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

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtaccaccactcctatttcactaaaaaaaatttggcctttactgaacattggtcttgcgaccactcctatttctactacggtaaataaccatgaaaaacttaatcagGAATAACCACGGTGATACCCTGGTTGCGTCCTACTACCACTTGGTAAAGAACCATTCAGGCACTGCTGTTGGAGCTGAGTTGTCTCACAGCATGTCGAGA

Basic information

species Zea mays
transcript GRMZM2G155021_T01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G155021_T01 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os01g40570.1 (Oryza sativa), 3'ss of exon 5
--------------------------------gtgagtaccac----cactccta--tttcactaaaaaa--aatt------tggcctttactgaacattggtc-ttgcgacc---actcctatttc--------tactacggtaaataaccatgaaaaacttaatcagGAATAACCACGGTGATACCCTGGTTGCGTCCTACTACCACTTGGTAAAGAACCATTCAGGCACTGCTGTTGGAGCTGAGTTGTCTCACAGCATGTCGAGA
                                 | || ||  |     ||| | |  | | ||| | ||   ||||      |  | |||  ||   | ||||  ||| |  |   |||||| | ||        || |  ||||| | ||| |  ||  | |   |||||| || || ||||||||| || |||| |||||||||||| |||||||| |||||||   |||||| || ||||||||| |||| |||||| | || || 
gtaagtattgattctatgcatggttatcatatattagcactgcatgttacttccaagtctgactgagaagccaattccagaataacatttcttgtttactggttgttgtggtcattactcctgtatcagtttatttagtttggtaactgaccttacaattcctgtccagGAACAATCATGGTGATACCTTGATTGCATCCTACTACCACCTGGTAAAGCACCATTCGAACACTGCCGTAGGAGCTGAGCTGTCCCACAGCTTCTCAAGG
















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|76287240|gb|DV026808.1|DV026808
EST:     AACGCTGCCCTGAGCCTCACCAGTCCAGATCTTATTGCTTCCCTTCATCT                         GAATAACCACGGTGATACCCTGGTTGCGTCCTACTACCACTT
genomic: AACGCTGCCCTGAGCCTCACCAGTCCAGATCTTATTGCTTCCCTTCATCTgtgagtacca ... acttaatcagGAATAACCACGGTGATACCCTGGTTGCGTCCTACTACCACTT
EST: gi|18163717|gb|BM333556.1|BM333556
EST:     AACGCTGCCCTGAGCCTCACCAGTCCAGATCTTATTGCTTCCCTTCATCT                         GAATAACCACGGTGATACCCTGGTTGCGTCCTACTACCACTTGGTAAAGAA
genomic: AACGCTGCCCTGAGCCTCACCAGTCCAGATCTTATTGCTTCCCTTCATCTgtgagtacca ... acttaatcagGAATAACCACGGTGATACCCTGGTTGCGTCCTACTACCACTTGGTAAAGAA
EST: gi|13126669|gb|BG317239.1|BG317239
EST:     AACGCTGCCCTGAGCCTCACCAGTCCAGATCTTATTGCTTCCCTTCATCT                         GAATAACCACGGTGATACCCTGGTTGCGTCCTACTACCACTTGGTAAAGAA
genomic: AACGCTGCCCTGAGCCTCACCAGTCCAGATCTTATTGCTTCCCTTCATCTgtgagtacca ... acttaatcagGAATAACCACGGTGATACCCTGGTTGCGTCCTACTACCACTTGGTAAAGAA
EST: gi|17931060|gb|BM268020.1|BM268020
EST:     AACGCTGCCCTGAGCCTCACCAGTCCAGATCTTATTGCTTCCCTTCATCT                         GAATAACCACGGTGATACCCTGGTTGCGTCCTACTACCACTTGGTAAAGAA
genomic: AACGCTGCCCTGAGCCTCACCAGTCCAGATCTTATTGCTTCCCTTCATCTgtgagtacca ... acttaatcagGAATAACCACGGTGATACCCTGGTTGCGTCCTACTACCACTTGGTAAAGAA
EST: gi|71432321|gb|DR813371.1|DR813371
EST:     AACGCTGCCCTGAGCCTCACCAGTCCAGATCTTATTGCTTCCCTTCATCT                         GAATAACCACGGTGATACCCTGGTTGCGTCCTACTACCACTTGGTAAAGAA
genomic: AACGCTGCCCTGAGCCTCACCAGTCCAGATCTTATTGCTTCCCTTCATCTgtgagtacca ... acttaatcagGAATAACCACGGTGATACCCTGGTTGCGTCCTACTACCACTTGGTAAAGAA
EST: gi|71425209|gb|DR806571.1|DR806571
EST:     AACGCTGCCCTGAGCCTCACCAGTCCAGATCTTATTGCTTCCCTTCATCT                         GAATAACCACGGTGATACCCTGGTTGCGTCCTACTACCACTTGGTAAAGAA
genomic: AACGCTGCCCTGAGCCTCACCAGTCCAGATCTTATTGCTTCCCTTCATCTgtgagtacca ... acttaatcagGAATAACCACGGTGATACCCTGGTTGCGTCCTACTACCACTTGGTAAAGAA
EST: gi|211256214|gb|FL477687.1|FL477687
EST:     CACCAGTCCAGATCTTATTGCTTCCCTTCATCT                         GAATAACCACGGTGATACCCTGGTTGCGTCCTACTACCACCTGGTAAAGAA
genomic: CACCAGTCCAGATCTTATTGCTTCCCTTCATCTgtgagtacca ... acttaatcagGAATAACCACGGTGATACCCTGGTTGCGTCCTACTACCACTTGGTAAAGAA
EST: gi|211472941|gb|FL454238.1|FL454238
EST:     GAGCCTCACCAGTCCAGATCTTATTGCTTCCCTTCATCT                         GAATAACCACGGTGATACCCTGGTTGCGTCCTACTACCACCTGGTAAAGAA
genomic: GAGCCTCACCAGTCCAGATCTTATTGCTTCCCTTCATCTgtgagtacca ... acttaatcagGAATAACCACGGTGATACCCTGGTTGCGTCCTACTACCACTTGGTAAAGAA
EST: gi|78112262|gb|DV530656.1|DV530656
EST:     AACGCTGCCCTGAGCCTCACCAGTCCAGATCTTATTGCTTCCCTTCATCT                         GAATAACCACGGTGATACCCTGGTTGCGTCCTACTACCACTTGGTAAAGAA
genomic: AACGCTGCCCTGAGCCTCACCAGTCCAGATCTTATTGCTTCCCTTCATCTgtgagtacca ... acttaatcagGAATAACCACGGTGATACCCTGGTTGCGTCCTACTACCACTTGGTAAAGAA
EST: gi|18171153|gb|BM340993.1|BM340993
EST:     AACGCTGCCNTGAGCCTCACCAGTCCAGATCTTATTGCTTCCCTTCATCT                         GAATAACCACGGTGATACCCTGGTTGCGTCCTACTACCACTTGGTAAAGAA
genomic: AACGCTGCCCTGAGCCTCACCAGTCCAGATCTTATTGCTTCCCTTCATCTgtgagtacca ... acttaatcagGAATAACCACGGTGATACCCTGGTTGCGTCCTACTACCACTTGGTAAAGAA
EST: gi|67041269|gb|CO467524.1|CO467524
EST:     AACGCTGCCCTGAGCCTCACCAGTCCAGATCTTATTGCTTCCCTTCATCT                         GAATAACCACGGTGATACCCTGGTTGCGTCCTACTACCACCTGGTAAAGAA
genomic: AACGCTGCCCTGAGCCTCACCAGTCCAGATCTTATTGCTTCCCTTCATCTgtgagtacca ... acttaatcagGAATAACCACGGTGATACCCTGGTTGCGTCCTACTACCACTTGGTAAAGAA
EST: gi|21987817|gb|BQ779345.1|BQ779345
EST:     AACGCTGCCCTGAGCCTCACCAGTCCAGATCTTATTGCTTTCCTTCATCT                         GAATAACCACGGTGATACCCTGGTTGCGT
genomic: AACGCTGCCCTGAGCCTCACCAGTCCAGATCTTATTGCTTCCCTTCATCTgtgagtacca ... acttaatcagGAATAACCACGGTGATACCCTGGTTGCGT
EST: gi|20512879|gb|BQ280071.1|BQ280071
EST:     AACGCTGCCCTGAGCCTCACCAGTCCAGATCTTATTGCTTCCCTTCATCT                         GAATAACCACGGTGATACCCTGGTTGCGTCCTACTACCACCTGGTAAAGAA
genomic: AACGCTGCCCTGAGCCTCACCAGTCCAGATCTTATTGCTTCCCTTCATCTgtgagtacca ... acttaatcagGAATAACCACGGTGATACCCTGGTTGCGTCCTACTACCACTTGGTAAAGAA
EST: gi|86468687|gb|DY235057.1|DY235057
EST:     AACGCTGCCCTGAGCCTCACCAGTCCAGATCTTATTGCTTCCCTTCATCT                         GAATAACCACGGTGATACCCTGGTTGCGTCCTACTACCACTTGGTAAAGAA
genomic: AACGCTGCCCTGAGCCTCACCAGTCCAGATCTTATTGCTTCCCTTCATCTgtgagtacca ... acttaatcagGAATAACCACGGTGATACCCTGGTTGCGTCCTACTACCACTTGGTAAAGAA
EST: gi|101397701|gb|EB820731.1|EB820731
EST:     AACGCTGCCCTGAGCCTCACCAGTCCAGATCTTATTGCTTCCCTTCATCT                         GAATAACCACGGTGATACCCTGGTTGCGTCCTACTACCACTTGGTAAAGAA
genomic: AACGCTGCCCTGAGCCTCACCAGTCCAGATCTTATTGCTTCCCTTCATCTgtgagtacca ... acttaatcagGAATAACCACGGTGATACCCTGGTTGCGTCCTACTACCACTTGGTAAAGAA
EST: gi|88752281|gb|DY536422.1|DY536422
EST:     AACGCTGCCCTGAGCCTCACCAGTCCAGATCTTATTGCTTCCCTTCATCT                         GAATAACCACGGTGATACCCTGGGTGCCTCCTACTACCACTTGGAAAAGAA
genomic: AACGCTGCCCTGAGCCTCACCAGTCCAGATCTTATTGCTTCCCTTCATCTgtgagtacca ... acttaatcagGAATAACCACGGTGATACCCTGGTTGCGTCCTACTACCACTTGGTAAAGAA
EST: gi|18169247|gb|BM339087.1|BM339087
EST:     AACGCTGCCCTGAGCCTCACCAGTCCAGATCTTATTGCTTCCCTTCATCT                         GAATAACCACGGTGATACCCTGGTTGCGTCCTACTACCACTTGGTAAAGAA
genomic: AACGCTGCCCTGAGCCTCACCAGTCCAGATCTTATTGCTTCCCTTCATCTgtgagtacca ... acttaatcagGAATAACCACGGTGATACCCTGGTTGCGTCCTACTACCACTTGGTAAAGAA
EST: gi|22472298|gb|BU036778.1|BU036778
EST:     AACGCTGCCCTGAGCCTCACCAGTCCAGATCTTATTGCTTCCCTTCATCT                         GAATAACCACGGNGATACCCTGGTTGCGTCCTACTACCACCTGGTAAAGAA
genomic: AACGCTGCCCTGAGCCTCACCAGTCCAGATCTTATTGCTTCCCTTCATCTgtgagtacca ... acttaatcagGAATAACCACGGTGATACCCTGGTTGCGTCCTACTACCACTTGGTAAAGAA
EST: gi|18172842|gb|BM348230.1|BM348230
EST:     AACGCTGCCNTGAGCCTCACCAGTCCAGATCTTATTGCTTCCCTTCATCT                         GAATAACCACGGTGATACCCTGGTTGCGTCCTACTACCACTTGGTAAAGAA
genomic: AACGCTGCCCTGAGCCTCACCAGTCCAGATCTTATTGCTTCCCTTCATCTgtgagtacca ... acttaatcagGAATAACCACGGTGATACCCTGGTTGCGTCCTACTACCACTTGGTAAAGAA
EST: gi|74244464|gb|DT652378.1|DT652378
EST:     AACGCTGCCCTGAGCCTCACCAGTCCAGATCTTATTGCTTCCCTTCATCT                         GAATAACCACGGTGATACCCTGGTTGCGTCCTACTACCACCTGGTAAAGAA
genomic: AACGCTGCCCTGAGCCTCACCAGTCCAGATCTTATTGCTTCCCTTCATCTgtgagtacca ... acttaatcagGAATAACCACGGTGATACCCTGGTTGCGTCCTACTACCACTTGGTAAAGAA
EST: gi|101397692|gb|EB820730.1|EB820730
EST:     AACGCTGCCCTGAGCCTCACCAGTCCAGATCTTATTGCTTCCCTTCATCT                         GAATAACCACGGTGATACCCTGGTTGCGTCCTACTACCACTTGGTAAAGAA
genomic: AACGCTGCCCTGAGCCTCACCAGTCCAGATCTTATTGCTTCCCTTCATCTgtgagtacca ... acttaatcagGAATAACCACGGTGATACCCTGGTTGCGTCCTACTACCACTTGGTAAAGAA
EST: gi|211331695|gb|FL020930.1|FL020930
EST:     AACGCTGCCCTGAGCCTCACCAGTCCAGATCTTATTGCTTCCCTTCATCT                         GAATAACCACGGTGATACCCTGGTTGCGTCCTACTACCACCTGGTAAAGAA
genomic: AACGCTGCCCTGAGCCTCACCAGTCCAGATCTTATTGCTTCCCTTCATCTgtgagtacca ... acttaatcagGAATAACCACGGTGATACCCTGGTTGCGTCCTACTACCACTTGGTAAAGAA
EST: gi|91874353|gb|EB404310.1|EB404310
EST:     AACGCTGCCCTGAGCCTCACCAGTCCAGATCTTATTGCTTCCCTTCATCT                         GAATAACCACGGTGATACCCTGGTTGCGTCCTACTACCACTTGGTAAAGAA
genomic: AACGCTGCCCTGAGCCTCACCAGTCCAGATCTTATTGCTTCCCTTCATCTgtgagtacca ... acttaatcagGAATAACCACGGTGATACCCTGGTTGCGTCCTACTACCACTTGGTAAAGAA
EST: gi|17932337|gb|BM269297.1|BM269297
EST:     AACGCTGCCATGAGCCTCACCAGTCCAGATCTTATTGCTTCCCTTCATCT                         GAATAACCACGGTGATACCCTGGTTGCGTCCTACTACCACTTGGTAAAGAA
genomic: AACGCTGCCCTGAGCCTCACCAGTCCAGATCTTATTGCTTCCCTTCATCTgtgagtacca ... acttaatcagGAATAACCACGGTGATACCCTGGTTGCGTCCTACTACCACTTGGTAAAGAA
EST: gi|67020552|gb|CO449301.1|CO449301
EST:     ACGCTGCCCTGAGCCT-ACCCAGTCCAGATCTTATTGCTTCCCTTCATCT                         GAATAACCACGGTGATACCCTGGTTGCGTCCTACTACCACCTGGTAAAGAA
genomic: ACGCTGCCCTGAGCCTCACC-AGTCCAGATCTTATTGCTTCCCTTCATCTgtgagtacca ... acttaatcagGAATAACCACGGTGATACCCTGGTTGCGTCCTACTACCACTTGGTAAAGAA
EST: gi|78112263|gb|DV530657.1|DV530657
EST:     AACGCTGCCCTGAGCCTCACCAGTCCAGATCTTATTGCTTCCCTTCATCT                         GAATAACCACGGTGATACCCTGGTTGCGTCCTACTACCACTTGGTAAAGAA
genomic: AACGCTGCCCTGAGCCTCACCAGTCCAGATCTTATTGCTTCCCTTCATCTgtgagtacca ... acttaatcagGAATAACCACGGTGATACCCTGGTTGCGTCCTACTACCACTTGGTAAAGAA
EST: gi|211118738|gb|FL431817.1|FL431817
EST:     TGCTTCCCTTCATCT                         GAATAACCACGGTGATACCCTGGTTGCGTCCTACTACCACCTGGTAAAGAA
genomic: TGCTTCCCTTCATCTgtgagtacca ... acttaatcagGAATAACCACGGTGATACCCTGGTTGCGTCCTACTACCACTTGGTAAAGAA
EST: gi|18167874|gb|BM337714.1|BM337714
EST:     AACGCTGCCATGAGCCTCACCAGTCCAGATCTTATTGCTTCCCTTCATCT                         GAATAACCACGGTGATACCCTGGTTGCGTCCTACTACCACTTGGTAAAGAA
genomic: AACGCTGCCCTGAGCCTCACCAGTCCAGATCTTATTGCTTCCCTTCATCTgtgagtacca ... acttaatcagGAATAACCACGGTGATACCCTGGTTGCGTCCTACTACCACTTGGTAAAGAA
EST: gi|71425206|gb|DR806570.1|DR806570
EST:     AACGCTGCCCTGAGCCTCACCAGTCCAGATCTTATTGCTTCCCTTCATCT                         GAATAACCACGGTGATACCCTGGTTGCGTCCTACTACCACTTGGTAAAGAA
genomic: AACGCTGCCCTGAGCCTCACCAGTCCAGATCTTATTGCTTCCCTTCATCTgtgagtacca ... acttaatcagGAATAACCACGGTGATACCCTGGTTGCGTCCTACTACCACTTGGTAAAGAA
EST: gi|71432320|gb|DR813370.1|DR813370
EST:     AACGCTGCCCTGAGCCTCACCAGTCCAGATCTTATTGCTTCCCTTCATCT                         GAATAACCACGGTGATACCCTGGTTGCGTCCTACTACCACTTGGTAAAGAA
genomic: AACGCTGCCCTGAGCCTCACCAGTCCAGATCTTATTGCTTCCCTTCATCTgtgagtacca ... acttaatcagGAATAACCACGGTGATACCCTGGTTGCGTCCTACTACCACTTGGTAAAGAA
EST: gi|4834979|gb|AI670205.1|AI670205
EST:     AGCCTCACCAGTCCAGATCTTATTGCTTCCCTTCATCT                         GAATAACCACGGTGATACCCTGGTTGCGTCCTACTACCACCTGGTAAAGAA
genomic: AGCCTCACCAGTCCAGATCTTATTGCTTCCCTTCATCTgtgagtacca ... acttaatcagGAATAACCACGGTGATACCCTGGTTGCGTCCTACTACCACTTGGTAAAGAA
EST: gi|78124064|gb|DV542448.1|DV542448
EST:     AACGCTGCCCTGAGCCTCACCAGTCCAGATCTTATTGCTTCCCTTCATCT                         GAATAACCACGGTGATACCCTGGTTGCGTCCTACTACCACTTGGTAAAGAA
genomic: AACGCTGCCCTGAGCCTCACCAGTCCAGATCTTATTGCTTCCCTTCATCTgtgagtacca ... acttaatcagGAATAACCACGGTGATACCCTGGTTGCGTCCTACTACCACTTGGTAAAGAA

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), 47 (downstream exon)
Score: 79

TCGGCGTTGATGTCTCATTTGATACGGCGACTAGCGATTTCACCAAGTACAACGCTGCCCTGAGCCTCACCAGTCCAGATCTTATTGCTTCCCTTCATCTgtgagtacca ... acttaatcagGAATAACCACGGTGATACCCTGGTTGCGTCCTACTACCACTTGGTAAAGAACCATTCAGGCACTGCTGTTGGAGCTGAGTTGTCTCACAGCATGTCGAGA


Block sizes: 46 (upstream exon), 47 (downstream exon)
Score: 97

TCGGCGTTGATGTCTCATTTGATACGGCGACTAGCGATTTCACCAAGTACAACGCTGCCCTGAGCCTCACCAGTCCAGATCTTATTGCTTCCCTTCATCTgtgagtacca ... acttaatcagGAATAACCACGGTGATACCCTGGTTGCGTCCTACTACCACTTGGTAAAGAACCATTCAGGCACTGCTGTTGGAGCTGAGTTGTCTCACAGCATGTCGAGA


Block sizes: 46 (upstream exon), 48 (downstream exon)
Score: 61

TCGGCGTTGATGTCTCATTTGATACGGCGACTAGCGATTTCACCAAGTACAACGCTGCCCTGAGCCTCACCAGTCCAGATCTTATTGCTTCCCTTCATCTgtgagtacca ... acttaatcagGAATAACCACGGTGATACCCTGGTTGCGTCCTACTACCACTTGGTAAAGAACCATTCAGGCACTGCTGTTGGAGCTGAGTTGTCTCACAGCATGTCGAGA


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 196

TCGGCGTTGATGTCTCATTTGATACGGCGACTAGCGATTTCACCAAGTACAACGCTGCCCTGAGCCTCACCAGTCCAGATCTTATTGCTTCCCTTCATCTgtgagtacca ... acttaatcagGAATAACCACGGTGATACCCTGGTTGCGTCCTACTACCACTTGGTAAAGAACCATTCAGGCACTGCTGTTGGAGCTGAGTTGTCTCACAGCATGTCGAGA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcttgcgaccactcctatttctactacggtaaataaccatgaaaaacttaatcagGAATAACCACGGTGATACCCTGGTTGCGTCCTACTACCACTTGGTAAAGAACCATTCAGGCACTGCTGTTGGAGCTGAGTTGTCTCACAGCATGTCGAGA
                              aaataac  putative branch site (score: 196)
                                      atgaaaaacttaat  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagtaccaccactcctatttcactaaaaaaaatttggcctttactgaacattggtcttgcgaccactcctatttctactacggtaaataaccatgaaaaacttaatcagGAATAACCACGGTGATACCCTGGTTGCGTCCTACTACCACTTGGTAAAGAACCATTCAGGCACTGCTGTTGGAGCTGAGTTGTCTCACAGCATGTCGAGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGA