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

TCCTCCAGTGCAGGCAGTCCCATCATTCCCTTCTTCATTTCCCCATCTCTTCGCTGGCAAGGACCAACTGCGGTGTCTTATCCCATGTGCAATAGATCAGgtacaaacatctttggtaaaatggtctttactagtataagtgattgtatataaacttgctagcatacttgtaatatttttgttagtgtaaatttctgaac...

Basic information

species Zea mays
transcript GRMZM2G002687_T01
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G002687_T01 (Zea mays), 5'ss of exon 5
lower sequence: LOC_Os12g35570.3 (Oryza sativa), 5'ss of exon 5
TCCTCCAGTGCAGGCAGTCCCATCATTCCCTTCTTCATTTCCCCATCTCTTCGCTGGCAAGGACCAACTGCGGTGTCTTATCCCATGTGCAATAGATCAGgtacaaacatctttggtaaaatggtctttactagtataagtgattgtatataaacttgctagcatacttgtaatatttttgttagtgtaaatttctgaac---
|||||| ||||| || || ||||||||||||||||||||||| ||||||||| |||| || |||||||| |||||  | ||||||||||||||||| |||||| |||||| | |||       |  |  | |  |    |||| | | |      |||   || |     |  |  | |  |     |   | |  ||||   
TCCTCCTGTGCAAGCGGTTCCATCATTCCCTTCTTCATTTCCACATCTCTTCTCTGGGAATGACCAACTACGGTGCTTAATCCCATGTGCAATAGACCAGgtataaacatatctgggctccctgattccatttctccctgtgaatttgtg---gtttggctgcctttccatgctgctatcatgccatttcgtctaggaacaca
















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|67015552|gb|CO444301.1|CO444301
EST:     GCTGGGCA-GGACCAACTGCNGTGTCTTATCCCATGTGNCA-TAGATCAG                         GATCCATATTTTAGGATGACTCGTGATGTTGCTCCTAGAATTGGNTATCAN
genomic: GCTGG-CAAGGACCAACTGCGGTGTCTTATCCCATGTG-CAATAGATCAGgtacaaacat ... tcttctgcagGATCCATATTTTAGGATGACTCGTGATGTTGCTCCTAGAATTGGTTATCAG
EST: gi|37395551|gb|CF635056.1|CF635056
EST:     ACTGCGGTGTC-TATCCCATGTGCAATAGATCAG                         GATCCATATTTTAGGATGACTCGTGATGTTGCTCCTAGAATTGGTTATCAG
genomic: ACTGCGGTGTCTTATCCCATGTGCAATAGATCAGgtacaaacat ... tcttctgcagGATCCATATTTTAGGATGACTCGTGATGTTGCTCCTAGAATTGGTTATCAG
EST: gi|67037924|gb|CO464466.1|CO464466
EST:     TCGCTGGCAGGGACCA-CTGCGGTGTCTTATCC-ATGTGCAATAGATCAG                         GATCCATATTTTAGGATGACTCGTGATGTTGCTCCTAGAATGGGTTAT
genomic: TCGCTGGCAAGGACCAACTGCGGTGTCTTATCCCATGTGCAATAGATCAGgtacaaacat ... tcttctgcagGATCCATATTTTAGGATGACTCGTGATGTTGCTCCTAGAATTGGTTAT
EST: gi|6020814|gb|AW065742.1|AW065742
EST:     TCGCTGGCAAGGACCAACTGCGGTGTCTTATCCCATGTGCAATAGATCAG                         GATCCATATTTTAGGATGACTCGTGATGTTGCTCCTAGAATTGGNTATCAG
genomic: TCGCTGGCAAGGACCAACTGCGGTGTCTTATCCCATGTGCAATAGATCAGgtacaaacat ... tcttctgcagGATCCATATTTTAGGATGACTCGTGATGTTGCTCCTAGAATTGGTTATCAG
EST: gi|149010069|gb|EE041876.2|EE041876
EST:     TCGCTGGCAAGGACCAACTGCGGTGTCTTATCCCATGTGCAATAGATCAG                         GATCCATATTTTA
genomic: TCGCTGGCAAGGACCAACTGCGGTGTCTTATCCCATGTGCAATAGATCAGgtacaaacat ... tcttctgcagGATCCATATTTTA
EST: gi|149010068|gb|EE041875.2|EE041875
EST:     TATCCCATGTGCAATAGATCAG                         GATCCATATTTTAGGATGACTCGTGATGTTGCTCCTAGAATTGGTTATCAG
genomic: TATCCCATGTGCAATAGATCAGgtacaaacat ... tcttctgcagGATCCATATTTTAGGATGACTCGTGATGTTGCTCCTAGAATTGGTTATCAG
EST: gi|149108285|gb|EE292625.2|EE292625
EST:     TTATCCCATGTGCAATAGATCAG                         GATCCATATTTTAGGATGACTCGTGATGTTGCTCCTAGAATTGGTTATCAG
genomic: TTATCCCATGTGCAATAGATCAGgtacaaacat ... tcttctgcagGATCCATATTTTAGGATGACTCGTGATGTTGCTCCTAGAATTGGTTATCAG
EST: gi|111192905|gb|EE291041.1|EE291041
EST:     CATGTGCAATAGATCAG                         GATCCATATTTTAGGATGACTCGTGATGTTGCTCCTAGAATTGGTTATCAG
genomic: CATGTGCAATAGATCAGgtacaaacat ... tcttctgcagGATCCATATTTTAGGATGACTCGTGATGTTGCTCCTAGAATTGGTTATCAG
EST: gi|110520053|gb|EE024360.1|EE024360
EST:     ATGTGCAATAGATCAG                         GATCCATATTTTAGGATGACTCGTGATGTTGCTCCTAGAATTGGTTATCAG
genomic: ATGTGCAATAGATCAGgtacaaacat ... tcttctgcagGATCCATATTTTAGGATGACTCGTGATGTTGCTCCTAGAATTGGTTATCAG
EST: gi|9953035|gb|BE639618.1|BE639618
EST:     TCGCTGGCAAGGACCAACTGCGGTGTCTTATCCCATGTGCAATAGATCAG                         GATCCATATTTTA
genomic: TCGCTGGCAAGGACCAACTGCGGTGTCTTATCCCATGTGCAATAGATCAGgtacaaacat ... tcttctgcagGATCCATATTTTA
EST: gi|149073833|gb|EE162155.2|EE162155
EST:     CATGTGCAATAGATCAG                         GATCCATATTTTAGGATGACTCGTGATGTTGCTCCTAGAATTGGTTATCAG
genomic: CATGTGCAATAGATCAGgtacaaacat ... tcttctgcagGATCCATATTTTAGGATGACTCGTGATGTTGCTCCTAGAATTGGTTATCAG
EST: gi|60354415|gb|DN221388.1|DN221388
EST:     ATGTGCAATAGATCAG                         GATCCATATTTTAGGATGACTCGTGATGTTGCTCCTAGAATTGGTTATCAG
genomic: ATGTGCAATAGATCAGgtacaaacat ... tcttctgcagGATCCATATTTTAGGATGACTCGTGATGTTGCTCCTAGAATTGGTTATCAG
EST: gi|91049846|gb|EB160264.1|EB160264
EST:     TCGCTGGCAAGGACCAACTGCGGTGTCTTATCCCATGTGCAATAGATCAG                         GATCCATATTTTAGGATGACTCGTGATGTTGCTCCTAGAATTGGTTATCAG
genomic: TCGCTGGCAAGGACCAACTGCGGTGTCTTATCCCATGTGCAATAGATCAGgtacaaacat ... tcttctgcagGATCCATATTTTAGGATGACTCGTGATGTTGCTCCTAGAATTGGTTATCAG
EST: gi|211139771|gb|FL315903.1|FL315903
EST:     TCGCTGGCAAGGACCAACTGCGGTGTCTTATCCCATGTGCAATAGATCAG                         GATCCATATTTTAGGATGACTCGTGATGTTGCTCCTAGAATTG-TTATCAG
genomic: TCGCTGGCAAGGACCAACTGCGGTGTCTTATCCCATGTGCAATAGATCAGgtacaaacat ... tcttctgcagGATCCATATTTTAGGATGACTCGTGATGTTGCTCCTAGAATTGGTTATCAG
EST: gi|149073834|gb|EE162156.2|EE162156
EST:     TCGCTGGCAAAGACCAACTGCGGTGTCTTATCCCCTGTGCAATAGATCAG                         GATCCATATTTTAGGATGA
genomic: TCGCTGGCAAGGACCAACTGCGGTGTCTTATCCCATGTGCAATAGATCAGgtacaaacat ... tcttctgcagGATCCATATTTTAGGATGA
EST: gi|67014073|gb|CO442822.1|CO442822
EST:     GCTGGCAATGACCAACTGCNGTGTNCT-ATCCCATGTGNCA-TAGATCAG                         GATCCATATTTTAGGATGACTCGTGATGTTGCTCCTANAATTG-TTATCAG
genomic: GCTGGCAAGGACCAACTGCGGTGT-CTTATCCCATGTG-CAATAGATCAGgtacaaacat ... tcttctgcagGATCCATATTTTAGGATGACTCGTGATGTTGCTCCTAGAATTGGTTATCAG

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), 47 (downstream exon)
Score: 194

TCCTCCAGTGCAGGCAGTCCCATCATTCCCTTCTTCATTTCCCCATCTCTTCGCTGGCAAGGACCAACTGCGGTGTCTTATCCCATGTGCAATAGATCAGgtacaaacat ... tcttctgcagGATCCATATTTTAGGATGACTCGTGATGTTGCTCCTAGAATTGGTTATCAGAAACCATCACTGATTGAATCTAGATTTTTTCCTGCTCTTCAG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 217

TCCTCCAGTGCAGGCAGTCCCATCATTCCCTTCTTCATTTCCCCATCTCTTCGCTGGCAAGGACCAACTGCGGTGTCTTATCCCATGTGCAATAGATCAGgtacaaacat ... tcttctgcagGATCCATATTTTAGGATGACTCGTGATGTTGCTCCTAGAATTGGTTATCAGAAACCATCACTGATTGAATCTAGATTTTTTCCTGCTCTTCAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 196

TCCTCCAGTGCAGGCAGTCCCATCATTCCCTTCTTCATTTCCCCATCTCTTCGCTGGCAAGGACCAACTGCGGTGTCTTATCCCATGTGCAATAGATCAGgtacaaacat ... tcttctgcagGATCCATATTTTAGGATGACTCGTGATGTTGCTCCTAGAATTGGTTATCAGAAACCATCACTGATTGAATCTAGATTTTTTCCTGCTCTTCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 174

TCCTCCAGTGCAGGCAGTCCCATCATTCCCTTCTTCATTTCCCCATCTCTTCGCTGGCAAGGACCAACTGCGGTGTCTTATCCCATGTGCAATAGATCAGgtacaaacat ... tcttctgcagGATCCATATTTTAGGATGACTCGTGATGTTGCTCCTAGAATTGGTTATCAGAAACCATCACTGATTGAATCTAGATTTTTTCCTGCTCTTCAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TCCTCCAGTGCAGGCAGTCCCATCATTCCCTTCTTCATTTCCCCATCTCTTCGCTGGCAAGGACCAACTGCGGTGTCTTATCCCATGTGCAATAGATCAGgtacaaacatctttggtaaaatggtctttactagtataagtgattgtatataaacttgctagcatacttgtaatatttttgttagtgtaaatttctgaac

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGATCA