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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atctactgatgaattccttgactttaaattggtatttgtgaggtgtatagcaccagcaggacaatgtttagttcatatcatcttttgacagtatatttagGTTCCAGGAATTGTCTTTGCAAGAGGGCCCGCGGTTGCTGTGTTGATTCTTTTGGAGTCGAATGGAGAAACATATGCTGTGCTTACCGAACAG

Basic information

species Zea mays
transcript GRMZM2G069008_T03
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G069008_T04 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os06g03910.1 (Oryza sativa), 3'ss of exon 2
-atctactgatgaattccttgactttaaattggtatttgtgaggtgtatagcaccagcaggaca-atgtttagttcatatcatcttttgacagtatatttagGTTCCAGGAATTGTCTTTGCAAGAGGGCCCGCGGTTGCTGTGTTGATTCTTTTGGAGTCGAATGGAGAAACATATGCTGTGCTTACCGAACAG
 ||    ||  | ||   |||| ||  |  ||||  ||||   |  |  |     ||| |      ||| || |  || |    |||||||| |||||  || ||||||||||||| |||||||||||||| || |||||||||||||||||||||||||| || ||  |||| || ||||| ||||| ||||||
tattccttgtagcatg--ttgaattagatgtggtcgttgtataggattcaaagtaagcggattttgtgtgtattatattttgagttttgacaatatatccagATTCCAGGAATTGTATTTGCAAGAGGGCCTGCTGTTGCTGTGTTGATTCTTTTGGAGTCTAAAGGGCAAACTTACGCTGTTCTTACAGAACAG

upper sequence: GRMZM2G069008_T04 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA05G04150.1 (Glycine max), 3'ss of exon 3
------------------------------------------------atctactgatgaattccttga-ctttaaattggtatttgtgaggtgta----tagcaccagcaggac-aatgtttagttcatatcatcttttgaca-----gtatatttagGTTCCAGGAATTGTCTTTGCAAGAGGGCCCGCGGTTGCTGTGTTGATTCTTTTGGAGTCGAATGGAGAAACATATGCTGTGCTTACCGAACAG
                                                 | |  |  | |   |  ||| ||   ||   ||||   |   || ||    |||    || |   | |||| | | |||||    |  | | | |     | ||  |||||||||||| ||||| ||||||||||| || || || ||||||||||| ||  |||| ||  | || || || |||||||| ||||| ||||||
gtatgagatggtttacatacaagtataaatctatgttggcatgttttcctgtgttagtaatggcagtgagctgcgaaccagtatgcatattgtctacttttagacttagtacacctaatgctgatttcattcttttatattaaactaaagcattattagGTTCCAGGTATTGTGTTTGCAAGAGGACCAGCTGTGGCTGTGTTGATGCTCCTGGAATCAGAGGGTGAGACTTATGCTGTTCTTACTGAACAG
















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|76926121|gb|DV170728.1|DV170728
EST:     GCTTTCTCAAGTTCAAGGCTGATATCGTGGACGAGGAAACCAAAACCAAG                         GTTCCAGGAATTGTCTTTGCAAGAGGGCCCGCGGTTGCTGTGTTGATTCTT
genomic: GCTTTCTCAAGTTCAAGGCTGATATCGTGGACGAGGAAACCAAAACCAAGgtgattgctt ... gtatatttagGTTCCAGGAATTGTCTTTGCAAGAGGGCCCGCGGTTGCTGTGTTGATTCTT
EST: gi|211274431|gb|FL232523.1|FL232523
EST:     GCTTTCTCAAGTTCAAGGCTGATATCGTGGACGAGGAAACCAAAACCAAG                         GTTCCAGGAATTGTCTTTGCAAGAGGGCCCGCGGTTGCTGTGTTGATTCTT
genomic: GCTTTCTCAAGTTCAAGGCTGATATCGTGGACGAGGAAACCAAAACCAAGgtgattgctt ... gtatatttagGTTCCAGGAATTGTCTTTGCAAGAGGGCCCGCGGTTGCTGTGTTGATTCTT
EST: gi|149096586|gb|EE182344.2|EE182344
EST:     GCTTTCTCAAGTTCAAGGCTGATATCGTGGACGAGGAAACCAAAACCAAG                         GTTCCAGGAATTGTCTTTGCAAGAGGGCCCGCGGTTGCTGTGTTGATTCTT
genomic: GCTTTCTCAAGTTCAAGGCTGATATCGTGGACGAGGAAACCAAAACCAAGgtgattgctt ... gtatatttagGTTCCAGGAATTGTCTTTGCAAGAGGGCCCGCGGTTGCTGTGTTGATTCTT
EST: gi|211274434|gb|FL232526.1|FL232526
EST:     GCTTTCTCAAGTTCAAGGCTGATATCGTGGACGAGGAAACCAAAACCAAG                         GTTCCAGGAATTGTCTTTGCAAGAGGGCCCGCGGTTGCTGTGT
genomic: GCTTTCTCAAGTTCAAGGCTGATATCGTGGACGAGGAAACCAAAACCAAGgtgattgctt ... gtatatttagGTTCCAGGAATTGTCTTTGCAAGAGGGCCCGCGGTTGCTGTGT
EST: gi|211274435|gb|FL232527.1|FL232527
EST:     GCTTTCTCAAGTTCAAGGCTGATATCGTGGACGAGGAAACCAAAACCAAG                         GTTCCAGGAATTGTCTTTGCAAGAGGG
genomic: GCTTTCTCAAGTTCAAGGCTGATATCGTGGACGAGGAAACCAAAACCAAGgtgattgctt ... gtatatttagGTTCCAGGAATTGTCTTTGCAAGAGGG
EST: gi|211274436|gb|FL232528.1|FL232528
EST:     GCTTTCTCAAGTTCAAGGCTGATATCGTGGACGAGGAAACCAAAACCAAG                         GTTCCAGGAATTGTCTTTGCAAGAKGGCCCGCGGTTGCTGTGTTGATTC
genomic: GCTTTCTCAAGTTCAAGGCTGATATCGTGGACGAGGAAACCAAAACCAAGgtgattgctt ... gtatatttagGTTCCAGGAATTGTCTTTGCAAGAGGGCCCGCGGTTGCTGTGTTGATTC
EST: gi|149074765|gb|EE163195.2|EE163195
EST:     GCTTTCTCAAGTTCAAGGCTGATATCGTGGACGAGGAAACCAAAACCAAG                         GTTCCAGGAATTGTCTTTGCAAGAGGGCCCGCGGTTGCTGTGTTGATTCTT
genomic: GCTTTCTCAAGTTCAAGGCTGATATCGTGGACGAGGAAACCAAAACCAAGgtgattgctt ... gtatatttagGTTCCAGGAATTGTCTTTGCAAGAGGGCCCGCGGTTGCTGTGTTGATTCTT
EST: gi|211274445|gb|FL232537.1|FL232537
EST:     GCCTTCTCAAGTTCAAGGCTGATATCGTGGACGAGGAAACCAAAACCAAG                         GTTCCAGGAATTGTCTTTGCAAGAGGGCCTGCGGTTGCTG
genomic: GCTTTCTCAAGTTCAAGGCTGATATCGTGGACGAGGAAACCAAAACCAAGgtgattgctt ... gtatatttagGTTCCAGGAATTGTCTTTGCAAGAGGGCCCGCGGTTGCTG
EST: gi|211274441|gb|FL232533.1|FL232533
EST:     GCTTTCTCAAGTTCAAGGCTGATATCGTGGACGAGGAAACCAAAACCAAG                         GTTCCAGGAATTGTCTTTGCAAGAGGGCCCG
genomic: GCTTTCTCAAGTTCAAGGCTGATATCGTGGACGAGGAAACCAAAACCAAGgtgattgctt ... gtatatttagGTTCCAGGAATTGTCTTTGCAAGAGGGCCCG
EST: gi|78087424|gb|DV515817.1|DV515817
EST:     GCTTTCTCAAGTTCAAGGCTGATATCGTGGACGAGGAAACCAAAACCAAG                         GTTCCAGGAATTGTCTTTGCAAGAGGGCCCGCGGTTGCTGTGTTGATTCTT
genomic: GCTTTCTCAAGTTCAAGGCTGATATCGTGGACGAGGAAACCAAAACCAAGgtgattgctt ... gtatatttagGTTCCAGGAATTGTCTTTGCAAGAGGGCCCGCGGTTGCTGTGTTGATTCTT
EST: gi|211276250|gb|FL232539.1|FL232539
EST:     GCTTTCTCAAGTTCAAGGCTGATATCGTGGACGAGGAAACCAAAACCAAG                         GTTCCAGGAATTGTCTTTGCAAGAGGGCCCGCGGTTGCTGTGTTGATTCTT
genomic: GCTTTCTCAAGTTCAAGGCTGATATCGTGGACGAGGAAACCAAAACCAAGgtgattgctt ... gtatatttagGTTCCAGGAATTGTCTTTGCAAGAGGGCCCGCGGTTGCTGTGTTGATTCTT
EST: gi|6021120|gb|AW066048.1|AW066048
EST:     GCTTTCTCAAGTTCAAGGCTGATATCGTGGACGAGGAAACCAAAACCAAG                         GTTCCAGGAATTGTCTTTGCAAGAGGGCCCGCGGTTGCTGTGTTGATTCTT
genomic: GCTTTCTCAAGTTCAAGGCTGATATCGTGGACGAGGAAACCAAAACCAAGgtgattgctt ... gtatatttagGTTCCAGGAATTGTCTTTGCAAGAGGGCCCGCGGTTGCTGTGTTGATTCTT
EST: gi|148942502|gb|EC887517.2|EC887517
EST:     GCTTTCTCAAGTTCAAGGCTGATATCGTGGACGAGGAAACCAAAACCAAG                         GTTCCAGGAATTGTCTTTGCAAGAGGGCCCGCGGTTGCTGTGTTGATTCTT
genomic: GCTTTCTCAAGTTCAAGGCTGATATCGTGGACGAGGAAACCAAAACCAAGgtgattgctt ... gtatatttagGTTCCAGGAATTGTCTTTGCAAGAGGGCCCGCGGTTGCTGTGTTGATTCTT
EST: gi|91054277|gb|EB164695.1|EB164695
EST:     AACCAAAACCAAG                         GTTCCAGGAATTGTCTTTGCAAGAGGGCCCGCGGTTGCTGTGTTGATTCTT
genomic: AACCAAAACCAAGgtgattgctt ... gtatatttagGTTCCAGGAATTGTCTTTGCAAGAGGGCCCGCGGTTGCTGTGTTGATTCTT
EST: gi|211274437|gb|FL232529.1|FL232529
EST:     GCTTTCTCAAGTTCAAGGCTGATATCGTGGACGAGGAAACCAAAACCAAG                         GTTCCAGGAATTGTCTTTGCAAGAGGGCCCGCGGTTGCTGTGTTGATTCTT
genomic: GCTTTCTCAAGTTCAAGGCTGATATCGTGGACGAGGAAACCAAAACCAAGgtgattgctt ... gtatatttagGTTCCAGGAATTGTCTTTGCAAGAGGGCCCGCGGTTGCTGTGTTGATTCTT
EST: gi|67016855|gb|CO445604.1|CO445604
EST:     GCTTTCTCAAGTTCAAGGCTGATATCGTGGACGAGGAAACCAAAACCAAG                         GTTCCAGGAATTGTCTTTGCAAGAGGGCCCGCGGTTGCTGTGTTGATTCTT
genomic: GCTTTCTCAAGTTCAAGGCTGATATCGTGGACGAGGAAACCAAAACCAAGgtgattgctt ... gtatatttagGTTCCAGGAATTGTCTTTGCAAGAGGGCCCGCGGTTGCTGTGTTGATTCTT
EST: gi|148991430|gb|EE032932.2|EE032932
EST:     GCTTTCTCAAGTTCAAGGCTGATATCGTGGACGAGGAAACCAAAACCAAG                         GTTCCAGGAATTGTCTTTGCAAGAGGGCCCGCGGTTGCTGTGTTGATTCTT
genomic: GCTTTCTCAAGTTCAAGGCTGATATCGTGGACGAGGAAACCAAAACCAAGgtgattgctt ... gtatatttagGTTCCAGGAATTGTCTTTGCAAGAGGGCCCGCGGTTGCTGTGTTGATTCTT
EST: gi|211274440|gb|FL232532.1|FL232532
EST:     GCTTTCTCAAGTTCAAGGCTGATATCGTGGACGAGGAAACCAAAACCAAG                         GTTCCAGGAATTGTCTTTGCAAGAGGGCCCGCGGTTGCTGTGTTGATTCTT
genomic: GCTTTCTCAAGTTCAAGGCTGATATCGTGGACGAGGAAACCAAAACCAAGgtgattgctt ... gtatatttagGTTCCAGGAATTGTCTTTGCAAGAGGGCCCGCGGTTGCTGTGTTGATTCTT
EST: gi|148942503|gb|EC887518.2|EC887518
EST:     GCTTTCTCAAGTTCAAGGCTGATATCGTGGACGAGGAAACCAAAACCAAG                         GTTCCAGGAATTGTCTTTGCAAGAGGGCCCGCGGTTGCTGTGTTGATTCTT
genomic: GCTTTCTCAAGTTCAAGGCTGATATCGTGGACGAGGAAACCAAAACCAAGgtgattgctt ... gtatatttagGTTCCAGGAATTGTCTTTGCAAGAGGGCCCGCGGTTGCTGTGTTGATTCTT
EST: gi|149096585|gb|EE182343.2|EE182343
EST:     GCTTTCTCAAGTTCAAGGCTGATATCGTGGACGAGGAAACCAAAACCAAG                         GTTCCAGGAATTGTCTTTGCAAGAGGGCCCGCGGTTGCTGTGTTGATTCTT
genomic: GCTTTCTCAAGTTCAAGGCTGATATCGTGGACGAGGAAACCAAAACCAAGgtgattgctt ... gtatatttagGTTCCAGGAATTGTCTTTGCAAGAGGGCCCGCGGTTGCTGTGTTGATTCTT
EST: gi|149111714|gb|EE190861.2|EE190861
EST:     GCTTTCTCAAGTTCAAGGCTGATATCGTGGACGAGGAAACCAAAACCAAG                         GTTCCAGGAATTGTCTTTGCAAGAGGGCCCGCGGTTGCTGTGTTGATTCTT
genomic: GCTTTCTCAAGTTCAAGGCTGATATCGTGGACGAGGAAACCAAAACCAAGgtgattgctt ... gtatatttagGTTCCAGGAATTGTCTTTGCAAGAGGGCCCGCGGTTGCTGTGTTGATTCTT
EST: gi|67042992|gb|CO469247.1|CO469247
EST:     GCTTTCTCAAGTTCAAGGCTGATATCGTGGACGAGGAAACCAAAACCAAG                         GTTCCAGGAATTGTCTTTGCAAGAGGGCCCGCGGTTGCTGTGTTGATTCTT
genomic: GCTTTCTCAAGTTCAAGGCTGATATCGTGGACGAGGAAACCAAAACCAAGgtgattgctt ... gtatatttagGTTCCAGGAATTGTCTTTGCAAGAGGGCCCGCGGTTGCTGTGTTGATTCTT
EST: gi|78082237|gb|DV510649.1|DV510649
EST:     GCTTTCTCAAGTTCAAGGCTGATATCGTGGACGAGGAAACCAAAACCAAG                         GTTCCAGGAATTGTCTTTGCAAGAGGGCCCGCGGTTGCTGTGTTGATTCTT
genomic: GCTTTCTCAAGTTCAAGGCTGATATCGTGGACGAGGAAACCAAAACCAAGgtgattgctt ... gtatatttagGTTCCAGGAATTGTCTTTGCAAGAGGGCCCGCGGTTGCTGTGTTGATTCTT
EST: gi|15313833|gb|BI478977.1|BI478977
EST:     GCTTTCTCAAGTTCAAGGCTGATATCGTGGACGAGGAAACCAAAACCAAG                         GTTCCAGGAATTGTCTTTGCAAGAGGGCCCGCGGTTGCTGTGTTGATTCTT
genomic: GCTTTCTCAAGTTCAAGGCTGATATCGTGGACGAGGAAACCAAAACCAAGgtgattgctt ... gtatatttagGTTCCAGGAATTGTCTTTGCAAGAGGGCCCGCGGTTGCTGTGTTGATTCTT
EST: gi|29543762|gb|CB604142.1|CB604142
EST:     GCTTTCTCAAGTTCAAGGCTGATATCGTGGACGAGGAAACCAAAACCAAG                         GTTCCAGGAATTGTCTTTGCAAGAGGGCCCGCGGTTGCTGTGTTGATTCTT
genomic: GCTTTCTCAAGTTCAAGGCTGATATCGTGGACGAGGAAACCAAAACCAAGgtgattgctt ... gtatatttagGTTCCAGGAATTGTCTTTGCAAGAGGGCCCGCGGTTGCTGTGTTGATTCTT
EST: gi|31355362|gb|CD439719.1|CD439719
EST:     TCTTTCTCAAGTTCAAGGCTGATATCGTGGACGAGGAAACCAAAACCAAG                         GTTCCAGGAATTGTCTTTGCAAGAGGGCCCGCGGTTGCTGTGTTGATTCTT
genomic: GCTTTCTCAAGTTCAAGGCTGATATCGTGGACGAGGAAACCAAAACCAAGgtgattgctt ... gtatatttagGTTCCAGGAATTGTCTTTGCAAGAGGGCCCGCGGTTGCTGTGTTGATTCTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatagcaccagcaggacaatgtttagttcatatcatcttttgacagtatatttagGTTCCAGGAATTGTCTTTGCAAGAGGGCCCGCGGTTGCTGTGTTGATTCTTTTGGAGTCGAATGGAGAAACATATGCTGTGCTTACCGAACAG
                                     ttttgac  putative branch site (score: 3)
                                            agtatattta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atctactgatgaattccttgactttaaattggtatttgtgaggtgtatagcaccagcaggacaatgtttagttcatatcatcttttgacagtatatttagGTTCCAGGAATTGTCTTTGCAAGAGGGCCCGCGGTTGCTGTGTTGATTCTTTTGGAGTCGAATGGAGAAACATATGCTGTGCTTACCGAACAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG