Skip to another splice site:
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 5'  3'   		2  
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 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATCTGCTGTACAAGGACTACAACACGCACCAGAAGTTCTCCCTCACCACCTGCTCCCCCAATGGCGTCgtgagtgccccctccctcctaatcaatcaccatttcctcctttacctgagcgcgcctccccagaggacaccgcactttatttgcgtagtccttagtggag...

Basic information

species Zea mays
transcript GRMZM2G155021_T01
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G155021_T01 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os01g40570.1 (Oryza sativa), 5'ss of exon 2
ATCTGCTGTACAAGGACTACAACACGCACCAGAAGTTCTCCCTCACCACCTGCTCCCCCAATGGCGTCgtgagtgccccctccctcctaatcaatcaccatttcctcctttacctgagcgcgc-ctccccagaggacaccgcactttatttgcgtagtccttagtggag
||||||| |||| |||||||   |||||||| |||||| |||||||||||||| ||||| | ||||||||||||  || | ||  |||  ||  || |  | |||  ||         | | | |        |     | |  ||| | | |      |   ||| | 
ATCTGCTTTACAGGGACTACGGGACGCACCACAAGTTCACCCTCACCACCTGCACCCCCGAGGGCGTCgtgagtatcctcccctccctc-tctctctctctctcccactcggatccgtcacccaccatttcttgtctggcacgatttgtattctcgtgtcggtgtgaat

upper sequence: GRMZM2G155021_T01 (Zea mays), 5'ss of exon 2
lower sequence: GLYMA09G37570.1 (Glycine max), 5'ss of exon 2
ATCTGCTGTACAAGGACTACAACACGCACCAGAAGTTCTCCCTCACCACCTGCTCCCCCAATGGCGTCgtgagtgccccctccctcctaatcaatcaccatttcctcctttacctgagcgcgcctccccagaggacaccgcactttatttgcgtagtccttagtggag------
||||||||| |||||||||| |||   ||||||||||| || ||||||||| ||| |||| ||| || |||||||     |   |  |||||  |||   |||      |  |   | | |    |     | |         |||  |   |   |  ||| ||||       
ATCTGCTGTTCAAGGACTACCACAGTGACCAGAAGTTCACCATCACCACCTACTCACCCACTGGAGTTgtgagtgtttttttt-ttttaatctttcaatttttg-----tggcacaaacacaatgcatggaatgggtatttgttttgctgttgggtttgttattggatgttctt
















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|211256321|gb|FL030999.1|FL030999
EST:     ACAACACGCACCAGAAGTTCTGCCTCACCACCTCCTCCCCCAATGGCGTC                         GCAATCACAGCCGCAGGAACAAGGAAAAATGAGTCCATCTTTGGTGAGCTT
genomic: ACAACACGCACCAGAAGTTCTCCCTCACCACCTGCTCCCCCAATGGCGTCgtgagtgccc ... tttcatacagGCAATCACAGCCGCAGGAACAAGGAAAAATGAGTCCATCTTTGGTGAGCTT
EST: gi|76287240|gb|DV026808.1|DV026808
EST:     ACAACACGCACCAGAAGTTCTCCCTCACCACCTGCTCCCCCAATGGCGTC                         GCAATCACAGCCGCAGGAACAAGGAAAAATGAGTCCATCTTTGGTGAGCTT
genomic: ACAACACGCACCAGAAGTTCTCCCTCACCACCTGCTCCCCCAATGGCGTCgtgagtgccc ... tttcatacagGCAATCACAGCCGCAGGAACAAGGAAAAATGAGTCCATCTTTGGTGAGCTT
EST: gi|211331694|gb|FL020929.1|FL020929
EST:     ACAACACGCACCAGAAGTTCTGCCTCACCACCTCCTCCCCCAATGGCGTC                         GCAATCACAGCCGCAGGAACAAGGAAAAATGAGTCCATCTTTGGTGAGCTT
genomic: ACAACACGCACCAGAAGTTCTCCCTCACCACCTGCTCCCCCAATGGCGTCgtgagtgccc ... tttcatacagGCAATCACAGCCGCAGGAACAAGGAAAAATGAGTCCATCTTTGGTGAGCTT
EST: gi|22521527|gb|BU080338.1|BU080338
EST:     ACAACACGCACCAGAAGTTCTGCCTCACCACCTCCTCCCCCAATGGCGTC                         GCAATCACAGCCGCAGGAACAAGGAAAAATGAGTCCATCTTTGGTGAGCTT
genomic: ACAACACGCACCAGAAGTTCTCCCTCACCACCTGCTCCCCCAATGGCGTCgtgagtgccc ... tttcatacagGCAATCACAGCCGCAGGAACAAGGAAAAATGAGTCCATCTTTGGTGAGCTT
EST: gi|13126669|gb|BG317239.1|BG317239
EST:     ACCTGCTCCCCCAATGGCGTC                         GCAATCACAGCCGCAGGAACAAGGAAAAATGAGTCCATCTTTGGTGAGCTT
genomic: ACCTGCTCCCCCAATGGCGTCgtgagtgccc ... tttcatacagGCAATCACAGCCGCAGGAACAAGGAAAAATGAGTCCATCTTTGGTGAGCTT
EST: gi|71432321|gb|DR813371.1|DR813371
EST:     ACAACACGCACCAGAAGTTCTCCCTCACCACCTGCTCCCCCAATGGCGTC                         GCAATCACAGCCGCAGGAACAAGGAAAAATGAGTCCATCTTTGGTGAGCTT
genomic: ACAACACGCACCAGAAGTTCTCCCTCACCACCTGCTCCCCCAATGGCGTCgtgagtgccc ... tttcatacagGCAATCACAGCCGCAGGAACAAGGAAAAATGAGTCCATCTTTGGTGAGCTT
EST: gi|211331700|gb|FL020935.1|FL020935
EST:     ACAACACGCACCAGAAGTTCTGCCTCACCACCTCCTCCCCCAATGGCGTC                         GCAATCACAGCCGCAGGAACAAGGAAAAATGAGTCCATCTTTGGTGAGCTT
genomic: ACAACACGCACCAGAAGTTCTCCCTCACCACCTGCTCCCCCAATGGCGTCgtgagtgccc ... tttcatacagGCAATCACAGCCGCAGGAACAAGGAAAAATGAGTCCATCTTTGGTGAGCTT
EST: gi|33102963|gb|CF062923.1|CF062923
EST:     ACAACACGCACCAGAAGTTCTCCCTCACCACCTGCTCCCCCAATGGCGTC                         GCAATCACAGCCGCAGGAACAAGGAAAAATGAGTCCATCTTTGGTGAGCTT
genomic: ACAACACGCACCAGAAGTTCTCCCTCACCACCTGCTCCCCCAATGGCGTCgtgagtgccc ... tttcatacagGCAATCACAGCCGCAGGAACAAGGAAAAATGAGTCCATCTTTGGTGAGCTT
EST: gi|71425209|gb|DR806571.1|DR806571
EST:     ACAACACGCACCAGAAGTTCTCCCTCACCACCTGCTCCCCCAATGGCGTC                         GCAATCACAGCCGCAGGAACAAGGAAAAATGAGTCCATCTTTGGTGAGCTT
genomic: ACAACACGCACCAGAAGTTCTCCCTCACCACCTGCTCCCCCAATGGCGTCgtgagtgccc ... tttcatacagGCAATCACAGCCGCAGGAACAAGGAAAAATGAGTCCATCTTTGGTGAGCTT
EST: gi|211331696|gb|FL020931.1|FL020931
EST:     ACAACACGCACCAGAAGTTCTGCCTCACCACCTCCTCCCCCAATGGCGTC                         GCAATCACAGCCGCAGGAACAAGGAAAAATGAGTCCATCTTTGGTGAGCTT
genomic: ACAACACGCACCAGAAGTTCTCCCTCACCACCTGCTCCCCCAATGGCGTCgtgagtgccc ... tttcatacagGCAATCACAGCCGCAGGAACAAGGAAAAATGAGTCCATCTTTGGTGAGCTT
EST: gi|67041269|gb|CO467524.1|CO467524
EST:     ACAACACGCACCAGAAGTTCTGCCTCACCACCTCCTCCCCCAATGGCGTC                         GCAATCACAGCCGCAGGAACAAGGAAAAATGAGTCCATCTTTGGTGAACTT
genomic: ACAACACGCACCAGAAGTTCTCCCTCACCACCTGCTCCCCCAATGGCGTCgtgagtgccc ... tttcatacagGCAATCACAGCCGCAGGAACAAGGAAAAATGAGTCCATCTTTGGTGAGCTT
EST: gi|21987817|gb|BQ779345.1|BQ779345
EST:     ACAACACGCACCAGAAGTTCTGCCTCACCACCTCCTCCCCCAATGGCGTC                         GCAATCACAGCCGCAGGAACAAGGAAAAATGAGTCCATCTTTGGTGAGCTT
genomic: ACAACACGCACCAGAAGTTCTCCCTCACCACCTGCTCCCCCAATGGCGTCgtgagtgccc ... tttcatacagGCAATCACAGCCGCAGGAACAAGGAAAAATGAGTCCATCTTTGGTGAGCTT
EST: gi|20512879|gb|BQ280071.1|BQ280071
EST:     ACAACACGCACCAGAAGTTCTGCCTCACCACCTCCTCCCCCAATGGCGTC                         GCAATCACAGCCGCAGGAACAAGGAAAAATGAGTCCATCTTTGGTGAGCTT
genomic: ACAACACGCACCAGAAGTTCTCCCTCACCACCTGCTCCCCCAATGGCGTCgtgagtgccc ... tttcatacagGCAATCACAGCCGCAGGAACAAGGAAAAATGAGTCCATCTTTGGTGAGCTT
EST: gi|211331704|gb|FL020939.1|FL020939
EST:     ACAACACGCACCAGAAGTTCTGCCTCACCACCTCCTCCCCCAATGGCGTC                         GCAATCACAGCCGCAG-AACAAGGAAAAATGAGTCCATCTTTGGTGAGCTT
genomic: ACAACACGCACCAGAAGTTCTCCCTCACCACCTGCTCCCCCAATGGCGTCgtgagtgccc ... tttcatacagGCAATCACAGCCGCAGGAACAAGGAAAAATGAGTCCATCTTTGGTGAGCTT
EST: gi|33102108|gb|CF062068.1|CF062068
EST:     ACAACACGCACCAGAAGTTCTCCCTCACCACCTGCTCCCCCAATGGCGTC                         GCAATCACAGCCGCAGGAACAAGGAAAAATGAGTCCATCTTTGGTGAGCTT
genomic: ACAACACGCACCAGAAGTTCTCCCTCACCACCTGCTCCCCCAATGGCGTCgtgagtgccc ... tttcatacagGCAATCACAGCCGCAGGAACAAGGAAAAATGAGTCCATCTTTGGTGAGCTT
EST: gi|101397701|gb|EB820731.1|EB820731
EST:     ACAACACGCACCAGAAGTTCTCCCTCACCACCTGCTCCCCCAATGGCGTC                         GCAATCACAGCCGCAGGAACAAGGAAAAATGAGTCCATCTTTGGTGAGCTT
genomic: ACAACACGCACCAGAAGTTCTCCCTCACCACCTGCTCCCCCAATGGCGTCgtgagtgccc ... tttcatacagGCAATCACAGCCGCAGGAACAAGGAAAAATGAGTCCATCTTTGGTGAGCTT
EST: gi|88752281|gb|DY536422.1|DY536422
EST:     ACAACACGCACCAGAAGTTCTCCCTCACCACCTGCTCCCCCAATGGCGTC                         GCAATCACAGCCGCAGGAACAAGGAAAAATGAGTCCATCTTTGGTGAGCTT
genomic: ACAACACGCACCAGAAGTTCTCCCTCACCACCTGCTCCCCCAATGGCGTCgtgagtgccc ... tttcatacagGCAATCACAGCCGCAGGAACAAGGAAAAATGAGTCCATCTTTGGTGAGCTT
EST: gi|22472298|gb|BU036778.1|BU036778
EST:     ACAACACGCACCAGAAGTTCTGCCTCACCACCTCCTCCCCCAATGGCGTC                         GCAATCACAGCCGCAGGAACAAGGAAAAATGAGTCCATCTTTGGTGAGCTT
genomic: ACAACACGCACCAGAAGTTCTCCCTCACCACCTGCTCCCCCAATGGCGTCgtgagtgccc ... tttcatacagGCAATCACAGCCGCAGGAACAAGGAAAAATGAGTCCATCTTTGGTGAGCTT
EST: gi|74244464|gb|DT652378.1|DT652378
EST:     ACAACACGCACCAGAAGTTCTCCCTCACCACCTCCTCCCCCAATGGCGTC                         GCAATCACAGCCGCAGGAACAAGGAAAAATGAGTCCATCTTTGGTGAGCTT
genomic: ACAACACGCACCAGAAGTTCTCCCTCACCACCTGCTCCCCCAATGGCGTCgtgagtgccc ... tttcatacagGCAATCACAGCCGCAGGAACAAGGAAAAATGAGTCCATCTTTGGTGAGCTT
EST: gi|211331699|gb|FL020934.1|FL020934
EST:     ACAACACGCACCAGAAGTTCTGCCTCACCACCTCCTCCCCCAATGGCGTC                         GCAATCACAGCCGCAGGAACAAGGAAAAATGAGTCCATCTTTGGTGAGCTT
genomic: ACAACACGCACCAGAAGTTCTCCCTCACCACCTGCTCCCCCAATGGCGTCgtgagtgccc ... tttcatacagGCAATCACAGCCGCAGGAACAAGGAAAAATGAGTCCATCTTTGGTGAGCTT
EST: gi|211331695|gb|FL020930.1|FL020930
EST:     ACAACACGCACCAGAAGTTCTGCCTCACCACCTCCTCCCCCAATGGCGTC                         GCAATCACAGCCGCAGGAACAAGGAAAAATGAGTCCATCTTTGGTGAGCTT
genomic: ACAACACGCACCAGAAGTTCTCCCTCACCACCTGCTCCCCCAATGGCGTCgtgagtgccc ... tttcatacagGCAATCACAGCCGCAGGAACAAGGAAAAATGAGTCCATCTTTGGTGAGCTT
EST: gi|37423435|gb|CF649445.1|CF649445
EST:     ACAACACGCACCAGAAGTTCTCCCTCACCACCTGCTCCCCCAATGGCGTC                         GCAATCACAGCCGCAGGAACAAGGAAAAATGAGTCCATCTTTGGTGAGCTT
genomic: ACAACACGCACCAGAAGTTCTCCCTCACCACCTGCTCCCCCAATGGCGTCgtgagtgccc ... tttcatacagGCAATCACAGCCGCAGGAACAAGGAAAAATGAGTCCATCTTTGGTGAGCTT
EST: gi|91874353|gb|EB404310.1|EB404310
EST:     ACAACACGCACCAGAAGTTCTCCCTCACCACCTGCTCCCCCAATGGCGTC                         GCAATCACAGCCGCAGGAACAAGGAAAAATGAGTCCATCTTTGGTGAGCTT
genomic: ACAACACGCACCAGAAGTTCTCCCTCACCACCTGCTCCCCCAATGGCGTCgtgagtgccc ... tttcatacagGCAATCACAGCCGCAGGAACAAGGAAAAATGAGTCCATCTTTGGTGAGCTT
EST: gi|67020552|gb|CO449301.1|CO449301
EST:     ACAACACGCACCAGAAGTTCTGCCTCACCACCTCCTCCCCCAATGGCGTC                         GCAATCACAGCCGCAGGAACAAGGAAAAATGAGTCCATCTTTGGTGAACTT
genomic: ACAACACGCACCAGAAGTTCTCCCTCACCACCTGCTCCCCCAATGGCGTCgtgagtgccc ... tttcatacagGCAATCACAGCCGCAGGAACAAGGAAAAATGAGTCCATCTTTGGTGAGCTT
EST: gi|78112263|gb|DV530657.1|DV530657
EST:     ACAACACGCACCAGAAGTTCTCCCTCACCACCTGCTCCCCCAATGGCGTC                         GCAATCACAGCCGCAGGAACAAGGAAAAATGAGTCCATCTTTGGTGAGCTT
genomic: ACAACACGCACCAGAAGTTCTCCCTCACCACCTGCTCCCCCAATGGCGTCgtgagtgccc ... tttcatacagGCAATCACAGCCGCAGGAACAAGGAAAAATGAGTCCATCTTTGGTGAGCTT
EST: gi|211331701|gb|FL020936.1|FL020936
EST:     ACAACACGCACCAGAAGTTCTGCCTCACCACCTCCTCCCCCAATGGCGTC                         GCAATCACAGCCGCAGGAACAAGGAAAAATGAGTCCATCTTTGGTGAGCTT
genomic: ACAACACGCACCAGAAGTTCTCCCTCACCACCTGCTCCCCCAATGGCGTCgtgagtgccc ... tttcatacagGCAATCACAGCCGCAGGAACAAGGAAAAATGAGTCCATCTTTGGTGAGCTT
EST: gi|33104262|gb|CF064222.1|CF064222
EST:     ACAACACGCACCAGAAGTTCTCCCTCACCACCTGCTCCCCCAATGGCGTC                         GCAATCACAGCCGCAGGAACAAGGAAAAATGAGTCCATCTTTGGTGAGCTT
genomic: ACAACACGCACCAGAAGTTCTCCCTCACCACCTGCTCCCCCAATGGCGTCgtgagtgccc ... tttcatacagGCAATCACAGCCGCAGGAACAAGGAAAAATGAGTCCATCTTTGGTGAGCTT
EST: gi|37425454|gb|CF650468.1|CF650468
EST:     ACAACACGCACCAGAAGTTCTCCCTGACCACCTGCGCCCCCAATGGCGTC                         GCAATCACAGCCGCAGGAACAAGGAAAAATGAGTCCATCTTTGGTGAGCTT
genomic: ACAACACGCACCAGAAGTTCTCCCTCACCACCTGCTCCCCCAATGGCGTCgtgagtgccc ... tttcatacagGCAATCACAGCCGCAGGAACAAGGAAAAATGAGTCCATCTTTGGTGAGCTT
EST: gi|32907826|gb|CF012639.1|CF012639
EST:     ACAACACGCACCAGAAGTTCTGCCTCACCACCTCCTCCCCCAATGGCGTC                         GCAATCACAGCCGCAGGAACAAGGAAAAATGAGTCCATCTTTGGTGAGCTT
genomic: ACAACACGCACCAGAAGTTCTCCCTCACCACCTGCTCCCCCAATGGCGTCgtgagtgccc ... tttcatacagGCAATCACAGCCGCAGGAACAAGGAAAAATGAGTCCATCTTTGGTGAGCTT

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: 49 (upstream exon), 48 (downstream exon)
Score: 36

ATCTGCTGTACAAGGACTACAACACGCACCAGAAGTTCTCCCTCACCACCTGCTCCCCCAATGGCGTCgtgagtgccc ... tttcatacagGCAATCACAGCCGCAGGAACAAGGAAAAATGAGTCCATCTTTGGTGAGCTTCACACCCAGATTAAGAACAAGAAATTGACAGTTGATGTCAAAGCAAACT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 84

ATCTGCTGTACAAGGACTACAACACGCACCAGAAGTTCTCCCTCACCACCTGCTCCCCCAATGGCGTCgtgagtgccc ... tttcatacagGCAATCACAGCCGCAGGAACAAGGAAAAATGAGTCCATCTTTGGTGAGCTTCACACCCAGATTAAGAACAAGAAATTGACAGTTGATGTCAAAGCAAACT


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 62

ATCTGCTGTACAAGGACTACAACACGCACCAGAAGTTCTCCCTCACCACCTGCTCCCCCAATGGCGTCgtgagtgccc ... tttcatacagGCAATCACAGCCGCAGGAACAAGGAAAAATGAGTCCATCTTTGGTGAGCTTCACACCCAGATTAAGAACAAGAAATTGACAGTTGATGTCAAAGCAAACT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 147

ATCTGCTGTACAAGGACTACAACACGCACCAGAAGTTCTCCCTCACCACCTGCTCCCCCAATGGCGTCgtgagtgccc ... tttcatacagGCAATCACAGCCGCAGGAACAAGGAAAAATGAGTCCATCTTTGGTGAGCTTCACACCCAGATTAAGAACAAGAAATTGACAGTTGATGTCAAAGCAAACT


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATCTGCTGTACAAGGACTACAACACGCACCAGAAGTTCTCCCTCACCACCTGCTCCCCCAATGGCGTCgtgagtgccccctccctcctaatcaatcaccatttcctcctttacctgagcgcgcctccccagaggacaccgcactttatttgcgtagtccttagtggag

- - - - - - - - - - - - - - - AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ccctccc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cctcccc