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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaacgtattagtaacattccatgcagtttagtcttacatatggagttacagtcataagtgcatatcctctgctgtatcttactgttacacttttcacctcagGTTTGCACATTCTACCAAAAAGGTGCATGCTCGTATGGTAGCCGTTGCAGATATGACCATGTCAAAGTTTCTCGTAACCCCACAGTGCCACCACCACGCC

Basic information

species Zea mays
transcript GRMZM2G395842_T02
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G395842_T02 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os06g21390.1 (Oryza sativa), 3'ss of exon 2
gtaacgtattagtaa-cattccatgcagtttagtcttacatatggagttacagtcataagtgcatatcctctgctgtatcttactgttacacttttcacctcagGTTTGCACATTCTACCAAAAAGGTGCATGCTCGTATGGTAGCCGTTGCAGATATGACCATGTCAAAGTTTCTCGTAACCCCACAGTGCCACCACCACGCC
|||| ||||||||||    |  |||   | |  | | |        |  | | | |  |||||| ||| ||| ||||  |||||| | |  |||     ||||||||||||| |||||||| |||||| ||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||| | |||||||   
gtaatgtattagtaaatgattgatgtgctctgatttcatt------gccatacttaacagtgcaaatcttctactgttccttactttgattcttacttgctcagGTTTGCACGTTCTACCAGAAAGGTTCATGCTCGTATGGTAGCCGTTGCCGATATGACCATGTCAAAGTTTCTCGTAACCCCACAGTGGCTCCACCACCAA

upper sequence: GRMZM2G395842_T02 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os06g21390.4 (Oryza sativa), 3'ss of exon 1
--gtaacgtattagtaa-cattccatgcagtttagtcttacatatggagttacagtcataagtgcatatcctctgctgtatcttactgttacacttttcacctcagGTTTGCACATTCTACCAAAAAGGTGCATGCTCGTATGGTAGCCGTTGCAGATATGACCATGTCAAAGTTTCTCGTAACCCCACAGTGCCACCACCACGCC
  |||| ||||||||||    |  |||   | |  | | |        |  | | | |  |||||| ||| ||| ||||  |||||| | |  |||     ||||||||||||| |||||||| |||||| ||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||| | |||||||   
atgtaatgtattagtaaatgattgatgtgctctgatttcatt------gccatacttaacagtgcaaatcttctactgttccttactttgattcttacttgctcagGTTTGCACGTTCTACCAGAAAGGTTCATGCTCGTATGGTAGCCGTTGCCGATATGACCATGTCAAAGTTTCTCGTAACCCCACAGTGGCTCCACCACCAA

upper sequence: GRMZM2G395842_T02 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA15G42750.1 (Glycine max), 3'ss of exon 2
gtaacgtattagtaacattccatgcagtttagtcttacatatggagttacagtcataagtgcatatcctctgctgtatcttactgttacacttttcacctcagGTTTGCACATTCTACCAAAAAGGTGCATGCTCGTATGGTAGCCGTTGCAGATATGACCATGTCAAAGTTTCTCGTAACCCCACAGTGCCACCACCACGCC
||     ||    |   |||  ||| |   |  | ||   ||  | | | | | ||   |  || ||        | | ||  ||||   ||  | |   ||| | |||||||| || || ||||| |  ||  | |||||||| || ||||||||||| |||||||||| ||||||  | |   |     | ||| |     
gttggtgatgcaaactcttctttgctgcaga-ccctattaattaattgataattatt--tagatttctctgataattttttcttgtttgtctcgttatgacagATATGCACATTTTATCAGAAAGGAGTCTGTGCTTATGGTAGTCGCTGCAGATATGATCATGTCAAAGCTTCTCGAGAGCAATCTTCTGCTCCATCTTCTT

upper sequence: GRMZM2G395842_T02 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA08G16340.1 (Glycine max), 3'ss of exon 2
gtaacgtattagtaacattccatgcagtttagtcttacatatggagttacagtcataagtgcatatcctctgctgtatcttactgttacacttttcacctcagGTTTGCACATTCTACCAAAAAGGTGCATGCTCGTATGGTAGCCGTTGCAGATATGACCATGTCAAAGTTTCTCGTAACCCCACAGTGCCACCACCACGCC
     || |  |   ||  |  | |  |   |     | ||   | | | ||  |||  | | | ||        | | ||  ||||   ||  | |   ||||| |||||||| || || ||||| |  ||  | |||||||| || ||||||||||| |||||||||| ||||||  | |   |     | ||| |     
-----gtttgtgatgcaaactcttctttgctgcagaccctactaattgatag--atatttacgtttctctgataattttttcttgttcttctcattatgacagGTATGCACATTTTATCAGAAAGGAGTCTGTGCTTATGGTAGTCGCTGCAGATATGATCATGTCAAAGCTTCTCGAGAGCAATCTTCTGCTCCATCTTCTT

upper sequence: GRMZM2G395842_T02 (Zea mays), 3'ss of exon 2
lower sequence: Vv13s0064g01090.t01 (Vitis vinifera), 3'ss of exon 3
gtaacgtattagtaacattccatgcagtttagtcttacatatggagttacagtcataagtgcatatcctctgctgtatc-ttactgttacactttt-cacctcagGTTTGCACATTCTACCAAAAAGGTGCATGCTCGTATGGTAGCCGTTGCAGATATGACCATGTCAAAGTTTCTCGTA---ACCCCACAGTGCCACCACCACGCC
                      |  | |||  |        | || ||  |  ||||| |  | |  |||   | |||| ||  |    ||  |||      ||| |||| || || || ||||||||||  ||||| |||||| | || ||||||||||| ||||| |||||||||| |    | ||  | |  ||| |  ||    
---------------------gtaaaattttctgactttcttagaattg-acccataaatctagaggctccattatatccttgtttcctcatctttgtgttacagATTTGTACCTTTTATCAAAAAGGTGTCTGCTCATATGGTGGTCGATGCAGATATGAACATGTTAAAGTTTCTCATTCTCAGCCTTCTGCTCCATCTTCAT---

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|211441986|gb|FL189209.1|FL189209
EST:     AAGGAGAGTACTGTGAATTCTCCCACGACTGGAGTGATCAAGCAAATAAT                         GTTTGCACATTCTACCAAAAAGGTGCATGCTCGTATGGTAGCCGTTGCAGA
genomic: AAGGAGAGTACTGTGAATTCTCCCACGACTGGAGTGATCAAGCAAATAATgtaacgtatt ... ttcacctcagGTTTGCACATTCTACCAAAAAGGTGCATGCTCGTATGGTAGCCGTTGCAGA
EST: gi|211441984|gb|FL189207.1|FL189207
EST:     AAGGAGAGTACTGTGAATTCTCCCACGACTGGAGTGATCAAGCAAATAAT                         GTTTGCACATTCTACCAAAAAGGTGCATGCTCGTATGGTAGCCGTTGCAGA
genomic: AAGGAGAGTACTGTGAATTCTCCCACGACTGGAGTGATCAAGCAAATAATgtaacgtatt ... ttcacctcagGTTTGCACATTCTACCAAAAAGGTGCATGCTCGTATGGTAGCCGTTGCAGA
EST: gi|211441982|gb|FL189205.1|FL189205
EST:     AAGGAGAGTACTGTGAATTCTCCCACGACTGGAGTGATCAAGCAAATAAT                         GGTTGCACATTCTACCAAAAAGGNGCATGCTCGTATGGTA
genomic: AAGGAGAGTACTGTGAATTCTCCCACGACTGGAGTGATCAAGCAAATAATgtaacgtatt ... ttcacctcagGTTTGCACATTCTACCAAAAAGGTGCATGCTCGTATGGTA
EST: gi|44682125|gb|CK787173.1|CK787173
EST:     AAGGAGAGTACTGTGAATTCTCCCACGACTGGAGTGATCAAGCAAATAAT                         GTTTGCACATTCTACCAAAAAGGTGCATGCTCGTATGGTAGCCGTTGCAGA
genomic: AAGGAGAGTACTGTGAATTCTCCCACGACTGGAGTGATCAAGCAAATAATgtaacgtatt ... ttcacctcagGTTTGCACATTCTACCAAAAAGGTGCATGCTCGTATGGTAGCCGTTGCAGA
EST: gi|211441987|gb|FL189210.1|FL189210
EST:     AAGGAGAGTACTGTGAATTCTCCCACGACTGGAGTGATCAAGCAAATAAT                         GTTTGCACATTCTACCAAAAAGGTGCATGCTCGTATGGTAGCCGTTGCAGA
genomic: AAGGAGAGTACTGTGAATTCTCCCACGACTGGAGTGATCAAGCAAATAATgtaacgtatt ... ttcacctcagGTTTGCACATTCTACCAAAAAGGTGCATGCTCGTATGGTAGCCGTTGCAGA
EST: gi|211441980|gb|FL189203.1|FL189203
EST:     AAGGAGAGTACTGTGAATTCTCCCACGACTGGAGTGATCAAGCAAATAAT                         GTTTGCACATTCTACCAAAAAGGTGCATGCTCGTATGGTAGCCGTTGCAGA
genomic: AAGGAGAGTACTGTGAATTCTCCCACGACTGGAGTGATCAAGCAAATAATgtaacgtatt ... ttcacctcagGTTTGCACATTCTACCAAAAAGGTGCATGCTCGTATGGTAGCCGTTGCAGA
EST: gi|88753027|gb|DY537168.1|DY537168
EST:     AAGGAGAGTACTGTGAATTCTCCCACGACTGGAGTGATCAAGCAAATAAT                         GTTTGCACATTCTACCAAAAAGGTGCATGCTCGTATGGTAGCCGTTGCAGA
genomic: AAGGAGAGTACTGTGAATTCTCCCACGACTGGAGTGATCAAGCAAATAATgtaacgtatt ... ttcacctcagGTTTGCACATTCTACCAAAAAGGTGCATGCTCGTATGGTAGCCGTTGCAGA
EST: gi|211441979|gb|FL189202.1|FL189202
EST:     AAGGAGAGTACTGTGAATTCTCCCACGACTGGAGTGATCAAGCAAATAAT                         GTTTGCACATTCTACCAAAAAGGTGCATGCTCGTATGGTANCCGTTGCAGA
genomic: AAGGAGAGTACTGTGAATTCTCCCACGACTGGAGTGATCAAGCAAATAATgtaacgtatt ... ttcacctcagGTTTGCACATTCTACCAAAAAGGTGCATGCTCGTATGGTAGCCGTTGCAGA
EST: gi|71435076|gb|DR816126.1|DR816126
EST:     AAGGAGAGTACTGTGAATTCTCCCACGACTGGAGTGATCAAGCAAATAAT                         GTTTGCACATTCTACCAAAAAGGTGCATGCTCGTATGGTAGCCGTTGCAGA
genomic: AAGGAGAGTACTGTGAATTCTCCCACGACTGGAGTGATCAAGCAAATAATgtaacgtatt ... ttcacctcagGTTTGCACATTCTACCAAAAAGGTGCATGCTCGTATGGTAGCCGTTGCAGA
EST: gi|211441978|gb|FL189201.1|FL189201
EST:     AAGGAGAGTACTGTGAATTCTCCCACGACTGGAGTGATCAAGCAAATAAT                         GTTTGCACATTCTACCAAAAAGGTGCATGCTCGTATGGTAGCCGTTGCAGA
genomic: AAGGAGAGTACTGTGAATTCTCCCACGACTGGAGTGATCAAGCAAATAATgtaacgtatt ... ttcacctcagGTTTGCACATTCTACCAAAAAGGTGCATGCTCGTATGGTAGCCGTTGCAGA
EST: gi|50333765|gb|CO528891.1|CO528891
EST:     AAGGAGAGTACTGTGAATTCTCCCACGACTGGAGTGATCAAGCAAATAAT                         GTTTGCACATTCTACCAAAAAGGTGCATGCTCGTATGGTAGCCGTTGCAGA
genomic: AAGGAGAGTACTGTGAATTCTCCCACGACTGGAGTGATCAAGCAAATAATgtaacgtatt ... ttcacctcagGTTTGCACATTCTACCAAAAAGGTGCATGCTCGTATGGTAGCCGTTGCAGA
EST: gi|89754462|gb|DY685237.1|DY685237
EST:     AAGGAGAGTACTGTGAATTCTCCCACGACTGGAGTGATCAAGCAAATAAT                         GTTTGCACATTCTACCAAAAAGG-GCATGCTCGTATGGTAGCCCTTGCAAA
genomic: AAGGAGAGTACTGTGAATTCTCCCACGACTGGAGTGATCAAGCAAATAATgtaacgtatt ... ttcacctcagGTTTGCACATTCTACCAAAAAGGTGCATGCTCGTATGGTAGCCGTTGCAGA
EST: gi|211441988|gb|FL189211.1|FL189211
EST:     AAGGAGAGTACTGTGAATTCTCCCACGACTGGAGTGATCAAGCAAATAAT                         GTTTGCACATTCTACCAAAAAGGNGCATGCTCGTATGGTAGCCGTTGCAGA
genomic: AAGGAGAGTACTGTGAATTCTCCCACGACTGGAGTGATCAAGCAAATAATgtaacgtatt ... ttcacctcagGTTTGCACATTCTACCAAAAAGGTGCATGCTCGTATGGTAGCCGTTGCAGA
EST: gi|78119832|gb|DV538216.1|DV538216
EST:     AAGGAGAGTACTGTGAATTCTCCCACGACTGGAGTGATCAAGCAAATAAT                         GTTTGCACATTCTACCAAAAAGGTGCATGCTCGTATGGTAGCCGTTGCAGA
genomic: AAGGAGAGTACTGTGAATTCTCCCACGACTGGAGTGATCAAGCAAATAATgtaacgtatt ... ttcacctcagGTTTGCACATTCTACCAAAAAGGTGCATGCTCGTATGGTAGCCGTTGCAGA
EST: gi|13557990|gb|BG549346.1|BG549346
EST:     AAGGAGAGTACTGTGAATTCTCCCACGACTGGAGTGATCAAGCAAATAAT                         GTTTGCACATTCTACCAAAAAGGTGCATGCTCGTATGGTAGCCGTTGCAGA
genomic: AAGGAGAGTACTGTGAATTCTCCCACGACTGGAGTGATCAAGCAAATAATgtaacgtatt ... ttcacctcagGTTTGCACATTCTACCAAAAAGGTGCATGCTCGTATGGTAGCCGTTGCAGA
EST: gi|74240963|gb|DT648877.1|DT648877
EST:     AAGGAGAGTACTGTGAATTCTCCCACGACTGGAGTGATCAAGCAAATAAT                         GTTTGCACATTCTACCAAAAAGGTGCATGCTCGTATGGTAGCCGTTGCAGA
genomic: AAGGAGAGTACTGTGAATTCTCCCACGACTGGAGTGATCAAGCAAATAATgtaacgtatt ... ttcacctcagGTTTGCACATTCTACCAAAAAGGTGCATGCTCGTATGGTAGCCGTTGCAGA
EST: gi|101389164|gb|EB816537.1|EB816537
EST:     AAGGAGAGTACTGTGAATTCTCCCACGACTGGAGTGATCAAGCAAATAAT                         GTTTGCACATTCTACCAAAAAGGTGCATGCTCGTATGGTAGCCGTTGCAGA
genomic: AAGGAGAGTACTGTGAATTCTCCCACGACTGGAGTGATCAAGCAAATAATgtaacgtatt ... ttcacctcagGTTTGCACATTCTACCAAAAAGGTGCATGCTCGTATGGTAGCCGTTGCAGA
EST: gi|89757793|gb|DY687242.1|DY687242
EST:     AAGGAGAGTACTGTGAATTCTCCCACGACTGGAGTGATCAAGCAAATAAT                         GTTTGCACATTCTACCAAAAAGGTGCATGCTCGTATGGTAGCCGTTGCAGA
genomic: AAGGAGAGTACTGTGAATTCTCCCACGACTGGAGTGATCAAGCAAATAATgtaacgtatt ... ttcacctcagGTTTGCACATTCTACCAAAAAGGTGCATGCTCGTATGGTAGCCGTTGCAGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acagtcataagtgcatatcctctgctgtatcttactgttacacttttcacctcagGTTTGCACATTCTACCAAAAAGGTGCATGCTCGTATGGTAGCCGTTGCAGATATGACCATGTCAAAGTTTCTCGTAACCCCACAGTGCCACCACCACGCC
                            atcttac  putative branch site (score: 3)
                                          cttttcacctc  putative PPT
                           tatctta  TA-rich tract