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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagtttgtacacatttgactgctactaatatgatgaattatttgcatgcctatctcatgatcagttgtacttaacttttttcttggtaattttatacgacagGTGACACACAGCATGCAAGTTCCTCTTTCCTATGCTGATGCTGTGATAGGGGCAGCTGGTGCCAGTATCAGCTACATCCGCAGGCATAGTGGAGCAACTA

Basic information

species Zea mays
transcript GRMZM2G130095_T02
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G130095_T02 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os12g40560.1 (Oryza sativa), 3'ss of exon 5
gttagtttgtacacatttgactgctactaatatgatgaattatttgcatgcctatctcatgatcagttgtacttaacttttttct-----tggtaattttatacgacagGTGACACACAGCATGCAAGTTCCTCTTTCCTATGCTGATGCTGTGATAGGGGCAGCTGGTGCCAGTATCAGCTACATCCGCAGGCATAGTGGAGCAACTA
|||||||  || | |||||||  ||   || || ||||| | |||    ||||     |   |   || |||| |  |||   |      || |  ||||||  ||||| | ||||||||||||||||||||||||||||| |||||||| ||||| |||||||||||||| |||||||||||||| |||||||||||||| ||||| |
gttagttgctaaaaatttgaccactgtgaacataatgaactgtttatgcgcctgctataaagtttcttttactgagttttcccccatatatgttgtttttatttgacagATAACACACAGCATGCAAGTTCCTCTTTCCTACGCTGATGCCGTGATTGGGGCAGCTGGTGCTAGTATCAGCTACATTCGCAGGCATAGTGGTGCAACAA

upper sequence: GRMZM2G130095_T02 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA19G43540.1 (Glycine max), 3'ss of exon 5
--gttagtttgtacacatttgactgctactaatatgatgaattatttgcatgcctatctcatgatcagttgtacttaacttttttcttggtaattttatacgacagGTGACACACAGCATGCAAGTTCCTCTTTCCTATGCTGATGCTGTGATAGGGGCAGCTGGTGCCAGTATCAGCTACATCCGCAGGCATAGTGGAGCAACTA
  || |    ||| | | ||   ||   || |  |  ||   | | |  |    |||  | |  |   |  ||   |    |||| ||| || |||     | ||| | || ||    |||||| ||||||| || |||||||||||||| || ||  ||||||| || ||||| ||||||||| |  |   |||||| || ||| 
aggtgatgcagtatatacttatatggacctgagttcctgttctttata-aaatttattactttttttatcataaagattaattttgttgttatttt-----ggcagATCACGCAGCAAATGCAAATTCCTCTATCTTATGCTGATGCTGTTATTGGAACAGCTGGAGCAAGTATAAGCTACATCAGACGAGCTAGTGGGGCTACTG

upper sequence: GRMZM2G130095_T02 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA03G40840.1 (Glycine max), 3'ss of exon 5
gttagtttgtacacatttgactgctactaatatgatgaattatttgcatgcctatctcatgatcagttgtacttaacttttttcttggtaattttatacgacagGTGACACACAGCATGCAAGTTCCTCTTTCCTATGCTGATGCTGTGATAGGGGCAGCTGGTGCCAGTATCAGCTACATCCGCAGGCATAGTGGAGCAACTA
|| |     || | | ||   ||   || || |  ||   | |||  |    | | | |   |   ||   | |||   |    ||  |   | | |  | ||| | || ||    |||||| ||||||| || |||||||||||||| || ||  ||||||| || ||||| ||||||||| |  |   |||||| || ||| 
gtgatgcaatatatacttatatggacctgatttcctg--ctctttataaattt-tattacctttttttaatcataaagatggattttattgctat-tgtggcagATCACGCAGCAAATGCAAATTCCTCTATCTTATGCTGATGCTGTTATTGGAACAGCTGGAGCAAGTATAAGCTACATCAGACGAGCTAGTGGGGCTACTG

upper sequence: GRMZM2G130095_T02 (Zea mays), 3'ss of exon 3
lower sequence: Vv07s0141g00800.t01 (Vitis vinifera), 3'ss of exon 5
gttagtttgtacacatttgactgctactaatatgatgaattatttgcatgcctatctcatgatcagttgtac-ttaacttttttcttggtaattttatacgacagGTGACACACAGCATGCAAGTTCCTCTTTCCTATGCTGATGCTGTGATAGGGGCAGCTGGTGCCAGTATCAGCTACATCCGCAGGCATAGTGGAGCAACTA
   |  ||| |  || ||  ||  || |   |  |   |||  |  ||    | |  |||       | ||  ||   | ||    ||||  ||   | |   || | |||||   ||||||||||||||| || ||||| |||||||| || |||||| ||||||  | ||| |||||  | ||| |    ||||| |||||||
aagaagttgcaagcagttc-ctattattttcacaac--attggtcacaattttttgacatatctgactttatgtttgatgttgctgtggtggtt--gttctgtagATCACACAGTACATGCAAGTTCCTCTATCATATGCAGATGCTGTAATTGGGGCATCTGGTGTAAATATAAGCTATGTACGCCGTACCAGTGGGGCAACTA

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|166565990|gb|EG281697.1|EG281697
EST:     CTCCAAGTGCTCCCCCAGGGAATCAAAACCAAGCACATGGGTCATCTCAG                         GTGACACACAGCAT
genomic: CTCCAAGTGCTCCCCCAGGGAATCAAAACCAAGCACATGGGTCATCTCAGgttagtttgt ... tatacgacagGTGACACACAGCAT
EST: gi|60397306|gb|DN230122.1|DN230122
EST:     CTCCAAGTGCTCCCCCAGGGAATCAAAACCAAGCACATGGGTCATCTCAG                         GTGACACACAGCATGCAAGTTCCTCTTTCCTATGCTGATGCTGTGATAGGG
genomic: CTCCAAGTGCTCCCCCAGGGAATCAAAACCAAGCACATGGGTCATCTCAGgttagtttgt ... tatacgacagGTGACACACAGCATGCAAGTTCCTCTTTCCTATGCTGATGCTGTGATAGGG
EST: gi|211479578|gb|FL296090.1|FL296090
EST:     CTCCAAGTGCTCCCCCASGGAATCAAAACCAAGCACATGGGTCATCTCAG                         GTGACACACAGCATGCAAGTTCCTCTTTCCTATGCTGATGCTGTGATAGGG
genomic: CTCCAAGTGCTCCCCCAGGGAATCAAAACCAAGCACATGGGTCATCTCAGgttagtttgt ... tatacgacagGTGACACACAGCATGCAAGTTCCTCTTTCCTATGCTGATGCTGTGATAGGG
EST: gi|78024287|gb|DV492674.1|DV492674
EST:     ATCAAAACCAAGCACATGGGTCATCTCAG                         GTGACACACAGCATGCAAGTTCCTCTTTCCTATGCTGATGCTGTGATAGGG
genomic: ATCAAAACCAAGCACATGGGTCATCTCAGgttagtttgt ... tatacgacagGTGACACACAGCATGCAAGTTCCTCTTTCCTATGCTGATGCTGTGATAGGG
EST: gi|76016914|gb|DT944084.1|DT944084
EST:     AAACCAAGCACATGGGTCATCTCAG                         GTGACACACAGCATGCAAGTTCCTCTTTCCTATGCTGATGCTGTGATAGGG
genomic: AAACCAAGCACATGGGTCATCTCAGgttagtttgt ... tatacgacagGTGACACACAGCATGCAAGTTCCTCTTTCCTATGCTGATGCTGTGATAGGG
EST: gi|78023469|gb|DV491856.1|DV491856
EST:     TCAAAACCAAGCACATGGGTCATCTCAG                         GTGACACACAGCATGCAAGTTCCTCTTTCCTATGCTGATGCTGTGATAGGG
genomic: TCAAAACCAAGCACATGGGTCATCTCAGgttagtttgt ... tatacgacagGTGACACACAGCATGCAAGTTCCTCTTTCCTATGCTGATGCTGTGATAGGG
EST: gi|32856049|gb|CD995730.1|CD995730
EST:     GGGTCATCTCAG                         GTGACACACAGCATGCAAGTTCCTCTTTCCTATGCTGATGCTGTGATAGGG
genomic: GGGTCATCTCAGgttagtttgt ... tatacgacagGTGACACACAGCATGCAAGTTCCTCTTTCCTATGCTGATGCTGTGATAGGG
EST: gi|5069761|gb|AI737726.1|AI737726
EST:     TGCTCCCCCAGGGAATCAAAACCAAGCACATGGGTCATCTCAG                         GTGACACACAGCATGCAAGTTCCTCTTTCCTATGCTGATGCTGTGATAGGG
genomic: TGCTCCCCCAGGGAATCAAAACCAAGCACATGGGTCATCTCAGgttagtttgt ... tatacgacagGTGACACACAGCATGCAAGTTCCTCTTTCCTATGCTGATGCTGTGATAGGG
EST: gi|149003743|gb|EE038968.2|EE038968
EST:     CCAAGTGCTCCCCCAGGGAATCAAAACCAAGCACATGGGTCATCTCAG                         GTGACACACAGCATGCAAGTTCCTCTTTCCTATGCTGATGCTGTGATAGGG
genomic: CCAAGTGCTCCCCCAGGGAATCAAAACCAAGCACATGGGTCATCTCAGgttagtttgt ... tatacgacagGTGACACACAGCATGCAAGTTCCTCTTTCCTATGCTGATGCTGTGATAGGG
EST: gi|60343040|gb|DN210013.1|DN210013
EST:     CTCCAAGTGCTCCCCCAGGGAATCAAAACCAAGCACATGGGTCATCTCAG                         GTGACACACAGCATGCAAGTTCCTCTTTCCTATGCTGATGCTGTGATAGGG
genomic: CTCCAAGTGCTCCCCCAGGGAATCAAAACCAAGCACATGGGTCATCTCAGgttagtttgt ... tatacgacagGTGACACACAGCATGCAAGTTCCTCTTTCCTATGCTGATGCTGTGATAGGG
EST: gi|74234411|gb|DT642325.1|DT642325
EST:     CTCCAAGTGCTCCCCCAGGGAATCAAAACCAAGCACATGGGTCATCTCAG                         GTGACACACAGCATGCAAGTTCCTCTTTCCTATGCTGATGCTGTGATAGGG
genomic: CTCCAAGTGCTCCCCCAGGGAATCAAAACCAAGCACATGGGTCATCTCAGgttagtttgt ... tatacgacagGTGACACACAGCATGCAAGTTCCTCTTTCCTATGCTGATGCTGTGATAGGG
EST: gi|18162011|gb|BM331850.1|BM331850
EST:     AAGTGCTCCCCCAGGGAATCAAAACCAAGCACATGGGTCATCTCAG                         GTGACACACAGCATGCAAGTTCCTCTTTCCTATGCTGATGCTGTGATAGGG
genomic: AAGTGCTCCCCCAGGGAATCAAAACCAAGCACATGGGTCATCTCAGgttagtttgt ... tatacgacagGTGACACACAGCATGCAAGTTCCTCTTTCCTATGCTGATGCTGTGATAGGG
EST: gi|60357837|gb|DN224810.1|DN224810
EST:     CTCCAAGTGCTCCCCCAGGGAATCAAAACCAAGCACATGGGTCATCTCAG                         GTGACACACAGCATGCAAGTTCCTCTTTCCTATGCTGATGCTGTGATAGGG
genomic: CTCCAAGTGCTCCCCCAGGGAATCAAAACCAAGCACATGGGTCATCTCAGgttagtttgt ... tatacgacagGTGACACACAGCATGCAAGTTCCTCTTTCCTATGCTGATGCTGTGATAGGG
EST: gi|149101966|gb|EE287480.2|EE287480
EST:     CTCCAAGTGCTCCCCCAGGGAATCAAAACCAAGCACATGGGTCATCTCAG                         GTGACACACAGCATGCAAGTTCCTCTTTCCTATGCTGATGCTGTGATAGGG
genomic: CTCCAAGTGCTCCCCCAGGGAATCAAAACCAAGCACATGGGTCATCTCAGgttagtttgt ... tatacgacagGTGACACACAGCATGCAAGTTCCTCTTTCCTATGCTGATGCTGTGATAGGG
EST: gi|60397147|gb|DN229963.1|DN229963
EST:     CTCCAAGTGCTCCCCCAGGGAATCAAAACCAAGCACATGGGTCATCTCAG                         GTGACACACAGCATGCAAGTTCCTCTTTCCTATGCTGATGCTGTGATAGGG
genomic: CTCCAAGTGCTCCCCCAGGGAATCAAAACCAAGCACATGGGTCATCTCAGgttagtttgt ... tatacgacagGTGACACACAGCATGCAAGTTCCTCTTTCCTATGCTGATGCTGTGATAGGG
EST: gi|113701552|gb|EE679056.1|EE679056
EST:     CTCCAAGTGCTCCCCCAGGGAATCAAAACCAAGCACATGGGTCATCTCAG                         GTGACACACAGCATGCAAGTTCCTCTTTCCTATGCTGATGCTGTGATAGGG
genomic: CTCCAAGTGCTCCCCCAGGGAATCAAAACCAAGCACATGGGTCATCTCAGgttagtttgt ... tatacgacagGTGACACACAGCATGCAAGTTCCTCTTTCCTATGCTGATGCTGTGATAGGG
EST: gi|93282653|gb|EB674917.1|EB674917
EST:     CTCCAAGTGCTCCCCCAGGGAATCAAAACCAAGCACATGGGTCATCTCAG                         GTGACACACAGCATGCAAGTTCCTCTTTCCTATGCTGATGCTGTGATAGGG
genomic: CTCCAAGTGCTCCCCCAGGGAATCAAAACCAAGCACATGGGTCATCTCAGgttagtttgt ... tatacgacagGTGACACACAGCATGCAAGTTCCTCTTTCCTATGCTGATGCTGTGATAGGG
EST: gi|166537501|gb|EG088453.1|EG088453
EST:     CCAAGCACATGGGTCATCTCAG                         GTGACACACAGCATGCAAGTTCCTCTTTCCTATGCTGATGCTGTGATAGGG
genomic: CCAAGCACATGGGTCATCTCAGgttagtttgt ... tatacgacagGTGACACACAGCATGCAAGTTCCTCTTTCCTATGCTGATGCTGTGATAGGG
EST: gi|30088103|gb|CB886308.1|CB886308
EST:     CTCCAAGTGCTCCCCCAGGGAATCAAAACCAAGCACATGGGTCATCTCAG                         GTGACACACAGCATGCAAGTTCCTCTTTCCTATGCTGATGCTGTGATAGGG
genomic: CTCCAAGTGCTCCCCCAGGGAATCAAAACCAAGCACATGGGTCATCTCAGgttagtttgt ... tatacgacagGTGACACACAGCATGCAAGTTCCTCTTTCCTATGCTGATGCTGTGATAGGG
EST: gi|24769920|gb|CA405049.1|CA405049
EST:     CTCCAAGTGCTCCCCCAGGGAATCAAAACCAAGCACATGGGTCATCTCAG                         GTGACACACAGCATGCAAGTTCCTCTTTCCTATGCTGATGCTGTGATAGGG
genomic: CTCCAAGTGCTCCCCCAGGGAATCAAAACCAAGCACATGGGTCATCTCAGgttagtttgt ... tatacgacagGTGACACACAGCATGCAAGTTCCTCTTTCCTATGCTGATGCTGTGATAGGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcctatctcatgatcagttgtacttaacttttttcttggtaattttatacgacagGTGACACACAGCATGCAAGTTCCTCTTTCCTATGCTGATGCTGTGATAGGGGCAGCTGGTGCCAGTATCAGCTACATCCGCAGGCATAGTGGAGCAACTA
                     acttaac  putative branch site (score: 3)
                            ttttttcttggtaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttagtttgtacacatttgactgctactaatatgatgaattatttgcatgcctatctcatgatcagttgtacttaacttttttcttggtaattttatacgacagGTGACACACAGCATGCAAGTTCCTCTTTCCTATGCTGATGCTGTGATAGGGGCAGCTGGTGCCAGTATCAGCTACATCCGCAGGCATAGTGGAGCAACTA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA