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'   		15  
 5'  3'   		16  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgcgccactcttttctctctctctctctcaagttggtgacaggatgacctctcatttcattatgggcaattgcagGTGGCTATGCTGCTGGATACTACAGTTACAAG

Basic information

species Zea mays
transcript GRMZM2G133919_T01
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G133919_T01 (Zea mays), 3'ss of exon 13
lower sequence: LOC_Os02g58340.1 (Oryza sativa), 3'ss of exon 13
gtttgcgccactcttttctctctct---ctctctcaagttggtgacaggatgac-ctctcatttcattatgggcaat-tgcagGTGGCTATGCTGCTGGATACTACAGTTACAAG
||||||    || |   ||   | |    ||  |||  |   |||| | |   | | ||  |||  |||| | |||| |||||| |||||||| |||||||||||||||||||||
gtttgcaatgctttaacctacatgtacattcattcatttatttgactgcagatctcactattttttttattgacaatctgcagGAGGCTATGCAGCTGGATACTACAGTTACAAG

upper sequence: GRMZM2G133919_T01 (Zea mays), 3'ss of exon 13
lower sequence: AT5G10540.1 (Arabidopsis thaliana), 3'ss of exon 13
------------------------------------gtttgcgccactcttttctctctctctctctcaagttggtgacaggatgacctctcatttcattat---gggcaattgcagGTGGCTATGCTGCTGGATACTACAGTTACAAG
                                    ||   ||  | || | |     | ||        |||  ||| ||  ||         ||||   |     |   |  ||||||| ||||| |||||||||||||||||||||
gtaacatccttaaacccgttttgttgtaacgcatccgtaaacgttagtcatgtgcagttatcgtaggtgcgtt--tgatagtttgtttcacttgttcaccttctcatgtcttgtcagGTGGTTATGCAGCTGGATACTACAGTTACAAG
















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|14243309|gb|BG841007.2|BG841007
EST:     TCCTCTGCCGGAGGACAGATTCCTGTGCAGCTTTAGCCATATTTTTGCAG                         GTGGCTATGCTGCTGGATACTACAGTTACAAG
genomic: TCCTCTGCCGGAGGACAGATTCCTGTGCAGCTTTAGCCATATTTTTGCAGgtttgcgcca ... gcaattgcagGTGGCTATGCTGCTGGATACTACAGTTACAAG
EST: gi|5871243|gb|AW017714.1|AW017714
EST:     TCCTCTGCCGGAGGACAGATTCCTGTGCAGCTTTAGCCATATTTTTGCAG                         GTGGCTATGCTGCTGGATACTACAGTTACAAG
genomic: TCCTCTGCCGGAGGACAGATTCCTGTGCAGCTTTAGCCATATTTTTGCAGgtttgcgcca ... gcaattgcagGTGGCTATGCTGCTGGATACTACAGTTACAAG
EST: gi|40335046|gb|CK369116.1|CK369116
EST:     TCCTCTGCCGGAGGACAGATTCCTGTGCAGCTTTAGCCATATTTTTGCAG                         GTGGCTATGCTGCTGGATACTACAGTTACAAG
genomic: TCCTCTGCCGGAGGACAGATTCCTGTGCAGCTTTAGCCATATTTTTGCAGgtttgcgcca ... gcaattgcagGTGGCTATGCTGCTGGATACTACAGTTACAAG
EST: gi|116824661|gb|EC868295.1|EC868295
EST:     TCCTCTGCCGGAGGACAGATTCCTGTGCAGCTTTAGCCATATTTTTGCAG                         GTGGCTATGCTGCTGGATACTACAGTTACAAG
genomic: TCCTCTGCCGGAGGACAGATTCCTGTGCAGCTTTAGCCATATTTTTGCAGgtttgcgcca ... gcaattgcagGTGGCTATGCTGCTGGATACTACAGTTACAAG
EST: gi|14244905|gb|BG842843.2|BG842843
EST:     TCCTCTGCCGGAGGACAGATTCCTGTGCAGCTTTAGCCATATTTTTGCAG                         GTGGCTATGCTGCTGGATACTACAGTTACAAG
genomic: TCCTCTGCCGGAGGACAGATTCCTGTGCAGCTTTAGCCATATTTTTGCAGgtttgcgcca ... gcaattgcagGTGGCTATGCTGCTGGATACTACAGTTACAAG
EST: gi|211206211|gb|FL245890.1|FL245890
EST:     TCCTCTGNCGGAGGACAGATTMCTGTGCAGCTTTAGCCATATTTTTGCAG                         GTGGCTATGCTGCTGGATACTACAGT
genomic: TCCTCTGCCGGAGGACAGATTCCTGTGCAGCTTTAGCCATATTTTTGCAGgtttgcgcca ... gcaattgcagGTGGCTATGCTGCTGGATACTACAGT
EST: gi|6020894|gb|AW065822.1|AW065822
EST:     TCCTCTGCCGGAGGACAGATTCCTGTGCAGCTTTAGCCATATTTTTGCAG                         GTGGCTATGCTGCTGGATACTACAGTTACAAG
genomic: TCCTCTGCCGGAGGACAGATTCCTGTGCAGCTTTAGCCATATTTTTGCAGgtttgcgcca ... gcaattgcagGTGGCTATGCTGCTGGATACTACAGTTACAAG
EST: gi|60401020|gb|DN233827.1|DN233827
EST:     TCCTCTGCCGGAGGACAGATTCCTGTGCAGCTTTAGCCATATTTTTGCAG                         GTGGCTATGCTGCTGGATACTACAGTTACAAG
genomic: TCCTCTGCCGGAGGACAGATTCCTGTGCAGCTTTAGCCATATTTTTGCAGgtttgcgcca ... gcaattgcagGTGGCTATGCTGCTGGATACTACAGTTACAAG
EST: gi|14242856|gb|BG840631.2|BG840631
EST:     TCCTCTGCCGGAGGACAGATTCCTGTGCAGCTTTAGCCATATTTTTGCAG                         GTGGCTATGCTGCTGGATACTACAGTTACAAG
genomic: TCCTCTGCCGGAGGACAGATTCCTGTGCAGCTTTAGCCATATTTTTGCAGgtttgcgcca ... gcaattgcagGTGGCTATGCTGCTGGATACTACAGTTACAAG
EST: gi|37382536|gb|CF628220.1|CF628220
EST:     TCCTCTGCCGGAGGACAGATTCCTGTGCAGCTTTAGCCATATTTTTGCAG                         GTGGCTATGCTGCTGGATACTACAGTTACAAG
genomic: TCCTCTGCCGGAGGACAGATTCCTGTGCAGCTTTAGCCATATTTTTGCAGgtttgcgcca ... gcaattgcagGTGGCTATGCTGCTGGATACTACAGTTACAAG
EST: gi|31997605|gb|CD661676.1|CD661676
EST:     TCCTCTGCCGGAGGACAGATTCCTGTGCAGCTTTAGCCATATTTTTGCAG                         GTGGCTATGCTGCTGGATACTACAGTTACAAG
genomic: TCCTCTGCCGGAGGACAGATTCCTGTGCAGCTTTAGCCATATTTTTGCAGgtttgcgcca ... gcaattgcagGTGGCTATGCTGCTGGATACTACAGTTACAAG
EST: gi|78021291|gb|DV489678.1|DV489678
EST:     TCCTCTGCCGGAGGACAGATTCCTGTGCAGCTTTAGCCATATTTTTGCAG                         GTGGCTATGCTGCTGGATACTACAGTTACAAG
genomic: TCCTCTGCCGGAGGACAGATTCCTGTGCAGCTTTAGCCATATTTTTGCAGgtttgcgcca ... gcaattgcagGTGGCTATGCTGCTGGATACTACAGTTACAAG
EST: gi|40336438|gb|CK370508.1|CK370508
EST:     TCCTCTGCCGGAGGACAGATTCCTGTGCAGCTTTAGCCATATTTTTGCAG                         GTGGCTATGCTGCTGGATACTACAGTTACAAG
genomic: TCCTCTGCCGGAGGACAGATTCCTGTGCAGCTTTAGCCATATTTTTGCAGgtttgcgcca ... gcaattgcagGTGGCTATGCTGCTGGATACTACAGTTACAAG
EST: gi|149075397|gb|EE163911.2|EE163911
EST:     TCCTCTGCCGGAGGACAGATTCCTGTGCAGCTTTAGCCATATTTTTGCAG                         GTGGCTATGCTGCTGGATACTACAGTTACAAG
genomic: TCCTCTGCCGGAGGACAGATTCCTGTGCAGCTTTAGCCATATTTTTGCAGgtttgcgcca ... gcaattgcagGTGGCTATGCTGCTGGATACTACAGTTACAAG
EST: gi|28982897|gb|BQ538418.2|BQ538418
EST:     TCCTCTGCCGGAGGACAGATTCCTGTGCAGCTTTAGCCATATTTTTGCAG                         GTGGCTATGCTGCTGGATACTACAGTTACAAG
genomic: TCCTCTGCCGGAGGACAGATTCCTGTGCAGCTTTAGCCATATTTTTGCAGgtttgcgcca ... gcaattgcagGTGGCTATGCTGCTGGATACTACAGTTACAAG
EST: gi|29543522|gb|CB603904.1|CB603904
EST:     TCCTCTGCCGGAGGACAGATTCCTGTGCAGCTTTAGCCATATTTTTGCAG                         GTGGCTATGCTGCTGGATACTACAGTTACAAG
genomic: TCCTCTGCCGGAGGACAGATTCCTGTGCAGCTTTAGCCATATTTTTGCAGgtttgcgcca ... gcaattgcagGTGGCTATGCTGCTGGATACTACAGTTACAAG
EST: gi|149009255|gb|EE153869.2|EE153869
EST:     TCTTTTGCCGGAGGACAGATTCCTGTGCAGCTTTAGCCATATTTTTGCAG                         GTGGCTATGCTGCTGGATACTACAGTTACAAG
genomic: TCCTCTGCCGGAGGACAGATTCCTGTGCAGCTTTAGCCATATTTTTGCAGgtttgcgcca ... gcaattgcagGTGGCTATGCTGCTGGATACTACAGTTACAAG
EST: gi|14244353|gb|BG842414.2|BG842414
EST:     TCCTCTGCCGGAGGACAGATTCCTGTGCAGCTTTAGCCATATTTTTGCAG                         GTGGCTATGCTGCTGGATACTACAGTTACAAG
genomic: TCCTCTGCCGGAGGACAGATTCCTGTGCAGCTTTAGCCATATTTTTGCAGgtttgcgcca ... gcaattgcagGTGGCTATGCTGCTGGATACTACAGTTACAAG
EST: gi|26456915|gb|CA828498.1|CA828498
EST:     TCCTCTGCCGGAGGACAGATTCCTGTGCAGCTTTAGCCATATTTTTGCAG                         GTGGCTATGCTGCTGGATACTACAGTTACA
genomic: TCCTCTGCCGGAGGACAGATTCCTGTGCAGCTTTAGCCATATTTTTGCAGgtttgcgcca ... gcaattgcagGTGGCTATGCTGCTGGATACTACAGTTACA
EST: gi|67025999|gb|CO454748.1|CO454748
EST:     CNCTCTGC-GGAGGACAGATTCCTGTGCAGCTTTAGCCATATTTTTGCAG                         GTGGCTATGCTGCTGGA-ACTACAGTTACAAG
genomic: C-CTCTGCCGGAGGACAGATTCCTGTGCAGCTTTAGCCATATTTTTGCAGgtttgcgcca ... gcaattgcagGTGGCTATGCTGCTGGATACTACAGTTACAAG
EST: gi|40335258|gb|CK369328.1|CK369328
EST:     TCCTCTGCCGGAGGACAGATTCCTGTGCAGCTTTAGCCATATTTTTGCAG                         GTGGCTATGCTGCTGGATACTACAGTTACAAG
genomic: TCCTCTGCCGGAGGACAGATTCCTGTGCAGCTTTAGCCATATTTTTGCAGgtttgcgcca ... gcaattgcagGTGGCTATGCTGCTGGATACTACAGTTACAAG
EST: gi|15589996|gb|BI674612.1|BI674612
EST:     TCCTCTGCCGGAGGACAGATTCCTGTGCAGCTTTAGCCATATTTTTGCAG                         GTGGCTATGCTGCTGGATACTACAGTTACAAG
genomic: TCCTCTGCCGGAGGACAGATTCCTGTGCAGCTTTAGCCATATTTTTGCAGgtttgcgcca ... gcaattgcagGTGGCTATGCTGCTGGATACTACAGTTACAAG
EST: gi|71758760|gb|DR956697.1|DR956697
EST:     TCCTCTGCCGGAGGACAGATTCCTGTGCAGCTTTAGCCATATTTTTGCAG                         GTGGCTATGCTGCTGGATACTACAGTTACAAG
genomic: TCCTCTGCCGGAGGACAGATTCCTGTGCAGCTTTAGCCATATTTTTGCAGgtttgcgcca ... gcaattgcagGTGGCTATGCTGCTGGATACTACAGTTACAAG
EST: gi|67022921|gb|CO451670.1|CO451670
EST:     TCCTCTGCCGGAGGACAGATTCCTGTGCAGCTTTAGCCATATTTTTGCAG                         GTGGCTATGCTGCTGGATACTACAGTTACAAG
genomic: TCCTCTGCCGGAGGACAGATTCCTGTGCAGCTTTAGCCATATTTTTGCAGgtttgcgcca ... gcaattgcagGTGGCTATGCTGCTGGATACTACAGTTACAAG
EST: gi|110220920|gb|EC902818.1|EC902818
EST:     TCCTCTGCCGGAGGACAGATTCCTGTGCAGCTTTAGCCATATTTTTGCAG                         GTGGCTATGCTGCTGGATACTACAGTTACAAG
genomic: TCCTCTGCCGGAGGACAGATTCCTGTGCAGCTTTAGCCATATTTTTGCAGgtttgcgcca ... gcaattgcagGTGGCTATGCTGCTGGATACTACAGTTACAAG

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), 48 (downstream exon)
Score: 227

TCCATATATGATGTGGACCAAAGAGTTGCAGAACGGACACAAGTTCTTGCTCCTCTGCCGGAGGACAGATTCCTGTGCAGCTTTAGCCATATTTTTGCAGgtttgcgcca ... gcaattgcagGTGGCTATGCTGCTGGATACTACAGTTACAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 251

TCCATATATGATGTGGACCAAAGAGTTGCAGAACGGACACAAGTTCTTGCTCCTCTGCCGGAGGACAGATTCCTGTGCAGCTTTAGCCATATTTTTGCAGgtttgcgcca ... gcaattgcagGTGGCTATGCTGCTGGATACTACAGTTACAAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 150

TCCATATATGATGTGGACCAAAGAGTTGCAGAACGGACACAAGTTCTTGCTCCTCTGCCGGAGGACAGATTCCTGTGCAGCTTTAGCCATATTTTTGCAGgtttgcgcca ... gcaattgcagGTGGCTATGCTGCTGGATACTACAGTTACAAG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 188

TCCATATATGATGTGGACCAAAGAGTTGCAGAACGGACACAAGTTCTTGCTCCTCTGCCGGAGGACAGATTCCTGTGCAGCTTTAGCCATATTTTTGCAGgtttgcgcca ... gcaattgcagGTGGCTATGCTGCTGGATACTACAGTTACAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctctctctcaagttggtgacaggatgacctctcatttcattatgggcaattgcagGTGGCTATGCTGCTGGATACTACAGTTACAAG
                                 atttcattat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttgcgccactcttttctctctctctctctcaagttggtgacaggatgacctctcatttcattatgggcaattgcagGTGGCTATGCTGCTGGATACTACAGTTACAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGGA