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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttcaatattgtttcattctgacattggttgcaatggaacatacacgtctctgtgcgtttggaaccatacatctatctaatcgttgcattatctcttgtagTGGAAGCACAATTGTTGGTATTGGTTCACCGGATCCTCCTGCATTCGTGTATGACGATGAAGACTACAAGGATGTTTTTGTGTCAG

Basic information

species Zea mays
transcript GRMZM5G859195_T02
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G859195_T01 (Zea mays), 3'ss of exon 9
lower sequence: LOC_Os01g58790.2 (Oryza sativa), 3'ss of exon 9
-ttcaatattgtttcattctgacattggttgcaa-tggaacatacacgtctctgtgcgtttggaaccatacatctatctaatcgttgcat-tatctcttgtagTGGAAGCACAATTGTTGGTATTGGTTCACCGGATCCTCCTGCATTCGTGTATGACGATGAAGACTACAAGGATGTTTTTGTGTCAG
  |  |  || | |  | |  | ||    |  |  |      ||     |  ||| |  |   ||   ||| |  || ||||  ||| || | |  |  | |||||||||||||||||||| ||||||||||| ||||| |||||||| |||||||| ||||| ||||||||||||  |||||||||||
ggtggaggttatatattgcatatatcaagtatatctatgttttatggaacattgttcaatcataaat-tacgtg-atataat-attgtatatgtaccacgcagTGGAAGCACAATTGTTGGGATTGGTTCACCAGATCCGCCTGCATTTGTGTATGATGATGATGACTACAAGGATACTTTTGTGTCAG

upper sequence: GRMZM5G859195_T01 (Zea mays), 3'ss of exon 9
lower sequence: AT2G26930.1 (Arabidopsis thaliana), 3'ss of exon 9
-ttcaatattgtttcatt--ctga-cattggttgcaatggaacatacacgtctctgtgcgtttggaaccatacatctatctaatcgttgcattatctcttg-tagTGGAAGCACAATTGTTGGTATTGGTTCACCGGATCCTCCTGCATTCGTGTATGACGATGAAGACTACAAGGATGTTTTTGTGTCAG
 |   ||  | | | ||   ||||  | || || |  | ||| |      | |   || |||  | |   |      || |  | || | || |   | |   ||||||||||| ||| | |||||||||||||| |||||||||  |||  | ||||| |||||||| |||||| | || ||  |||| |
ataagatcatatataatgagctgagtactgtttac--tagaataagagattataaatgagttgagtaat-tgtgctaattt--tggtgggatgaatgcataacagTGGAAGCACTATTATCGGTATTGGTTCACCAGATCCTCCTCAATTTATATATGATGATGAAGAATACAAGAACGTGTTCTTGTCTG

upper sequence: GRMZM5G859195_T01 (Zea mays), 3'ss of exon 9
lower sequence: Vv06s0009g02320.t01 (Vitis vinifera), 3'ss of exon 9
-ttca--atattgtttcattctgacattg--gttgcaatggaacatacacgtctctgtgcgtttggaaccatacatctatctaatcgttgcattatctcttgtagTGGAAGCACAATTGTTGGTATTGGTTCACCGGATCCTCCTGCATTCGTGTATGACGATGAAGACTACAAGGATGTTTTTGTGTCAG
 ||||  |      || ||    |||| |  ||| ||       |   || ||  |||   | |  | || ||  | | | |  || |||   ||| |  || ||||||||||| ||||| ||||||||||| || ||||||||   |||  | ||||| ||||| || ||  ||||||| ||| ||||||
attcatgaagacaattgatgtccacatggaagtttcatcatcttaattacatcattgt---tatacagccttaactgtgttt--tctttgacatatttgatgcagTGGAAGCACTATTGTGGGTATTGGTTCTCCAGATCCTCCACAATTTATCTATGATGATGATGAATATCAGGATGTGTTTTTGTCAG

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|149080471|gb|EE169501.2|EE169501
EST:     ATTATTGCAGCTGGCCGGGATGATTATAGTGCTGTTTTTATGTCAGGAAG                         TGGAAGCACAATTGTTGGTATTGGTTCACCGGATCCTCCTGCATTCGTGTA
genomic: ATTATTGCAGCTGGCCGGGATGATTATAGTGCTGTTTTTATGTCAGGAAGgtaaggatgg ... tctcttgtagTGGAAGCACAATTGTTGGTATTGGTTCACCGGATCCTCCTGCATTCGTGTA
EST: gi|13515641|gb|BG517917.1|BG517917
EST:     ATTATTGCAGCTGGCCGGGATGATTATAGTGCTGTTTTTATGTCAGGAAG                         TGGAAGCACAATTGTTGGTATTGGTTCACCGGATCCTCCTGCATTCGTGTA
genomic: ATTATTGCAGCTGGCCGGGATGATTATAGTGCTGTTTTTATGTCAGGAAGgtaaggatgg ... tctcttgtagTGGAAGCACAATTGTTGGTATTGGTTCACCGGATCCTCCTGCATTCGTGTA
EST: gi|32934305|gb|CF039117.1|CF039117
EST:     ATTATTGCAGCTGGCCGGGATGATTATAGTGCTGTTTTTATGTCAGGAAG                         TGGAAGCACAATTGTTGGTATTGGTTCACCGGATCCTCCTGCATTCGTGTA
genomic: ATTATTGCAGCTGGCCGGGATGATTATAGTGCTGTTTTTATGTCAGGAAGgtaaggatgg ... tctcttgtagTGGAAGCACAATTGTTGGTATTGGTTCACCGGATCCTCCTGCATTCGTGTA
EST: gi|149103616|gb|EE289016.2|EE289016
EST:     ATTATTGCAGCTGGCCGGGATGATTATAGTGCTGTTTTTATGTCAGGAAG                         TGGAAGCACAATTGTTGGTATTGGTTCCCCGGATCCTCCTGCATTCGTGTA
genomic: ATTATTGCAGCTGGCCGGGATGATTATAGTGCTGTTTTTATGTCAGGAAGgtaaggatgg ... tctcttgtagTGGAAGCACAATTGTTGGTATTGGTTCACCGGATCCTCCTGCATTCGTGTA
EST: gi|148969054|gb|EE019773.2|EE019773
EST:     ATTATTGCAGCTGGCCGGGATGATTATAGTGCTGTTTTTATTTCAGGAAG                         TGGAAGCACAATTGTTGGTATTGGTTCCCCGGATCCTCCTGCATTCGTGTA
genomic: ATTATTGCAGCTGGCCGGGATGATTATAGTGCTGTTTTTATGTCAGGAAGgtaaggatgg ... tctcttgtagTGGAAGCACAATTGTTGGTATTGGTTCACCGGATCCTCCTGCATTCGTGTA
EST: gi|4630582|gb|AI621456.1|AI621456
EST:     ATTATTGCAGCTGGCCGGGATGATTATAGTGCTGTTTTTATGTCAGGAAG                         TGGAAGCACAATTGTTGGTATTGGTTCACCGGATCCTCCTGCATTCGTGTA
genomic: ATTATTGCAGCTGGCCGGGATGATTATAGTGCTGTTTTTATGTCAGGAAGgtaaggatgg ... tctcttgtagTGGAAGCACAATTGTTGGTATTGGTTCACCGGATCCTCCTGCATTCGTGTA
EST: gi|16917892|gb|BM073477.1|BM073477
EST:     ATTATTGCAGCTGGCCGGGATGATTATAGTGCTGTTTTTATGTCAGGAAG                         TGGAAGCACAATTGTTGGTATTGGTTCACCGGATCCTCCTGCATTCGTGTA
genomic: ATTATTGCAGCTGGCCGGGATGATTATAGTGCTGTTTTTATGTCAGGAAGgtaaggatgg ... tctcttgtagTGGAAGCACAATTGTTGGTATTGGTTCACCGGATCCTCCTGCATTCGTGTA
EST: gi|12972415|gb|BG267970.1|BG267970
EST:     ATTATTGCAGCTGGCCGGGATGATTATAGTGCTGTTTTTATGTCAGGAAG                         TGGAAGCACAATTGTTGGTATTGGTTCACCGGATCCTCCTGCATTCGTGTA
genomic: ATTATTGCAGCTGGCCGGGATGATTATAGTGCTGTTTTTATGTCAGGAAGgtaaggatgg ... tctcttgtagTGGAAGCACAATTGTTGGTATTGGTTCACCGGATCCTCCTGCATTCGTGTA
EST: gi|76021626|gb|DT948796.1|DT948796
EST:     ATTATTGCAGCTGGCCGGGATGATTATAGTGCTGTTTTTATGTCAGGAAG                         TGGAAGCACAATTGTTGGTATTGGTTCACCGGATCCTCCTGCATTCGTGTA
genomic: ATTATTGCAGCTGGCCGGGATGATTATAGTGCTGTTTTTATGTCAGGAAGgtaaggatgg ... tctcttgtagTGGAAGCACAATTGTTGGTATTGGTTCACCGGATCCTCCTGCATTCGTGTA
EST: gi|13558407|gb|BG549763.1|BG549763
EST:     ATTATTGCAGCTGGCCGGGATGATTATAGTGCTGTTTTTATGTCAGGAAG                         TGGAAGCACAATTGTTGGTATTGGTTCACCGGATCCTCCTGCATTCGTGTA
genomic: ATTATTGCAGCTGGCCGGGATGATTATAGTGCTGTTTTTATGTCAGGAAGgtaaggatgg ... tctcttgtagTGGAAGCACAATTGTTGGTATTGGTTCACCGGATCCTCCTGCATTCGTGTA
EST: gi|211470049|gb|FL442815.1|FL442815
EST:     ATTATTGCAGCTGGCCGGGATGATTATAGTGCTGTTTTTATGTCAGGAAG                         TGGAAGCACAATTGTTGGTATTGGTTCACCGGATCCTCCTGCATTCGTGTA
genomic: ATTATTGCAGCTGGCCGGGATGATTATAGTGCTGTTTTTATGTCAGGAAGgtaaggatgg ... tctcttgtagTGGAAGCACAATTGTTGGTATTGGTTCACCGGATCCTCCTGCATTCGTGTA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtctctgtgcgtttggaaccatacatctatctaatcgttgcattatctcttgtagTGGAAGCACAATTGTTGGTATTGGTTCACCGGATCCTCCTGCATTCGTGTATGACGATGAAGACTACAAGGATGTTTTTGTGTCAG
                            atctaat  putative branch site (score: 3)
                                          ttatctctt  putative PPT
                           tatctaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttcaatattgtttcattctgacattggttgcaatggaacatacacgtctctgtgcgtttggaaccatacatctatctaatcgttgcattatctcttgtagTGGAAGCACAATTGTTGGTATTGGTTCACCGGATCCTCCTGCATTCGTGTATGACGATGAAGACTACAAGGATGTTTTTGTGTCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG
- - - - tgtttca
- - - - - - - -ttctgac
- - - - - - - - - - - - tggttgc
- - - - - - - - - - - - - - - - - - -acataca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ccataca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ttgcatt