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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AAAAGAAACCAAAGGAGGGTGACAACATTGTTCAGGATGCTCCTGCAGATATTCCTTCCCTCCTAGAATTGAAGCGTATCTACTATGAACTGATGATTCGgtatgtcatgcttctcaatctcaattagattaatgtactaccagtctgctatttcattgtcaattgtcattattctctcgtctacctgactacctctggaactgccaatttctttgttctattgaacactatggttcacaatgacattttatattggagccaatcataattcttcgttatctcatcacag

Basic information

species Zea mays
transcript GRMZM2G013750_T04
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G013750_T03 (Zea mays), 5'ss of exon 6
lower sequence: LOC_Os03g63430.1 (Oryza sativa), 5'ss of exon 6
AAAAGAAACCAAAGGAGGGTGACAACATTGTTCAGGATGCTCCTGCAGATATTCCTTCCCTCCTAGAATTGAAGCGTATCTACTATGAACTGATGATTCGgtatgtcatgcttctcaatctcaattagattaatgtactaccagtctgctatttcattgtcaattgtcattattctctcgtctacctgactacctctggaactgccaatttctttgttctattgaacactatggttcacaatgacattttatattggagccaatcataattcttcgttatctcatcacag
|||||||||| || || ||||| || ||||||||||| || || ||||| || ||||||||||| ||| ||||||| |||||||||||||||||||||||||||||| | || |||| |       ||| ||||  |  |  |||            |   |||  |  ||    |     |||||     |  ||   || |                                                                                       
AAAAGAAACCGAAAGAAGGTGATAATATTGTTCAGGAAGCCCCAGCAGAGATACCTTCCCTCCTGGAACTGAAGCGCATCTACTATGAACTGATGATTCGgtatgtcttcctgctcagtg------agactaattcatcatgagttcatgtcgcttctagtaatgttggttgaagttaatgctaccccctcaggtcgcaaaatata------------------------------------------------------------------------------------

upper sequence: GRMZM2G013750_T03 (Zea mays), 5'ss of exon 6
lower sequence: GLYMA06G15330.1 (Glycine max), 5'ss of exon 6
AAAAGAAACCAAAGGAGGGTGACAACATTGTTCAGGATGCTCCTGCAGATATTCCTTCCCTCCTAGAATTGAAGCGTATCTACTATGAACTGATGATTCGgtatgtcatgcttctca----atctcaattagattaatgtactaccagtctgctatttcattgtcaattgtcattattctctcgtctacctgactacctctggaactgccaatttctttgttctattgaacactatggttcacaatgacattttatattggagccaatcataattcttcgttatctcatcacag
| || || || || || ||||| ||  ||||| | || ||||||||||||||||| || || | ||| |||||||| |||||||||||||| |||||||||||  | || ||   |      ||| | || | ||  |  |    | | ||| ||     |  | || |||   | || |   || ||| |   || |  |                                                                                             
AGAAAAAGCCTAAAGAAGGTGATAATGTTGTTGAAGAAGCTCCTGCAGATATTCCATCTCTACCAGAGTTGAAGCGGATCTACTATGAACTAATGATTCGgtaactgattctctacttgttgtcttattttgcttgttcaatatgctgcctggtagggggtgttaaaatgtggatgttgttctgt-tacatagttatcggt---------------------------------------------------------------------------------------------

upper sequence: GRMZM2G013750_T03 (Zea mays), 5'ss of exon 6
lower sequence: GLYMA04G39520.1 (Glycine max), 5'ss of exon 6
AAAAGAAACCAAAGGAGGGTGACAACATTGTTCAGGATGCTCCTGCAGATATTCCTTCCCTCCTAGAATTGAAGCGTATCTACTATGAACTGATGATTCGgtatgtcatgcttctcaatctcaattagattaatgtactaccagtctgctatttcattgtcaattgtcattattctctcgtctacctgactacctctggaactgccaatttctttgttctattgaacactatggttcacaatgacattttatattggagccaatcataattcttcgttatctcatcacag
| || || || || || ||||| ||  ||||| | || |||||||  ||||| || || || |  || |||||||| |||||||||||||| |||||||||||   ||     ||   | | |  | | ||    |  |  || ||||||   |    |     ||| |  ||      ||    |||  |||      ||| |  |                                                                                   
AGAAAAAGCCTAAAGAAGGTGATAATGTTGTTGAAGAAGCTCCTGTTGATATACCATCTCTACCGGAGTTGAAGCGAATCTACTATGAACTAATGATTCGgta-accaattccctacttgttatcttgttttgcttgtt--caatctgcttcctggcag--gggtgttaaaatgtggatgttgttctg-ttac-----aaacagttatccg-------------------------------------------------------------------------------

upper sequence: GRMZM2G013750_T03 (Zea mays), 5'ss of exon 6
lower sequence: Vv07s0031g01970.t01 (Vitis vinifera), 5'ss of exon 6
AAAAGAAACCAAAGGAGGGTGACAACATTGTTCAGGATGCTCCTGCAGATATTCCTTCCCTCCTAGAATTGAAGCGTATCTACTATGAACTGATGATTCGgtatgtcatgcttctcaatctcaattagattaatgtactaccagtctgctatttcattgtcaattgtcattattctctcgtctacctgactacctctggaactgccaatttctttgttctattgaacactatggttcacaatgacattttatattggagccaatcataattcttcgttatctcatcacag
| || || || || || ||||| |   ||||  | || || || || || ||||||||  | | ||| |||||||| ||||||||||||||||||||| ||||| |   |   ||   | ||                           |||| |  | ||  |||| |||    ||| |  |   ||||| | | |  |  ||  |  || |||||| | ||   || |||                                                          
AGAAAAAGCCCAAAGAAGGTGATAGTGTTGTAGAAGAAGCACCAGCTGACATTCCTTCTTTGCCAGAGTTGAAGCGCATCTACTATGAACTGATGATTAGgtattttgggtgccttggtttcc-------------------------ttattcc--tatcttttgt-attgcattcttgctt---tgactgcatgtaaaggtgagagctt-tttgttat-ttattcaatata---------------------------------------------------------

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|60352441|gb|DN219414.1|DN219414
EST:     ATTCCTTCCCTCCTAGAATTGAAGCGTATCTACTATGAACTGATGATTCG                         ATATTACTTGCACAACAATGATTACCT
genomic: ATTCCTTCCCTCCTAGAATTGAAGCGTATCTACTATGAACTGATGATTCGgtatgtcatg ... ctcatcacagATATTACTTGCACAACAATGATTACCT
EST: gi|67017748|gb|CO446497.1|CO446497
EST:     ATTCCTTCCCTCCTAGAATTGAAGCGTATCTACTATGAACTGATGATTCG                         ATATTACTTGCACAAACA-TGATTACCTGNAAATCTGTCGTTG
genomic: ATTCCTTCCCTCCTAGAATTGAAGCGTATCTACTATGAACTGATGATTCGgtatgtcatg ... ctcatcacagATATTACTTGCACAA-CAATGATTACCTGGAAATCTGTCGTTG
EST: gi|149074396|gb|EE162784.2|EE162784
EST:     ATTCCTTCCCTCCTAGAATTGAAGCGTATCTACTATGAACTGATGATTCG                         ATATTACTTNGCACA-CAATGATTACCTGGAAATCTGTCGTTGTTACAAGG
genomic: ATTCCTTCCCTCCTAGAATTGAAGCGTATCTACTATGAACTGATGATTCGgtatgtcatg ... ctcatcacagATATTACTT-GCACAACAATGATTACCTGGAAATCTGTCGTTGTTACAAGG
EST: gi|5847143|gb|AW000222.1|AW000222
EST:     ATTCCTTCCCTCCTAGAATTGAAGCGTATCTACTATGAACTGATGATTCG                         ATATTACTTGCACAACAATGATTACCTGGAAATCTGTCGTTGTTACAAGGC
genomic: ATTCCTTCCCTCCTAGAATTGAAGCGTATCTACTATGAACTGATGATTCGgtatgtcatg ... ctcatcacagATATTACTTGCACAACAATGATTACCTGGAAATCTGTCGTTGTTACAAGGC
EST: gi|40337465|gb|CK371535.1|CK371535
EST:     ATTCCTTCCCTCCTAGAATTGAAGCGTATCTACTATGAACTGATGATTCG                         ATATTACTTGCACAACAATGATTACCTGGAAATCTGTCGTTGTTACAAGGC
genomic: ATTCCTTCCCTCCTAGAATTGAAGCGTATCTACTATGAACTGATGATTCGgtatgtcatg ... ctcatcacagATATTACTTGCACAACAATGATTACCTGGAAATCTGTCGTTGTTACAAGGC
EST: gi|60345832|gb|DN212805.1|DN212805
EST:     ATTCCTTCCCTCCTAGAATTGAAGCGTATCTACTATGAACTGATGATTCG                         ATATTACTTGCACAACAATGATTACCTGGAAATCTGTCGTTGTTACAAGGC
genomic: ATTCCTTCCCTCCTAGAATTGAAGCGTATCTACTATGAACTGATGATTCGgtatgtcatg ... ctcatcacagATATTACTTGCACAACAATGATTACCTGGAAATCTGTCGTTGTTACAAGGC
EST: gi|149078169|gb|EE166920.2|EE166920
EST:     TTCCTTCCCTCCTAGAATTTGA-GCGTATCTACTATGAACTGATGATTCG                         ATATTACTTGCACAACAATGATTACCTGGAAATCTGTCGTTG
genomic: TTCCTTCCCTCCTAGAATT-GAAGCGTATCTACTATGAACTGATGATTCGgtatgtcatg ... ctcatcacagATATTACTTGCACAACAATGATTACCTGGAAATCTGTCGTTG
EST: gi|60349290|gb|DN216263.1|DN216263
EST:     ATTCCTTCCCTCCTAGAATTGAAGCGTATCTACTATGAACTGATGATTCG                         ATATTACTTGCACAACAATGATTACCTGGAAATCTGTCGTTGTTACAAGGC
genomic: ATTCCTTCCCTCCTAGAATTGAAGCGTATCTACTATGAACTGATGATTCGgtatgtcatg ... ctcatcacagATATTACTTGCACAACAATGATTACCTGGAAATCTGTCGTTGTTACAAGGC
EST: gi|60358924|gb|DN225897.1|DN225897
EST:     ATTCCTTCCCTCCTAGAATTGAAGCGTATCTACTATGAACTGATGATTCG                         ATATTACTTGCACAACAATGATTACCTGGAAATCTGTCGTTGTTACAAGGC
genomic: ATTCCTTCCCTCCTAGAATTGAAGCGTATCTACTATGAACTGATGATTCGgtatgtcatg ... ctcatcacagATATTACTTGCACAACAATGATTACCTGGAAATCTGTCGTTGTTACAAGGC
EST: gi|148945727|gb|EC891006.2|EC891006
EST:     ATTCCTTCCCTCCTAGAATTGAAGCGTATCTACTATGAACTGATGATTCG                         ATATTACTTGCACAACAATGATTACCTGGAAATCTGTCGT
genomic: ATTCCTTCCCTCCTAGAATTGAAGCGTATCTACTATGAACTGATGATTCGgtatgtcatg ... ctcatcacagATATTACTTGCACAACAATGATTACCTGGAAATCTGTCGT
EST: gi|211088675|gb|FL328946.1|FL328946
EST:     ATTCCTTCCCTCCTAGAATTGAAGCGTATCTACTATGAACTGATGATTCG                         ATATTACTTGCACAACAATGATTACCTGGAAATCTGTCGTTGTTACAAGTC
genomic: ATTCCTTCCCTCCTAGAATTGAAGCGTATCTACTATGAACTGATGATTCGgtatgtcatg ... ctcatcacagATATTACTTGCACAACAATGATTACCTGGAAATCTGTCGTTGTTACAAGGC
EST: gi|67021450|gb|CO450199.1|CO450199
EST:     ATTCCTTCCCTCCTAGAATTGAAGCGTATCTACTATGAACTGATGATTCG                         ATATTACTTGCACAACAATGATTACCTGGAAATCTGTCGTTGTTACAAGGC
genomic: ATTCCTTCCCTCCTAGAATTGAAGCGTATCTACTATGAACTGATGATTCGgtatgtcatg ... ctcatcacagATATTACTTGCACAACAATGATTACCTGGAAATCTGTCGTTGTTACAAGGC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AAAAGAAACCAAAGGAGGGTGACAACATTGTTCAGGATGCTCCTGCAGATATTCCTTCCCTCCTAGAATTGAAGCGTATCTACTATGAACTGATGATTCGgtatgtcatgcttctcaatctcaattagattaatgtactaccagtctgctatttcattgtcaattgtcattattctctcgtctacctgactacctctggaactgccaatttctttgttctattgaacactatggttcacaatgacattttatattggagccaatcataattcttcgttatctcatcacag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC