | | | | |||| | | ||| ||||| || |||||||| ||||||||||||||||| | ||||| || || || || || || || || || |||||||||||||| ||||||||||| || |
actaagtccttattcttcatcatat-caagtgcggtcggttatct-gttttgtcttctaacatcaagcatgtctaactaaacttttatataattgtttgcagGCGGTATGCACAGAAGCTGGAATGTTTGCTCTAAGGGAGAGGAGAGTACATGTGACACAAGAAGATTTTGAGATGGCAGTGGCAAAGGTGATGAAAAAGG

upper sequence: GRMZM2G107362_T04 (Zea mays), 3'ss of exon 8
lower sequence: Vv09s0002g05800.t01 (Vitis vinifera), 3'ss of exon 8
tttcaatgcttattaccaagcatttgtgatcgttatagttcctatagctttgtgtttgtgtttcagactttttcctttcatttttttggtgttggtt--cagGCCGTCTGCACAGAGGCTGGAATGTTTGCTCTTCGTGAGAGAAGGGTGCACGTTACCCAGGAGGACTTCGAGATGGCAGTGGCCAAGGTGATGAAGAAAG
| | | | || ||| ||| | || | | || | || | | | | || | | || | ||| || ||| ||||| || |||||||| || || ||||||||| | | ||||| ||||| ||||| || ||||| || ||||||||||| || ||||| ||||||||||| |
ctgactttcctgccttcataggtttttgaatataatggaaaccat--ttacttgcatagatctgatacctctcggattgagcatttgaacttttgtttgcagGCGGTATGCACAGAAGCAGGGATGTTTGCTTTGAGGGAGAGGAGGGTTCACGTAACACAGGAAGATTTCGAGATGGCTGTAGCCAAAGTGATGAAGAAGG

upper sequence: GRMZM2G107362_T04 (Zea mays), 3'ss of exon 8
lower sequence: PP1S7016_1V6.1 (Physcomitrella patens), 3'ss of exon 3
--------------------------tttcaatgcttattaccaagcatttgtgatcgttatag-ttcctatagctttgtgtttgtgtttcagactttttcctttcatttttttggtgttggttca----gGCCGTCTGCACAGAGGCTGGAATGTTTGCTCTTCGTGAGAGAAGGGTGCACGTTACCCAGGAGGACTTCGAGATGGCAGTGGCCAAGGTGATGAAGAAAG
|| | | || | | | | | || || | | || | | ||| || | || || || | | ||| | ||| |||| ||| || |||||||||||||| ||||||||||| ||||| | | || || || || || ||||||||||||||||| ||||| |||||||||||||| |
gtagctacaaacctacagtatctagggtttatttctggtagtgatacgaaggaagctgctagaggcttttgtattatgttatttaaaattttggctgttcgtttatactaattttttattgcttcaatcagGCTGTATGCACAGAGGCTGGCATGTTTGCTCTACGTGAACGGCGTGTACATGTGACACAAGAGGACTTCGAGATGGCTGTGGCTAAGGTGATGAAGAAGG

upper sequence: GRMZM2G107362_T04 (Zea mays), 3'ss of exon 8
lower sequence: EFJ28638 (Selaginella moellendorffii), 3'ss of exon 7
tttcaatgcttattaccaagcatttgtgatcgttatagttcctatagctttgtgtttgtgtttcagactttttcctttcatttttttggtgttggttcagGCCGTCTGCACAGAGGCTGGAATGTTTGCTCTTCGTGAGAGAAGGGTGCACGTTACCCAGGAGGACTTCGAGATGGCAGTGGCCAAGGTGATGAAGAAAG
|||||||| | || ||| || || ||| | || | | | ||| |||||||| | | ||||| || ||||| |||||||||||||||||||| || ||||| | || || || |||||||| || ||||| ||||| |||||||| ||||||||||| |
---------------------gtttgtgatgctcgcg----ctttag-ttggtccttg-acgacggagtgtgtttttttttttttttgctctc----cagGCGGTGTGCACGGAGGCTGGAATGTTTGCTCTGCGAGAGAGGCGCGTTCATGTCACCCAGGAAGATTTCGACATGGCGGTGGCCAAAGTGATGAAGAAGG

upper sequence: GRMZM2G107362_T04 (Zea mays), 3'ss of exon 8
lower sequence: EFJ04162 (Selaginella moellendorffii), 3'ss of exon 6
tttcaatgcttattaccaagcatttgtgatcgttatagttcctatagctttgtgtttgtgtttcagactttttcctttcatttttttggtgttggttcagGCCGTCTGCACAGAGGCTGGAATGTTTGCTCTTCGTGAGAGAAGGGTGCACGTTACCCAGGAGGACTTCGAGATGGCAGTGGCCAAGGTGATGAAGAAAG
|||||||| | || ||| || || ||| | || | | | ||| |||||||| | | ||||| || ||||| |||||||||||||||||||| || ||||| | || || || |||||||| |||||||| ||| | |||||||| ||||||||||| |
---------------------gtttgtgatgctcgcg----ctttag-ttggtccttg-acgacggagtgtgtttttttttttttttgctctc----cagGCGGTGTGCACGGAGGCTGGAATGTTTGCTCTGCGAGAGAGGCGCGTTCATGTCACCCAGGAAGACTTCGACATGCCGGTGGCCAAAGTGATGAAGAAGG

upper sequence: GRMZM2G107362_T04 (Zea mays), 3'ss of exon 8
lower sequence: EFJ20576 (Selaginella moellendorffii), 3'ss of exon 7
tttcaatgcttattaccaagcatttgtgatcgttatagttcctatagctttgtgtttgtgtttcagactttttcctttcatttttttggtgttggttcagGCCGTCTGCACAGAGGCTGGAATGTTTGCTCTTCGTGAGAGAAGGGTGCACGTTACCCAGGAGGACTTCGAGATGGCAGTGGCCAAGGTGATGAAGAAAG
|||||||| | || ||| || || ||| | || | | | ||| |||||||| | | ||||| || ||||| |||||||||||||||||||| || ||||| | || || || |||||||| |||||||| ||||| |||||||| ||||||||||| |
---------------------gtttgtgatgctcgcg----ctttag-ttggtccttg-acgacggagtgtgtttttttttttttttgctctc----cagGCGGTGTGCACGGAGGCTGGAATGTTTGCTCTGCGAGAGAGGCGCGTTCATGTCACCCAGGAAGACTTCGACATGGCGGTGGCCAAAGTGATGAAGAAGG

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|166525245|gb|EG101803.1|EG101803
EST:     CTCAGGAGCTGAGCTCAAG                         GCCGTCTGCACAGAGGCTGGAATGTTTGCTCTTCGTGAGAGAAGGGTGCAC
genomic: CTCAGGAGCTGAGCTCAAGgtttgttaat ... gttggttcagGCCGTCTGCACAGAGGCTGGAATGTTTGCTCTTCGTGAGAGAAGGGTGCAC
EST: gi|32843443|gb|CD983124.1|CD983124
EST:     TGAAAAAGATCGCGGAAAAGATGAATGGGGCCTCAGGAGCTGAGCTCAAG                         GCCGTCTGCACAGAGGCTGGAATGTTTGCTCTCCGTGAGAGAAGGGTGCAC
genomic: TGAAAAAGATCGCGGAAAAGATGAATGGGGCCTCAGGAGCTGAGCTCAAGgtttgttaat ... gttggttcagGCCGTCTGCACAGAGGCTGGAATGTTTGCTCTTCGTGAGAGAAGGGTGCAC
EST: gi|6827684|gb|AW331327.1|AW331327
EST:     TGAAAAAGATCGCGGAAAAGATGAATGGGGCCTCAGGAGCTGAGCTCAAG                         GCCGTCTGCNCAGAGGCTGGAATGTTTGCTCTTCGTGAGAGAAGGGTGCAC
genomic: TGAAAAAGATCGCGGAAAAGATGAATGGGGCCTCAGGAGCTGAGCTCAAGgtttgttaat ... gttggttcagGCCGTCTGCACAGAGGCTGGAATGTTTGCTCTTCGTGAGAGAAGGGTGCAC
EST: gi|5847445|gb|AW000524.1|AW000524
EST:     TGAAAAAGATCGCGGAAAAGATGAATGGGGCCTCAGGAGCTGAGCTCAAG                         GCCGTCTGCACAGAGGCT
genomic: TGAAAAAGATCGCGGAAAAGATGAATGGGGCCTCAGGAGCTGAGCTCAAGgtttgttaat ... gttggttcagGCCGTCTGCACAGAGGCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agctttgtgtttgtgtttcagactttttcctttcatttttttggtgttggttcagGCCGTCTGCACAGAGGCTGGAATGTTTGCTCTTCGTGAGAGAAGGGTGCACGTTACCCAGGAGGACTTCGAGATGGCAGTGGCCAAGGTGATGAAGAAAG
                              tttcattttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tttcaatgcttattaccaagcatttgtgatcgttatagttcctatagctttgtgtttgtgtttcagactttttcctttcatttttttggtgttggttcagGCCGTCTGCACAGAGGCTGGAATGTTTGCTCTTCGTGAGAGAAGGGTGCACGTTACCCAGGAGGACTTCGAGATGGCAGTGGCCAAGGTGATGAAGAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA