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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGCACTTCAAAACCAGCCAATTGTCAATGCTGTCATTGATGGTGATGACATCATATACAGAGACTACGTAGACATCAGTGTTGCTGTTGGCACTTCCAAGgtaccatattgcttacttgctactctggtgactgatgtatcatctttcttgtacctagaactagaaaagccaaaatggcctatagtttggggtggtcagagtatttactatgtatatcactaattgtaatatttttcag

Basic information

species Zea mays
transcript GRMZM2G079538_T03
intron # 11
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G079538_T01 (Zea mays), 5'ss of exon 10
lower sequence: LOC_Os04g32330.1 (Oryza sativa), 5'ss of exon 11
TGCACTTCAAAACCAGCCAATTGTCAATGCTGTCATTGATGGTGATGACATCATATACAGAGACTACGTAGACATCAGTGTTGCTGTTGGCACTTCCAAGgtaccatattgcttacttgctactctggtgactg-atgtatcatctttc--ttgtacc-tagaactagaaaagccaaaatggcctata-gtttggggtggtcagagtatttactatgtatatcactaattgtaatatttttcag
 |||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||| || |||||||||||||||||||| |||||||||||| | |  | | |||| |   || || ||| |  |   |||||| |    |||     ||  ||    | || ||   |    || |  |      | |                                            
AGCACTTCAAAACCAACCAATTGTCAATGCTGTCATTGATGGTGATGACATCATATACAGAGACTATGTTGACATCAGTGTTGCTGTTGGTACTTCCAAGgtaacttgatacgtactagtc-ctgtgttgaatccaaagatcatcctctgattgggttataagacatacatagtcactgtcatgtacatatccattttag--------------------------------------------

upper sequence: GRMZM2G079538_T01 (Zea mays), 5'ss of exon 10
lower sequence: GLYMA14G02530.2 (Glycine max), 5'ss of exon 13
TGCACTTCAAAACCAGCCAATTGTCAATGCTGTCATTGATGGTGATGACATCATATACAGAGACTACGTAGACATCAGTGTTGCTGTTGGCACTTCCAAGgtaccatattgcttacttgctactctggtgactgatgtatcatctttcttgtacctagaactagaaaagccaaaatggcctatagtttggggtggtcagagtatttactatgtatatcactaattgtaatatttttcag
|||||| ||| | ||||| ||||||||||| ||||||||||||||||| || ||||||||||| ||  |||| |||||  | |||||||| ||||| |||||          |||   || ||  |  |   |    | |||| |   ||||       ||| || ||  |||      |  ||   ||   || | | |    |  | || | | | |                    
TGCACTCCAACATCAGCCGATTGTCAATGCAGTCATTGATGGTGATGATATTATATACAGAGATTATATAGATATCAGCATAGCTGTTGGTACTTCGAAGgttt--------ttatcagccacctttatcttt----tctcatttactttgttt-----acttgagaaatcaat-caatcattatactgtcttgatgaaac--ctagccatctctgtgat-------------------

upper sequence: GRMZM2G079538_T01 (Zea mays), 5'ss of exon 10
lower sequence: GLYMA02G46200.1 (Glycine max), 5'ss of exon 13
TGCACTTCAAAACCAGCCAATTGTCAATGCTGTCATTGATGGTGATGACATCATATACAGAGACTACGTAGACATCAGTGTTGCTGTTGGCACTTCCAAGgtaccatattgcttacttgctactctggtgactgatgtatcatctttcttgtacctagaactagaaaagccaaaatggcctatagtttggggtggtcagagtatttactatgtatatcactaattgtaatatttttcag
|||||| ||| | ||||| ||||||||||| ||||||||||||||||| || ||||||||||| ||  |||| |||||  | |||||||| ||| | |||||          |||   || ||  |  |   |  | | | |  ||  || |    |||| |  |  |  ||  ||    ||   ||||  |          |||| |                               
TGCACTCCAACATCAGCCGATTGTCAATGCAGTCATTGATGGTGATGATATTATATACAGAGATTATATAGATATCAGCATAGCTGTTGGTACTCCAAAGgttt--------ttatcagccacctttatcttttctcttttactttgtttatgtagagaaatcaatcaatcattatactatact-tttgatgaaacttagccatttgcg------------------------------

upper sequence: GRMZM2G079538_T01 (Zea mays), 5'ss of exon 10
lower sequence: AT4G26910.3 (Arabidopsis thaliana), 5'ss of exon 8
TGCACTTCAAAACCAGCCAATTGTCAATGCTGTCATTGATGGTGATGACATCATATACAGAGACTACGTAGACATCAGTGTTGCTGTTGGCACTTCCAAGgta---ccatattgcttacttgctactctggtgactgatgtatcatctttcttgtacctagaactagaaaagccaaaatggcctatagtttggggtggtcagagtatttactatgtatatcactaattgtaatatttttcag
 || |||||  | || ||| |||| ||||| || ||||| || ||||| ||||||||||||||||| || || |||||| | |||||||| || || |||||     || |||  |||  |   | |    ||    |  | ||||  || |||     |    ||    || |  |||    | |   ||| |||        |||  |                                
CGCCCTTCAGCATCAACCAGTTGTAAATGCAGTTATTGACGGGGATGATATCATATACAGAGACTATGTGGATATCAGTATCGCTGTTGGTACCTCTAAGgttagttcacattctttagctatcattggtttgtgctaaatttcattcttattgcgatcatg--tatgtgaggctgaat--tttttttcttgtggtctct----tatccag-------------------------------

upper sequence: GRMZM2G079538_T01 (Zea mays), 5'ss of exon 10
lower sequence: AT5G55070.1 (Arabidopsis thaliana), 5'ss of exon 13
TGCACTTCAAAACCAGCCAATTGTCAATGCTGTCATTGATGGTGATGACATCATATACAGAGACTACGTAGACATCAGTGTTGCTGTTGGCACTTCCAAGgtaccatattgcttacttgctactctggtgactgatgtatcatctttcttgtacctagaactagaaaagccaaaatggcctatagtttggggtggtcagagtatttactatgtatatcactaattgtaatatttttcag
||| || ||  |||| ||  | || ||||| || || ||||| ||||| ||||| |||||||||||||| || |||||| | |||||||| || || |||||      ||| || |    | || | |  | |||   || || |   |||  | |     |   | ||     || |  |    ||    |||    |  |                                     
TGCCCTCCAGCACCAACCTGTAGTAAATGCAGTTATCGATGGAGATGATATCATTTACAGAGACTACGTGGATATCAGTATCGCTGTTGGTACCTCTAAGgt------ttgtttccgcaattcttttgacattgagtgataatatcatttgggctt----ttgagatagttttgattgattcctcttctctgtgtattgtatcccag--------------------------------

upper sequence: GRMZM2G079538_T01 (Zea mays), 5'ss of exon 10
lower sequence: PP1S2_220V6.1 (Physcomitrella patens), 5'ss of exon 7
TGCACTTCAAAACCAGCCAATTGTCAATGCTGTCATTGATGGTGATGACATCATATACAGAGACTACGTAGACATCAGTGTTGCTGTTGGCACTTCCAAGgtaccata-ttgcttacttgctactctggtgac--tgatgtatcatcttt-cttgtacctagaactagaaaagccaaaatggcctatagtttggggtggt-cagagtatttactat----gtatatcactaattg---taatatttttcag------------------------
||||||| |  |    ||    || ||||| || || ||||| ||||| |||||||||||||||||| | ||||||||  |||||||||| |||   |||||  || |  | | ||     || | |    |   |  |  | || |    ||| | | ||  |  |     |  ||  | |  | |  | |  |   || || |   ||   |||    | |  | |   | ||   ||  || ||| |                         
TGCACTTAAGCAATTTCCTGCAGTAAATGCGGTAATCGATGGAGATGATATCATATACAGAGACTACATTGACATCAGCATTGCTGTTGGAACTAAAAAGgtttcagaacttcataaacaatagtttatacatatttttaaaacaccagcacttatgcttatgagcacctgtgggaattttggttttgttctcagaccgttcataactttccttattacagcacgtgatggactgaactaggatatttaatgatgcgtgcatcttcttcgttcag

upper sequence: GRMZM2G079538_T01 (Zea mays), 5'ss of exon 10
lower sequence: PP1S154_6V6.2 (Physcomitrella patens), 5'ss of exon 11
TGCACTTCAAAACCAGCCAATTGTCAATGCTGTCATTGATGGTGATGACATCATATACAGAGACTACGTAGACATCAGTGTTGCTGTTGGCACTTCCAAGgtaccatattgcttacttgctactctggtgactgatgtatcatctttcttgtacctagaactagaaaagccaaaatggcctatagtttggggtggtcagagtatttact-atgtatatcactaattgtaatatttttcag
||||||  |  |    ||   |||||||||||| |||||||| ||||||||||| ||| |||| ||||| ||||||||  |||||||||| ||  |||| |||    | | |  ||||| | |    |||     ||| ||||  |      || || |  | ||  | || ||   || |      |  | |  | ||||||| |  | |||||                         
TGCACTCAAGCAATTTCCTGCTGTCAATGCTGTAATTGATGGAGATGACATCATCTACCGAGATTACGTTGACATCAGCATTGCTGTTGGTACAGCCAAAgta----agttcaaacttggttcaaatgtg-----tgtttcattgtcaacacacgtaaa--ttgatgatcctaacaagctt-----ctatgttactaagagtatcttttcatgtag------------------------

upper sequence: GRMZM2G079538_T01 (Zea mays), 5'ss of exon 10
lower sequence: EFJ31629 (Selaginella moellendorffii), 5'ss of exon 7
TGCACTTCAAAACCAGCCAATTGTCAATGCTGTCATTGATGGTGATGACATCATATACAGAGACTACGTAGACATCAGTGTTGCTGTTGGCACTTCCAAGgtaccatattgcttacttgctactctggtgactgatgtatcatctttcttgtacctagaactagaaaagccaaaatggcctatagtttggggtggtcagagtatttactatgtatatcactaattgtaatatttttcag
 ||  | ||    |||||  |||| || ||||| || || || ||||||||||| |||||||||||||| ||||||||  |||||||||| ||| | ||||||   |  || |  |              ||  || |    | |      |    ||                                                                                 
CGCTTTGCAGGCGCAGCCCGTTGTAAACGCTGTGATCGACGGAGATGACATCATTTACAGAGACTACGTCGACATCAGCATTGCTGTTGGAACTCCAAAGgtattgtcatgttctcggagactaaaaaaaaccaattttgtttttccacgttgtgcag---------------------------------------------------------------------------------

upper sequence: GRMZM2G079538_T01 (Zea mays), 5'ss of exon 10
lower sequence: EFJ38519 (Selaginella moellendorffii), 5'ss of exon 7
TGCACTTCAAAACCAGCCAATTGTCAATGCTGTCATTGATGGTGATGACATCATATACAGAGACTACGTAGACATCAGTGTTGCTGTTGGCACTTCCAAGgtaccatattgcttacttgctactctggtgactgatgtatcatctttcttgtacctagaactagaaaagccaaaatggcctatagtttggggtggtcagagtatttactatgtatatcactaattgtaatatttttcag
 ||  | ||    |||||  |||| || ||||| || || || ||||||||||| |||||||||||||| ||||||||  |||||||||| ||| | ||||||   |  || |  || |           ||     | |  | ||||       |  |                                                                                
CGCTTTGCAGGCGCAGCCCGTTGTAAACGCTGTGATCGACGGAGATGACATCATTTACAGAGACTACGTCGACATCAGCATTGCTGTTGGAACTCCAAAGgtattgtcatgtt--ctcggagactcaaaaacaccaattttgtttttccacgttgtgcag-------------------------------------------------------------------------------

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|211104575|gb|FL031921.1|FL031921
EST:     TCATATACAGAGACTACGTAGACATCAGTGTTGCTGTTGGCACTTCCAAG                         GGCCTTGTGGTTCCTGTTATCCGAGATGCTGATACCATGAACTTTGCTGAC
genomic: TCATATACAGAGACTACGTAGACATCAGTGTTGCTGTTGGCACTTCCAAGgtaccatatt ... tatttttcagGGCCTTGTGGTTCCTGTTATCCGAGATGCTGATACCATGAACTTTGCTGAC
EST: gi|6102024|gb|AW126494.1|AW126494
EST:     TCATATCCAGAGACTACGTAGACATCAGTGTTGCTGTTGGCACTTCCAAG                         GGCCTTGTGGTTCCTGTTATCCGAGATGCTGATACCATGAACTTTGCTGAC
genomic: TCATATACAGAGACTACGTAGACATCAGTGTTGCTGTTGGCACTTCCAAGgtaccatatt ... tatttttcagGGCCTTGTGGTTCCTGTTATCCGAGATGCTGATACCATGAACTTTGCTGAC
EST: gi|110528815|gb|EE032999.1|EE032999
EST:     ACGTAGACATCAGTGTTGCTGTTGGCACTTCCAAG                         GGCCTTGTGGTTCCTGTTATCCGAGATGGTGATACCATGAACTTTGCTGAC
genomic: ACGTAGACATCAGTGTTGCTGTTGGCACTTCCAAGgtaccatatt ... tatttttcagGGCCTTGTGGTTCCTGTTATCCGAGATGCTGATACCATGAACTTTGCTGAC
EST: gi|31363969|gb|CD448324.1|CD448324
EST:     TCATATACAGAGACTACGTAGACATCAGTGTTGCTGTTGGCACTTCCAAG                         GGCCTTGTGGTTCCTGTTATCCGAGATGCTGATACCATGAACTTTGCTGAC
genomic: TCATATACAGAGACTACGTAGACATCAGTGTTGCTGTTGGCACTTCCAAGgtaccatatt ... tatttttcagGGCCTTGTGGTTCCTGTTATCCGAGATGCTGATACCATGAACTTTGCTGAC
EST: gi|6021309|gb|AW066237.1|AW066237
EST:     TCATATACAGAGACTACGTAGACATCAGTGTTGCTGTTGGCACTTCCAAG                         GGCCTTGTGGTTCCTGTTATCCGAGATGCTGATACCATGAACTTTGCTGAC
genomic: TCATATACAGAGACTACGTAGACATCAGTGTTGCTGTTGGCACTTCCAAGgtaccatatt ... tatttttcagGGCCTTGTGGTTCCTGTTATCCGAGATGCTGATACCATGAACTTTGCTGAC
EST: gi|31358903|gb|CD443260.1|CD443260
EST:     CATATACAGAGACTACGTAGACATCAGTGGTGCGTGGTGGCACTTCCAAG                         GGCCTTGTGGTTCCTGTTATCCGAGATGCTGATACCATGAACTTTGCTGAC
genomic: CATATACAGAGACTACGTAGACATCAGTGTTGC-TGTTGGCACTTCCAAGgtaccatatt ... tatttttcagGGCCTTGTGGTTCCTGTTATCCGAGATGCTGATACCATGAACTTTGCTGAC
EST: gi|211169880|gb|FL077609.1|FL077609
EST:     TCATATACAGAGACTACGTAGACATCAGTGTTGCTGTTGGCACTTCCAAG                         GGCCTTGTGGTTCCTGTTATCCGAGATGCTGATACCATGAACTTTGCTGAC
genomic: TCATATACAGAGACTACGTAGACATCAGTGTTGCTGTTGGCACTTCCAAGgtaccatatt ... tatttttcagGGCCTTGTGGTTCCTGTTATCCGAGATGCTGATACCATGAACTTTGCTGAC
EST: gi|32830086|gb|CD969764.1|CD969764
EST:     TCATATACAGAGACTACGTAGACATCAGTGTTGCTGTTGGCACTTCCAAG                         GGCCTTGTGGTTCCTGTTATCCGAGATGCTGATACCATGAACTTTGCTGAC
genomic: TCATATACAGAGACTACGTAGACATCAGTGTTGCTGTTGGCACTTCCAAGgtaccatatt ... tatttttcagGGCCTTGTGGTTCCTGTTATCCGAGATGCTGATACCATGAACTTTGCTGAC
EST: gi|13558100|gb|BG549456.1|BG549456
EST:     TCATATACAGAGACTACGTAGACATCAGTGTTGCTGTTGGCACTTCCAAG                         GGCCTTGTGGTTCCTGTTATCCGAGATGCTGATACCATGAACTTTGCTGAC
genomic: TCATATACAGAGACTACGTAGACATCAGTGTTGCTGTTGGCACTTCCAAGgtaccatatt ... tatttttcagGGCCTTGTGGTTCCTGTTATCCGAGATGCTGATACCATGAACTTTGCTGAC
EST: gi|32942914|gb|CF047733.1|CF047733
EST:     TCATATACGGAGACTACGTAGACATCAGTGTTGCTGTTGGCACTTCCAAG                         GGCCTTGTGGTTCCTGTTATCCGAGATGCTGATACCATGAACTTTGCTGAC
genomic: TCATATACAGAGACTACGTAGACATCAGTGTTGCTGTTGGCACTTCCAAGgtaccatatt ... tatttttcagGGCCTTGTGGTTCCTGTTATCCGAGATGCTGATACCATGAACTTTGCTGAC
EST: gi|60358853|gb|DN225826.1|DN225826
EST:     TCATATACAGAGACTACGTAGACATCAGTGTTGCTGTTGGCACTTCCAAG                         GGCCTTGTGGTTCCTGTTATCCGAGATGCTGATACCATGAACTTTGCTGAC
genomic: TCATATACAGAGACTACGTAGACATCAGTGTTGCTGTTGGCACTTCCAAGgtaccatatt ... tatttttcagGGCCTTGTGGTTCCTGTTATCCGAGATGCTGATACCATGAACTTTGCTGAC
EST: gi|6227238|gb|AW155837.1|AW155837
EST:     TCATATACAGAGACTACGTAGACATCAGTGTTGCTGTTGGCACTTCCAAG                         GGCCTTGTGGTTCCTGTTATCCGAGATGCTGATACCATGAACTTTGCTGAC
genomic: TCATATACAGAGACTACGTAGACATCAGTGTTGCTGTTGGCACTTCCAAGgtaccatatt ... tatttttcagGGCCTTGTGGTTCCTGTTATCCGAGATGCTGATACCATGAACTTTGCTGAC
EST: gi|32829046|gb|CD968724.1|CD968724
EST:     TCATATACAGAGACTACGTAGACATCAGTGTTGCTGTTGGCACTTCCAAG                         GGCCTTGTGGTTCCTGTTATCCGAGATGCTGATACCATGAACTTTGCTGAC
genomic: TCATATACAGAGACTACGTAGACATCAGTGTTGCTGTTGGCACTTCCAAGgtaccatatt ... tatttttcagGGCCTTGTGGTTCCTGTTATCCGAGATGCTGATACCATGAACTTTGCTGAC
EST: gi|32828877|gb|CD968555.1|CD968555
EST:     TCATATACAGAGACTACGTAGACATCAGTGTTGCTGTTGGCACTTCCAAG                         GGCCTTGTGGTTCCTGTTATCCGAGATGCTGATACCATGAACTTTGCTGAC
genomic: TCATATACAGAGACTACGTAGACATCAGTGTTGCTGTTGGCACTTCCAAGgtaccatatt ... tatttttcagGGCCTTGTGGTTCCTGTTATCCGAGATGCTGATACCATGAACTTTGCTGAC
EST: gi|211169873|gb|FL077602.1|FL077602
EST:     TCATATACAGAGACTACGTAGACATCAGTGTTGCTGTTGGCACTTCCAAG                         GGCCTTGTGGTTCCTGTTATCCGAGATGCTGATACCATGAACTTTGCTGAC
genomic: TCATATACAGAGACTACGTAGACATCAGTGTTGCTGTTGGCACTTCCAAGgtaccatatt ... tatttttcagGGCCTTGTGGTTCCTGTTATCCGAGATGCTGATACCATGAACTTTGCTGAC
EST: gi|148978724|gb|EE026282.2|EE026282
EST:     TTGCTGTTGGCACTTCCAAG                         GGCCTTGTGGTTCCTGTTATCCGAGATGCTGATACCATGAACTTTGCTGAC
genomic: TTGCTGTTGGCACTTCCAAGgtaccatatt ... tatttttcagGGCCTTGTGGTTCCTGTTATCCGAGATGCTGATACCATGAACTTTGCTGAC
EST: gi|8368148|gb|BE051093.1|BE051093
EST:     CAGAGACTACGTAGACATCAGTGTTGCTGTTGGCACTTCCAAG                         GGCCTTGTGGTTCCTGTTATCCGAGATGCTGATACCATGAACTTTGCTGAC
genomic: CAGAGACTACGTAGACATCAGTGTTGCTGTTGGCACTTCCAAGgtaccatatt ... tatttttcagGGCCTTGTGGTTCCTGTTATCCGAGATGCTGATACCATGAACTTTGCTGAC
EST: gi|14548407|gb|BI096736.1|BI096736
EST:     TCATATACAGAGACTACGTAGACATCAGTGTTGCTGTTGGCACTTCCAAG                         GGCCTTGTGGTTCCTGTTATCCGAGATGCTGATACCATGAACTTTGCTGAC
genomic: TCATATACAGAGACTACGTAGACATCAGTGTTGCTGTTGGCACTTCCAAGgtaccatatt ... tatttttcagGGCCTTGTGGTTCCTGTTATCCGAGATGCTGATACCATGAACTTTGCTGAC
EST: gi|13558537|gb|BG549893.1|BG549893
EST:     TCATATACAGAGACTACGTAGACATCAGTGTTGCTGTTGGCACTTCCAAG                         GGCCTTGTGGTTCCTGTTATCCGAGATGCTGATACCATGAACTTTGCTGAC
genomic: TCATATACAGAGACTACGTAGACATCAGTGTTGCTGTTGGCACTTCCAAGgtaccatatt ... tatttttcagGGCCTTGTGGTTCCTGTTATCCGAGATGCTGATACCATGAACTTTGCTGAC
EST: gi|32867030|gb|CF006712.1|CF006712
EST:     TCATATACAGAGACTACGTAGACATCAGTGTTGCTGTTGGCACTTCCAAG                         GGCCTTGTGGTTCCTGTTATCCGAGATGCTGATACCATGAACTTTGCTGAC
genomic: TCATATACAGAGACTACGTAGACATCAGTGTTGCTGTTGGCACTTCCAAGgtaccatatt ... tatttttcagGGCCTTGTGGTTCCTGTTATCCGAGATGCTGATACCATGAACTTTGCTGAC
EST: gi|67019048|gb|CO447797.1|CO447797
EST:     TCATATACAGAGACTACGTAGACATCAGTGTTGCTGTTGGCACTTCCAAG                         GGCCTTGTGGTTCCTGTTATCCGAGATGCTGATACCATGAACTTTGCTGAC
genomic: TCATATACAGAGACTACGTAGACATCAGTGTTGCTGTTGGCACTTCCAAGgtaccatatt ... tatttttcagGGCCTTGTGGTTCCTGTTATCCGAGATGCTGATACCATGAACTTTGCTGAC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGCACTTCAAAACCAGCCAATTGTCAATGCTGTCATTGATGGTGATGACATCATATACAGAGACTACGTAGACATCAGTGTTGCTGTTGGCACTTCCAAGgtaccatattgcttacttgctactctggtgactgatgtatcatctttcttgtacctagaactagaaaagccaaaatggcctatagtttggggtggtcagagtatttactatgtatatcactaattgtaatatttttcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT