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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTCTTTCAGCTTCACTAAATGTTAGGATAGTTTATCTGGACATCATGAGGCCATTTGCTGAATCAACTTTGTTAGGgtgagaacgagatgctatttacttgacattgtcatgccaatggttgcaccatctttatagtaaaaacataatctctctcttttctctcattgctgattttttatgtcttcactttggtcag

Basic information

species Zea mays
transcript GRMZM2G140917_T01
intron # 14
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G140917_T01 (Zea mays), 5'ss of exon 14
lower sequence: LOC_Os06g48770.2 (Oryza sativa), 5'ss of exon 12
GTCTTTCAGCTTCACTAAATGTTAGGATAGTTTATCTGGACATCATGAGGCCATTTGCTGAATCAACTTTGTTAGGgtgagaacgagatgctatttacttgacattgtcatgccaatggttgcaccatctttatagtaaaaacataatctctctcttttctctcattgctgattttttatgtcttcactttggtcag
| || ||||| |||||||||||||||||||||||||| ||||||||||||||||||||||||||||||||| ||||||||||        || ||||  |              | || |||||  | | ||| ||||||              | | | | | |||||| ||||   ||| ||||  |   |  ||
GGCTATCAGCATCACTAAATGTTAGGATAGTTTATCTAGACATCATGAGGCCATTTGCTGAATCAACTTTGCTAGGgtgagatgc-----ctgtttatct--------------actgtttgcaggagccttagagtaaag-------------catcttttttattgcttattt---atgccttcgttgatggtag

upper sequence: GRMZM2G140917_T01 (Zea mays), 5'ss of exon 14
lower sequence: GLYMA17G24420.1 (Glycine max), 5'ss of exon 12
GTCTTTCAGCTTCACTAAATGTTAGGATAGTTTATCTGGACATCATGAGGCCATTTGCTGAATCAACTTTGTTAGGgtgagaa--cgagatgctatttacttgacattgtcatgccaatggttgcaccatctttatagtaaaaacataatctctctcttttctctcattgctgattttttatgtcttcactttggtcag
| |||||  |  |  | |||||  | ||||| ||| ||||||| |||||||||||||||||||||  ||||   |||||||    |   |   | | |  |||  |||          | ||| |    |      |  | |   | | |  |                                              
GGCTTTCTTCCACCATGAATGTACGAATAGTATATATGGACATTATGAGGCCATTTGCTGAATCAGTTTTGAGTGGgtgagtcttctgaaaattttctgattggtatttattacttgcttgtttcctttttggctgaacagaggtacacttgccag-------------------------------------------

upper sequence: GRMZM2G140917_T01 (Zea mays), 5'ss of exon 14
lower sequence: AT5G24810.2 (Arabidopsis thaliana), 5'ss of exon 13
GTCTTTCAGCTTCACTAAATGTTAGGATAGTTTATCTGGACATCATGAGGCCATTTGCTGAATCAACTTTGTTAGGgtgagaacgagatgctatttacttgacattgtcatgccaatggttgcaccatctttatagtaaaaacataatctctctcttttctctcattgctgattttttatgtcttcactttggtcag
| |||||| || |  | |||||| |||| |||||||||||||||||||| |||||||| |||||   | ||||||||| || ||    ||  ||||    |    | | ||    ||   |     || | |   |||  | |||||| |   | ||                                        
GACTTTCATCTACTATGAATGTTCGGATTGTTTATCTGGACATCATGAGACCATTTGCCGAATCTGTTCTGTTAGGgtaagcaccct-tggaatttggcagctcattttatt---atctctttgtgatatatcccgtacgaccataatgtgggttttcag-------------------------------------

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|211142855|gb|FL032416.1|FL032416
EST:     ATAGTTTATCTGGACATCATGAGGCCATCTGCTGAATCAACTTTGTTAGG                         GAGTTTGACACACGGACAAATACCTAACAGTCAGTGGATTTTTGACTCACC
genomic: ATAGTTTATCTGGACATCATGAGGCCATTTGCTGAATCAACTTTGTTAGGgtgagaacga ... ctttggtcagGAGTTTGACACACGGACAAATACCTAACAGTCAGTGGATTTTTGACTCACC
EST: gi|211402616|gb|FL252144.1|FL252144
EST:     ATAGTTTATCTGGACATCATGAGGCCATCTGCTGAATCAACTTTGTTAGG                         GAGTTTGACACACGGACAAATACCTAACAGTCAGTGGATTTTTGACTCACC
genomic: ATAGTTTATCTGGACATCATGAGGCCATTTGCTGAATCAACTTTGTTAGGgtgagaacga ... ctttggtcagGAGTTTGACACACGGACAAATACCTAACAGTCAGTGGATTTTTGACTCACC
EST: gi|211145716|gb|FL032440.1|FL032440
EST:     ATAGTTTATCTGGACATCATGAGGCCATCTGCTGAATCAACTTTGTTAGG                         GAGTTTGACACACGGACAAATACCTAACAGTCAGTGGATTTTTGACTCACC
genomic: ATAGTTTATCTGGACATCATGAGGCCATTTGCTGAATCAACTTTGTTAGGgtgagaacga ... ctttggtcagGAGTTTGACACACGGACAAATACCTAACAGTCAGTGGATTTTTGACTCACC
EST: gi|211144291|gb|FL032433.1|FL032433
EST:     GTTTATCTGGACATCATGAGGCCATTTGCTGAATCATTTTTTGGTAAGG
genomic: GTTTATCTGGACATCATGAGGCCATTTGCTGAATCAACTTT-GTTA-GG
EST: gi|89763775|gb|DY690831.1|DY690831
EST:     ATAGTTTATCTGGACATCATGAGGCCATTTGCTGAATCAACTTTGTTAGG                         GAGTTTGACACACGGACAAATACCTAACAGTCAGTGGATTTTTGACTCACC
genomic: ATAGTTTATCTGGACATCATGAGGCCATTTGCTGAATCAACTTTGTTAGGgtgagaacga ... ctttggtcagGAGTTTGACACACGGACAAATACCTAACAGTCAGTGGATTTTTGACTCACC
EST: gi|211145718|gb|FL032442.1|FL032442
EST:     TAGTTTATCTGGACATCATGAGGCCATCTGCTGAATCAACTTTTGTTAGG                         GAGTTTGACACACGGACAAATACCTAACAGTCAGTGGATTTTTGACTCAC
genomic: TAGTTTATCTGGACATCATGAGGCCATTTGCTGAATCAACTTT-GTTAGGgtgagaacga ... ctttggtcagGAGTTTGACACACGGACAAATACCTAACAGTCAGTGGATTTTTGACTCAC
EST: gi|148966697|gb|EE017760.2|EE017760
EST:     ATAGTTTATCTGGACATCATGAGGCCATTTGCTGAATCAACTTTGTTAGG                         GAGTTTGACACACGGACAAATACCTAACAGTCAGTGGATTTTTGACTCACC
genomic: ATAGTTTATCTGGACATCATGAGGCCATTTGCTGAATCAACTTTGTTAGGgtgagaacga ... ctttggtcagGAGTTTGACACACGGACAAATACCTAACAGTCAGTGGATTTTTGACTCACC
EST: gi|211144288|gb|FL032430.1|FL032430
EST:     ATAGTTTATCTGGACATCATGAGGCCATCTGCTGAATCAACTTTGTTAGG                         GAGTTTGACACACGGACAAATACCTAACAGTCAGTGGATTTTTGACTCACC
genomic: ATAGTTTATCTGGACATCATGAGGCCATTTGCTGAATCAACTTTGTTAGGgtgagaacga ... ctttggtcagGAGTTTGACACACGGACAAATACCTAACAGTCAGTGGATTTTTGACTCACC
EST: gi|211145719|gb|FL032443.1|FL032443
EST:     ATAGTTTATCTGGACATCATGAGGCCATCTGCTGAATCAACTTTGTTAGG                         GAGTTTGACACACGGACAAATACCTAACAGTCAGTGGATTTTTGACTCACC
genomic: ATAGTTTATCTGGACATCATGAGGCCATTTGCTGAATCAACTTTGTTAGGgtgagaacga ... ctttggtcagGAGTTTGACACACGGACAAATACCTAACAGTCAGTGGATTTTTGACTCACC
EST: gi|211144285|gb|FL032427.1|FL032427
EST:     ATAGTTTATCTGGACATCATGAGGCCATCTGCTGAATCAACTTTGTTAGG                         GAGTTTGACACNCGGACNAATACCTAACAGTCAGTGGATTTTTGACTCACC
genomic: ATAGTTTATCTGGACATCATGAGGCCATTTGCTGAATCAACTTTGTTAGGgtgagaacga ... ctttggtcagGAGTTTGACACACGGACAAATACCTAACAGTCAGTGGATTTTTGACTCACC
EST: gi|211145714|gb|FL032438.1|FL032438
EST:     ATAGTTTATCTGGACATCATGAGGCCATCTGCTGAATCAACTTTGTTAGG                         GAGTTTGACACACGGACAAATACCCTAACAGTCAGTGGATTTTTGACTCAC
genomic: ATAGTTTATCTGGACATCATGAGGCCATTTGCTGAATCAACTTTGTTAGGgtgagaacga ... ctttggtcagGAGTTTGACACACGGACAAATACC-TAACAGTCAGTGGATTTTTGACTCAC
EST: gi|211145713|gb|FL032437.1|FL032437
EST:     ATAGTTTATCTGGACATCATGAGGCCATCTGCTGAATCAACTTTGTTAGG                         GAGTTTGACACACGGACAAATACCTAACAGTCAGNGGATTTTTGACTCACC
genomic: ATAGTTTATCTGGACATCATGAGGCCATTTGCTGAATCAACTTTGTTAGGgtgagaacga ... ctttggtcagGAGTTTGACACACGGACAAATACCTAACAGTCAGTGGATTTTTGACTCACC
EST: gi|211144294|gb|FL032436.1|FL032436
EST:     ATAGTTTATCTGGACATCATGAGGCCATCTGCTGAATCAACTTTGTTAGG                         GAGTTTGACACACGGACAAATACCTAACAGTCAGTGGATTTTTGACTCACC
genomic: ATAGTTTATCTGGACATCATGAGGCCATTTGCTGAATCAACTTTGTTAGGgtgagaacga ... ctttggtcagGAGTTTGACACACGGACAAATACCTAACAGTCAGTGGATTTTTGACTCACC
EST: gi|211144287|gb|FL032429.1|FL032429
EST:     ATAGTTTATCTGGACATCATGAGGCCATCTGCTGAATCAACTTTGTTAGG                         GAGTTTGACACACGGACAAATACCTAACAGTCAGTGGATTTTTGACTCACC
genomic: ATAGTTTATCTGGACATCATGAGGCCATTTGCTGAATCAACTTTGTTAGGgtgagaacga ... ctttggtcagGAGTTTGACACACGGACAAATACCTAACAGTCAGTGGATTTTTGACTCACC
EST: gi|211145717|gb|FL032441.1|FL032441
EST:     ATAGTTTATCTGGACATCATGAGGCCATCTGCTGAATCAACTTTGTTAGG                         GAGTTTGACACACGGACAAATACCTAACAGTCAGTGGATTTTTGACTCACC
genomic: ATAGTTTATCTGGACATCATGAGGCCATTTGCTGAATCAACTTTGTTAGGgtgagaacga ... ctttggtcagGAGTTTGACACACGGACAAATACCTAACAGTCAGTGGATTTTTGACTCACC
EST: gi|211144283|gb|FL032425.1|FL032425
EST:     ATAGTTTATCTGGACATCATGAGGCCATCTGCTGAATCAACTTTGTTAGG                         GAGTTTGACACACGGACAAATACCTAACAGTCAGTGGATTTTTGACTCACC
genomic: ATAGTTTATCTGGACATCATGAGGCCATTTGCTGAATCAACTTTGTTAGGgtgagaacga ... ctttggtcagGAGTTTGACACACGGACAAATACCTAACAGTCAGTGGATTTTTGACTCACC
EST: gi|211142856|gb|FL032417.1|FL032417
EST:     ATAGTTTATCTGGACATCATGAGGCCATCTGCTGAATCAACTTTGTTAGG                         GAGTTTGACACACGGACAAATACCTAACAGTCAGTGGATTTTTGACTCACC
genomic: ATAGTTTATCTGGACATCATGAGGCCATTTGCTGAATCAACTTTGTTAGGgtgagaacga ... ctttggtcagGAGTTTGACACACGGACAAATACCTAACAGTCAGTGGATTTTTGACTCACC
EST: gi|211144292|gb|FL032434.1|FL032434
EST:     ATAGTTTATCTGGACATCATGAGGCCATCTGCTGAATCAACTTTGTTAGG                         GAGTTTGACACACGGACAAATACCTAACAGTCAGTGGATTTTTGACTCACC
genomic: ATAGTTTATCTGGACATCATGAGGCCATTTGCTGAATCAACTTTGTTAGGgtgagaacga ... ctttggtcagGAGTTTGACACACGGACAAATACCTAACAGTCAGTGGATTTTTGACTCACC
EST: gi|211145720|gb|FL032444.1|FL032444
EST:     ATAGTTTATCTGGACATCATGAGGCCATCTGCTGAATCAACTTTGNTAGG                         GAGTTTGACACACGGACAAATACCTAACAGTCAGTGGATTTTTGACTCACC
genomic: ATAGTTTATCTGGACATCATGAGGCCATTTGCTGAATCAACTTTGTTAGGgtgagaacga ... ctttggtcagGAGTTTGACACACGGACAAATACCTAACAGTCAGTGGATTTTTGACTCACC
EST: gi|211142860|gb|FL032421.1|FL032421
EST:     ATAGTTTATCTGGACATCATGAGGCCATTTGCTGAATCA-CTTTGTTAGG                         GAGTTTGACACACG
genomic: ATAGTTTATCTGGACATCATGAGGCCATTTGCTGAATCAACTTTGTTAGGgtgagaacga ... ctttggtcagGAGTTTGACACACG
EST: gi|211144290|gb|FL032432.1|FL032432
EST:     ATAGTTTATCTGGACATCATGAGGCCATCTGCTGAATCAACTTTGTTAGG                         GAGTNTGACACACGGACAAATACCTAACAGTCAGTGGATTTTTGACTCACC
genomic: ATAGTTTATCTGGACATCATGAGGCCATTTGCTGAATCAACTTTGTTAGGgtgagaacga ... ctttggtcagGAGTTTGACACACGGACAAATACCTAACAGTCAGTGGATTTTTGACTCACC
EST: gi|67017334|gb|CO446083.1|CO446083
EST:     ATAGTTTATCTGGACATCATGAGGCCATTTGCTGAATCAACTTTGTTAGG                         GAGTTTGACACACGGACAAATACCTAACAGTCAGTGGATTTTTGACTCACC
genomic: ATAGTTTATCTGGACATCATGAGGCCATTTGCTGAATCAACTTTGTTAGGgtgagaacga ... ctttggtcagGAGTTTGACACACGGACAAATACCTAACAGTCAGTGGATTTTTGACTCACC
EST: gi|211142857|gb|FL032418.1|FL032418
EST:     ATAGTTTATCTGGACATCATGAGGCCATCTGCTGAATCAACTTTGTTAGG                         GAGTTTGACACACGGACAAATACCTAACAGTCAGTGGATTTTTGACTCACC
genomic: ATAGTTTATCTGGACATCATGAGGCCATTTGCTGAATCAACTTTGTTAGGgtgagaacga ... ctttggtcagGAGTTTGACACACGGACAAATACCTAACAGTCAGTGGATTTTTGACTCACC
EST: gi|211142859|gb|FL032420.1|FL032420
EST:     ATAGTTTATCTGGACATCATGAGGCCATCTGCTGAATCAACTTTGTTAGG                         GAGTTTGACACACGGACAAATACCTAACAGTCAGTGGATTTTTGACTCACC
genomic: ATAGTTTATCTGGACATCATGAGGCCATTTGCTGAATCAACTTTGTTAGGgtgagaacga ... ctttggtcagGAGTTTGACACACGGACAAATACCTAACAGTCAGTGGATTTTTGACTCACC
EST: gi|211144282|gb|FL032424.1|FL032424
EST:     ATAGTTTATCTGGACATCATGAGGCCATCTGCTGAATCAACTTTGTTAGG                         GAGTTTGACAC
genomic: ATAGTTTATCTGGACATCATGAGGCCATTTGCTGAATCAACTTTGTTAGGgtgagaacga ... ctttggtcagGAGTTTGACAC

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), 46 (downstream exon)
Score: 47

GTCTTTCAGCTTCACTAAATGTTAGGATAGTTTATCTGGACATCATGAGGCCATTTGCTGAATCAACTTTGTTAGGgtgagaacga ... ctttggtcagGAGTTTGACACACGGACAAATACCTAACAGTCAGTGGATTTTTGACTCACCTGCTAACTCTGATGTGGAGTCTAAACTGAGAAATTATCTGCTTGAGTTG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 233

GTCTTTCAGCTTCACTAAATGTTAGGATAGTTTATCTGGACATCATGAGGCCATTTGCTGAATCAACTTTGTTAGGgtgagaacga ... ctttggtcagGAGTTTGACACACGGACAAATACCTAACAGTCAGTGGATTTTTGACTCACCTGCTAACTCTGATGTGGAGTCTAAACTGAGAAATTATCTGCTTGAGTTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 282

GTCTTTCAGCTTCACTAAATGTTAGGATAGTTTATCTGGACATCATGAGGCCATTTGCTGAATCAACTTTGTTAGGgtgagaacga ... ctttggtcagGAGTTTGACACACGGACAAATACCTAACAGTCAGTGGATTTTTGACTCACCTGCTAACTCTGATGTGGAGTCTAAACTGAGAAATTATCTGCTTGAGTTG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 270

GTCTTTCAGCTTCACTAAATGTTAGGATAGTTTATCTGGACATCATGAGGCCATTTGCTGAATCAACTTTGTTAGGgtgagaacga ... ctttggtcagGAGTTTGACACACGGACAAATACCTAACAGTCAGTGGATTTTTGACTCACCTGCTAACTCTGATGTGGAGTCTAAACTGAGAAATTATCTGCTTGAGTTG