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'   		12  
 5'  3'   		13  
 5'  3'   		14  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtatccccgtgttcttggttcgccttgtttcagagatttgcaagccaggcagcttcaacgatagagtaggcaaccacgtttgttacatgagggtttgtgtatcttgtgtgaccagATACCATCTAGCTGAGAAGAAGATCCCTTCCATCCATGGGTTCACAACGGGCCTGAAGCTGGAACAGTTTATATTCGACGCCTTCACTTACTCCCCATCC

Basic information

species Zea mays
transcript GRMZM2G019986_T04
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G019986_T04 (Zea mays), 3'ss of exon 12
lower sequence: LOC_Os04g52370.2 (Oryza sativa), 3'ss of exon 12
gtgagtatccccgtgttcttggttcgccttgtttcagagatttgcaagccaggcagcttcaacgatagagtaggcaaccacgtttgttacatgaggg-tttgtgtatcttgtgtgaccagATACCATCTAGCTGAGAAGAAGATCCCTTCCATCCATGGGTTCACAACGGGCCTGAAGCTGGAACAGTTTATATTCGACGCCTTCACTTACTCCCCATCC
                ||||  |  |    ||   ||  || |  ||  | |  |||| || |  |     |  | |     |||||  ||   |   |||    | ||| |||| |||| || ||||| ||||||||||||||||||||||||||||||| | ||| |||| ||||||| ||||||| |||||||||||| |||| |||||||||||||
---------------ctcttcctaagaaa-gtgagagccatgtttaaaactgcaagctccatcatt----cattctattgtatttgtagcacatgaaatttacaaaacttttgtgtccagTTATCATCTTGCTGAGAAGAAGATCCCTTCCATCCATGGGTACGCAATGGGCTTGAAGCTTGAACAGTATATATTCGACGCGTTCAGTTACTCCCCATCC
















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|149111355|gb|EE294858.2|EE294858
EST:     ACTCTGGACTTCTTGAACCAAGTGGCGAACAGCCTCGAGAAGGACAGTGT                         ATACCATCTAGCTGAGAAGAAGATCCCTTCCATCCATGGGTTCACAACGGG
genomic: ACTCTGGACTTCTTGAACCAAGTGGCGAACAGCCTCGAGAAGGACAGTGTgtgagtatcc ... gtgtgaccagATACCATCTAGCTGAGAAGAAGATCCCTTCCATCCATGGGTTCACAACGGG
EST: gi|78089271|gb|DV517645.1|DV517645
EST:     ACTCTGGACTTCTTGAACCAAGTGGCGAACAGCCTCGAGAAGGACAGTGT                         ATACCATCTAGCTGAGAAGAAGATCCCTTCCATCCATGGGTTCACAACGGG
genomic: ACTCTGGACTTCTTGAACCAAGTGGCGAACAGCCTCGAGAAGGACAGTGTgtgagtatcc ... gtgtgaccagATACCATCTAGCTGAGAAGAAGATCCCTTCCATCCATGGGTTCACAACGGG
EST: gi|211210620|gb|FL436849.1|FL436849
EST:     ACTCTGGACTTCTTGAACCAAGTGGCGAACAGCCTCGAGAAGGACAGTGT                         ATACCATCTAGCTGAGAAGAAGATCCCTTCCATCCATGGGTTCACAACGGG
genomic: ACTCTGGACTTCTTGAACCAAGTGGCGAACAGCCTCGAGAAGGACAGTGTgtgagtatcc ... gtgtgaccagATACCATCTAGCTGAGAAGAAGATCCCTTCCATCCATGGGTTCACAACGGG
EST: gi|110497708|gb|EE015394.1|EE015394
EST:     ACTCTGGACTTCTTGAACCAAGTGGCGAACAGCCTCGAGAAGGACAGGGT                         ATACCATCTAGCTGAGAAGAAGATCCCTTCCATCCATGGGTTCACAACGGG
genomic: ACTCTGGACTTCTTGAACCAAGTGGCGAACAGCCTCGAGAAGGACAGTGTgtgagtatcc ... gtgtgaccagATACCATCTAGCTGAGAAGAAGATCCCTTCCATCCATGGGTTCACAACGGG
EST: gi|5124174|gb|AI745798.1|AI745798
EST:     ACTCTGGACTTCTTGAACCAAGTGGCGAACAGCCTCGAGAAGGACAGTGT                         ATATCATCTAGCTGAGAAGAAGATCCCTTCCATCCATGGGTTCACAACGGG
genomic: ACTCTGGACTTCTTGAACCAAGTGGCGAACAGCCTCGAGAAGGACAGTGTgtgagtatcc ... gtgtgaccagATACCATCTAGCTGAGAAGAAGATCCCTTCCATCCATGGGTTCACAACGGG
EST: gi|211288805|gb|FL433953.1|FL433953
EST:     CTCGAGAAGGACAGTGT                         ATACCATCTAGCTGAGAAGAAGATCCCTTCCATCCATGGGTTCACAACGGG
genomic: CTCGAGAAGGACAGTGTgtgagtatcc ... gtgtgaccagATACCATCTAGCTGAGAAGAAGATCCCTTCCATCCATGGGTTCACAACGGG
EST: gi|16379775|gb|BI993142.1|BI993142
EST:     ACTCTGGACTTCTTGAACCAAGTGGCGAACAGCCTCGAGAAGGACAGTGT                         ATACCATCTAGCTGAGAAGAAGATCCCTTCCATCCATGGGTTCACAACGGG
genomic: ACTCTGGACTTCTTGAACCAAGTGGCGAACAGCCTCGAGAAGGACAGTGTgtgagtatcc ... gtgtgaccagATACCATCTAGCTGAGAAGAAGATCCCTTCCATCCATGGGTTCACAACGGG
EST: gi|71774723|gb|DR972601.1|DR972601
EST:     ACTCTGGACTTCTTGAACCAAGTGGCGAACAGCCTCGAGAAGGACAGTGT                         ATACCATCTAGCTGAGAAGAAGATCCCTTCCATCCATGGGTTCACAACGGG
genomic: ACTCTGGACTTCTTGAACCAAGTGGCGAACAGCCTCGAGAAGGACAGTGTgtgagtatcc ... gtgtgaccagATACCATCTAGCTGAGAAGAAGATCCCTTCCATCCATGGGTTCACAACGGG
EST: gi|148935255|gb|EC879292.2|EC879292
EST:     ACTCTGGACTTCTTGAACCAAGTGGCGAACAGCCTCGAGAAGGACAGTGT                         ATACCATCTAGCTGAGAAGAAGATCCCTTCCATCCATGGGTTCACAACGGG
genomic: ACTCTGGACTTCTTGAACCAAGTGGCGAACAGCCTCGAGAAGGACAGTGTgtgagtatcc ... gtgtgaccagATACCATCTAGCTGAGAAGAAGATCCCTTCCATCCATGGGTTCACAACGGG
EST: gi|18166601|gb|BM336440.1|BM336440
EST:     ACTCTGGACTTCTTGAACCAAGTGGCGAACAGCCTCGAGAAGGACAGTGT                         ATACCATCTAGCTGAGAAGAAGATCCCTTCCATCCATGGGTTCACAACGGG
genomic: ACTCTGGACTTCTTGAACCAAGTGGCGAACAGCCTCGAGAAGGACAGTGTgtgagtatcc ... gtgtgaccagATACCATCTAGCTGAGAAGAAGATCCCTTCCATCCATGGGTTCACAACGGG
EST: gi|110214878|gb|EC896775.1|EC896775
EST:     ATTCTGGACTTCTTGAACCAAGTGGCGAACAGCCTCGAGAAGGACAGTGT                         ATACCATCTAGCTGAGAAGAAGATCCCTTCCATCCATGGGTTCACAACGGG
genomic: ACTCTGGACTTCTTGAACCAAGTGGCGAACAGCCTCGAGAAGGACAGTGTgtgagtatcc ... gtgtgaccagATACCATCTAGCTGAGAAGAAGATCCCTTCCATCCATGGGTTCACAACGGG
EST: gi|40335845|gb|CK369915.1|CK369915
EST:     ACTCTGGACTTCTTGAACCAAGTGGCGAACAGCCTCGAGAAGGACAGTGT                         ATATCATCTAGCTGAGAAGAAGATCCCTTCCATCCATGGGTTCACAACGGG
genomic: ACTCTGGACTTCTTGAACCAAGTGGCGAACAGCCTCGAGAAGGACAGTGTgtgagtatcc ... gtgtgaccagATACCATCTAGCTGAGAAGAAGATCCCTTCCATCCATGGGTTCACAACGGG
EST: gi|149102321|gb|EE287688.2|EE287688
EST:     ACTCTGGACTTCTTGAACCAAGTGGCGAACAGCCTCGAGAAGGACAGTGT                         ATACCATCTAGCTGAGAAGAAGATCCCTTCCATCCATGGGTTCACAACGGG
genomic: ACTCTGGACTTCTTGAACCAAGTGGCGAACAGCCTCGAGAAGGACAGTGTgtgagtatcc ... gtgtgaccagATACCATCTAGCTGAGAAGAAGATCCCTTCCATCCATGGGTTCACAACGGG
EST: gi|67018099|gb|CO446848.1|CO446848
EST:     ACTCTGGACTTCTTGAACCAAGTGGCGAACAGCCTCGAGAAGGACAGTGT                         ATACCATCTAGCTGAGAAGAAGATCCCTTCCATCCATGGGTTCACAACGGG
genomic: ACTCTGGACTTCTTGAACCAAGTGGCGAACAGCCTCGAGAAGGACAGTGTgtgagtatcc ... gtgtgaccagATACCATCTAGCTGAGAAGAAGATCCCTTCCATCCATGGGTTCACAACGGG
EST: gi|37375243|gb|CF624047.1|CF624047
EST:     ACTCTGGACTTCTTGAACCAAGTGGCGAACAGCCTCGAGAAGGACAGTGT                         ATATCATCTAGCTGAGAAGAAGATCCCTTCCATCCATGGGTTCACAACGGG
genomic: ACTCTGGACTTCTTGAACCAAGTGGCGAACAGCCTCGAGAAGGACAGTGTgtgagtatcc ... gtgtgaccagATACCATCTAGCTGAGAAGAAGATCCCTTCCATCCATGGGTTCACAACGGG
EST: gi|17931736|gb|BM268696.1|BM268696
EST:     ACTCTGGACTTCTTGAACCAAGTGGCGAACAGCCTCGAGAAGGACAGTGT                         ATACCATCTAGCTGAGAAGAAGATCCCTTCCATCCATGGGTTCACAACGGG
genomic: ACTCTGGACTTCTTGAACCAAGTGGCGAACAGCCTCGAGAAGGACAGTGTgtgagtatcc ... gtgtgaccagATACCATCTAGCTGAGAAGAAGATCCCTTCCATCCATGGGTTCACAACGGG
EST: gi|40303710|gb|CK348097.1|CK348097
EST:     ACTCTGGACTTCTTGAACCAAGTGGCGAACAGCCTCGAGAAGGACAGTGT                         ATATCATCTAGCTGAGAAGAAGATCCCTTCCATCCATGGGTTCACAACGGG
genomic: ACTCTGGACTTCTTGAACCAAGTGGCGAACAGCCTCGAGAAGGACAGTGTgtgagtatcc ... gtgtgaccagATACCATCTAGCTGAGAAGAAGATCCCTTCCATCCATGGGTTCACAACGGG

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 3 RNA-Seq libraries.


Block sizes: 40 (upstream exon), 21 (downstream exon)
Score: 12

ATCTGCCTGCACATGTTCACTCTGGACTTCTTGAACCAAGTGGCGAACAGCCTCGAGAAGGACAGTGTgtgagtatcc ... gtgtgaccagATACCATCTAGCTGAGAAGAAGATCCCTTCCATCCATGGGTTCACAACGGGCCTGAAGCTGGAACAGTTTATATTCGACGCCTTCACTTACTCCCCATCC


Block sizes: 40 (upstream exon), 34 (downstream exon)
Score: 4

ATCTGCCTGCACATGTTCACTCTGGACTTCTTGAACCAAGTGGCGAACAGCCTCGAGAAGGACAGTGTgtgagtatcc ... gtgtgaccagATACCATCTAGCTGAGAAGAAGATCCCTTCCATCCATGGGTTCACAACGGGCCTGAAGCTGGAACAGTTTATATTCGACGCCTTCACTTACTCCCCATCC


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 39

ATCTGCCTGCACATGTTCACTCTGGACTTCTTGAACCAAGTGGCGAACAGCCTCGAGAAGGACAGTGTgtgagtatcc ... gtgtgaccagATACCATCTAGCTGAGAAGAAGATCCCTTCCATCCATGGGTTCACAACGGGCCTGAAGCTGGAACAGTTTATATTCGACGCCTTCACTTACTCCCCATCC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atagagtaggcaaccacgtttgttacatgagggtttgtgtatcttgtgtgaccagATACCATCTAGCTGAGAAGAAGATCCCTTCCATCCATGGGTTCACAACGGGCCTGAAGCTGGAACAGTTTATATTCGACGCCTTCACTTACTCCCCATCC
                  tttgtta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagtatccccgtgttcttggttcgccttgtttcagagatttgcaagccaggcagcttcaacgatagagtaggcaaccacgtttgttacatgagggtttgtgtatcttgtgtgaccagATACCATCTAGCTGAGAAGAAGATCCCTTCCATCCATGGGTTCACAACGGGCCTGAAGCTGGAACAGTTTATATTCGACGCCTTCACTTACTCCCCATCC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA