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'   		11  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtatttttctcattgccccattcttttgcatttttgcacttaatgatggaatccaattttctggtgctaatagattatttatgtcaaacattagGGTATTCCAGTAACAGCTGAAATTGCTGTTCCAATTGGTGGTCAAGGGGCAAACACAACTGATCGAGCTCCTACTGGGGAAGCTGGTCTCTCTGGGATTC

Basic information

species Zea mays
transcript GRMZM2G143462_T06
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G143462_T06 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os02g08300.2 (Oryza sativa), 3'ss of exon 6
gtatgtatttttctcattgccccattcttttgcatttttgcacttaatgatggaatccaattttctggtgctaatagat------tatttatgtcaaacattagGGTATTCCAGTAACAGCTGAAATTGCTGTTCCAATTGGTGGTCAAGGGGCAAACACAACTGATCGAGCTCCTACTGGGGAAGCTGGTCTCTCTGGGATTC
                        |||| || |  |  || |  |  |  |         ||||||   | ||||||||      | ||| |  |||||||||||| |||||| | ||||| ||  |||||||||||   ||||||||||||||||||||||| || | | || ||||| |||||||  |||| ||||| ||||
-------------------gtatgttctgtttc-ctcctgtaaatgtttgttattcttttttttctaacgttaatagataatgtttgtttctcccaaacattagGGCATTCCAATTACAGCGGAGGTTGCTGTTCCAGCAGGTGGTCAAGGGGCAAACACAACCGAGCCATCTTCTACTAGGGAAGCCAGTCTGTCTGGAATTC
















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|211394218|gb|FL229512.1|FL229512
EST:     TCCGTGCCGCTTACAACAACCCCGAACGTGCTGTTGAATACCTCTACTCT                         GGTATTCCAGTAACAGCTGAAATTGCTGTTCCAATTGSTGGTCAAGGGGCA
genomic: TCCGTGCCGCTTACAACAACCCCGAACGTGCTGTTGAATACCTCTACTCTgtatgtattt ... caaacattagGGTATTCCAGTAACAGCTGAAATTGCTGTTCCAATTGGTGGTCAAGGGGCA
EST: gi|74242202|gb|DT650116.1|DT650116
EST:     TCCGTGCCGCTTACAACAACCCCGAACGTGCTGTTGAATACCTCTACTCT                         GGTATTCCAGTAACAGCTGAAATTGCTGTTCCAATTGGTGGTCAAGGGGCA
genomic: TCCGTGCCGCTTACAACAACCCCGAACGTGCTGTTGAATACCTCTACTCTgtatgtattt ... caaacattagGGTATTCCAGTAACAGCTGAAATTGCTGTTCCAATTGGTGGTCAAGGGGCA
EST: gi|148995692|gb|EE034914.2|EE034914
EST:     TCCGTGCCGCTTACAACAACCCCGAACGTGCTGTTGAATACCTCTACTCT                         GGTATTCCAGTAACAGCTGAAATTGCTG
genomic: TCCGTGCCGCTTACAACAACCCCGAACGTGCTGTTGAATACCTCTACTCTgtatgtattt ... caaacattagGGTATTCCAGTAACAGCTGAAATTGCTG
EST: gi|89759371|gb|DY688230.1|DY688230
EST:     TCCGTGCCGCTTACAACAACCCCGAACGTGCTGTTGAATACCTCTACTCT                         GGTATTCCAGTAACAGCTGAAATTGCTGTTCCCATTGGTGGTCAAGGGGCA
genomic: TCCGTGCCGCTTACAACAACCCCGAACGTGCTGTTGAATACCTCTACTCTgtatgtattt ... caaacattagGGTATTCCAGTAACAGCTGAAATTGCTGTTCCAATTGGTGGTCAAGGGGCA
EST: gi|71764241|gb|DR962178.1|DR962178
EST:     TCCGTGCCGCTTACAACAACCCCGAACGTGCTGTTGAATACCTCTACTCT                         GGTATTCCAGTAACAGCTGAAATTGCTGTTCCAATTGGTGGTCAAGGGGCA
genomic: TCCGTGCCGCTTACAACAACCCCGAACGTGCTGTTGAATACCTCTACTCTgtatgtattt ... caaacattagGGTATTCCAGTAACAGCTGAAATTGCTGTTCCAATTGGTGGTCAAGGGGCA
EST: gi|32936801|gb|CF041620.1|CF041620
EST:     TCCGTGCCGCTTACAACAACCCCGAACGTGCTGTTGAATACCTCTACTCT                         GGTATTCCAGTAACAGCTGAAATTGCTGTTCCAATTGGTGGTCAAGGGGCA
genomic: TCCGTGCCGCTTACAACAACCCCGAACGTGCTGTTGAATACCTCTACTCTgtatgtattt ... caaacattagGGTATTCCAGTAACAGCTGAAATTGCTGTTCCAATTGGTGGTCAAGGGGCA
EST: gi|211488314|gb|FK957004.1|FK957004
EST:     TCCGTGCCGCTTACAACA-CCCCGAACGTGCTGTTGAATACCTCTACTCT                         GGTATTCCAGTAACAGCTNGAATTTGCTGTCCCANTTGGTGGTCAAGGGGC
genomic: TCCGTGCCGCTTACAACAACCCCGAACGTGCTGTTGAATACCTCTACTCTgtatgtattt ... caaacattagGGTATTCCAGTAACAGCT-GAAATTGCTGTTCCAATTGGTGGTCAAGGGGC
EST: gi|148947026|gb|EC892323.2|EC892323
EST:     TCCGTGCCGCTTACAACAACCCCGAACGTGCTGTTGAATACCTCTACTCT                         GGTATTCCAGTAACAGCTGAAATTGCTGTTCCAATTGGGTGGTCAAGGGGC
genomic: TCCGTGCCGCTTACAACAACCCCGAACGTGCTGTTGAATACCTCTACTCTgtatgtattt ... caaacattagGGTATTCCAGTAACAGCTGAAATTGCTGTTCCAATTGG-TGGTCAAGGGGC
EST: gi|89758471|gb|DY687642.1|DY687642
EST:     TCCGTGCCGCTTACAACAACCCCGAACGTGCTGTTGAATACCTCTACTCT                         GGTATTCCAGTAACAGCTGAAATTGCTGTTCCAATTGGTGGTCAAGGGGCA
genomic: TCCGTGCCGCTTACAACAACCCCGAACGTGCTGTTGAATACCTCTACTCTgtatgtattt ... caaacattagGGTATTCCAGTAACAGCTGAAATTGCTGTTCCAATTGGTGGTCAAGGGGCA
EST: gi|89761592|gb|DY689541.1|DY689541
EST:     TCCGTGCCGCTTACAACAACCCCGAACGTGCTGTTGAATACCTCTACTCT                         GGTATTCCAGTAACAGCTGAAATTGCTGTTTCCA-TTGGTGGTCAAGG
genomic: TCCGTGCCGCTTACAACAACCCCGAACGTGCTGTTGAATACCTCTACTCTgtatgtattt ... caaacattagGGTATTCCAGTAACAGCTGAAATTGCTGTT-CCAATTGGTGGTCAAGG
EST: gi|19272554|gb|BM888810.1|BM888810
EST:     TCCGTGCCGCTTACAACAACCCCGAACGTGCTGTTGAATACCTCTACTCT                         GGTATTCCAGTAACAGCTGAAATTGCTGTTCCAATTGGTGGTCAAGGTGCA
genomic: TCCGTGCCGCTTACAACAACCCCGAACGTGCTGTTGAATACCTCTACTCTgtatgtattt ... caaacattagGGTATTCCAGTAACAGCTGAAATTGCTGTTCCAATTGGTGGTCAAGGGGCA
EST: gi|211394219|gb|FL229513.1|FL229513
EST:     TCCGTGCCGCTTACAACAACCCCGAACGTGCTGNTGAATACCTCTACTCT                         GGTATTCCAGTAACAGCTGAAATTGCTGTTCCAATTGGTGGTCAAGGGGCA
genomic: TCCGTGCCGCTTACAACAACCCCGAACGTGCTGTTGAATACCTCTACTCTgtatgtattt ... caaacattagGGTATTCCAGTAACAGCTGAAATTGCTGTTCCAATTGGTGGTCAAGGGGCA
EST: gi|211394220|gb|FL229514.1|FL229514
EST:     TCCGTGCCGCTTACAACAACCCCGAACGTGCTGTTGAATACCTCTACTCT                         GGTATTCCAGTAACAGCTGAAATTGCTGTTCCAATTGGTGGTCAAGGGGCA
genomic: TCCGTGCCGCTTACAACAACCCCGAACGTGCTGTTGAATACCTCTACTCTgtatgtattt ... caaacattagGGTATTCCAGTAACAGCTGAAATTGCTGTTCCAATTGGTGGTCAAGGGGCA
EST: gi|78111156|gb|DV529553.1|DV529553
EST:     TCCGTGCCGCTTACAACAACCCCGAACGTGCTGTTGAATACCTCTACTCT                         --TA----A----CAGCTGAAATTGCTGTTCCAATTGGTGGTCAAGGGGCA
genomic: TCCGTGCCGCTTACAACAACCCCGAACGTGCTGTTGAATACCTCTACTCTgtatgtattt ... caaacattagGGTATTCCAGTAACAGCTGAAATTGCTGTTCCAATTGGTGGTCAAGGGGCA
EST: gi|148999208|gb|EE036127.2|EE036127
EST:     TCCGTGCCGCTTACAACAACCCCGAACGTGCTGTTGAATACCTCTACTCT                         GGTATTCCAGTAACAGCTGAAATTGCTGTTCCAATTGGTGGTCAAGGGGCA
genomic: TCCGTGCCGCTTACAACAACCCCGAACGTGCTGTTGAATACCTCTACTCTgtatgtattt ... caaacattagGGTATTCCAGTAACAGCTGAAATTGCTGTTCCAATTGGTGGTCAAGGGGCA
EST: gi|22489727|gb|BU049650.1|BU049650
EST:     TCCGTGCCGCTTACAACAACCCCGAACGTGCTGTTGAATACCTCTACTCT                         GGTATTCCAGTAACAGCTGAAATTGCTGTTCCAATTGGTGGTCAAGGGGCA
genomic: TCCGTGCCGCTTACAACAACCCCGAACGTGCTGTTGAATACCTCTACTCTgtatgtattt ... caaacattagGGTATTCCAGTAACAGCTGAAATTGCTGTTCCAATTGGTGGTCAAGGGGCA
EST: gi|93280956|gb|EB673220.1|EB673220
EST:     TCCGTGCCGCTTACAACAACCCCGAACGTGCTGTTGAATACCTCTACTCT                         GGTATTCCAGTAACAGCTGAAATTGCTGTTTCCA-TTGGTGGGTCA-GGGG
genomic: TCCGTGCCGCTTACAACAACCCCGAACGTGCTGTTGAATACCTCTACTCTgtatgtattt ... caaacattagGGTATTCCAGTAACAGCTGAAATTGCTGTT-CCAATTGGTGG-TCAAGGGG
EST: gi|2615440|gb|AA661449.1|AA661449
EST:     GCCGCTTACAACAACCCCGAANGTGCTGTTGAATACCTCTACTCT                         GGTATTCCAGTAACAGCTGAAATTGNTGTTCCAATTGGTGGTCAANGGGCA
genomic: GCCGCTTACAACAACCCCGAACGTGCTGTTGAATACCTCTACTCTgtatgtattt ... caaacattagGGTATTCCAGTAACAGCTGAAATTGCTGTTCCAATTGGTGGTCAAGGGGCA
EST: gi|149095756|gb|EE181396.2|EE181396
EST:     TCCGTGCCGCTTACAACAACCCCGAACGTGCTGTTGAATACCTCTACTCT                         GGTATTCCAGTAACAGCTGAAATTGCTGTTCCAATTGGTGGTCAAGGGGCA
genomic: TCCGTGCCGCTTACAACAACCCCGAACGTGCTGTTGAATACCTCTACTCTgtatgtattt ... caaacattagGGTATTCCAGTAACAGCTGAAATTGCTGTTCCAATTGGTGGTCAAGGGGCA
EST: gi|19822693|gb|BQ048717.1|BQ048717
EST:     TCCGTGCCGCTTACAACAACCCCGAACGTGCTGTTGAATACCTCTACTCT                         GGTATTCCAGTAACAGCTGAAATTGCTGTTCCAATTGGTGGTCAAGGGGCA
genomic: TCCGTGCCGCTTACAACAACCCCGAACGTGCTGTTGAATACCTCTACTCTgtatgtattt ... caaacattagGGTATTCCAGTAACAGCTGAAATTGCTGTTCCAATTGGTGGTCAAGGGGCA
EST: gi|76912415|gb|DV164721.1|DV164721
EST:     TCCGTGCCGCTTACAACAACCCCGAACGTGCTGTTGAATACCTCTACTCT                         GGTATTCCAGTAACAGCTGAAATTGCTGTTCCNATTGGT
genomic: TCCGTGCCGCTTACAACAACCCCGAACGTGCTGTTGAATACCTCTACTCTgtatgtattt ... caaacattagGGTATTCCAGTAACAGCTGAAATTGCTGTTCCAATTGGT

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: 236

AATGGAGATGGGTGGGGGCAGTTGGGACAAAGATAAAGTCCAAAGGGCTCTCCGTGCCGCTTACAACAACCCCGAACGTGCTGTTGAATACCTCTACTCTgtatgtattt ... caaacattagGGTATTCCAGTAACAGCTGAAATTGCTGTTCCAATTGGTGGTCAAGGGGCAAACACAACTGATCGAGCTCCTACTGGGGAAGCTGGTCTCTCTGGGATTC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 97

AATGGAGATGGGTGGGGGCAGTTGGGACAAAGATAAAGTCCAAAGGGCTCTCCGTGCCGCTTACAACAACCCCGAACGTGCTGTTGAATACCTCTACTCTgtatgtattt ... caaacattagGGTATTCCAGTAACAGCTGAAATTGCTGTTCCAATTGGTGGTCAAGGGGCAAACACAACTGATCGAGCTCCTACTGGGGAAGCTGGTCTCTCTGGGATTC


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 78

AATGGAGATGGGTGGGGGCAGTTGGGACAAAGATAAAGTCCAAAGGGCTCTCCGTGCCGCTTACAACAACCCCGAACGTGCTGTTGAATACCTCTACTCTgtatgtattt ... caaacattagGGTATTCCAGTAACAGCTGAAATTGCTGTTCCAATTGGTGGTCAAGGGGCAAACACAACTGATCGAGCTCCTACTGGGGAAGCTGGTCTCTCTGGGATTC


Block sizes: 45 (upstream exon), 48 (downstream exon)
Score: 92

AATGGAGATGGGTGGGGGCAGTTGGGACAAAGATAAAGTCCAAAGGGCTCTCCGTGCCGCTTACAACAACCCCGAACGTGCTGTTGAATACCTCTACTCTgtatgtattt ... caaacattagGGTATTCCAGTAACAGCTGAAATTGCTGTTCCAATTGGTGGTCAAGGGGCAAACACAACTGATCGAGCTCCTACTGGGGAAGCTGGTCTCTCTGGGATTC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttaatgatggaatccaattttctggtgctaatagattatttatgtcaaacattagGGTATTCCAGTAACAGCTGAAATTGCTGTTCCAATTGGTGGTCAAGGGGCAAACACAACTGATCGAGCTCCTACTGGGGAAGCTGGTCTCTCTGGGATTC
                         tgctaat  putative branch site (score: 92)
                            taatagattatttatg  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgtatttttctcattgccccattcttttgcatttttgcacttaatgatggaatccaattttctggtgctaatagattatttatgtcaaacattagGGTATTCCAGTAACAGCTGAAATTGCTGTTCCAATTGGTGGTCAAGGGGCAAACACAACTGATCGAGCTCCTACTGGGGAAGCTGGTCTCTCTGGGATTC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG