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

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TACTCTCTGCAAGGCCCGAGAGCGCGAGCAATTTTGTCAAGGTGGACTCCATCTTTGGCCCGgtaatggctgatgcagtagtaaatcttatgctaatgggacagctggtgtgcaaatgctagcaatgaatggaaaaaagttaattggtcagatgccatttgt...

Basic information

species Zea mays
transcript GRMZM2G177914_T02
intron # 3
splice site 5'
intron type U2

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|19822213|gb|BQ048237.1|BQ048237
EST:     GGCCCGAGAGCGCGAGCAATTTTGTCAAGGTGGACTCCATCTTTGGCCCG                         GGAACAAAAATGGTCTACAAGCATTTGGCCACACTATACTTTGTTTTTGTC
genomic: GGCCCGAGAGCGCGAGCAATTTTGTCAAGGTGGACTCCATCTTTGGCCCGgtaatggctg ... cgctttgcagGGAACAAAAATGGTCTACAAGCATTTGGCCACACTATACTTTGTTTTTGTC
EST: gi|211467096|gb|FK972975.1|FK972975
EST:     GGCCCGAGAGCGCGAGCAATTTTGTCAAGGTGGACTCCATCTTTGGCCCG                         GGAACAAAAATGGTCTACAAGCATTTGGCCACACTATACTTTGTTTTTGTT
genomic: GGCCCGAGAGCGCGAGCAATTTTGTCAAGGTGGACTCCATCTTTGGCCCGgtaatggctg ... cgctttgcagGGAACAAAAATGGTCTACAAGCATTTGGCCACACTATACTTTGTTTTTGT-
EST: gi|211469619|gb|FK972986.1|FK972986
EST:     GGCCCGAGAGCGCGAGCAATTTTGTCAAGGTGGACTCCATCTTTGGCCCG                         GGAACAAAAATGGTCTACAAGCATTTGGCCACACTATACTTTGTTTTTGTC
genomic: GGCCCGAGAGCGCGAGCAATTTTGTCAAGGTGGACTCCATCTTTGGCCCGgtaatggctg ... cgctttgcagGGAACAAAAATGGTCTACAAGCATTTGGCCACACTATACTTTGTTTTTGTC
EST: gi|211467101|gb|FK972980.1|FK972980
EST:     GGCCCGAGAGCGCGAGGAATTTTGTCAAGGTGGACTCCATCTTTGGCCCG                         GGAACAAAAATGGTCTACAAGCATTTGGCCACACTATACTTTGTTTT-G--
genomic: GGCCCGAGAGCGCGAGCAATTTTGTCAAGGTGGACTCCATCTTTGGCCCGgtaatggctg ... cgctttgcagGGAACAAAAATGGTCTACAAGCATTTGGCCACACTATACTTTGTTTTTGTC
EST: gi|211467098|gb|FK972977.1|FK972977
EST:     GGCCCGAGAGCGCGAGCAATTTTGTCAAGGTGGACTCCATCTTTGGCCCG                         GGAACAAAAATGGTCTACAAGCATTTGGCCACACTATACTTTGTT
genomic: GGCCCGAGAGCGCGAGCAATTTTGTCAAGGTGGACTCCATCTTTGGCCCGgtaatggctg ... cgctttgcagGGAACAAAAATGGTCTACAAGCATTTGGCCACACTATACTTTGTT
EST: gi|211472153|gb|FK973002.1|FK973002
EST:     GGCCCGAGAGCGCGAGCAATTTTGTCAAGGTGGACTCCATCTTTGGCCCG                         GGAACAAAAATGGTCTACAAGCA
genomic: GGCCCGAGAGCGCGAGCAATTTTGTCAAGGTGGACTCCATCTTTGGCCCGgtaatggctg ... cgctttgcagGGAACAAAAATGGTCTACAAGCA
EST: gi|211472152|gb|FK973001.1|FK973001
EST:     GGCCCGAGAGCGCGAGCAATTTTGTCAAGGTGGACTCCATCTTTGGCCCG                         GGAACAAAAATGGTCTACAAGCATTTGGCCACACTATACTTT
genomic: GGCCCGAGAGCGCGAGCAATTTTGTCAAGGTGGACTCCATCTTTGGCCCGgtaatggctg ... cgctttgcagGGAACAAAAATGGTCTACAAGCATTTGGCCACACTATACTTT
EST: gi|211472150|gb|FK972999.1|FK972999
EST:     GGCCCGAGAGCGCGAGCAATTTTGTCAAGGTGGACTCCATCTTTGGCCCG                         GGAACAAAAATGGTCTACAAGCA
genomic: GGCCCGAGAGCGCGAGCAATTTTGTCAAGGTGGACTCCATCTTTGGCCCGgtaatggctg ... cgctttgcagGGAACAAAAATGGTCTACAAGCA
EST: gi|211469626|gb|FK972993.1|FK972993
EST:     GGCCCGAGAGCGCGAGCAATTTTGTCAAGGTGGACTCCATCTTTGGCCCG                         GGAACAAAAATGGTCTACAAGCATTTGGCCACACTATACTTTGTTTTTGTC
genomic: GGCCCGAGAGCGCGAGCAATTTTGTCAAGGTGGACTCCATCTTTGGCCCGgtaatggctg ... cgctttgcagGGAACAAAAATGGTCTACAAGCATTTGGCCACACTATACTTTGTTTTTGTC
EST: gi|76011356|gb|DT938526.1|DT938526
EST:     GGCCCGAGAGCGCGAGCAATTTTGTCAAGGTGGACTCCATCTTTGGCCCG                         GGAACAAAAATGGTCTACAAGCATTTGGCCACACTATACTTTGTTTTTGTC
genomic: GGCCCGAGAGCGCGAGCAATTTTGTCAAGGTGGACTCCATCTTTGGCCCGgtaatggctg ... cgctttgcagGGAACAAAAATGGTCTACAAGCATTTGGCCACACTATACTTTGTTTTTGTC
EST: gi|211469628|gb|FK972995.1|FK972995
EST:     GGCCCGAGAGCGCGAGCAATTTTGTCAAGGTGGACTCCATCTTTGGCCCG                         GGAACAAAAATGGTCTACAAGCATTTG
genomic: GGCCCGAGAGCGCGAGCAATTTTGTCAAGGTGGACTCCATCTTTGGCCCGgtaatggctg ... cgctttgcagGGAACAAAAATGGTCTACAAGCATTTG
EST: gi|211472147|gb|FK972996.1|FK972996
EST:     GGCCCGAGAGCGCGAGCAATTTTGTCAAGGTGGACTCCATCTTTGGCCCG                         GGAACAAAAATGGTCTACAAGCATTTGGCCACACTATACTTTGTTTTTGTC
genomic: GGCCCGAGAGCGCGAGCAATTTTGTCAAGGTGGACTCCATCTTTGGCCCGgtaatggctg ... cgctttgcagGGAACAAAAATGGTCTACAAGCATTTGGCCACACTATACTTTGTTTTTGTC
EST: gi|71429421|gb|DR810471.1|DR810471
EST:     GGCCCGAGAGCGCGAGCAATTTTGTCAAGGTGGACTCCATCTTTGGCCCG                         GGAACAAAAATGGTCTACAAGCATTTGGCCACACTATACTTTG
genomic: GGCCCGAGAGCGCGAGCAATTTTGTCAAGGTGGACTCCATCTTTGGCCCGgtaatggctg ... cgctttgcagGGAACAAAAATGGTCTACAAGCATTTGGCCACACTATACTTTG

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: 223

TACTCTCTGCAAGGCCCGAGAGCGCGAGCAATTTTGTCAAGGTGGACTCCATCTTTGGCCCGgtaatggctg ... cgctttgcagGGAACAAAAATGGTCTACAAGCATTTGGCCACACTATACTTTGTTTTTGTCTTTGATAGCTCTGAGAACGAGCTTGCCATGCTCGACCTCGTACAAGGTA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 394

TACTCTCTGCAAGGCCCGAGAGCGCGAGCAATTTTGTCAAGGTGGACTCCATCTTTGGCCCGgtaatggctg ... cgctttgcagGGAACAAAAATGGTCTACAAGCATTTGGCCACACTATACTTTGTTTTTGTCTTTGATAGCTCTGAGAACGAGCTTGCCATGCTCGACCTCGTACAAGGTA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 458

TACTCTCTGCAAGGCCCGAGAGCGCGAGCAATTTTGTCAAGGTGGACTCCATCTTTGGCCCGgtaatggctg ... cgctttgcagGGAACAAAAATGGTCTACAAGCATTTGGCCACACTATACTTTGTTTTTGTCTTTGATAGCTCTGAGAACGAGCTTGCCATGCTCGACCTCGTACAAGGTA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 354

TACTCTCTGCAAGGCCCGAGAGCGCGAGCAATTTTGTCAAGGTGGACTCCATCTTTGGCCCGgtaatggctg ... cgctttgcagGGAACAAAAATGGTCTACAAGCATTTGGCCACACTATACTTTGTTTTTGTCTTTGATAGCTCTGAGAACGAGCTTGCCATGCTCGACCTCGTACAAGGTA


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TACTCTCTGCAAGGCCCGAGAGCGCGAGCAATTTTGTCAAGGTGGACTCCATCTTTGGCCCGgtaatggctgatgcagtagtaaatcttatgctaatgggacagctggtgtgcaaatgctagcaatgaatggaaaaaagttaattggtcagatgccatttgt

- - - - - - - - - - - - - - - - - - - - GGTGGA