Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgtcttgtatcgctcatcatggtcatttaggcatgcatcgacatgaacagggtgagtgtgacctagctcgtcgtcgctttggcagCTCCGGCGACAGGGGGCTCAAGCCTCTGTTCGTGATCCCTCATGAGAAGCACAGAGATGAAATCGAGGAGGAGGTGGGGGACGACACAAGCATCCTGTTC

Basic information

species Zea mays
transcript GRMZM2G328908_T01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G328908_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os08g17390.1 (Oryza sativa), 3'ss of exon 3
---------------------------------gtgtcttgtatcgctcat-catggtcatttaggcatgcatcgacatgaa-cagggtgagtgtgacctagctcgtcgtcgctttggcagCTCCGGCGACAGGGGGCTCAAGCCTCTGTTCGTGATCCCTCATGAGAAGCACAGAGATGAAATCGAGGAGGAGGTGGGGGACGACACAAGCATCCTGTTC
                                   | ||  | |  | | | |||   ||  | || |   || |  |  |   ||    |  |  |   |  | || || |  |||||||||| |  ||||  || || ||||||||||| |||||||||||| |||||||||| || ||  | ||||||   |||||| | ||||| |  |||||||||
gtttttcacctcacctcactcactcactcaagcacggctgctcttacacttacatttccagcttggtaccgattgtgagaaggtagaactaaagccaaaaaaatggtggt-gtcttggcagCTCTGAAGACAATGGTCTGAAGCCTCTGTTTGTGATCCCTCATCAGAAGCACAGGGAAGAGGTTGAGGAGACTGTGGGGAAGGACACCAATATCCTGTTC
















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|7135782|gb|AW498263.1|AW498263
EST:     GACTGCCTTCTTCCCCTCGGGCACTGGGCTCAGATAGCCAAGGAAATCAG                         CTCCGGCGACAGGGGGCTCAAGCCTCTGTTCGTGATCCCTCATGAGAAGCA
genomic: GACTGCCTTCTTCCCCTCGGGCACTGGGCTCAGATAGCCAAGGAAATCAGgtgtcttgta ... gctttggcagCTCCGGCGACAGGGGGCTCAAGCCTCTGTTCGTGATCCCTCATGAGAAGCA
EST: gi|18650231|gb|BM499050.1|BM499050
EST:     GGGCTCAGATAGCCAAGGAAATCAG                         CTCCGGCGACAGGGGGCTCAAGCCTCTGTTCGTGATCCCTCATGAGAAGCA
genomic: GGGCTCAGATAGCCAAGGAAATCAGgtgtcttgta ... gctttggcagCTCCGGCGACAGGGGGCTCAAGCCTCTGTTCGTGATCCCTCATGAGAAGCA
EST: gi|148991813|gb|EE033399.2|EE033399
EST:     GACTGCCTTCTTCCCCTCGGGCACTGGGCTCAGATAGCCAAGGAAATCAG                         CTCCGGCGACA
genomic: GACTGCCTTCTTCCCCTCGGGCACTGGGCTCAGATAGCCAAGGAAATCAGgtgtcttgta ... gctttggcagCTCCGGCGACA
EST: gi|4647713|gb|AI622788.1|AI622788
EST:     CAGATAGCCAAGGAAATCAG                         CTCCGGCGACAGGGGGCTCAAGCCTCTGTTCGTGATCCCTCATGAGAAGCA
genomic: CAGATAGCCAAGGAAATCAGgtgtcttgta ... gctttggcagCTCCGGCGACAGGGGGCTCAAGCCTCTGTTCGTGATCCCTCATGAGAAGCA
EST: gi|149040130|gb|EE046781.2|EE046781
EST:     CAGATAGCCAAGGAAATCAG                         CTCCGGCGACAGGGGGCTCAAGCCTCTGTTCGTGATCCCTCATGAGAAGCA
genomic: CAGATAGCCAAGGAAATCAGgtgtcttgta ... gctttggcagCTCCGGCGACAGGGGGCTCAAGCCTCTGTTCGTGATCCCTCATGAGAAGCA
EST: gi|16919363|gb|BM074154.1|BM074154
EST:     GACTGCCTTCTTCCCCTCGGGCACTGGGCTCAGATAGCCAAGGAAATCAG                         CTCCGGCGACAGGGGGCTCAAGCCTCTGTTCGTGATCCCTCATGAGAAGCA
genomic: GACTGCCTTCTTCCCCTCGGGCACTGGGCTCAGATAGCCAAGGAAATCAGgtgtcttgta ... gctttggcagCTCCGGCGACAGGGGGCTCAAGCCTCTGTTCGTGATCCCTCATGAGAAGCA
EST: gi|110219083|gb|EC900981.1|EC900981
EST:     TCCCCTCGGGCACTGGGCTCAGATAGCCAAGGAAATCAG                         CTCCGGCGACAGGGGGCTCAAGCCTCTGTTCGTGATCCCTCATGAGAAGCA
genomic: TCCCCTCGGGCACTGGGCTCAGATAGCCAAGGAAATCAGgtgtcttgta ... gctttggcagCTCCGGCGACAGGGGGCTCAAGCCTCTGTTCGTGATCCCTCATGAGAAGCA
EST: gi|13490371|gb|BG517135.1|BG517135
EST:     GACTGCCTTCTTCCCCTCGGGCACTGGGCTCAGATAGCCAAGGAAATCAG                         CTCCGGCGACAGGGGGCTCAAGC
genomic: GACTGCCTTCTTCCCCTCGGGCACTGGGCTCAGATAGCCAAGGAAATCAGgtgtcttgta ... gctttggcagCTCCGGCGACAGGGGGCTCAAGC
EST: gi|32849587|gb|CD989268.1|CD989268
EST:     GACTGCCTTCTTCCCCTCGGGCACTGGGCTCAGATAGCCAAGGAAATCAG                         CTCCGGCGACAGGGGGCTCAAGCCTCTGTTCGTGATCCCTCATGAGAAGCA
genomic: GACTGCCTTCTTCCCCTCGGGCACTGGGCTCAGATAGCCAAGGAAATCAGgtgtcttgta ... gctttggcagCTCCGGCGACAGGGGGCTCAAGCCTCTGTTCGTGATCCCTCATGAGAAGCA
EST: gi|116820958|gb|EC864226.1|EC864226
EST:     GACTGCCTTCTTCCCCTCGGGCACTGGGCTCAGATAGCCAAGGAAATCAG                         CTCCGGCGACAGGGGGCTCAAGCCTCTGTTCGTGATCCCTCATGAGAAGCA
genomic: GACTGCCTTCTTCCCCTCGGGCACTGGGCTCAGATAGCCAAGGAAATCAGgtgtcttgta ... gctttggcagCTCCGGCGACAGGGGGCTCAAGCCTCTGTTCGTGATCCCTCATGAGAAGCA
EST: gi|149081398|gb|EE170514.2|EE170514
EST:     ACTGCCTTCTTTCCCCTCGG-CACTGGGCTCAGATAGCCAAGGAAATCAG                         CTCCGGCGACAGGGGGCTCAAGCCTCTGTTCGTGATCCCTCATG
genomic: ACTGCCTTCTT-CCCCTCGGGCACTGGGCTCAGATAGCCAAGGAAATCAGgtgtcttgta ... gctttggcagCTCCGGCGACAGGGGGCTCAAGCCTCTGTTCGTGATCCCTCATG
EST: gi|148934032|gb|EC878040.2|EC878040
EST:     GACTGCCTTCTTCCCCTCGGGCACTGGGCTCAGATAGCCAAGGAAATCAG                         CTCCGGCGACAGGGGGCTCAAGCCTCTGTTCGTGATCCCTCATGAGAAGCA
genomic: GACTGCCTTCTTCCCCTCGGGCACTGGGCTCAGATAGCCAAGGAAATCAGgtgtcttgta ... gctttggcagCTCCGGCGACAGGGGGCTCAAGCCTCTGTTCGTGATCCCTCATGAGAAGCA
EST: gi|13126121|gb|BG316691.1|BG316691
EST:     GACTGCCTTCTTCCCCTCGGGCACTGGGCTCAGATAGCCAAGGAAATCAG                         CTCCGGCGACAGGGGGCTCAAGCCTCTGTTCGTGATCCCTCATGAGAAGCA
genomic: GACTGCCTTCTTCCCCTCGGGCACTGGGCTCAGATAGCCAAGGAAATCAGgtgtcttgta ... gctttggcagCTCCGGCGACAGGGGGCTCAAGCCTCTGTTCGTGATCCCTCATGAGAAGCA
EST: gi|148996082|gb|EE035341.2|EE035341
EST:     GACTGCCTTCTTCCCCTCGGGCACTGGGCTCAGATAGCCAAGGAAATCAG                         CTCCGGCGACAGGGGGCTCAAGCCTCTGTTCGTGATCCCTCATGAGAAGCA
genomic: GACTGCCTTCTTCCCCTCGGGCACTGGGCTCAGATAGCCAAGGAAATCAGgtgtcttgta ... gctttggcagCTCCGGCGACAGGGGGCTCAAGCCTCTGTTCGTGATCCCTCATGAGAAGCA
EST: gi|13490410|gb|BG517174.1|BG517174
EST:     GACTGCCTTCTTCCCCTCGGGCACTGGGCTCAGATAGCCAAGGAAATCAG                         CTCCGGCGACAGGGGGCTCAAGCCTCTGTTCGTGATCCCTCATGAGAAGCA
genomic: GACTGCCTTCTTCCCCTCGGGCACTGGGCTCAGATAGCCAAGGAAATCAGgtgtcttgta ... gctttggcagCTCCGGCGACAGGGGGCTCAAGCCTCTGTTCGTGATCCCTCATGAGAAGCA
EST: gi|148934031|gb|EC878039.2|EC878039
EST:     ACTGCCTTCTTCCCCTCGGGCACTGGGCTCAGATAGCCAAAGGAA-TCAG                         CTCCGGCGACAGGGGGCTCAAGCCTCTGTTCGTGATCCCTCATG
genomic: ACTGCCTTCTTCCCCTCGGGCACTGGGCTCAGATAGCCAA-GGAAATCAGgtgtcttgta ... gctttggcagCTCCGGCGACAGGGGGCTCAAGCCTCTGTTCGTGATCCCTCATG
EST: gi|13126546|gb|BG317116.1|BG317116
EST:     TGCCTTCTTCCCCTCGGGCACTGGGCTCAGATAGCCAAGGAAATCAG                         CTCCGGCGACAGGGGGCTCAAGCCTCTGTTCGTGATCCCTCATGAGAAGCA
genomic: TGCCTTCTTCCCCTCGGGCACTGGGCTCAGATAGCCAAGGAAATCAGgtgtcttgta ... gctttggcagCTCCGGCGACAGGGGGCTCAAGCCTCTGTTCGTGATCCCTCATGAGAAGCA
EST: gi|149040129|gb|EE046780.2|EE046780
EST:     GACTGCCTTCTTCCCCTCGGGCACTGGGCTCAGATAGCCAAGGAAATCAG                         CTCCGGCGACAGGGGGCTCAAGCCTCTGTTCGTGA
genomic: GACTGCCTTCTTCCCCTCGGGCACTGGGCTCAGATAGCCAAGGAAATCAGgtgtcttgta ... gctttggcagCTCCGGCGACAGGGGGCTCAAGCCTCTGTTCGTGA

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 2 RNA-Seq libraries.


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 153

ACGGCATCGCCTCTGACTCCGTCGCCAACATGAAGTCCAGAGGCGACGACGACTGCCTTCTTCCCCTCGGGCACTGGGCTCAGATAGCCAAGGAAATCAGgtgtcttgta ... gctttggcagCTCCGGCGACAGGGGGCTCAAGCCTCTGTTCGTGATCCCTCATGAGAAGCACAGAGATGAAATCGAGGAGGAGGTGGGGGACGACACAAGCATCCTGTTC


Block sizes: 48 (upstream exon), 45 (downstream exon)
Score: 37

ACGGCATCGCCTCTGACTCCGTCGCCAACATGAAGTCCAGAGGCGACGACGACTGCCTTCTTCCCCTCGGGCACTGGGCTCAGATAGCCAAGGAAATCAGgtgtcttgta ... gctttggcagCTCCGGCGACAGGGGGCTCAAGCCTCTGTTCGTGATCCCTCATGAGAAGCACAGAGATGAAATCGAGGAGGAGGTGGGGGACGACACAAGCATCCTGTTC




<











 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcatgcatcgacatgaacagggtgagtgtgacctagctcgtcgtcgctttggcagCTCCGGCGACAGGGGGCTCAAGCCTCTGTTCGTGATCCCTCATGAGAAGCACAGAGATGAAATCGAGGAGGAGGTGGGGGACGACACAAGCATCCTGTTC
                                           tcgcttt  CT-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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgtcttgtatcgctcatcatggtcatttaggcatgcatcgacatgaacagggtgagtgtgacctagctcgtcgtcgctttggcagCTCCGGCGACAGGGGGCTCAAGCCTCTGTTCGTGATCCCTCATGAGAAGCACAGAGATGAAATCGAGGAGGAGGTGGGGGACGACACAAGCATCCTGTTC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG