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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...catgattgaatttgaatcattgggttagtgtttgcatatagtcatacgcatttgggacatcattaggactatgtctaaacctgctggtctttattttcagATCAAGATTCAGTGCGTCTGTTGGCTGTTGAAGGCTGTGCTGCCCTTGGTAAATTGTTGGAACCACAAGATTGCGTAGCACACATTCTTCCAGTCATTGT

Basic information

species Zea mays
transcript GRMZM2G164352_T04
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G164352_T04 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA09G31760.1 (Glycine max), 3'ss of exon 3
--catgattgaatttgaatcattgggttagtgtttgcatatagtcatacgcatttgggacatcattaggactatgtctaaacctgctggtctttatttt--cagATCAAGATTCAGTGCGTCTGTTGGCTGTTGAAGGCTGTGCTGCCCTTGGTAAATTGTTGGAACCACAAGATTGCGTAGCACACATTCTTCCAGTCATTGT
    | |||   |  | |   ||   ||| ||| |   |  |||  |   |   ||| |   |||    | ||  |    |  |  |  || || || |  ||||||||||||| || || ||  | |||||||| || ||||| || || || |||||||||||||| ||||||||||| ||||| |||||||| ||||| ||
atgttcatttgttaagtagtgttattttactgtgttttttaagt--tgatctgctggaagtgcat--acattaactgatgatttttttatccttgttcttgcagATCAAGATTCTGTTCGGCTACTTGCTGTTGAGGGTTGTGCAGCTCTGGGGAAATTGTTGGAACCTCAAGATTGCGTGGCACATATTCTTCCTGTCATAGT

upper sequence: GRMZM2G164352_T04 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA20G24790.1 (Glycine max), 3'ss of exon 3
---------------------------catgattgaa---tttgaatcattgggttagtgtttgcatatagtcatacgcatttgggacatcattaggactatgtctaaacctgctggtct-------ttatttt----cagATCAAGATTCAGTGCGTCTGTTGGCTGTTGAAGGCTGTGCTGCCCTTGGTAAATTGTTGGAACCACAAGATTGCGTAGCACACATTCTTCCAGTCATTGT
                             |   || |   | |   ||||| |  |  |   |   || |    |     | | | | |   |   || | |   | |  |   |  | |       | || ||    ||||||||||||| ||  |  |||||||||| || ||||||||||| ||||| ||  ||||||| ||||||||||| || ||||| || || || || |||||
gtaattgaatacatatttcttgttctttgtagatggaaagtgtctgtcatttgtctgttacatatttacatgtgtgattgtgttgtagagtctcctgaatgtactttactcctttaatatgcaattgtaatcttggaacagATCAAGATTCTGTCAGATTGTTGGCTGTGGAGGGCTGTGCTGCTCTTGGCAAGCTGTTGGAGCCACAAGATTGTGTTGCACATATACTCCCGGTTATTGT

upper sequence: GRMZM2G164352_T04 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA07G10000.1 (Glycine max), 3'ss of exon 2
--catgattgaatttgaatcattgggttagtgtttgcatatagtc-atacgcatttgggacatcattaggactatgtctaaacctgctggtctttattttc--agATCAAGATTCAGTGCGTCTGTTGGCTGTTGAAGGCTGTGCTGCCCTTGGTAAATTGTTGGAACCACAAGATTGCGTAGCACACATTCTTCCAGTCATTGT
    | |||   |  | |   ||   ||| ||| |   |  |||  || |||   ||| |   |||    | ||  |       |  |  || || ||     |||||||||||| || || ||  | |||||||| || ||||| || || || |||||||||||||| |||||||| || ||||| |||||||| ||||| ||
atgttcatttgttgagtagtgttattttactgtgttttttaagttgatccgc---tggaagtgcat--acattaactgatggtttttttatccttgttcctgtagATCAAGATTCTGTTCGGCTACTTGCTGTTGAGGGTTGTGCAGCTCTGGGAAAATTGTTGGAACCTCAAGATTGTGTGGCACATATTCTTCCTGTCATAGT

upper sequence: GRMZM2G164352_T04 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA10G42250.1 (Glycine max), 3'ss of exon 3
-----------------------------------------------catgattgaat-ttgaatcattgggttagt-gtttgcatatagtcatacgcatttgggacatcattaggactatgtctaaacctgctggtctttattttcagATCAAGATTCAGTGCGTCTGTTGGCTGTTGAAGGCTGTGCTGCCCTTGGTAAATTGTTGGAACCACAAGATTGCGTAGCACACATTCTTCCAGTCATTGT
                                               |||  |||  | ||| ||  ||   || || || ||  | |  |        |   | |  |  ||    || | |  | |  || ||   | |     ||||||||||||| ||  |  |||||||||| || ||||||||||| ||||| ||  ||||||| ||||||||||| || ||||| || || || || |||||
gtaattgaatacatatttcttgttctttgtagatggaaagtgtctgtcatttttgtctattgcatatttacattggttgtgtgattgtgttgtagaatctcctgaatgtactttc--ctcttttaatatgtgttgtaatcttggaacagATCAAGATTCTGTCAGATTGTTGGCTGTGGAGGGCTGTGCTGCTCTTGGCAAGCTGTTGGAGCCACAAGATTGTGTTGCACATATACTCCCGGTTATTGT

upper sequence: GRMZM2G164352_T04 (Zea mays), 3'ss of exon 3
lower sequence: AT1G25490.1 (Arabidopsis thaliana), 3'ss of exon 3
--------------------------------------------------------------------------------catgattgaatttgaatcattgggttagtgtttgc----atatagt-----catacgcatttgggaca--tcattaggactatgtctaaacctgctggtctttat------tttcagATCAAGATTCAGTGCGTCTGTTGGCTGTTGAAGGCTGTGCTGCCCTTGGTAAATTGTTGGAACCACAAGATTGCGTAGCACACATTCTTCCAGTCATTGT
                                                                                   |||   |||||||| | |       ||||||     ||||| |     | |||   ||  | |    |  ||    || ||  || |   | |   |||||       ||||||| |||||||| ||| | || |||||||||||||| ||||| || ||||| || ||||||||||| || ||||| || |||| |||| | || || |||||
gtacttaatgtttgaatatatcgtactttatatgtgctcatcacttagaaatagtttgcatagacccaagagtatggtaaagagatcacatttgaattaataaac-gctgtttgatgaaatatattggatacttacctcttcagaaatgtttgttttatctgtgcttatattggttaaactttaaccttcatttcagACCAAGATTCTGTGAGACTATTGGCTGTTGAAGGGTGTGCAGCTCTTGGAAAGTTGTTGGAACCTCAGGATTGTGTTGCACGCATTTTACCTGTTATTGT

upper sequence: GRMZM2G164352_T04 (Zea mays), 3'ss of exon 3
lower sequence: AT1G13320.3 (Arabidopsis thaliana), 3'ss of exon 3
catgattgaatttgaatcattgggttagtgtttgcatatagtcatacgcat-ttgggacatcat--taggactatgtctaa--acctgctggtctttattttcagATCAAGATTCAGTGCGTCTGTTGGCTGTTGAAGGCTGTGCTGCCCTTGGTAAATTGTTGGAACCACAAGATTGCGTAGCACACATTCTTCCAGTCATTGT
      |||| || |             ||| | ||| |   | |  |  | ||   | || ||  ||  ||    | |||  | ||  | | | ||  | |||||||||||||| ||  |  | ||||||||||| || |||||||| ||||| ||||||||||| || || || || || |||||||||||||| || |||||
-----ctgaagttaagcagaattacggttgtctacatctcagcttcagtgtctttttatattataatattacagattttaagtatcttattgacattgatatcagATCAAGATTCGGTTAGATTATTGGCTGTTGAGGGTTGTGCTGCTCTTGGGAAATTGTTGGAGCCCCAGGACTGTGTTGCACACATTCTTCCTGTGATTGT

upper sequence: GRMZM2G164352_T04 (Zea mays), 3'ss of exon 3
lower sequence: Vv17s0000g03870.t01 (Vitis vinifera), 3'ss of exon 4
catgattgaatttgaatcattgggttagtgtttgcatatagtcatac-gcatttgggaca-tcattaggactatgtctaaacctgctggtctttattttcagATCAAGATTCAGTGCGTCTGTTGGCTGTTGAAGGCTGTGCTGCCCTTGGTAAATTGTTGGAACCACAAGATTGCGTAGCACACATTCTTCCAGTCATTGT
 ||||   | ||    |  ||  |||  ||   | || |  | |||  | |  |  || |  |||| ||  | |      ||    |  | || |||| ||||||||||||| ||  |  | ||||||||||| || ||||| || || || ||  |||||||||| |||||||| |||||||| |||||||| || |||||
aatgacaaagttgtttttctttcgtttttgccggtatttttttatattggaagtatgatagccatttgggttgttagcttaca-atttattttcattt-cagATCAAGATTCTGTTAGGTTATTGGCTGTTGAGGGTTGTGCAGCTCTCGGAAAGCTGTTGGAACCTCAAGATTGTGTAGCACATATTCTTCCCGTAATTGT

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|32831601|gb|CD971279.1|CD971279
EST:     TCATTTGAAGACAGAAATAATGTCAATATTTGATGATTTAACCCAAGATG                         ATCAAGATTCAGTGCGTCTGTTGGCTGTTGAAGGCTGTGCTGCCCTTGGTA
genomic: TCATTTGAAGACAGAAATAATGTCAATATTTGATGATTTAACCCAAGATGgtacattcta ... ttattttcagATCAAGATTCAGTGCGTCTGTTGGCTGTTGAAGGCTGTGCTGCCCTTGGTA
EST: gi|33091965|gb|CF051959.1|CF051959
EST:     TCATTTGAAGACAGAAATAATGTCAATATTTGATGACTTAACCCAAGATG                         ATCAAGATTCAGTGCGTTTGTTGGCTGTTGAAGGTTGTGCTGCTCTTGGTA
genomic: TCATTTGAAGACAGAAATAATGTCAATATTTGATGATTTAACCCAAGATGgtacattcta ... ttattttcagATCAAGATTCAGTGCGTCTGTTGGCTGTTGAAGGCTGTGCTGCCCTTGGTA
EST: gi|21088918|gb|BQ401231.1|BQ401231
EST:     TCATTTGAAGACAGAAATAATGTCAATATTTGATGATTTAACCCAAGATG                         ATCAAGATTCAGTGCGTCTGTTGGCTGTTGAAGGCTGTGCTGCCCTTGGTA
genomic: TCATTTGAAGACAGAAATAATGTCAATATTTGATGATTTAACCCAAGATGgtacattcta ... ttattttcagATCAAGATTCAGTGCGTCTGTTGGCTGTTGAAGGCTGTGCTGCCCTTGGTA
EST: gi|22473017|gb|BU037497.1|BU037497
EST:     TCATTTGAAGACAGAAATAATGTCAATATTTGATGATTTAACCCAAGATG                         ATCAAGATTCAGTGCGTCTGTTGGCTGTTGAAGGCTGTGCTGCCCTTGGTA
genomic: TCATTTGAAGACAGAAATAATGTCAATATTTGATGATTTAACCCAAGATGgtacattcta ... ttattttcagATCAAGATTCAGTGCGTCTGTTGGCTGTTGAAGGCTGTGCTGCCCTTGGTA
EST: gi|211520937|gb|FL382784.1|FL382784
EST:     TCATTTGAAGACAGAAATAATGTCAATATTTGATGATTTAACCCAAGATG                         ATCAAGATTCAGTGCGTCTGTTGGCTGTTGAAGGCTGTGCTGCCCTTGGTA
genomic: TCATTTGAAGACAGAAATAATGTCAATATTTGATGATTTAACCCAAGATGgtacattcta ... ttattttcagATCAAGATTCAGTGCGTCTGTTGGCTGTTGAAGGCTGTGCTGCCCTTGGTA
EST: gi|32940030|gb|CF044849.1|CF044849
EST:     TCATTTGAAGACAGAAATAATGTCAATATTTGATGATTTAACCCAAGATG                         ATCAAGATTCAGTGCGTCTGTTGGCTGTTGAAGGCTGTGCTGCCCTTGGTA
genomic: TCATTTGAAGACAGAAATAATGTCAATATTTGATGATTTAACCCAAGATGgtacattcta ... ttattttcagATCAAGATTCAGTGCGTCTGTTGGCTGTTGAAGGCTGTGCTGCCCTTGGTA
EST: gi|32830645|gb|CD970323.1|CD970323
EST:     TCATTTGAAGACAGAAATAATGTCAATATTTGATGATTTAACCCAAGATG                         ATCAAGATTCAGTGCGTCTGTTGGCTGTTGAAGGCTGTGCTGCCCTTGGTA
genomic: TCATTTGAAGACAGAAATAATGTCAATATTTGATGATTTAACCCAAGATGgtacattcta ... ttattttcagATCAAGATTCAGTGCGTCTGTTGGCTGTTGAAGGCTGTGCTGCCCTTGGTA
EST: gi|32938569|gb|CF043388.1|CF043388
EST:     TCATTTGAAGACAGAAATAATGTCAATATTTGATGATTTAACCCAAGATG                         ATCAAGATTCAGTGCGTCTGTTGGCTGTTGAAGGCTGTGCTGCCCTTGGTA
genomic: TCATTTGAAGACAGAAATAATGTCAATATTTGATGATTTAACCCAAGATGgtacattcta ... ttattttcagATCAAGATTCAGTGCGTCTGTTGGCTGTTGAAGGCTGTGCTGCCCTTGGTA
EST: gi|26456172|gb|CA827755.1|CA827755
EST:     TCATTTGAAGACAGAAATAATGTCAATATTTGATGATTTAACCCAAGATG                         ATCAAGATTCA
genomic: TCATTTGAAGACAGAAATAATGTCAATATTTGATGATTTAACCCAAGATGgtacattcta ... ttattttcagATCAAGATTCA
EST: gi|22935744|gb|BU572019.1|BU572019
EST:     TCATTTGAAGACAGAAATAATGTCAATATTTGATGATTTAACCCAAGATG                         ATCAAGATTCAGGGCGTCTGTTGGCTGTTGAAGGCTGTGCTGCCCTTGGTA
genomic: TCATTTGAAGACAGAAATAATGTCAATATTTGATGATTTAACCCAAGATGgtacattcta ... ttattttcagATCAAGATTCAGTGCGTCTGTTGGCTGTTGAAGGCTGTGCTGCCCTTGGTA
EST: gi|31349427|gb|CD433784.1|CD433784
EST:     TCATTTGAAGACAGAAATAATGTCAATATTTGATGATTTAACCCAAGATG                         ATCAAGATTCAGTGCGTCTGTTGGCTGTTGAAGGCTGTGCTGCCCTTGGTA
genomic: TCATTTGAAGACAGAAATAATGTCAATATTTGATGATTTAACCCAAGATGgtacattcta ... ttattttcagATCAAGATTCAGTGCGTCTGTTGGCTGTTGAAGGCTGTGCTGCCCTTGGTA
EST: gi|32847343|gb|CD987024.1|CD987024
EST:     TCATTTGAAGACAGAAATAATGTCAATATTTGATGATTTAACCCAAGATG                         ATCAAGATTCAGTGCGTCTGTTGGCTGTTGAAGGCTGTGCTGCCCTTGGTA
genomic: TCATTTGAAGACAGAAATAATGTCAATATTTGATGATTTAACCCAAGATGgtacattcta ... ttattttcagATCAAGATTCAGTGCGTCTGTTGGCTGTTGAAGGCTGTGCTGCCCTTGGTA
EST: gi|31356642|gb|CD440999.1|CD440999
EST:     TCATTTGAAGACAGAAATAATGTCAATATTTGATGATTTAACCCAAGATG                         ATCAAGATTCAGTGCGTCTGTTGGCTGTTGAAGGCTGTGCTGCCCTTGGTA
genomic: TCATTTGAAGACAGAAATAATGTCAATATTTGATGATTTAACCCAAGATGgtacattcta ... ttattttcagATCAAGATTCAGTGCGTCTGTTGGCTGTTGAAGGCTGTGCTGCCCTTGGTA
EST: gi|211194221|gb|FL384750.1|FL384750
EST:     TCATTTGAAGACAGAAATAATGTCAATATTTGATGATTTAACCCAAGATG                         ATCAAGATTCAGTGCGTCTGTTGGCTGTTGAAGGCTGTGCTGCCCTTGGTA
genomic: TCATTTGAAGACAGAAATAATGTCAATATTTGATGATTTAACCCAAGATGgtacattcta ... ttattttcagATCAAGATTCAGTGCGTCTGTTGGCTGTTGAAGGCTGTGCTGCCCTTGGTA
EST: gi|19770363|gb|BQ035084.1|BQ035084
EST:     TCATTTGAAGACAGAAATAATGTCAATATTTGATGATTTAACCCAAGATG                         ATCAAGATTCAGTGCGTCTGTTGGCTGTTGAAGGCTGTGCTGCCCTTGGTA
genomic: TCATTTGAAGACAGAAATAATGTCAATATTTGATGATTTAACCCAAGATGgtacattcta ... ttattttcagATCAAGATTCAGTGCGTCTGTTGGCTGTTGAAGGCTGTGCTGCCCTTGGTA
EST: gi|32831720|gb|CD971398.1|CD971398
EST:     TCATTTGAAGACAGAAATAATGTCAATATTTGATGATTTAACCCAAGATG                         ATCAAGATTCAGTGCGTCTG
genomic: TCATTTGAAGACAGAAATAATGTCAATATTTGATGATTTAACCCAAGATGgtacattcta ... ttattttcagATCAAGATTCAGTGCGTCTG
EST: gi|213188056|gb|FM186556.1|FM186556
EST:     TCATTTGAAGACAGAAATAATGTNNNTATTTGATGATTTAACCCAAGATG                         ATCAAGATTCAGTGCGTCTGTTGGCTGTTGAAGGCTGTGCTGCCCTTGGTA
genomic: TCATTTGAAGACAGAAATAATGTCAATATTTGATGATTTAACCCAAGATGgtacattcta ... ttattttcagATCAAGATTCAGTGCGTCTGTTGGCTGTTGAAGGCTGTGCTGCCCTTGGTA
EST: gi|32829962|gb|CD969640.1|CD969640
EST:     ATTTGATGATTTAACCCAAGATG                         ATCAAGATTCAGTGCGTCTGTTGGCTGTTGAAGGCTGTGCTGCCCTTGGTA
genomic: ATTTGATGATTTAACCCAAGATGgtacattcta ... ttattttcagATCAAGATTCAGTGCGTCTGTTGGCTGTTGAAGGCTGTGCTGCCCTTGGTA
EST: gi|32851452|gb|CD991133.1|CD991133
EST:     TCATTTGAAGACAGAAATAATGTCAATATTTGATGATTTAACCCAAGATG                         ATCAAGATTCAGTGCGTCTGTTGGCTGTTGAAGGCTGTGCTGCCCTTGGTA
genomic: TCATTTGAAGACAGAAATAATGTCAATATTTGATGATTTAACCCAAGATGgtacattcta ... ttattttcagATCAAGATTCAGTGCGTCTGTTGGCTGTTGAAGGCTGTGCTGCCCTTGGTA
EST: gi|211356091|gb|FL413289.1|FL413289
EST:     TCATTTGAAGACAGAAATAATGTCAATATTTGATGATTTAACCCAAGATG                         ATCAAGATTCAGTGCGTCTGTTGGCTGTTGAAGGCTGTGCTGCCCTTGGNA
genomic: TCATTTGAAGACAGAAATAATGTCAATATTTGATGATTTAACCCAAGATGgtacattcta ... ttattttcagATCAAGATTCAGTGCGTCTGTTGGCTGTTGAAGGCTGTGCTGCCCTTGGTA
EST: gi|211150174|gb|FL390449.1|FL390449
EST:     TCATTTGAAGACAGAAATAATGTCAATATTTGATGATTTAACCCAAGATG                         ATCAAGATTCAGTGCGTCTGTTGGCTGTTGAAGGCTGTGCTGCCCTTGGTA
genomic: TCATTTGAAGACAGAAATAATGTCAATATTTGATGATTTAACCCAAGATGgtacattcta ... ttattttcagATCAAGATTCAGTGCGTCTGTTGGCTGTTGAAGGCTGTGCTGCCCTTGGTA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acgcatttgggacatcattaggactatgtctaaacctgctggtctttattttcagATCAAGATTCAGTGCGTCTGTTGGCTGTTGAAGGCTGTGCTGCCCTTGGTAAATTGTTGGAACCACAAGATTGCGTAGCACACATTCTTCCAGTCATTGT
                           gtctaaa  putative branch site (score: 3)
                                          tctttattttc  putative PPT
                                          tctttatttt  TA-rich tract