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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGCAAATGAGGAGTCCTTAAGCAGAAAGGACATATTGGAGAGGGTTGATAGGTGGATGTCAGCATGTGAAGAAGAAAGCTGGCTTGAAGACTACAGCCGGgtatgctgcttattcatttttgtgatttgtgtctcatggaagatgccaagccgtactttagctcctggcaattcttgaaattgcattattttttatatacttgctgttgtcttcacttcgtgtcctatcacaaggttctgacgtctatgctatcttaattaaccgcag

Basic information

species Zea mays
transcript GRMZM2G112337_T04
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G112337_T04 (Zea mays), 5'ss of exon 7
lower sequence: LOC_Os06g40840.1 (Oryza sativa), 5'ss of exon 7
AGCAAATGAGGAGTCCTTAAGCAGAAAGGACATATTGGAGAGGGTTGATAGGTGGATGTCAGCATGTGAAGAAGAAAGCTGGCTTGAAGACTACAGCCGGgta-tgctgcttattcatttttgtgatttgtgtctcatggaa---gatgccaagccgtactttagctcctggcaattcttgaaattgcattattttttatatacttgctgttgtcttcacttcgtgtcctatcacaaggttctgacgtctatgctatcttaattaaccgcag
|||||| || ||| | |||||||||||||||| |||||| |||||| ||||||||||||||||| |||||||| ||||||||||||||||| |||| |||| | ||| || | | || | || | | | | || || | ||| | | | | ||||| ||| |||
AGCAAAAGAAGAGGCACTAAGCAGAAAGGACATTCTGGAGAAGGTTGAAAGGTGGATGTCAGCATGCGAAGAAGAGAGCTGGCTTGAAGACTATAGCCAGgtaataaaaagtatacagtat-gtaacttcttcattgtttgatctcattaacagtcatacatctttacattgatattctgataatggcag----------------------------------------------------------------------------------

upper sequence: GRMZM2G112337_T04 (Zea mays), 5'ss of exon 7
lower sequence: GLYMA08G43450.1 (Glycine max), 5'ss of exon 14
AGCAAATGAGGAGTCCTTAAGCAGAAAGGACATATTGGAGAGGGTTGATAGGTGGATGTCAGCATGTGAAGAAGAAAGCTGGCTTGAAGACTACAGCCGGgtatgc-tgcttattcatttttgtgatttgtgtctca-tggaagatgccaagccgtactttagctcctggcaattcttgaaattgcattattttttatatacttgctgttgtcttcacttcgtgtcctatcacaaggttctgacgtctatgctatcttaattaaccgcag
||| || || || | |||||| ||| || |||||||| | |||||| | ||||||||||||||||||||||| || |||||||||||||| | ||||| | | | ||| || | | | | | | | | || | | | | | | || | | || ||| || | || | | || |
AGCGAAAGAAGAAGCTTTAAGCCAAAAAGAAATATTGGACAAGGTTGAGAAATGGATGTCAGCATGTGAAGAAGAGAGTTGGCTTGAAGACTATAATAGGgtacttataatcaaccatcttcat--tctatatttgagtctctaatatcttgttgcatgcttacatct--taggtggaaaagttgaatcacttg--agaatctaac----------------------------------------------------------------

upper sequence: GRMZM2G112337_T04 (Zea mays), 5'ss of exon 7
lower sequence: GLYMA02G46450.3 (Glycine max), 5'ss of exon 7
AGCAAATGAGGAGTCCTTAAGCAGAAAGGACATATTGGAGAGGGTTGATAGGTGGATGTCAGCATGTGAAGAAGAAAGCTGGCTTGAAGACTACAGCCGGgtatgctgcttattcatttt--tgtgatttgtgtctcatggaagatgccaagccgtactttagctcctggcaattcttgaaattgcattattttttatatacttgctgttgtcttcacttcgtgtcctatcacaaggttctgacgtctatgctatcttaattaaccgcag
|||||| || || | |||||| |||| || |||||||| | |||||| | |||||||||||||||||||||||||| ||||||||||| || | |||||| | | || | | | ||| | ||| | ||| | || | | | |||| | | ||||| | |
AGCAAAAGAAGAAGCTTTAAGCCGAAAAGATATATTGGACAAGGTTGAGAAATGGATGTCAGCATGTGAAGAAGAAAGTTGGCTTGAAGATTATAATCGGgtacttaaaatctcgcttctgctttattttttttctgagtttgaatgattggttgtgcacagtcgtggatagagaggtgaagtagtattatgatcagaac----------------------------------------------------------------------

upper sequence: GRMZM2G112337_T04 (Zea mays), 5'ss of exon 7
lower sequence: GLYMA02G46450.2 (Glycine max), 5'ss of exon 7
---------------------------------------------------------AGCAAATGAGGAGTCCTTAAGCAGAAAGGACATATTGGAGAGGGTTGATAGGTGGATGTCAGCATGTGAAGAAGAAAGCTGGCTTGAAGACTACAGCCGGgtatgctgcttattcatttttgtgatttgtgtctcatggaagatgccaagccgtactttagctcctggcaattcttgaaattgcattattttttatatacttgctgttgtcttcacttcgtgtcctatcacaaggttctgacgtctatgctatcttaattaaccgcag
|||||| || || | |||||| |||| || |||||||| | |||||| | |||||||||||||||||||||||||| ||||||||||| || | |||||| | || || || ||| | | | | || |
TTCAGGAAACATTGAACCAACTGAATTACTGGCTGACATGGACAATCAGATAGCAACAGCAAAAGAAGAAGCTTTAAGCCGAAAAGATATATTGGACAAGgttgagaaatggatgtcagcatgtgaagaagaaagttggcttgaagattataatcgggtacttaa---aatctcgcttctgctttattttttttctgagtttg--------------------------------------------------------------------------------------------------------------------------

upper sequence: GRMZM2G112337_T04 (Zea mays), 5'ss of exon 7
lower sequence: GLYMA14G02180.4 (Glycine max), 5'ss of exon 7
AGCAAATGAGGAGTCCTTAAGCAGAAAGGACATATTGGAGAGGGTTGATAGGTGGATGTCAGCATGTGAAGAAGAAAGCTGGCTTGAAGACTACAGCCGGgtatgctgcttattcatttttgtgatttgtgtctcatggaagatgccaagccgtactttagctcctggcaattcttgaaattgcattattttttatatacttgctgttgtcttcacttcgtgtcctatcacaaggttctgacgtctatgctatcttaattaaccgcag
|||||| || || | ||||| ||| || |||||||| | |||||| | ||||||||||||||||| ||||| || |||||||||||||| | ||||||| | || || || ||| | |||| | | || | | | | | | | || | | ||||| | | || || |
AGCAAAAGAAGAAGCTGTAAGCCAAAAAGATATATTGGACAAGGTTGAGAAATGGATGTCAGCATGTGATGAAGAGAGTTGGCTTGAAGACTATAACCGGgtacttaa---aatctcgcttctgctttatttctctttctgagtttgaatagagaggtgaagtagtagta-ttatgatcagaacattaaatccttta-accagag---------------------------------------------------------------

upper sequence: GRMZM2G112337_T04 (Zea mays), 5'ss of exon 7
lower sequence: AT5G55230.2 (Arabidopsis thaliana), 5'ss of exon 6
AGCAAATGAGGAGTCCTTAAGCAGAAAGGACATATTGGAGAGGGTTGATAGGTGGATGTCAGCATGTGAAGAAGAAAGCTGGCTTGAAGACTACAGCCGGgtatgctgcttattcatttttgtgatttgtgtctcatggaagatgccaagccgtactttagctcctggc-aattcttgaaattgcattattttttatatacttgctgttgtcttcacttcgtgtcctatcacaaggttctgacgtctatgctatcttaattaaccgcag
|| || || || | || || ||||| || |||||||| | || || | ||||||||||| ||||| ||||| |||||||| |||||||||| |||||| ||| || |||| | | | | ||| | || ||| || ||| || |||||| || |||| | | || | |
GGCTAAGGAAGAAGCATTTAGTAGAAAAGATATATTGGACCGAGTCGAGAAATGGATGTCAGCTTGTGAGGAAGAGAGCTGGCTAGAAGACTACAATCGGgtaa--tgcata---atttctctcagtcactcactatgatacatcataag----acattaactttaaattggatcttgagctttttcatggttttgttttctgagagcag-----------------------------------------------------------

upper sequence: GRMZM2G112337_T04 (Zea mays), 5'ss of exon 7
lower sequence: Vv19s0090g01230.t01 (Vitis vinifera), 5'ss of exon 6
AGCAAATGAGGAGTCCTTAAGCAGAAAGGACATATTGGAGAGGGTTGATAGGTGGATGTCAGCATGTGAAGAAGAAAGCTGGCTTGAAGACTACAGCCGGgtatgctgcttattcatttttgtgatttgtgtctcatggaagatgccaagccgtactttagctcctggcaattcttgaaattgcattattttttatatacttgctgttgtcttcacttcgtgtcctatcacaaggttctgacgtctatgctatcttaattaaccgcag
|||||| || ||| | || ||||||||||| ||||| || | |||||| | ||||||||||| ||||||||||| || |||||||||||||||| ||||||| || | | | | | | | |||| | || |||| ||| | | || | ||| | |||| | | | |||||
AGCAAAGGAAGAGGCTTTCAGCAGAAAGGATATATTAGACAAGGTTGAGAAATGGATGTCAGCTTGTGAAGAAGAGAGTTGGCTTGAAGACTACAATCGGgtatcctctctctctctctctctccccctccctccctgga------ttcgttgtggattagatcc--accttgattaggaatgc-tcatttgtgctctctgcaatgttg-----------------------------------------------------------

upper sequence: GRMZM2G112337_T04 (Zea mays), 5'ss of exon 7
lower sequence: PP1S135_53V6.1 (Physcomitrella patens), 5'ss of exon 7
AGCAAATGAGGAGTCCTTAAGCAGAAAGGACATATTGGAGAGGGTTGATAGGTGGATGTCAGCATGTGAAGAAGAAAGCTGGCTTGAAGACTACAGCCGGgtatgctgcttattcatttttgtgatttgtgtctcatggaagatgccaagccgtactttagctcctggcaattcttgaaattgcattattttttatatacttgctgttgtcttcacttcgtgtcctatcacaaggttctgacgtctatgctatcttaattaaccgcag
||||| || ||| ||||| ||||||||| || | || | |||||||||||| |||||||| ||| | |||||||| ||||||||| |||| | || | || || | | | | | |||| | | ||| ||||| | | || || || ||||| | || | |||| | || || | | ||
GGCAAAAGAAGAGGTAGCTAGCAGGAAGGACATAATGATTTTATTGGAAAAGTGGATGTCAGCTTGTGAAGAGGAAGGTTGGCTTGAGGACTACAGCAAGgtactcaact--cttatcttcttcgtatat-tgtcatagt--gtagcaa-ttttacttcaaagttttt---ttgctgcaaa-gcattctcgttcgttgcagcactgtcggctgagtttgatcatgcgttgcag-----------------------------------

upper sequence: GRMZM2G112337_T04 (Zea mays), 5'ss of exon 7
lower sequence: EFJ24960 (Selaginella moellendorffii), 5'ss of exon 7
AGCAAATGAGGAGTCCTTAAGCAGAAAGGACATATTGGAGAGGGTTGATAGGTGGATGTCAGCATGTGAAGAAGAAAGCTGGCTTGAAGACTACAGCCGGgtatgctgcttattc-atttttgtgatttgtgtctcatggaagatgccaagccgtactttagctcctggcaattcttgaaattgcattattttttatatacttgctgttgtcttcacttcgtgtcctatcacaaggttctgacgtctatgctatcttaattaaccgcag
|| || || || || | | ||| | || ||| |||| || | || | ||||| ||||||||||||||||| ||||||||||| |||| |||||| ||| | |||| | ||| | | || | ||
GGCGAAGGAAGAATCACTCGGTAGACAAGATATAATGGAAAGAATGGAACGATGGATTAGTGCATGTGAAGAAGAAAGTTGGCTTGAAGAATACAATAAGgtatgagcgttacgctatttcacttattcattttcgattgtag------------------------------------------------------------------------------------------------------------------------------

upper sequence: GRMZM2G112337_T04 (Zea mays), 5'ss of exon 7
lower sequence: EFJ15410 (Selaginella moellendorffii), 5'ss of exon 5
AGCAAATGAGGAGTCCTTAAGCAGAAAGGACATATTGGAGAGGGTTGATAGGTGGATGTCAGCATGTGAAGAAGAAAGCTGGCTTGAAGACTACAGCCGGgtatgctgcttattc-atttttgtgatttgtgtctcatggaagatgccaagccgtactttagctcctggcaattcttgaaattgcattattttttatatacttgctgttgtcttcacttcgtgtcctatcacaaggttctgacgtctatgctatcttaattaaccgcag
|| || || || || | |||| || ||| |||| || | || ||||||| || |||||||||||||||||||||||||| ||||| |||||| |||| | |||| | ||| | | || | || |||||| ||| | |||| | | |||| | || | || ||| |
GGCGAAGGAAGAATCACTCGACAGACGAGATATAATGGAAAGAATGGAACGGTGGATTAGCGCGTGTGAAGAAGAAAGCTGGCTTGAAGAATACAGTAAGgtatgagcgttatgctatttcacttattcattttcgattgtaggatgaaagccg--cttcaat-----gcaac-cagaggagcacatttgaatcta-aaacgtgcagaa------------------------------------------------------------

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|88756750|gb|DY540891.1|DY540891
EST:     GGTGGATGTCAGCATGTGAAGAAGAAAGCTGGCTTGAAGACTACAGCCGG                         GACGATAACAGGTACAGTGCAACTCGGGGTGCACATCTGAATCTGAAGCGT
genomic: GGTGGATGTCAGCATGTGAAGAAGAAAGCTGGCTTGAAGACTACAGCCGGgtatgctgct ... ttaaccgcagGACGATAACAGGTACAGTGCAACTCGGGGTGCACATCTGAATCTGAAGCGT
EST: gi|148995697|gb|EE034920.2|EE034920
EST:     GGTGGATGTCAGCATGTGAAGAAGAAAGCTGGCTTGAAGACTACAGCCGG                         GACGATAACAGGTACAGTGCAACTCGGGGTGCACATCTGAATCTGAAGCGT
genomic: GGTGGATGTCAGCATGTGAAGAAGAAAGCTGGCTTGAAGACTACAGCCGGgtatgctgct ... ttaaccgcagGACGATAACAGGTACAGTGCAACTCGGGGTGCACATCTGAATCTGAAGCGT
EST: gi|71771989|gb|DR969926.1|DR969926
EST:     GGTGGATGTCAGCATGTGAAGAAGAAAGCTGGCTTGAAGACTACAGCCGG                         GACGATAACAGGTACAGTGCAACTCGGGGTGCACATCTGAATCTGAAGCGT
genomic: GGTGGATGTCAGCATGTGAAGAAGAAAGCTGGCTTGAAGACTACAGCCGGgtatgctgct ... ttaaccgcagGACGATAACAGGTACAGTGCAACTCGGGGTGCACATCTGAATCTGAAGCGT
EST: gi|67021761|gb|CO450510.1|CO450510
EST:     GGTGGATGTCAGCATGTGAAGAAGAAAGCTGGCTTGAAGACTACAGCCGG                         GACGATAACAGGTACAGTGCAACTCGGGGTGCACATCTGAATCTGAAGCGT
genomic: GGTGGATGTCAGCATGTGAAGAAGAAAGCTGGCTTGAAGACTACAGCCGGgtatgctgct ... ttaaccgcagGACGATAACAGGTACAGTGCAACTCGGGGTGCACATCTGAATCTGAAGCGT
EST: gi|71773221|gb|DR971130.1|DR971130
EST:     GGTGGATGTCAGCATGTGAAGAAGAAAGCTGGCTTGAAGACTACAGCCGG                         GACGATAACAGGTACAGTGCAACTCGGGGTGCACATCTGAATCTGAAGCGT
genomic: GGTGGATGTCAGCATGTGAAGAAGAAAGCTGGCTTGAAGACTACAGCCGGgtatgctgct ... ttaaccgcagGACGATAACAGGTACAGTGCAACTCGGGGTGCACATCTGAATCTGAAGCGT
EST: gi|148928684|gb|EC873287.2|EC873287
EST:     GGTGGATGTCAGCATGTGAAGAAGAAAGCTGGCTTGAAGACTACAGCCGG                         GACGATAACAGGTACAGTGCAACTCGGGGTGCACATCTGAATCTGAAGCGT
genomic: GGTGGATGTCAGCATGTGAAGAAGAAAGCTGGCTTGAAGACTACAGCCGGgtatgctgct ... ttaaccgcagGACGATAACAGGTACAGTGCAACTCGGGGTGCACATCTGAATCTGAAGCGT
EST: gi|89249959|gb|DY621745.1|DY621745
EST:     GGTGGATGTCAGCATGTGAAGAAGAAAGCTGGCTTGAAGACTACAGCCGG                         GACGATAACAGGTACAGTGCAACTCGGGGTGCACATCTGAATCTGAAGCGT
genomic: GGTGGATGTCAGCATGTGAAGAAGAAAGCTGGCTTGAAGACTACAGCCGGgtatgctgct ... ttaaccgcagGACGATAACAGGTACAGTGCAACTCGGGGTGCACATCTGAATCTGAAGCGT
EST: gi|71306089|gb|DR789194.1|DR789194
EST:     GGTGGATGTCAGCATGTGAAGAAGAAAGCTGGCTTGAAGACTACAGCCGG                         GACGATAACAGGTACAGTGCAACTCGGGGTGCACATCTGAATCTGAAGCGT
genomic: GGTGGATGTCAGCATGTGAAGAAGAAAGCTGGCTTGAAGACTACAGCCGGgtatgctgct ... ttaaccgcagGACGATAACAGGTACAGTGCAACTCGGGGTGCACATCTGAATCTGAAGCGT
EST: gi|71435944|gb|DR816994.1|DR816994
EST:     GGTGGATGTCAGCATGTGAAGAAGAAAGCTGGCTTGAAGACTACAGCC-G                         GACGATAACAGGTACAGTGCAACTCGGGGTGCACATCTGAATCTGAAGCGT
genomic: GGTGGATGTCAGCATGTGAAGAAGAAAGCTGGCTTGAAGACTACAGCCGGgtatgctgct ... ttaaccgcagGACGATAACAGGTACAGTGCAACTCGGGGTGCACATCTGAATCTGAAGCGT
EST: gi|149098529|gb|EE184515.2|EE184515
EST:     GGTGGATGTCAGCATGTGAAGAAGAAAGCTGGCTTGAAGACTACAGCCGG                         GACGATAACAGGTACAGTGCAACTCGGGGTGCACATCTGAATCTGAAGCGT
genomic: GGTGGATGTCAGCATGTGAAGAAGAAAGCTGGCTTGAAGACTACAGCCGGgtatgctgct ... ttaaccgcagGACGATAACAGGTACAGTGCAACTCGGGGTGCACATCTGAATCTGAAGCGT
EST: gi|60351440|gb|DN218413.1|DN218413
EST:     GGTGGATGTCAGCATGTGAAGAAGAAAGCTGGCTTGAAGACTACAGCCGG                         GACGATAACAGGTACAGTGCAACTCGGGGTGCACATCTGAATCTGAAGCGT
genomic: GGTGGATGTCAGCATGTGAAGAAGAAAGCTGGCTTGAAGACTACAGCCGGgtatgctgct ... ttaaccgcagGACGATAACAGGTACAGTGCAACTCGGGGTGCACATCTGAATCTGAAGCGT
EST: gi|149078381|gb|EE167156.2|EE167156
EST:     GGTGGATGTCAGCATGTGAAGAAGAAAGCTGGCTTGAAGACTACAGCCGG                         GACGATAACAGGTACAGTGCAACTCGGGGTGCACATCTGAATCTGAAGCGT
genomic: GGTGGATGTCAGCATGTGAAGAAGAAAGCTGGCTTGAAGACTACAGCCGGgtatgctgct ... ttaaccgcagGACGATAACAGGTACAGTGCAACTCGGGGTGCACATCTGAATCTGAAGCGT
EST: gi|89763677|gb|DY690772.1|DY690772
EST:     GGTGGATGTCAGCATGTGAAGAAGAAAGCTGGCTTGAAGACTACAGCCGG                         GACGATAACAGGTACAGTGCAACTCGGGGTGCACATCTGAATCTGAAGCGT
genomic: GGTGGATGTCAGCATGTGAAGAAGAAAGCTGGCTTGAAGACTACAGCCGGgtatgctgct ... ttaaccgcagGACGATAACAGGTACAGTGCAACTCGGGGTGCACATCTGAATCTGAAGCGT
EST: gi|67020793|gb|CO449542.1|CO449542
EST:     GGTGGATGTCAGCATGTGAAGAAGAAAGCTGGCTTGAAGACTACAGCCGG                         GACGATAACAGGTACAGTGCAACTCGGGGTGCACATCTGAATCTGAAGCGT
genomic: GGTGGATGTCAGCATGTGAAGAAGAAAGCTGGCTTGAAGACTACAGCCGGgtatgctgct ... ttaaccgcagGACGATAACAGGTACAGTGCAACTCGGGGTGCACATCTGAATCTGAAGCGT
EST: gi|149088740|gb|EE177864.2|EE177864
EST:     GGTGGATGTCAGCATGTGAAGAAGAAAGCTGGCTTGAAGACTACAGCCGG                         GACGATAACAGGTACAGTGCAACTCGGGGTGCACATCTGAATCTGAAGCGT
genomic: GGTGGATGTCAGCATGTGAAGAAGAAAGCTGGCTTGAAGACTACAGCCGGgtatgctgct ... ttaaccgcagGACGATAACAGGTACAGTGCAACTCGGGGTGCACATCTGAATCTGAAGCGT
EST: gi|194716932|gb|FK934091.1|FK934091
EST:     GGTGGATGTCAGCATGTGAAGAAGAAAGCTGGCTTGAAGACTACAGCCGG                         GACGATAACAGGT
genomic: GGTGGATGTCAGCATGTGAAGAAGAAAGCTGGCTTGAAGACTACAGCCGGgtatgctgct ... ttaaccgcagGACGATAACAGGT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGCAAATGAGGAGTCCTTAAGCAGAAAGGACATATTGGAGAGGGTTGATAGGTGGATGTCAGCATGTGAAGAAGAAAGCTGGCTTGAAGACTACAGCCGGgtatgctgcttattcatttttgtgatttgtgtctcatggaagatgccaagccgtactttagctcctggcaattcttgaaattgcattattttttatatacttgctgttgtcttcacttcgtgtcctatcacaaggttctgacgtctatgctatcttaattaaccgcag

- - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA