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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatctggctcagtgttgctgccactagtttaccgtatgtttttacttgctaagttgctaaccctggtcgagcttcatcagAAACTGGAGGGCATGCAGTGGACAATTCACCAGGTGGAGATGGACCTGAAACCTCACCATGACCACGCAGCTGTTTAAGTCCACATCTGTTGGAGGCCAT

Basic information

species Zea mays
transcript GRMZM2G068277_T02
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G068277_T01 (Zea mays), 3'ss of exon 8
lower sequence: LOC_Os02g02690.1 (Oryza sativa), 3'ss of exon 12
gtaatctggctcagtgttgctgccactagtttaccgtatgtttttacttgctaagttgctaaccctggtcgagcttcatcagAAACTGGAGGGCATGCAGTGGACAATTCACCAGGTGGAGATGGACCTGAAACCTCACCATGACCACGCAGCTGTTTAAG-TCCACATCTGTTGGAGGCCAT
||||| || |||| | | | | |||||| ||| ||| |||| | | || || |||||||||||||||||| ||||| ||||| ||||| || ||||| ||||| |||||||||||||| |||| ||| || | |||| ||| |||| ||
gtaatttgactcatcttcatcattatcaatgagtaccatgtttga---tgcatcattgacaacca-atttaaactgca---gAAACTGGAGGGCATGCAATGGACGATTCATCAGGTCGAAATGGATCTGAAGCCTCACCATGACCATGCAGATGTCTAGGCTCCATCTCTCCAGGAGTGCA-

upper sequence: GRMZM2G068277_T01 (Zea mays), 3'ss of exon 8
lower sequence: EFJ09056 (Selaginella moellendorffii), 3'ss of exon 11
gtaatctggctcagtgttgctgccactagtttaccgtatgtttttacttgctaagttgctaaccctggtcgagcttcatcagAAACTGGAGGGCATGCAGTGGACAATTCACCAGGTGGAGATGGACCTGAAACCTCACCATGACCACGCAGCTGTTTAAGTCCACATCTGTTGGAGGCCAT
|| || | | | | | ||| | || | || | | | | ||| |||||||||||||| || ||||||||||| ||||||||||||||||| || | || || || ||
---------------gtgagagcaa--aatcgtgggcagcctttgatatgttgggtggt--------gacaaactta--cagAAACTGGAGGGAATTCAGTGGACAATAAGACAGGTGGAGATGGACCTCAATAATGGACACGAGCAT-TAG------------------------------
















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|211432853|gb|FL453388.1|FL453388
EST:     TAGATCCACGGTTCGATGTGATTGCGAGGCAGTACCACGAGATTGTAAAG                         AAACTGGAGGGCATGCAGTGGACAATTCACCAGGTGGAGATGGACCTGAAA
genomic: TAGATCCACGGTTCGATGTGATTGCGAGGCAGTACCACGAGATTGTAAAGgtaatctggc ... gcttcatcagAAACTGGAGGGCATGCAGTGGACAATTCACCAGGTGGAGATGGACCTGAAA
EST: gi|60400409|gb|DN233216.1|DN233216
EST:     TAGATCCACGGTTCGATGTGATTGCGAGGCAGTACCACGAGATTGTAAAG                         AAACTGGAGGGCATGCAGTGGACAATTCACCAGGTGGAGATGGACCTGAAA
genomic: TAGATCCACGGTTCGATGTGATTGCGAGGCAGTACCACGAGATTGTAAAGgtaatctggc ... gcttcatcagAAACTGGAGGGCATGCAGTGGACAATTCACCAGGTGGAGATGGACCTGAAA
EST: gi|32788560|gb|CD940796.1|CD940796
EST:     GATCCACGGTTCGATGTGATTGCGAGGCAGTACCACGAGATTGTAAAG                         AAACTGGAGGGCATGCAGTGGACAATTCACCAGGTGGAGATGGACCTGAAA
genomic: GATCCACGGTTCGATGTGATTGCGAGGCAGTACCACGAGATTGTAAAGgtaatctggc ... gcttcatcagAAACTGGAGGGCATGCAGTGGACAATTCACCAGGTGGAGATGGACCTGAAA
EST: gi|211359393|gb|FL440514.1|FL440514
EST:     TAGATCCACGGTTCGATGTGATTGCGAGGCAGTACCACGAGATTGTAAAG                         AAACTGGAGGGCATGCAGTGGACAATTCACCAGGTGGAGATGGACCTGAAA
genomic: TAGATCCACGGTTCGATGTGATTGCGAGGCAGTACCACGAGATTGTAAAGgtaatctggc ... gcttcatcagAAACTGGAGGGCATGCAGTGGACAATTCACCAGGTGGAGATGGACCTGAAA
EST: gi|71428336|gb|DR809386.1|DR809386
EST:     TAGATCCACGGTTCGATGTGATTGCGAGGCAGTACCACGAGATTGTAAAG                         AAACTGGAGGGCATGCAGTGGACAATTCACCAGGTGGAGATGGACCTGAAA
genomic: TAGATCCACGGTTCGATGTGATTGCGAGGCAGTACCACGAGATTGTAAAGgtaatctggc ... gcttcatcagAAACTGGAGGGCATGCAGTGGACAATTCACCAGGTGGAGATGGACCTGAAA
EST: gi|60401584|gb|DN234391.1|DN234391
EST:     TAGATCCACGGTTCGATGTGATTGCGAGGCAGTACCACGAGATTGTAAAG                         AAACTGGAGGGCATGCAGTGGACAATTCACCAGGTGGAGATGGACCTGAAA
genomic: TAGATCCACGGTTCGATGTGATTGCGAGGCAGTACCACGAGATTGTAAAGgtaatctggc ... gcttcatcagAAACTGGAGGGCATGCAGTGGACAATTCACCAGGTGGAGATGGACCTGAAA
EST: gi|71443220|gb|DR824270.1|DR824270
EST:     TAGATCCACGGTTCGATGTGATTGCGAGGCAGTACCACGAGATTGTAAAG                         AAACTGGAGGGCATGCAGTGGACAATTCACCAGGTGGAGATGGACCTGAAA
genomic: TAGATCCACGGTTCGATGTGATTGCGAGGCAGTACCACGAGATTGTAAAGgtaatctggc ... gcttcatcagAAACTGGAGGGCATGCAGTGGACAATTCACCAGGTGGAGATGGACCTGAAA
EST: gi|32797207|gb|CD949443.1|CD949443
EST:     GTTCGATGTGATTGCAAGGCAGTACCACGAGATTGTAAAG                         AAACTGGAGGGCATGCAGTGGACAATTCACCAGGTGGAGATGGACCTGAAA
genomic: GTTCGATGTGATTGCGAGGCAGTACCACGAGATTGTAAAGgtaatctggc ... gcttcatcagAAACTGGAGGGCATGCAGTGGACAATTCACCAGGTGGAGATGGACCTGAAA
EST: gi|76281959|gb|DV021527.1|DV021527
EST:     TAGATCCACGGTTCGATGTGATTGCGAGGCAGTACCACGAGATTGTAAAG                         AAACTGGAGGGCATGCAGTGGACAATTCACCAGGTGGAGATGGACCTGAAA
genomic: TAGATCCACGGTTCGATGTGATTGCGAGGCAGTACCACGAGATTGTAAAGgtaatctggc ... gcttcatcagAAACTGGAGGGCATGCAGTGGACAATTCACCAGGTGGAGATGGACCTGAAA
EST: gi|78122195|gb|DV540579.1|DV540579
EST:     TAGATCCACGGTTCGATGTGATTGCGAGGCAGTACCACGAGATTGTAAAG                         AAACTGGAGGGCATGCAGTGGACAATTCACCAGGTGGAGATGGACCTGAAA
genomic: TAGATCCACGGTTCGATGTGATTGCGAGGCAGTACCACGAGATTGTAAAGgtaatctggc ... gcttcatcagAAACTGGAGGGCATGCAGTGGACAATTCACCAGGTGGAGATGGACCTGAAA
EST: gi|32802117|gb|CD954353.1|CD954353
EST:     GATCCACGGTTCGATGTGATTGCAAGGCAGTACCACGAGATTGTAAAG                         AAACTGGAGGGCATGCAGTGGACAATTCACCAGGTGGAGATGGACCTGAAA
genomic: GATCCACGGTTCGATGTGATTGCGAGGCAGTACCACGAGATTGTAAAGgtaatctggc ... gcttcatcagAAACTGGAGGGCATGCAGTGGACAATTCACCAGGTGGAGATGGACCTGAAA
EST: gi|50331676|gb|CO526802.1|CO526802
EST:     TAGATCCACGGTTCGATGTGATTGCGAGGCAGTACCACGAGATTGTAAAG                         AAACTGGAGGGCATGCAGTGGACAATTCACCAGGTGGAGATGGACCTGAAA
genomic: TAGATCCACGGTTCGATGTGATTGCGAGGCAGTACCACGAGATTGTAAAGgtaatctggc ... gcttcatcagAAACTGGAGGGCATGCAGTGGACAATTCACCAGGTGGAGATGGACCTGAAA
EST: gi|32796987|gb|CD949223.1|CD949223
EST:     GATCCCCGGTTCGATGTGATTGCAAGGCAGTACCACGAGATTGTAAAG                         AAACTGGAGGGCATGCAGTGGACAATTCACCAGGTGGAGATGGACCTGAAA
genomic: GATCCACGGTTCGATGTGATTGCGAGGCAGTACCACGAGATTGTAAAGgtaatctggc ... gcttcatcagAAACTGGAGGGCATGCAGTGGACAATTCACCAGGTGGAGATGGACCTGAAA
EST: gi|110488821|gb|EE012728.1|EE012728
EST:     TAGATCCACGGTTCGATGTGATTGCGAGGCAGTACCACGAGATTGTAAAG                         AAACTGGAGGGCATGCAGTGGACAATTCACCAGGTGGAGATGGACCTGAAA
genomic: TAGATCCACGGTTCGATGTGATTGCGAGGCAGTACCACGAGATTGTAAAGgtaatctggc ... gcttcatcagAAACTGGAGGGCATGCAGTGGACAATTCACCAGGTGGAGATGGACCTGAAA
EST: gi|32806979|gb|CD959213.1|CD959213
EST:     GATCTACGGTTCGATGTGATTGCAAGGCAGTACCACGAGATTGTAAAG                         AAACTGGAGGGCATGCAGTGGACAATTCACCAGGTGGAGATGGACCTGAAA
genomic: GATCCACGGTTCGATGTGATTGCGAGGCAGTACCACGAGATTGTAAAGgtaatctggc ... gcttcatcagAAACTGGAGGGCATGCAGTGGACAATTCACCAGGTGGAGATGGACCTGAAA
EST: gi|45568053|gb|CK985878.1|CK985878
EST:     TAGATCCACGGTTCGATGTGATTGCGAGGCAGTACCACGAGATTGTAAAG                         AAACTGGAGGGCATGCAGTGGACAATTCACCAGGTGGAGATGGACCTGAAA
genomic: TAGATCCACGGTTCGATGTGATTGCGAGGCAGTACCACGAGATTGTAAAGgtaatctggc ... gcttcatcagAAACTGGAGGGCATGCAGTGGACAATTCACCAGGTGGAGATGGACCTGAAA
EST: gi|32797216|gb|CD949452.1|CD949452
EST:     GATCCACGGTTCGATGTGATTGCAAGGCAGTACCACGAGATTGTAAAG                         AAACTGGAGGGCATGCAGTGGACAATTCACCAGGTGGAGATGGACCTGAAA
genomic: GATCCACGGTTCGATGTGATTGCGAGGCAGTACCACGAGATTGTAAAGgtaatctggc ... gcttcatcagAAACTGGAGGGCATGCAGTGGACAATTCACCAGGTGGAGATGGACCTGAAA
EST: gi|148948940|gb|EC894359.2|EC894359
EST:     TAGATCCACGGTTCGATGTGATTGCGAGGCAGTACCACGAGATTGTAAAG                         AAACTGGAGGGCATGCAGTGGACAATTCACCAGGTGGAGATGGACCTGAAA
genomic: TAGATCCACGGTTCGATGTGATTGCGAGGCAGTACCACGAGATTGTAAAGgtaatctggc ... gcttcatcagAAACTGGAGGGCATGCAGTGGACAATTCACCAGGTGGAGATGGACCTGAAA
EST: gi|32797109|gb|CD949345.1|CD949345
EST:     GATCCGCGGTTCGATGTGATTGCAAGGCAGTACCACGAGATTGTAAAG                         AAACTGGAGGGCATGCAGTGGACAATTCACCAGGTGGAGATGGACCTGAAA
genomic: GATCCACGGTTCGATGTGATTGCGAGGCAGTACCACGAGATTGTAAAGgtaatctggc ... gcttcatcagAAACTGGAGGGCATGCAGTGGACAATTCACCAGGTGGAGATGGACCTGAAA
EST: gi|110504829|gb|EE017437.1|EE017437
EST:     TAGATCCACGGTTCGATGTGATTGCGAGGCAGTACCACGAGATTGTAAAG                         AAACTGGAGGGCATGCAGTGGACAATTCACCAGGTGGAGATGGACCTGAAA
genomic: TAGATCCACGGTTCGATGTGATTGCGAGGCAGTACCACGAGATTGTAAAGgtaatctggc ... gcttcatcagAAACTGGAGGGCATGCAGTGGACAATTCACCAGGTGGAGATGGACCTGAAA
EST: gi|60347346|gb|DN214319.1|DN214319
EST:     TAGATCCACGGTTCGATGTGATTGCGAGGCAGTACCACGAGATTGTAAAG                         AAACTGGAGGGCATGCAGTGGACAATTCACCAGGTGGAGATGGACCTGAAA
genomic: TAGATCCACGGTTCGATGTGATTGCGAGGCAGTACCACGAGATTGTAAAGgtaatctggc ... gcttcatcagAAACTGGAGGGCATGCAGTGGACAATTCACCAGGTGGAGATGGACCTGAAA
EST: gi|50324448|gb|CO519574.1|CO519574
EST:     TAGATCCACGGTTCGATGTGATTGCGAGGCAGTACCACGAGATTGTAAAG                         AAACTGGAGGGCATGCAGTGGACAATTCACCAGGTGGAGATGGACCTGAAA
genomic: TAGATCCACGGTTCGATGTGATTGCGAGGCAGTACCACGAGATTGTAAAGgtaatctggc ... gcttcatcagAAACTGGAGGGCATGCAGTGGACAATTCACCAGGTGGAGATGGACCTGAAA
EST: gi|211359065|gb|FL430712.1|FL430712
EST:     TAGATCCACGGTTCGATGTGATTGCGAGGCAGTACCACGAGATTGTAAAG                         AAACTGGAGGGCATGCAGTGGACAATTCACCAGGTGGAGATGGACCTGAAA
genomic: TAGATCCACGGTTCGATGTGATTGCGAGGCAGTACCACGAGATTGTAAAGgtaatctggc ... gcttcatcagAAACTGGAGGGCATGCAGTGGACAATTCACCAGGTGGAGATGGACCTGAAA
EST: gi|44900277|gb|CK826822.1|CK826822
EST:     TAGATCCACGGTTCGATGTGATTGCGAGGCAGTACCACGAGATTGTAAAG                         AAACTGGAGGGCATGCAGTGGACAATTCACCAGGTGGAGATGGACCTGAAA
genomic: TAGATCCACGGTTCGATGTGATTGCGAGGCAGTACCACGAGATTGTAAAGgtaatctggc ... gcttcatcagAAACTGGAGGGCATGCAGTGGACAATTCACCAGGTGGAGATGGACCTGAAA
EST: gi|5915607|gb|AW053248.1|AW053248
EST:     TAGATCCACGGTTCGATGTGATTGCGAGGCAGTACCACGAGATTGTAAAG                         AAACTGGAGGGCATGCAGTGGACAATTCACCAGGTGGAGATGGACCTGAAA
genomic: TAGATCCACGGTTCGATGTGATTGCGAGGCAGTACCACGAGATTGTAAAGgtaatctggc ... gcttcatcagAAACTGGAGGGCATGCAGTGGACAATTCACCAGGTGGAGATGGACCTGAAA
EST: gi|211478808|gb|FL379717.1|FL379717
EST:     TAGATCCACGGTTCGATGTGATTGCGAGGCAGTACCACGAGATTGTAAAG                         AAACTGGAGGGCATGCAGTGGACAATTCACCAGGTGGAGATGGACCTGAAA
genomic: TAGATCCACGGTTCGATGTGATTGCGAGGCAGTACCACGAGATTGTAAAGgtaatctggc ... gcttcatcagAAACTGGAGGGCATGCAGTGGACAATTCACCAGGTGGAGATGGACCTGAAA
EST: gi|74237081|gb|DT644995.1|DT644995
EST:     TAGATCCACGGTTCGATGTGATTGCGAGGCAGTACCACGAGATTGTAAAG                         AAACTGGAGGGCATGCAGTGGACAATTCACCAGGTGGAGATGGACCTGAAA
genomic: TAGATCCACGGTTCGATGTGATTGCGAGGCAGTACCACGAGATTGTAAAGgtaatctggc ... gcttcatcagAAACTGGAGGGCATGCAGTGGACAATTCACCAGGTGGAGATGGACCTGAAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agtttaccgtatgtttttacttgctaagttgctaaccctggtcgagcttcatcagAAACTGGAGGGCATGCAGTGGACAATTCACCAGGTGGAGATGGACCTGAAACCTCACCATGACCACGCAGCTGTTTAAGTCCACATCTGTTGGAGGCCAT
                             tgctaac  putative branch site (score: 1)
 cttcatc  putative PPT
 tatgttttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaatctggctcagtgttgctgccactagtttaccgtatgtttttacttgctaagttgctaaccctggtcgagcttcatcagAAACTGGAGGGCATGCAGTGGACAATTCACCAGGTGGAGATGGACCTGAAACCTCACCATGACCACGCAGCTGTTTAAGTCCACATCTGTTGGAGGCCAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG