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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttgttccagcttacagattgaaatatcctgagcagatatcaaattattttagtcacgagttcttcatgctgaatatctttgtcccttgtgcagTATGCTTTTAATATATTCTCACACAATGCACCAGTTCTTGAGAATGGGTATAACGAGGAGGAAATGAAAATGGTGAAGGAGACCAGGAAAATTTGG

Basic information

species Zea mays
transcript GRMZM2G076885_T01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G076885_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os03g55280.1 (Oryza sativa), 3'ss of exon 3
gttgttccagcttacagattgaaatatcctgagcagatatcaaattattttagtcacgagttcttcatgctgaatatctttgtcccttgtgcagTATGCTTTTAATATATTCTCACACAATGCACCAGTTCTTGAGAATGGGTATAACGAGGAGGAAATGAAAATGGTGAAGGAGACCAGGAAAATTTGG
         | |   |   |  |||||||||  || |   || ||||||||     | |||       ||||||| |  || ||| ||||||||||||||||||||||||| ||||| ||||||||| || |||| |||||||| || |||||||| ||||| ||||||||||||||||| ||||| |||
---------gttctaattctataatatcctggacacacgccagattatttt-----caagtca-----gctgaatttgcttctcc-ttgtgcagTATGCTTTTAATATATTTTCACATAATGCACCAATTGTTGAAAATGGGTACAATGAGGAGGAGATGAAGATGGTGAAGGAGACCAGAAAAATCTGG

upper sequence: GRMZM2G076885_T01 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA05G34420.1 (Glycine max), 3'ss of exon 3
gttgttccagcttacagattgaaatatcctgagcaga--tatcaaattattttagtcacgagttcttcatgctgaatatctttgtcccttgtgcagTATGCTTTTAATATATTCTCACACAATGCACCAGTTCTTGAGAATGGGTATAACGAGGAGGAAATGAAAATGGTGAAGGAGACCAGGAAAATTTGG
                | ||| |  || |||  ||    | ||   | |||   |     ||  || | |  ||| |    ||||   || ||||||||||||||||| |||||||||| |||||  | ||||||   || || | ||| || || |||||||||||||| ||||||||||||||||| |||
----------------gtttgcacaattctgtacatgcctctcttgtgattgatgctttaagaactacttcatga-tggtgttgttgtttttgcagTATGCTTTTAATCTATTCTCACATAATGCGTCTGTTCTTTCAAAGGGATTTAATGAAGAAGAAATGAAAATGGTCAAGGAGACCAGGAAAATCTGG

upper sequence: GRMZM2G076885_T01 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA08G05250.1 (Glycine max), 3'ss of exon 3
gttgttccagcttacagattgaaatatcctgagcagatatcaaattattttagt--cacgagttcttcatgctgaatatctttgtcccttgtgcagTATGCTTTTAATATATTCTCACACAATGCACCAGTTCTTGAGAATGGGTATAACGAGGAGGAAATGAAAATGGTGAAGGAGACCAGGAAAATTTGG
                | ||| |  || |||  ||    ||   | |||||  |      ||  || | | |||| |     |||   || ||||||||||||||||| ||||||| || |||||  | ||||||   ||||| ||||| || || |||||||||||||| ||||||||||||||||| |||
----------------gtttgcacaattctgtacatgcctctcgtgattttgatgctttaagaactacttcctga-tgctgctgttgttt-tgcagTATGCTTTTAATCTATTCTCGCATAATGCGTCTGTTCTTTCAAATGGATATAATGAAGAAGAAATGAAAATGGTCAAGGAGACCAGGAAAATCTGG

upper sequence: GRMZM2G076885_T01 (Zea mays), 3'ss of exon 3
lower sequence: AT1G14810.1 (Arabidopsis thaliana), 3'ss of exon 3
------gttgttccagcttacagattgaaatatcc-tgagcagat-atcaaattattttagtcacgagttcttcatgctgaatatctttgtcccttgtgcagTATGCTTTTAATATATTCTCACACAATGCACCAGTTCTTGAGAATGGGTATAACGAGGAGGAAATGAAAATGGTGAAGGAGACCAGGAAAATTTGG
      | |      ||||| || ||| | |     || || ||| || ||||   |||      ||||  |   || ||  | | | |||   || |||||||||| |||||  | || ||||| ||||| ||  ||||||| || || || ||||| |||||||||||| | ||||||||||| ||||| || |||
gtgagtgcttaatttgcttatagtttgtatttcgaatgtgctgattatgaaatccctttt----tgagtaat--gtgatggttttgtatgttg-ttctgcagTATGCATTTAACTTGTTTTCACATAATGCTCCTATTCTTGACAACGGTTACAACGAAGAGGAAATGAAACTTGTGAAGGAGACAAGGAAGATCTGG

upper sequence: GRMZM2G076885_T01 (Zea mays), 3'ss of exon 3
lower sequence: Vv01s0011g05860.t01 (Vitis vinifera), 3'ss of exon 3
----gttgttccagcttacagattga--aatatcctgagcag-atatcaaattattttagtcacgagttcttcatgctgaatatctt---------tgtcccttgtgcagTATGCTTTTAATATATTCTCACACAATGCACCAGTTCTTGAGAATGGGTATAACGAGGAGGAAATGAAAATGGTGAAGGAGACCAGGAAAATTTGG
    ||     ||   ||||  || |  ||| |    || |  | | ||||| |||||       |  |  |      ||||| | |         | | | |  ||||||||||||||||| | || |||||||||||||| ||||||   |||||||| || || |||||||||||| | || || ||||| |||||||| |||
gtttgtctactcattatacatgtttaccaatttgacaagaattacaacaaatgattttgtattttatctagttgcctagaataacctcttaatacatatacttcatgcagTATGCTTTTAATCTCTTTTCACACAATGCACCTGTTCTTCCAAATGGGTACAATGAAGAGGAAATGAAATTAGTAAAAGAGACAAGGAAAATCTGG

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|18964615|gb|BM661107.1|BM661107
EST:     GTCTTGGAAGGGAAGGCGCCAACATGCAACATTTTCAAACAGCAG                         TATGCTTTTAATATATTCTCACACAATGCACCAGTTCTTGAGAATGGGTAT
genomic: GTCTTGGAAGGGAAGGCGCCAACATGCAACATTTTCAAACAGCAGgttgttccag ... ccttgtgcagTATGCTTTTAATATATTCTCACACAATGCACCAGTTCTTGAGAATGGGTAT
EST: gi|7216942|gb|AW563049.1|AW563049
EST:     GTCTTGGAAGGGAAGGCGCCAACATGCAACATTTTCAAACAGCAG                         TATGCTTTTAATATATTCTCACACAATGCACCAGTTCTTGAGAATGGGTAT
genomic: GTCTTGGAAGGGAAGGCGCCAACATGCAACATTTTCAAACAGCAGgttgttccag ... ccttgtgcagTATGCTTTTAATATATTCTCACACAATGCACCAGTTCTTGAGAATGGGTAT
EST: gi|76292292|gb|DV031860.1|DV031860
EST:     GTCTTGGAAGGGAAGGCGCCAACATGCAACATTTTCAAACAGCAG                         TATGCTTTTAATATATTCTCACACAATGCACCAGTTCTTGAGAATGGGTAT
genomic: GTCTTGGAAGGGAAGGCGCCAACATGCAACATTTTCAAACAGCAGgttgttccag ... ccttgtgcagTATGCTTTTAATATATTCTCACACAATGCACCAGTTCTTGAGAATGGGTAT
EST: gi|5714254|gb|AI944239.1|AI944239
EST:     TTTTC-AACAGCAG                         TATGCTTTTAATATATTCTCACNCAATGCNCCAGTTCTTGAGAATGGGTAT
genomic: TTTTCAAACAGCAGgttgttccag ... ccttgtgcagTATGCTTTTAATATATTCTCACACAATGCACCAGTTCTTGAGAATGGGTAT
EST: gi|7216973|gb|AW563095.1|AW563095
EST:     GTCTTGGAAGGGAAGGCGCCAACATGCAACATTTTCAAACAGCAG                         TATGCTTTTAATATATTCTCACACAATGCACCAGTTCTTGAGAATGGGTAT
genomic: GTCTTGGAAGGGAAGGCGCCAACATGCAACATTTTCAAACAGCAGgttgttccag ... ccttgtgcagTATGCTTTTAATATATTCTCACACAATGCACCAGTTCTTGAGAATGGGTAT
EST: gi|93011814|gb|EB637334.1|EB637334
EST:     GTCTTGGAAGGGAAGGCGCCAACATGCAACATTTTCAAACAGCAG                         TATGCTTTTAATATATTCTCACACAATGCACCAGTTCTTGAGAATGGGTAT
genomic: GTCTTGGAAGGGAAGGCGCCAACATGCAACATTTTCAAACAGCAGgttgttccag ... ccttgtgcagTATGCTTTTAATATATTCTCACACAATGCACCAGTTCTTGAGAATGGGTAT
EST: gi|88749457|gb|DY533598.1|DY533598
EST:     GAAGGGAAGGCGCCAACATGCAACATTTTCAAACAGCAG                         TATGCTTTTAATATATTCTCACACAATGCACCAGTTCTTGAGAATGGGTAT
genomic: GAAGGGAAGGCGCCAACATGCAACATTTTCAAACAGCAGgttgttccag ... ccttgtgcagTATGCTTTTAATATATTCTCACACAATGCACCAGTTCTTGAGAATGGGTAT

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: 132

GTCTTGGAAGGGAAGGCGCCAACATGCAACATTTTCAAACAGCAGgttgttccag ... ccttgtgcagTATGCTTTTAATATATTCTCACACAATGCACCAGTTCTTGAGAATGGGTATAACGAGGAGGAAATGAAAATGGTGAAGGAGACCAGGAAAATTTGG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 137

GTCTTGGAAGGGAAGGCGCCAACATGCAACATTTTCAAACAGCAGgttgttccag ... ccttgtgcagTATGCTTTTAATATATTCTCACACAATGCACCAGTTCTTGAGAATGGGTATAACGAGGAGGAAATGAAAATGGTGAAGGAGACCAGGAAAATTTGG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 124

GTCTTGGAAGGGAAGGCGCCAACATGCAACATTTTCAAACAGCAGgttgttccag ... ccttgtgcagTATGCTTTTAATATATTCTCACACAATGCACCAGTTCTTGAGAATGGGTATAACGAGGAGGAAATGAAAATGGTGAAGGAGACCAGGAAAATTTGG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 83

GTCTTGGAAGGGAAGGCGCCAACATGCAACATTTTCAAACAGCAGgttgttccag ... ccttgtgcagTATGCTTTTAATATATTCTCACACAATGCACCAGTTCTTGAGAATGGGTATAACGAGGAGGAAATGAAAATGGTGAAGGAGACCAGGAAAATTTGG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcaaattattttagtcacgagttcttcatgctgaatatctttgtcccttgtgcagTATGCTTTTAATATATTCTCACACAATGCACCAGTTCTTGAGAATGGGTATAACGAGGAGGAAATGAAAATGGTGAAGGAGACCAGGAAAATTTGG
                                   tatctttgtccctt  CT-rich tract
     ttattttagt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttgttccagcttacagattgaaatatcctgagcagatatcaaattattttagtcacgagttcttcatgctgaatatctttgtcccttgtgcagTATGCTTTTAATATATTCTCACACAATGCACCAGTTCTTGAGAATGGGTATAACGAGGAGGAAATGAAAATGGTGAAGGAGACCAGGAAAATTTGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA