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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTGATTTTGTATCGGTTGGAAGCCGTTGATCTGAGGAGAATGACAGATGAAGAAAAGATCGCATTCTGGGTCAACATACACAATGCTTTGCTGATGCATgtaatactctactgattgtagttcgccaaaaatttcttggcacttgacgtgctttgttcttgatggggtcccattgtaatactttcacag

Basic information

species Zea mays
transcript GRMZM5G843914_T02
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G843914_T01 (Zea mays), 5'ss of exon 8
lower sequence: LOC_Os03g55890.1 (Oryza sativa), 5'ss of exon 8
GTTGATTTTGTATCGGTTGGAAGCCGTTGATCTGAGGAGAATGACAGATGAAGAAAAGATCGCATTCTGGGTCAACATACACAATGCTTTGCTGATGCATgtaatact-ctactgattgtagttcgccaaaaatttcttggca----cttgacgtgctttgttcttgatggggtcccattgtaatactttcacag
|||||||||||| ||||||||| |||| ||||| |||||||||||  | ||||||||||| ||||||||||||||||||||||| ||   ||||||||||||||| || |||||| ||  ||||| | | ||||||||  |||    ||  |  || ||| || || |||||      ||||| ||| | |||||
GTTGATTTTGTACCGGTTGGAAACCGTCGATCTCAGGAGAATGACGAACGAAGAAAAGATTGCATTCTGGGTCAACATACACAACGCCCAGCTGATGCATgtaatgcttctactgttt-cagttcactacaaatttct-agcattgtctcaagttgtttttttgttaatgggtataatttgtactacctccacag

upper sequence: GRMZM5G843914_T01 (Zea mays), 5'ss of exon 8
lower sequence: GLYMA11G06610.1 (Glycine max), 5'ss of exon 3
GTTGATTTTGTATCGGTTGGAAGCCGTTGATCTGAGGAGAATGACAGATGAAGAAAAGATCGCATTCTGGGTCAACATACACAATGCTTTGCTGATGCATgtaatactctactgattgtagttcgccaaaaatttcttggcacttgacgtgctttgttcttgatggggtcccattgtaatactttcacag-----------
||   || | | |||||| ||||  || || |   | ||  |||   | || || ||||| || || ||| |||||||||||||||||||  |||||||||||||    || | ||| || |    ||| ||| | ||      | |  |  ||     |||||  | |    || ||||   |||               
GTCACTTATTTGTCGGTTAGAAGAAGTAGACCCCGGCAGGTTGAAGCACGAGGAGAAGATAGCTTTTTGGATCAACATACACAATGCTTTAGTGATGCATgtaat---ttatt-attatact--atcaagaatatgtttcagtgtaatatttttcccatttgattag-ttgtgttataatttgttctttcgtttctaatag

upper sequence: GRMZM5G843914_T01 (Zea mays), 5'ss of exon 8
lower sequence: GLYMA01G38680.1 (Glycine max), 5'ss of exon 9
GTTGATTTTGTATCGGTTGGAAGCCGTTGATCTGAGGAGAATGACAGATGAAGAAAAGATCGCATTCTGGGTCAACATACACAATGCTTTGCTGATGCATgtaatactctactgattgtagttcgccaaaaatttct---tggcacttgacgtgctttgttc--ttgatggggtcccattgtaatactttcacag------
||   || | | ||| || ||||  || || |   | ||  ||| | | || || ||||| || || ||| |||||||||||||||||||  |||||||||||||    || |  ||    |     | |   ||||   |   ||||  |        ||   ||  | ||||   | | |  |  |||           
GTCACTTATTTGTCGATTAGAAGAAGTAGACCCCGGCAGGTTGAAACACGAGGAGAAGATAGCTTTTTGGATCAACATACACAATGCTTTAGTGATGCATgtaatttattatt--ttactatcaagaatatgcttctgtataatactttcccattcccatttgattagttgggttataatttgttcttttgtttctaatag

upper sequence: GRMZM5G843914_T01 (Zea mays), 5'ss of exon 8
lower sequence: GLYMA16G25820.1 (Glycine max), 5'ss of exon 6
GTTGATTTTGTATCGGTTGGAAGCCGTTGATCTGAGGAGAATGACAGATGAAGAAAAGATCGCATTCTGGGTCAACATACACAATGCTTTGCTGATGCATgtaatactctactgattgtagttcgccaaaaatttcttggcacttgacgtgctttgttcttgat-ggggtcccattgtaatactttcacag----------
 |   || | | ||  || ||||  || ||||   |||   ||| | |||| || ||| | || |||||| |||||||||||||||||||| |||||||||||||    || |  |  |   ||   | |||||||     | | |   | | ||  ||||||| | |||   | | |  | ||||    |          
ATCACTTATTTCTCAATTAGAAGAAGTAGATCCTGGGAAGTTGAAACATGAGGAGAAGTTAGCTTTCTGGATCAACATACACAATGCTTTGGTGATGCATgtaat----tattattact--ctcaaaacaaatttccctttattagttttccatttctcttgattgaggttataatatgct-cttttttggtttctaatag

upper sequence: GRMZM5G843914_T01 (Zea mays), 5'ss of exon 8
lower sequence: GLYMA02G06790.1 (Glycine max), 5'ss of exon 7
GTTGATTTTGTATCGGTTGGAAGCCGTTGATCTGAGGAGAATGACAGATGAAGAAAAGATCGCATTCTGGGTCAACATACACAATGCTTTGCTGATGCATgtaat-actctactgattgtagttcgccaaaaatttcttggcacttgacgtgctttgttcttgatggggtcccattgtaatact---ttcacag---
||   || | | ||  || ||||  || ||||   |||   ||| | | || || ||| | || |||||| |||||||||||||||||||| ||||||||||||| | | |     |   |            |||||| |   |  |  |||| |    |   || |||   | | |  |  |   ||   |    
GTCACTTATTTGTCAATTAGAAGAAGTAGATCCTGGGAAGTTGAAAAACGAGGACAAGTTAGCTTTCTGGATCAACATACACAATGCTTTGGTGATGCATgtaattattatcactctcaaaacaatgtttccctttcttagttttcca-atgctctcacttcattgaggttataatatgtttttgggtttctaatag

upper sequence: GRMZM5G843914_T01 (Zea mays), 5'ss of exon 8
lower sequence: Vv00s0207g00120.t01 (Vitis vinifera), 5'ss of exon 9
GTTGATTTTGTATCGGTTGGAAGCCGTTGATCTGAGGAGAATGACAGATGAAGAAAAGATCGCATTCTGGGTCAACATACACAATGCTTTGCTGATGCATgtaatactc--tactgattgtagttcgc------caaaaatttcttg-------gcacttgacgtgctttgttcttgatggggtcccattgtaatactttcacag
 |   || | | ||| || ||||  || ||||||||||  |||| | |||| |||||||| ||||||||| |||||||||| ||||| ||| |||||||||||||  ||  |  |||||  | |  |       |||  ||  ||||       |    | | |||   || |  ||||  |  |   ||  | |  ||  ||||
ATCACTTATTTCTCGATTAGAAGAAGTGGATCTGAGGAAGATGAAACATGAGGAAAAGATAGCATTCTGGATCAACATACATAATGCATTGGTGATGCATgtaatgatccttcttgattaaactatgaaatttgcaaggataccttgtttaaaagtttctaatgtgaaatgataatgataagagcttctt--actctttgaacag

upper sequence: GRMZM5G843914_T01 (Zea mays), 5'ss of exon 8
lower sequence: Vv00s0207g00150.t01 (Vitis vinifera), 5'ss of exon 6
GTTGATTTTGTATCGGTTGGAAGCCGTTGATCTGAGGAGAATGACAGATGAAGAAAAGATCGCATTCTGGGTCAACATACACAATGCTTTGCTGATGCATgtaatactctac--tgattgtagttcgc------caaaaatttcttg-------gcacttgacgtgctttgttcttgatggggtcccattgtaatactttcacag
 |   || | | ||| || ||||  || ||||||||||  |||| | |||| |||||||| || |||||| |||||||||| ||||| ||| |||||||||||||  || |   |||||  | |  |       ||   ||  ||||       |    | | |||   || |  ||||  |  |   ||  | |  ||  ||||
ATCACTTATTTCTCGATTAGAAGAAGTGGATCTGAGGAAGATGAAACATGAGGAAAAGATAGCGTTCTGGATCAACATACATAATGCATTGGTGATGCATgtaatgatccatcttgattaaactatgaaatttgcagggataccttgtttaaaagtttctaatgtgaaatgataatgataagagcttctt--actctttgaacag

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|71431420|gb|DR812470.1|DR812470
EST:     AAGAAAAGATCGCATTCTGGGTCAACATACACAATGCTTTGCTGATGCAT                         GCTTATCTGAAGAATGGCGTCCCACAGAACAATCTAAAGAAAACATCCCTA
genomic: AAGAAAAGATCGCATTCTGGGTCAACATACACAATGCTTTGCTGATGCATgtaatactct ... actttcacagGCTTATCTGAAGAATGGCGTCCCACAGAACAATCTAAAGAAAACATCCCTA
EST: gi|74241581|gb|DT649495.1|DT649495
EST:     GGTCAACATACACAATGCTTTGCTGATGCAT                         GCTTATCTGAAGAATGGCGTCCCACAGAACAATCTAAAGAAAACATCCCTA
genomic: GGTCAACATACACAATGCTTTGCTGATGCATgtaatactct ... actttcacagGCTTATCTGAAGAATGGCGTCCCACAGAACAATCTAAAGAAAACATCCCTA
EST: gi|71431421|gb|DR812471.1|DR812471
EST:     AAGAAAAGATCGCATTCTGGGTCAACATACACAATGCTTTGCTGATGCAT                         GCTTATCTGAAGAATGGCGTCCCACAGAACAATCTAAAGAAAACATCCCTA
genomic: AAGAAAAGATCGCATTCTGGGTCAACATACACAATGCTTTGCTGATGCATgtaatactct ... actttcacagGCTTATCTGAAGAATGGCGTCCCACAGAACAATCTAAAGAAAACATCCCTA
EST: gi|88756881|gb|DY541022.1|DY541022
EST:     AAGAAAAGATCGCATTCTGGGTCAACATACACAATGCTTTGCTGATGCAT                         GCTTATCTGAAGAATGGCGTCCCACAGAACAATCTAAAGAAAACATCCCTA
genomic: AAGAAAAGATCGCATTCTGGGTCAACATACACAATGCTTTGCTGATGCATgtaatactct ... actttcacagGCTTATCTGAAGAATGGCGTCCCACAGAACAATCTAAAGAAAACATCCCTA
EST: gi|78123668|gb|DV542052.1|DV542052
EST:     AAAGATCGCATTCTGGGTCAACATACACAATGCTTTGCTGATGCAT                         GCTTATCTGAAGAATGGCGTCCCACAGAACAATCTAAAGAAAACATCCCTA
genomic: AAAGATCGCATTCTGGGTCAACATACACAATGCTTTGCTGATGCATgtaatactct ... actttcacagGCTTATCTGAAGAATGGCGTCCCACAGAACAATCTAAAGAAAACATCCCTA
EST: gi|101391015|gb|EB817443.1|EB817443
EST:     AAGAAAAGATCGCATTCTGGGTCAACATACACAATGCTTTGCTGATGCAT                         GCTTATCTGAAGAATGGCGTCCCACAGAACAATCTAAAGAAAACATCCCTA
genomic: AAGAAAAGATCGCATTCTGGGTCAACATACACAATGCTTTGCTGATGCATgtaatactct ... actttcacagGCTTATCTGAAGAATGGCGTCCCACAGAACAATCTAAAGAAAACATCCCTA
EST: gi|211041651|gb|FL024100.1|FL024100
EST:     AAGAAAAGATCGCATTCTGGGTCAACATACACAATGCTTTGCTGATGCAT                         GCTTATCTGAAGAATGGCGTCCCACAGAACAATCTAAAGAAAACATCCCTA
genomic: AAGAAAAGATCGCATTCTGGGTCAACATACACAATGCTTTGCTGATGCATgtaatactct ... actttcacagGCTTATCTGAAGAATGGCGTCCCACAGAACAATCTAAAGAAAACATCCCTA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTTGATTTTGTATCGGTTGGAAGCCGTTGATCTGAGGAGAATGACAGATGAAGAAAAGATCGCATTCTGGGTCAACATACACAATGCTTTGCTGATGCATgtaatactctactgattgtagttcgccaaaaatttcttggcacttgacgtgctttgttcttgatggggtcccattgtaatactttcacag

- - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT