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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGGAGACTTGGGATATGCATCAGAGCTTGGAAACTATGCAGAGTATAGTGGTGCTCCTAATGAGGAGGAGGTTCTGAATTATTCTAGAGTTGTTCTTGATgtaagcaaacattgtaaccttgtcaatgctgctcttaactccaccttaggaccatcatctggttgggacaatgttaggatcatctgctaaccatacaattaaatgtag

Basic information

species Zea mays
transcript GRMZM2G107082_T01
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G107082_T01 (Zea mays), 5'ss of exon 8
lower sequence: LOC_Os11g47330.1 (Oryza sativa), 5'ss of exon 8
TGGAGACTTGGGATATGCATCAGAGCTTGGAAACTATGCAGAGTATAGTGGTGCTCCTAATGAGGAGGAGGTTCTGAATTATTCTAGAGTTGTTCTTGATgtaagcaaacat--tgtaaccttgtcaatgctgctcttaactccaccttaggaccatcatctggttgggacaatgttaggatcatctgctaaccatacaattaaatgtag
||||| ||||||||||| ||||| | |||||||||||||||||||| |||||||| |||||||||||||||||| | ||| ||||||| || ||||||||||||| || | ||||| | | | | |||| ||||| | || || || | || || || ||
CGGAGATTTGGGATATGCTTCAGAATTAGGAAACTATGCAGAGTATAGCGGTGCTCCCAATGAGGAGGAGGTTCTGCAGTATGCTAGAGTAGTACTTGATgtaagcactcaagatataaccataaccacatttctctccactcccttgttatgtca--atttgttaatgataacattcaatgcag-------------------------

upper sequence: GRMZM2G107082_T01 (Zea mays), 5'ss of exon 8
lower sequence: LOC_Os11g47120.1 (Oryza sativa), 5'ss of exon 8
TGGAGACTTGGGATATGCATCAGAGCTTGGAAACTATGCAGAGTATAGTGGTGCTCCTAATGAGGAGGAGGTTCTGAATTATTCTAGAGTTGTTCTTGATgtaagcaaaca--ttgtaaccttgtcaatgctgctcttaactccaccttaggaccatcatctggttgggacaatgttaggatcatctgctaaccatacaattaaatgtag
| | | |||||||||||||||||| |||||||| || ||||||||||||||| | ||| ||||||| || ||||||||||||| || | ||||| | | | | |||| ||||| | || || || | || || || ||
-----------------------AATTAGAAAACTATGCAGAGTATAGCGGTGCTCCCAACGAGGAGGAGGTTCTGCAGTATGCTAGAGTAGTACTTGATgtaagcactcaagatataaccataaccacatttctctccactcccttgttatgtca--atttgttaatgataacattcaatgcag-------------------------

upper sequence: GRMZM2G107082_T01 (Zea mays), 5'ss of exon 8
lower sequence: AT1G09430.1 (Arabidopsis thaliana), 5'ss of exon 9
TGGAGACTTGGGATATGCATCAGAGCTTGGAAACTATGCAGAGTATAGTGGTGCTCCTAATGAGGAGGAGGTTCTGAATTATTCTAGAGTTGTTCTTGATgtaagcaaacattgtaaccttgtcaatgctgctc-ttaactccaccttaggaccatcatctggttg-ggac--aatgttaggatcatctgctaaccatacaattaaatgtag
||| || || || ||||||||||||||||||||||| |||||||||||||| || ||||||||||| ||||| | | ||| | |||||||| ||||||| || | | |||| | | | || || | || | | | | ||| || ||| || |||
TGGGGATTTAGGTTATGCATCAGAGCTTGGAAACTACGCAGAGTATAGTGGAGCACCTAATGAGGAAGAGGTGTTACAATATGCAAGAGTTGTCATTGATgtgagtcatggcaaagaacttggccttttccttaattgtttctatctataaaattttagagattcacagaccaaacgttcgggctttctcag--------------------

upper sequence: GRMZM2G107082_T01 (Zea mays), 5'ss of exon 8
lower sequence: Vv14s0060g00550.t01 (Vitis vinifera), 5'ss of exon 9
TGGAGACTTGGGATATGCATCAGAGCTTGGAAACTATGCAGAGTATAGTGGTGCTCCTAATGAGGAGGAGGTTCTGAATTATTCTAGAGTTGTTCTTGATgtaagcaaacattgtaaccttgtcaatgctgctcttaactcca---ccttaggaccatcatctggttgggacaatgttaggatcatctgctaaccatacaattaaatgtag
|||||| ||||| ||||| ||||||||||| |||||||||||||||||||| ||||| |||||||| ||||| || | ||| | |||||||||||||||||||| || || ||| ||| || || | | || || | || | || ||| || | ||| || | | || ||| ||| | | | ||
TGGAGATTTGGGTTATGCGTCAGAGCTTGGTAACTATGCAGAGTATAGTGGAGCTCCGAATGAGGAAGAGGTGTTGCAATATGCCAGAGTTGTTCTTGATgtaagaaattatg--aactttggcatacct--tttgggcttcagctctttgttaaaatttgctgcttaaaataattttcatttgttgtgg-aacaatatactctt-tacag

upper sequence: GRMZM2G107082_T01 (Zea mays), 5'ss of exon 8
lower sequence: PP1S7_156V6.2 (Physcomitrella patens), 5'ss of exon 10
TGGAGACTTGGGATATGCATCAGAGCTTGGAAACTATGCAGAGTATAGTGGTGCTCCTAATGAGGAGGAGGTTCTGAATTATTCTAGAGTTGTTCTTGATgtaag--caaacattgtaaccttgtcaatgct--gctcttaactccaccttaggaccatcatctggt-tgggacaatgttaggatca-tctgct-aaccatacaattaaatgtag-------------------------------------------------------------
||||||||| || | ||| ||||| || |||||||| |||||||||||||| |||||||| || || || | | | | | | | |||||||||| | ||| | | || | | || | | | || ||| | | || || | | | |||| ||| | ||| | | | || | |||
TGGAGACTTAGGCTTTGCTAGTGAGCTGGGTAACTATGCGGAGTATAGTGGTGCGCCTAATGAAGAAGAAACCCTTCACTTTGCACGTGCCCTAATTGATgtaagttctttcataacatacatgaaaccacctagcccactagtatgagctatgactagtagtaagtctgtctcgcagagaaaatcaatctaatcaactacaaattttgacgtatctgtgaagcatctatttgtttagaggatcagccctagttctgacctagttctttttgttag

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|6056658|gb|AW091063.1|AW091063
EST:     GTGCTCCTAATGAGGAGGAGGTTCTGAATTATTCTAGAGTTGTACTTGAT                         TGTGCAACTGCTGA
genomic: GTGCTCCTAATGAGGAGGAGGTTCTGAATTATTCTAGAGTTGTTCTTGATgtaagcaaac ... ttaaatgtagTGTGCAACTGCTGA
EST: gi|211099628|gb|FL031896.1|FL031896
EST:     GTGCTCCTAATGAGGAGGAGGTTCTGAATTATTCTAGAGTTGTTCTTGAT                         TGTGCAACTGCTGATCCTGATGGCCGCAAGAGAGCCCTTCTCATTGGAGGT
genomic: GTGCTCCTAATGAGGAGGAGGTTCTGAATTATTCTAGAGTTGTTCTTGATgtaagcaaac ... ttaaatgtagTGTGCAACTGCTGATCCTGATGGCCGCAAGAGAGCCCTTCTCATTGGAGGT
EST: gi|6851489|gb|AW352499.1|AW352499
EST:     GTGCTCCTAATGAGGAGGAGGTTCTGAATTATTCTAGAGTTGTACTTGAT                         TGTGCAACTGCTGACCCTGATGGCCGCAAGAGAGCCCTTCTCATTGGAGGT
genomic: GTGCTCCTAATGAGGAGGAGGTTCTGAATTATTCTAGAGTTGTTCTTGATgtaagcaaac ... ttaaatgtagTGTGCAACTGCTGATCCTGATGGCCGCAAGAGAGCCCTTCTCATTGGAGGT
EST: gi|60357576|gb|DN224549.1|DN224549
EST:     GTGCTCCTAATGAGGAGGAGGTTCTGAATTATTCTAGAGTTGTTCTTGAT                         TGTGCAACTGCTGATCCTGATGGCCGCAAGAGAGCCCTTCTCATTGGAGGT
genomic: GTGCTCCTAATGAGGAGGAGGTTCTGAATTATTCTAGAGTTGTTCTTGATgtaagcaaac ... ttaaatgtagTGTGCAACTGCTGATCCTGATGGCCGCAAGAGAGCCCTTCTCATTGGAGGT
EST: gi|4966766|gb|AI691622.1|AI691622
EST:     GTGCTCCTAATGAGGAGGAGGTTCTGAATTATTCTAGAGTTGTACTTGAT                         TGTGCANCTGCTGATCCTGATGGCCGCAAGAGAGCCCTTCTCATTGGAGGT
genomic: GTGCTCCTAATGAGGAGGAGGTTCTGAATTATTCTAGAGTTGTTCTTGATgtaagcaaac ... ttaaatgtagTGTGCAACTGCTGATCCTGATGGCCGCAAGAGAGCCCTTCTCATTGGAGGT
EST: gi|60352571|gb|DN219544.1|DN219544
EST:     GTGCTCCTAATGAGGAGGAGGTTCTGAATTATTCTAGAGTTGTTCTTGAT                         TGTGCAACTGCTGATCCTGATGGCCGCAAGAGAGCCCTTCTCATTGGAGGT
genomic: GTGCTCCTAATGAGGAGGAGGTTCTGAATTATTCTAGAGTTGTTCTTGATgtaagcaaac ... ttaaatgtagTGTGCAACTGCTGATCCTGATGGCCGCAAGAGAGCCCTTCTCATTGGAGGT
EST: gi|60354935|gb|DN221908.1|DN221908
EST:     GTGCTCCTAATGAGGAGGAGGTTCTGAATTATTCTAGAGTTGTTCTTGAT                         TGTGCAACTGCTGATCCTGATGGCCGCAAGAGAGCCCTTCTCATTGGAGGT
genomic: GTGCTCCTAATGAGGAGGAGGTTCTGAATTATTCTAGAGTTGTTCTTGATgtaagcaaac ... ttaaatgtagTGTGCAACTGCTGATCCTGATGGCCGCAAGAGAGCCCTTCTCATTGGAGGT
EST: gi|148953531|gb|EE153040.2|EE153040
EST:     GTGCTCCTAATGAGGAGGAGGTTCTGAATTATTCTAGAGTTGTTCTTGAT                         TGTGCAACTGCTGATCCTGATGGCCGCAAGAGAGCCCTTCTCATTGGAGGT
genomic: GTGCTCCTAATGAGGAGGAGGTTCTGAATTATTCTAGAGTTGTTCTTGATgtaagcaaac ... ttaaatgtagTGTGCAACTGCTGATCCTGATGGCCGCAAGAGAGCCCTTCTCATTGGAGGT
EST: gi|211099629|gb|FL031897.1|FL031897
EST:     GTGCTCCTAATGAGGAGGAGGTTCTGAATTATTCTAGAGTTGTTCTTGAT                         TGTGCAACTGCTGATCCTGATGGCCGCAAGAGAGCCCTTCTCATTGGAGGT
genomic: GTGCTCCTAATGAGGAGGAGGTTCTGAATTATTCTAGAGTTGTTCTTGATgtaagcaaac ... ttaaatgtagTGTGCAACTGCTGATCCTGATGGCCGCAAGAGAGCCCTTCTCATTGGAGGT
EST: gi|13177932|gb|BG349115.1|BG349115
EST:     GTGCTCCTAATGAGGAGGAGGTTCTGAATTATTCTAGAGTTGTTCTTGAT                         TGTGCAACTGCTGATCCTGATGGCCGCAAGAGAGCCCTTCTCATTGGAGGT
genomic: GTGCTCCTAATGAGGAGGAGGTTCTGAATTATTCTAGAGTTGTTCTTGATgtaagcaaac ... ttaaatgtagTGTGCAACTGCTGATCCTGATGGCCGCAAGAGAGCCCTTCTCATTGGAGGT
EST: gi|60398717|gb|DN231533.1|DN231533
EST:     GTGCTCCTAATGAGGAGGAGGTTCTGAATTATTCTAGAGTTGTTCTTGAT                         TGTGCAACTGCTGATCCTGATGGCCGCAAGAGAGCCCTTCTCATTGGAGGT
genomic: GTGCTCCTAATGAGGAGGAGGTTCTGAATTATTCTAGAGTTGTTCTTGATgtaagcaaac ... ttaaatgtagTGTGCAACTGCTGATCCTGATGGCCGCAAGAGAGCCCTTCTCATTGGAGGT
EST: gi|113703225|gb|EE680729.1|EE680729
EST:     GTGCTCCTAATGAGGAGGAGGTTCTGAATTATTCTAGAGTTGTTCTTGAT                         TGTGCAACTGCTGATCCTGATGGCCGCAAGAGAGCCCTTCTCATTGGAGGT
genomic: GTGCTCCTAATGAGGAGGAGGTTCTGAATTATTCTAGAGTTGTTCTTGATgtaagcaaac ... ttaaatgtagTGTGCAACTGCTGATCCTGATGGCCGCAAGAGAGCCCTTCTCATTGGAGGT
EST: gi|32851220|gb|CD990901.1|CD990901
EST:     GTGCTCCTAATGAGGAGGAGGTTCTGAATTATTCTAGAGTTGTACTTGAT                         TGTGCAACTGCTGACCCTGATGGCCGCAAGAGAGCCCTTCTCATTGGAGGT
genomic: GTGCTCCTAATGAGGAGGAGGTTCTGAATTATTCTAGAGTTGTTCTTGATgtaagcaaac ... ttaaatgtagTGTGCAACTGCTGATCCTGATGGCCGCAAGAGAGCCCTTCTCATTGGAGGT
EST: gi|13177931|gb|BG349114.1|BG349114
EST:     GAATTATTCTAGAGTTGTTCTTGAT                         TGTGCAACTGCTGATCCTGATGGCCGCAAGAGAGCCCTTCTCATTGGAGGT
genomic: GAATTATTCTAGAGTTGTTCTTGATgtaagcaaac ... ttaaatgtagTGTGCAACTGCTGATCCTGATGGCCGCAAGAGAGCCCTTCTCATTGGAGGT
EST: gi|5922366|gb|AW055655.1|AW055655
EST:     GTGCTCCTAATGAGGAGGAGGTTCTGAATTATTCTAGAGTTGTACTTGAT                         TGTGCAACTGCTGATCCTGATGGCCGCAAGAGAGCCCTTCTCATTGGAGGT
genomic: GTGCTCCTAATGAGGAGGAGGTTCTGAATTATTCTAGAGTTGTTCTTGATgtaagcaaac ... ttaaatgtagTGTGCAACTGCTGATCCTGATGGCCGCAAGAGAGCCCTTCTCATTGGAGGT
EST: gi|4827542|gb|AI668234.1|AI668234
EST:     GTGCTCCTAATGAGGAGGAGGTTCTGAATTATTCTAGAGTTGTACTTGAT                         TGTGCAACTGCTGATCCTGATGGCCGCAAGAGAGCCCTTCTCATTGGAGGT
genomic: GTGCTCCTAATGAGGAGGAGGTTCTGAATTATTCTAGAGTTGTTCTTGATgtaagcaaac ... ttaaatgtagTGTGCAACTGCTGATCCTGATGGCCGCAAGAGAGCCCTTCTCATTGGAGGT
EST: gi|211182330|gb|FL049127.1|FL049127
EST:     GTGCTCCTAATGAGGAGGAGGTTCTGAATTATTCTAGAGTTGTTCTTGAT                         TGTKCAACTGCTGATCCTGATGGCCGCAAGAKAGCCCTTCTCATTGGAGGT
genomic: GTGCTCCTAATGAGGAGGAGGTTCTGAATTATTCTAGAGTTGTTCTTGATgtaagcaaac ... ttaaatgtagTGTGCAACTGCTGATCCTGATGGCCGCAAGAGAGCCCTTCTCATTGGAGGT
EST: gi|5871775|gb|AW018246.1|AW018246
EST:     GTGCTCCTAATGAGGAGGAGGTTCTGAATTATTCTAGAGTTGTACTTGAT                         TGTGCAACTGCTGACCCTGATGGCCGCAAGAGAGCCCTTCTCATTGGAGGT
genomic: GTGCTCCTAATGAGGAGGAGGTTCTGAATTATTCTAGAGTTGTTCTTGATgtaagcaaac ... ttaaatgtagTGTGCAACTGCTGATCCTGATGGCCGCAAGAGAGCCCTTCTCATTGGAGGT
EST: gi|211123624|gb|FL002523.1|FL002523
EST:     TGCTCCTAATGAGGGAG-AGGGTCTGAATTATNCTAGAGTTGTTCTTGAT                         TGTGCAACTGCTGATCCTGATGGCCG-AAGAGAAGCCCTTCTCATTGGAGG
genomic: TGCTCCTAATGAGG-AGGAGGTTCTGAATTATTCTAGAGTTGTTCTTGATgtaagcaaac ... ttaaatgtagTGTGCAACTGCTGATCCTGATGGCCGCAAGAGA-GCCCTTCTCATTGGAGG
EST: gi|60401566|gb|DN234373.1|DN234373
EST:     GTGCTCCTAATGAGGAGGAGGTTCTGAATTATTCTAGAGTTGTTCTTGAT                         TGTGCAACTGCTGATCCTGATGGCCGCAAGAGAGCCCTTCTCATTGGAGGT
genomic: GTGCTCCTAATGAGGAGGAGGTTCTGAATTATTCTAGAGTTGTTCTTGATgtaagcaaac ... ttaaatgtagTGTGCAACTGCTGATCCTGATGGCCGCAAGAGAGCCCTTCTCATTGGAGGT
EST: gi|78024963|gb|DV493350.1|DV493350
EST:     GTGCTCCTAATGAGGAGGAGGTTCTGAATTATTCTAGAGTTGTACTTGAT                         TGTGCAACTGCTGATCCTGATGGCCGCAAGAGAGCCCTTCTCATTGGAGGT
genomic: GTGCTCCTAATGAGGAGGAGGTTCTGAATTATTCTAGAGTTGTTCTTGATgtaagcaaac ... ttaaatgtagTGTGCAACTGCTGATCCTGATGGCCGCAAGAGAGCCCTTCTCATTGGAGGT
EST: gi|50332311|gb|CO527437.1|CO527437
EST:     GTGCTCCTAATGAGGAGGAGGTTCTGAATTATTCTAGAGTTGTTCTTGAT                         TGTGCAACTGCTGATCCTGATGGCCGCAAGAGAGCCCTTCTCATTGGAGGT
genomic: GTGCTCCTAATGAGGAGGAGGTTCTGAATTATTCTAGAGTTGTTCTTGATgtaagcaaac ... ttaaatgtagTGTGCAACTGCTGATCCTGATGGCCGCAAGAGAGCCCTTCTCATTGGAGGT
EST: gi|6012698|gb|AW062135.1|AW062135
EST:     GTGCTCCTAATGAGGAGGAGGTTCTGAATTATTCTAGAGTTGTACTTGAT                         TGTGCAACTGCTGATCCTGATGGCCGCAAGAGAGCCCTTCTCATTGGAG-T
genomic: GTGCTCCTAATGAGGAGGAGGTTCTGAATTATTCTAGAGTTGTTCTTGATgtaagcaaac ... ttaaatgtagTGTGCAACTGCTGATCCTGATGGCCGCAAGAGAGCCCTTCTCATTGGAGGT
EST: gi|16378083|gb|BI992269.1|BI992269
EST:     GTGCTCCTAATGAGGAGGAGGTTCTGAATTATTCTAGAGTTGTTCTTGAT                         TGTGCAACTGCTGATCCTGATGGCCGCAAGAGAGCCCTTCTCATTGGAGGT
genomic: GTGCTCCTAATGAGGAGGAGGTTCTGAATTATTCTAGAGTTGTTCTTGATgtaagcaaac ... ttaaatgtagTGTGCAACTGCTGATCCTGATGGCCGCAAGAGAGCCCTTCTCATTGGAGGT
EST: gi|60395413|gb|DN228283.1|DN228283
EST:     GTGCTCCTAATGAGGAGGAGGTTCTGAATTATTCTAGAGTTGTTCTTGAT                         TGTGCAACTGCTGATCCTGATGGCCGCAAGAGAGCCCTTCTCATTGGAGGT
genomic: GTGCTCCTAATGAGGAGGAGGTTCTGAATTATTCTAGAGTTGTTCTTGATgtaagcaaac ... ttaaatgtagTGTGCAACTGCTGATCCTGATGGCCGCAAGAGAGCCCTTCTCATTGGAGGT
EST: gi|211420152|gb|FL463211.1|FL463211
EST:     GTGCTCCTAATGAGGAGGAGGTTCTGAATTATTCTAGAGTTGTTCTTGAT                         TGTGCAACTGCTGATCCTGATGGCCGCAAGAGAGCCCTTCTCATTGGAGGT
genomic: GTGCTCCTAATGAGGAGGAGGTTCTGAATTATTCTAGAGTTGTTCTTGATgtaagcaaac ... ttaaatgtagTGTGCAACTGCTGATCCTGATGGCCGCAAGAGAGCCCTTCTCATTGGAGGT
EST: gi|211481515|gb|FL480068.1|FL480068
EST:     GTGCTCCTAATGAGGAGGAGGTTCTGAATTATTCTAGAGTTGTTCTTGAT                         TGTGCAACTGCTGATCCTGATGGCCGCAAGAGAGCCCTTCTCATTGGAGGT
genomic: GTGCTCCTAATGAGGAGGAGGTTCTGAATTATTCTAGAGTTGTTCTTGATgtaagcaaac ... ttaaatgtagTGTGCAACTGCTGATCCTGATGGCCGCAAGAGAGCCCTTCTCATTGGAGGT
EST: gi|113703355|gb|EE680859.1|EE680859
EST:     GTGCTCCTAATGAGGAGGAGGTTCTGAATTATTCTAGAGTTGTTCTTGAT                         TGTGCAACTGCTGATCCTGATGGCCGCAAGAGAGCCCTTCTCATTGGAGGT
genomic: GTGCTCCTAATGAGGAGGAGGTTCTGAATTATTCTAGAGTTGTTCTTGATgtaagcaaac ... ttaaatgtagTGTGCAACTGCTGATCCTGATGGCCGCAAGAGAGCCCTTCTCATTGGAGGT
EST: gi|211182333|gb|FL049130.1|FL049130
EST:     TTCTAGAGTTGTTCTTGAT                         TGTGCAACTGCTGATCCTGATGGCCGCAAGAGAGCCCTTCTCATTGGAGGT
genomic: TTCTAGAGTTGTTCTTGATgtaagcaaac ... ttaaatgtagTGTGCAACTGCTGATCCTGATGGCCGCAAGAGAGCCCTTCTCATTGGAGGT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGGAGACTTGGGATATGCATCAGAGCTTGGAAACTATGCAGAGTATAGTGGTGCTCCTAATGAGGAGGAGGTTCTGAATTATTCTAGAGTTGTTCTTGATgtaagcaaacattgtaaccttgtcaatgctgctcttaactccaccttaggaccatcatctggttgggacaatgttaggatcatctgctaaccatacaattaaatgtag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG