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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_T01
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

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 4 RNA-Seq libraries.


Block sizes: 48 (upstream exon), 47 (downstream exon)
Score: 79

AGTTCTTTGCAAGTTCTTCATGCATGGAGCTTGCTTGAAAGGAGAGTACTGTGAATTCTCCCACGACTGGAGTGATCAAGCAAATAATgtaacgtatt ... ttcacctcagGTTTGCACATTCTACCAAAAAGGTGCATGCTCGTATGGTAGCCGTTGCAGATATGACCATGTCAAAGTTTCTCGTAACCCCACAGTGCCACCACCACGCC


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 107

AGTTCTTTGCAAGTTCTTCATGCATGGAGCTTGCTTGAAAGGAGAGTACTGTGAATTCTCCCACGACTGGAGTGATCAAGCAAATAATgtaacgtatt ... ttcacctcagGTTTGCACATTCTACCAAAAAGGTGCATGCTCGTATGGTAGCCGTTGCAGATATGACCATGTCAAAGTTTCTCGTAACCCCACAGTGCCACCACCACGCC


Block sizes: 41 (upstream exon), 49 (downstream exon)
Score: 73

AGTTCTTTGCAAGTTCTTCATGCATGGAGCTTGCTTGAAAGGAGAGTACTGTGAATTCTCCCACGACTGGAGTGATCAAGCAAATAATgtaacgtatt ... ttcacctcagGTTTGCACATTCTACCAAAAAGGTGCATGCTCGTATGGTAGCCGTTGCAGATATGACCATGTCAAAGTTTCTCGTAACCCCACAGTGCCACCACCACGCC


Block sizes: 47 (upstream exon), 48 (downstream exon)
Score: 79

AGTTCTTTGCAAGTTCTTCATGCATGGAGCTTGCTTGAAAGGAGAGTACTGTGAATTCTCCCACGACTGGAGTGATCAAGCAAATAATgtaacgtatt ... ttcacctcagGTTTGCACATTCTACCAAAAAGGTGCATGCTCGTATGGTAGCCGTTGCAGATATGACCATGTCAAAGTTTCTCGTAACCCCACAGTGCCACCACCACGCC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acagtcataagtgcatatcctctgctgtatcttactgttacacttttcacctcagGTTTGCACATTCTACCAAAAAGGTGCATGCTCGTATGGTAGCCGTTGCAGATATGACCATGTCAAAGTTTCTCGTAACCCCACAGTGCCACCACCACGCC
                            atcttac  putative branch site (score: 79)
                                          cttttcacctc  putative PPT
                           tatctta  TA-rich tract