Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   		8  
 5'  3'   		9  
 5'  3'   		10  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGAGGAGGTAGAAGGCGAAAGAAGGGGAACCAAATCTTGGACGGGAACACATAGATTTCTTTGGTGGAGGAAGGAGGAGGGCAACAAGAGGAGGTTACAGgtatggacacccatctgttcttgctcctagatttggctgtttgttttttcggtttgttcttctctgttgctagtttgtgaccgcgaatgggcgtccttgg...

Basic information

species Zea mays
transcript GRMZM5G835235_T02
intron # 1
splice site 5'
intron type U2

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|13490381|gb|BG517145.1|BG517145
EST:     GGAGGAAGGAGGAGGGCAACAAGAGGAGGTTACAG                         GTAGCCCAATAGATCTACTGCTGTTGAGGGAGTTGATGCAAAGCTGAGTTG
genomic: GGAGGAAGGAGGAGGGCAACAAGAGGAGGTTACAGgtatggacac ... ccacttacagGTAGCCCAATAGATCTACTGCTGTTGAGGGAGTTGATGCAAAGCTGAGTTG
EST: gi|67039601|gb|CO465856.1|CO465856
EST:     GGAAGGAGGATGCCAACAAGAGGAGGTTACAG                         GTAGCCCAATAGATCTACTGCTGTTGAGGGAGTTGATGCAAAGCTGAGTTG
genomic: GGAAGGAGGAGGGCAACAAGAGGAGGTTACAGgtatggacac ... ccacttacagGTAGCCCAATAGATCTACTGCTGTTGAGGGAGTTGATGCAAAGCTGAGTTG
EST: gi|22819758|gb|BU499848.1|BU499848
EST:     ATAGATTTCTTTGGTGGAGGAAGGAGGAGGGCAACAAGAGGAGGTTACAG                         GTAGCCCAATAGATCTACTGCTGTTGAGGGAGTTGATGCAAAGCTGAGTTG
genomic: ATAGATTTCTTTGGTGGAGGAAGGAGGAGGGCAACAAGAGGAGGTTACAGgtatggacac ... ccacttacagGTAGCCCAATAGATCTACTGCTGTTGAGGGAGTTGATGCAAAGCTGAGTTG
EST: gi|211304795|gb|FL143344.1|FL143344
EST:     AGGAGGTTACAG                         GTAGCCCAATAGATCTACTGCTGTTGAGGGAGTTGATGCAAAGCTGAGTTG
genomic: AGGAGGTTACAGgtatggacac ... ccacttacagGTAGCCCAATAGATCTACTGCTGTTGAGGGAGTTGATGCAAAGCTGAGTTG
EST: gi|87156577|gb|DY401366.1|DY401366
EST:     ATAGATTTCTTTGGTGGAGGAAGGAGGAGGGCAACAAGAGGAGGTTACAG                         GTAGCCCAATAGATCTACTGCTGTTGAGGGAGTTGATGCAAAGCTGAGTTG
genomic: ATAGATTTCTTTGGTGGAGGAAGGAGGAGGGCAACAAGAGGAGGTTACAGgtatggacac ... ccacttacagGTAGCCCAATAGATCTACTGCTGTTGAGGGAGTTGATGCAAAGCTGAGTTG
EST: gi|211304794|gb|FL143343.1|FL143343
EST:     ATAGATTTCTTTGGTGGAGGAAGGAGGAGGGCAACAAGAGGAGGTTACAG                         GTAGCCCAATAGATCTACTGCTGTTGAGGGAGTTGATGCAAAGCTGAGTTG
genomic: ATAGATTTCTTTGGTGGAGGAAGGAGGAGGGCAACAAGAGGAGGTTACAGgtatggacac ... ccacttacagGTAGCCCAATAGATCTACTGCTGTTGAGGGAGTTGATGCAAAGCTGAGTTG
EST: gi|24773942|gb|CA409196.1|CA409196
EST:     ATAGATTTCTTTGGTGGAGGAAGGAGGAGGGCAACAAGAGGAGGCTACAG                         GTAGCCCAATAGATCTACTGCTGTTGAGGGAGTTGATGCAAAGCTGAGTTG
genomic: ATAGATTTCTTTGGTGGAGGAAGGAGGAGGGCAACAAGAGGAGGTTACAGgtatggacac ... ccacttacagGTAGCCCAATAGATCTACTGCTGTTGAGGGAGTTGATGCAAAGCTGAGTTG
EST: gi|211089520|gb|FL366816.1|FL366816
EST:     ATAGATTTCTTTGGTGGAGGAAGGAGGAGGGCAACAAGAGGAGGTTACAG                         GTAGCCCAATAGATCTACTGCTGTTGAGGGAGTTGATGCAAAGCTGAGTTG
genomic: ATAGATTTCTTTGGTGGAGGAAGGAGGAGGGCAACAAGAGGAGGTTACAGgtatggacac ... ccacttacagGTAGCCCAATAGATCTACTGCTGTTGAGGGAGTTGATGCAAAGCTGAGTTG
EST: gi|26559736|gb|CA831971.1|CA831971
EST:     ATAGATTTCTTTGGTGGAGGAAGGAGGAGGGCAACAAGAGGAGGTTACAG                         GTAGCCCAATAGATCTACTGCTGTTGAGGGAGTTGATGCAAAGCTGAGTTG
genomic: ATAGATTTCTTTGGTGGAGGAAGGAGGAGGGCAACAAGAGGAGGTTACAGgtatggacac ... ccacttacagGTAGCCCAATAGATCTACTGCTGTTGAGGGAGTTGATGCAAAGCTGAGTTG
EST: gi|32865540|gb|CF005222.1|CF005222
EST:     ATAGATTTCTTTGGTGGAGGAAGGAGGAGGGCAACAAGAGGAGGTTACAG                         GTAGCCCAATAGATCTACTGCTGTTGAGGGAGTTGATGCAAAGCTGAGTTG
genomic: ATAGATTTCTTTGGTGGAGGAAGGAGGAGGGCAACAAGAGGAGGTTACAGgtatggacac ... ccacttacagGTAGCCCAATAGATCTACTGCTGTTGAGGGAGTTGATGCAAAGCTGAGTTG
EST: gi|211304793|gb|FL143342.1|FL143342
EST:     ATAGATTTCTTTGGTGGAGGAAGGAGGAGGGCAACAAGAGGAGGTTACAG                         GTAGCCCAATAGATCTACTGCTGTTGAGGGAGTTGATGCAAAGCTGAGTTG
genomic: ATAGATTTCTTTGGTGGAGGAAGGAGGAGGGCAACAAGAGGAGGTTACAGgtatggacac ... ccacttacagGTAGCCCAATAGATCTACTGCTGTTGAGGGAGTTGATGCAAAGCTGAGTTG

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), 49 (downstream exon)
Score: 1531

GGAGGAGGTAGAAGGCGAAAGAAGGGGAACCAAATCTTGGACGGGAACACATAGATTTCTTTGGTGGAGGAAGGAGGAGGGCAACAAGAGGAGGTTACAGgtatggacac ... ccacttacagGTAGCCCAATAGATCTACTGCTGTTGAGGGAGTTGATGCAAAGCTGAGTTGCTGCGCGTTGGCTTTCTTTAGAGATGGCTTCAGCTGGTGTTGCCCCTTC


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 588

GGAGGAGGTAGAAGGCGAAAGAAGGGGAACCAAATCTTGGACGGGAACACATAGATTTCTTTGGTGGAGGAAGGAGGAGGGCAACAAGAGGAGGTTACAGgtatggacac ... ccacttacagGTAGCCCAATAGATCTACTGCTGTTGAGGGAGTTGATGCAAAGCTGAGTTGCTGCGCGTTGGCTTTCTTTAGAGATGGCTTCAGCTGGTGTTGCCCCTTC


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 581

GGAGGAGGTAGAAGGCGAAAGAAGGGGAACCAAATCTTGGACGGGAACACATAGATTTCTTTGGTGGAGGAAGGAGGAGGGCAACAAGAGGAGGTTACAGgtatggacac ... ccacttacagGTAGCCCAATAGATCTACTGCTGTTGAGGGAGTTGATGCAAAGCTGAGTTGCTGCGCGTTGGCTTTCTTTAGAGATGGCTTCAGCTGGTGTTGCCCCTTC


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 550

GGAGGAGGTAGAAGGCGAAAGAAGGGGAACCAAATCTTGGACGGGAACACATAGATTTCTTTGGTGGAGGAAGGAGGAGGGCAACAAGAGGAGGTTACAGgtatggacac ... ccacttacagGTAGCCCAATAGATCTACTGCTGTTGAGGGAGTTGATGCAAAGCTGAGTTGCTGCGCGTTGGCTTTCTTTAGAGATGGCTTCAGCTGGTGTTGCCCCTTC


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGAGGAGGTAGAAGGCGAAAGAAGGGGAACCAAATCTTGGACGGGAACACATAGATTTCTTTGGTGGAGGAAGGAGGAGGGCAACAAGAGGAGGTTACAGgtatggacacccatctgttcttgctcctagatttggctgtttgttttttcggtttgttcttctctgttgctagtttgtgaccgcgaatgggcgtccttgg

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG