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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttgttcaattgttctttgcaatgtcttacatgcacccttccttttttttataaccaaaatagaactaattgtttttcaatctgtgttctggaccaaatcttatagGGAGGAGTCAATAGAACATGAAGGGGATGATGAGATTTCTGTGCAGACAAGTCCACAAAAGTCCCTTGAGGAGGAATATTTGGAAACTGAAAAGAAG

Basic information

species Zea mays
transcript GRMZM2G102196_T01
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G102196_T01 (Zea mays), 3'ss of exon 11
lower sequence: LOC_Os01g06270.1 (Oryza sativa), 3'ss of exon 13
gttgttcaattgttctttgcaatgtcttacatgcacccttccttttttttataaccaaaatagaactaattgtttttcaatc-tgtgttctggaccaaatcttatagGGAGGAGTCAATAGAACATGAAGGGGATGATGAGATTTCTGTGCAGACAAGTCCACAAAAGTCCCTTGAGGAGGAATATTTGGAAACTGAAAAGAAG
||||  ||||||||||||   || |     || ||  || |  |    |       |||||    | |||  | || | |||  ||||| ||||| |||| || |||||| | ||||| |||||||||     |||| ||  | || |   ||||||||||||| || ||||||||||| ||||||||||||||||||||||||
gttggccaattgttctttttgatat-----atacaatctgcagtaaggtctgccagaaaatgaccccaatgatattgcgatcacgtgtt-tggacgaaat-ttgtagGGACGTGTCAACAGAACATGACA---ATGAGGAACTATCAGAAAAGACAAGTCCACAGAAATCCCTTGAGGAAGAATATTTGGAAACTGAAAAGAAG
















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|61119836|gb|DN560797.1|DN560797
EST:     ATTGAGCGGATACGCACATACGTGGATAATTTGGCAGTCTTAAACTCTAG                         GGAGGAGTCAATAGAACATGGAGGGGATGATGAGATTTCTGAGCAGACAAG
genomic: ATTGAGCGGATACGCACATACGTGGATAATTTGGCAGTCTTAAACTCTAGgttgttcaat ... aatcttatagGGAGGAGTCAATAGAACATGAAGGGGATGATGAGATTTCTGTGCAGACAAG
EST: gi|60354570|gb|DN221543.1|DN221543
EST:     ATTGAGCGGATACGCACATACGTGGATAATTTGGCAGTCTTAAACTCTAG                         GGAGGAGTCAATAGAACATGAAGGGGATGATGAGATTTCTGTGCAGACAAG
genomic: ATTGAGCGGATACGCACATACGTGGATAATTTGGCAGTCTTAAACTCTAGgttgttcaat ... aatcttatagGGAGGAGTCAATAGAACATGAAGGGGATGATGAGATTTCTGTGCAGACAAG
EST: gi|4621437|gb|AI612270.1|AI612270
EST:     ATTGAGCGGATACGCACATACGTGGATAATTTGGCAGTCTTAAACTCTAG                         GGAGGAGTCAATAGAACATGAAGGGGATGATGAGATTTCTGTGCAGACAAG
genomic: ATTGAGCGGATACGCACATACGTGGATAATTTGGCAGTCTTAAACTCTAGgttgttcaat ... aatcttatagGGAGGAGTCAATAGAACATGAAGGGGATGATGAGATTTCTGTGCAGACAAG
EST: gi|60339229|gb|DN206202.1|DN206202
EST:     ATTGAGCGGATACGCACATACGTGGATAATTTGGCAGTCTTAAACTCTAG                         GGAGGAGTCAATAGAACATGAAGGGGATGATGAGATTTCTGTGCAGACAAG
genomic: ATTGAGCGGATACGCACATACGTGGATAATTTGGCAGTCTTAAACTCTAGgttgttcaat ... aatcttatagGGAGGAGTCAATAGAACATGAAGGGGATGATGAGATTTCTGTGCAGACAAG
EST: gi|31352028|gb|CD436385.1|CD436385
EST:     CTTGAGCGGATACACACATACGTGGATAATTTGGCAGTCTTAAACTCTAG                         GGAGGAGTCAATAGAACATGGAGGGGATGATGAGATTTCTGAGCAGACAAG
genomic: ATTGAGCGGATACGCACATACGTGGATAATTTGGCAGTCTTAAACTCTAGgttgttcaat ... aatcttatagGGAGGAGTCAATAGAACATGAAGGGGATGATGAGATTTCTGTGCAGACAAG
EST: gi|60340698|gb|DN207671.1|DN207671
EST:     ATTGAGCGGATACGCACATACGTGGATAATTTGGCAGTCTTAAACTCTAG                         GGAGGAGTCAATAGAACATGAAGGGGATGATGAGATTTCTGTGCAGACAAG
genomic: ATTGAGCGGATACGCACATACGTGGATAATTTGGCAGTCTTAAACTCTAGgttgttcaat ... aatcttatagGGAGGAGTCAATAGAACATGAAGGGGATGATGAGATTTCTGTGCAGACAAG
EST: gi|60337011|gb|DN203984.1|DN203984
EST:     ATTGAGCGGATACGCACATACGTGGATAATTTGGCAGTCTTAAACTCTAG                         GGAGGAGTCAATAGAACATGAAGGGGATGATGAGATTTCTGTGCAGACAAG
genomic: ATTGAGCGGATACGCACATACGTGGATAATTTGGCAGTCTTAAACTCTAGgttgttcaat ... aatcttatagGGAGGAGTCAATAGAACATGAAGGGGATGATGAGATTTCTGTGCAGACAAG

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: 46 (upstream exon), 49 (downstream exon)
Score: 96

GAAGTTCTTAGCCCGTCAATTGAGCGGATACGCACATACGTGGATAATTTGGCAGTCTTAAACTCTAGgttgttcaat ... aatcttatagGGAGGAGTCAATAGAACATGAAGGGGATGATGAGATTTCTGTGCAGACAAGTCCACAAAAGTCCCTTGAGGAGGAATATTTGGAAACTGAAAAGAAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 90

GAAGTTCTTAGCCCGTCAATTGAGCGGATACGCACATACGTGGATAATTTGGCAGTCTTAAACTCTAGgttgttcaat ... aatcttatagGGAGGAGTCAATAGAACATGAAGGGGATGATGAGATTTCTGTGCAGACAAGTCCACAAAAGTCCCTTGAGGAGGAATATTTGGAAACTGAAAAGAAG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 143

GAAGTTCTTAGCCCGTCAATTGAGCGGATACGCACATACGTGGATAATTTGGCAGTCTTAAACTCTAGgttgttcaat ... aatcttatagGGAGGAGTCAATAGAACATGAAGGGGATGATGAGATTTCTGTGCAGACAAGTCCACAAAAGTCCCTTGAGGAGGAATATTTGGAAACTGAAAAGAAG


Block sizes: 45 (upstream exon), 48 (downstream exon)
Score: 118

GAAGTTCTTAGCCCGTCAATTGAGCGGATACGCACATACGTGGATAATTTGGCAGTCTTAAACTCTAGgttgttcaat ... aatcttatagGGAGGAGTCAATAGAACATGAAGGGGATGATGAGATTTCTGTGCAGACAAGTCCACAAAAGTCCCTTGAGGAGGAATATTTGGAAACTGAAAAGAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taaccaaaatagaactaattgtttttcaatctgtgttctggaccaaatcttatagGGAGGAGTCAATAGAACATGAAGGGGATGATGAGATTTCTGTGCAGACAAGTCCACAAAAGTCCCTTGAGGAGGAATATTTGGAAACTGAAAAGAAG
            aactaat  putative branch site (score: 118)
     aaaatagaactaattg  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttgttcaattgttctttgcaatgtcttacatgcacccttccttttttttataaccaaaatagaactaattgtttttcaatctgtgttctggaccaaatcttatagGGAGGAGTCAATAGAACATGAAGGGGATGATGAGATTTCTGTGCAGACAAGTCCACAAAAGTCCCTTGAGGAGGAATATTTGGAAACTGAAAAGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG