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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTATGCATACTTCAAAAAGCTGGATTACTTTTCCACAGAATgtaatgtctggatcttttttctgttcagttcttttcattttttcccgcattgaaggagaccactttattccaatatcagaaaatgctaggatgtcacttg...

Basic information

species Zea mays
transcript GRMZM2G402242_T03
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G402242_T02 (Zea mays), 5'ss of exon 7
lower sequence: LOC_Os02g52470.2 (Oryza sativa), 5'ss of exon 8
GTATGCATACTTCAAAAAGCTGGATTACTTTTCCACAGAATgtaatgtctggatcttttttctgttcagttcttt-----tcattttttcccgcattgaaggagaccactttattcca-atatcagaaaatgctaggatgtcacttg
||||||||| |||||||||||||| ||||| ||||||||||||||| |||   || ||  | |||  || | ||      ||| |   |  |    || |    | ||   | ||  | | |  || ||    |  | |        
GTATGCATATTTCAAAAAGCTGGACTACTTCTCCACAGAATgtaatttcttactccttcctatgtatagatgttcagcagtcactgactagcattctgtaaccaatcatgcttttatacacactagcaataattctgctaa------

upper sequence: GRMZM2G402242_T02 (Zea mays), 5'ss of exon 7
lower sequence: GLYMA04G00350.1 (Glycine max), 5'ss of exon 1
-----------------------------------------------------------GTATGCATACTTCAAAAAGCTGGATTACTTTTCCACAGAATgtaatgtctggatcttttttctgttcagttcttttcattttttcccgc-attgaaggagaccactttattc-caatatcagaaaatgctaggatgtcacttg
                                                           |||||| || ||||| ||||| |||||||||||||| ||||||||  |      |||| || |  ||  || |||||   | |  | || |   ||  |   |||| | |   ||||  |||                     
GATGGCCCCATTCCCCGATGCAAACCTTTCAAGTATACTTACGAGAAGGAGATTGTCATGTATGCTTATTTCAAGAAGCTCGATTACTTTTCCACCGAATgtaaccttc----ctttcttttcctc--ttattttcccctctaactgccaaacaaacatttcactctctctacaattccag---------------------

upper sequence: GRMZM2G402242_T02 (Zea mays), 5'ss of exon 7
lower sequence: GLYMA04G00350.3 (Glycine max), 5'ss of exon 1
----------------------------------------------------------------------------------------------------GTATGCATACTTCAAAAAGCTGGATTACTTTTCCACAGAATgtaatgtctggatcttttttctgttcagttcttttcattttttcccgc-attgaaggagaccactttattc-caatatcagaaaatgctaggatgtcacttg
                                                                                                    |||||| || ||||| ||||| |||||||||||||| ||||||||  |      |||| || |  ||  || |||||   | |  | || |   ||  |   |||| | |   ||||  |||                     
TTGCCAGATTGAGTAGATGCACCTCTATAACCACCGGTGAGGATGGCCCCATTCCCCGATGCAAACCTTTCAAGTATACTTACGAGAAGGAGATTGTCATgtatgcttatttcaagaagctcgattacttttccaccgaatgtaaccttc----ctttcttttcctc--ttattttcccctctaactgccaaacaaacatttcactctctctacaattccag---------------------

upper sequence: GRMZM2G402242_T02 (Zea mays), 5'ss of exon 7
lower sequence: AT2G44270.2 (Arabidopsis thaliana), 5'ss of exon 8
------GTATGCATACTTCAAAAAGCTGGATTACTTTTCCACAGAATgtaa-tgtctggatcttttttctgttcagttcttttcattttttcccgcattgaaggagaccactttattccaatatcagaaaatgctaggatgtcacttg-------
      |||||| || ||||| |||||||||||||| ||||| |||||||| |||       |   || | |  || | || ||  ||  |     || |    || | |  |      | | | |     |  |    | |     |       
CTTTACGTATGCTTATTTCAAGAAGCTGGATTACTTCTCCACTGAATgtaagtgtacaatcatcgattttttgtaggttttatctgttcctaagttatagtttcagccaatctctagttatttttatggcttattttttttttttgagtttgcag

upper sequence: GRMZM2G402242_T02 (Zea mays), 5'ss of exon 7
lower sequence: AT2G44270.1 (Arabidopsis thaliana), 5'ss of exon 7
GTATGCATACTTCAAAAAGCTGGATTACTTTTCCACAGAATgtaa-tgtctggatcttttttctgttcagttcttttcattttttcccgcattgaaggagaccactttattccaatatcagaaaatgctaggatgtcacttg-------
|||||| || ||||| |||||||||||||| ||||| |||||||| |||       |   || | |  || | || ||  ||  |     || |    || | |  |      | | | |     |  |    | |     |       
GTATGCTTATTTCAAGAAGCTGGATTACTTCTCCACTGAATgtaagtgtacaatcatcgattttttgtaggttttatctgttcctaagttatagtttcagccaatctctagttatttttatggcttattttttttttttgagtttgcag

upper sequence: GRMZM2G402242_T02 (Zea mays), 5'ss of exon 7
lower sequence: Vv18s0001g00440.t01 (Vitis vinifera), 5'ss of exon 7
--------------------------GTATGCATACTTCAAAAAGCTGGATTACTTTTCCACAGAATgtaa-tgtctggatcttttttctgttcagttcttttcattttttcccgcattgaaggagaccactttattccaatatcagaaaatgctaggatgtcacttg-
                          ||||||||| ||||||| ||| || ||||||||||| |||||||| |||     |   ||| |||||||   || ||    | || |    ||  |     || |||| ||||  |    |     | |    | |   |   
CTGCAAAACCTTAACCGGATTTACACGTATGCATATTTCAAAAGGCTAGACTACTTTTCCACCGAATgtaagtgttcattttcctttactgttcaag-ctcttatcctattactaggttttattcttccgcttt-ttccttttggggtgggagttgttttcttgttcat

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|71774415|gb|DR972293.1|DR972293
EST:     GTATGCATACTTCAAAAAGCTGGATTACTTTTTCACAGATT                         GCATCTATTCACCAAATGCATACCGTGGTTTTGCTC
genomic: GTATGCATACTTCAAAAAGCTGGATTACTTTTCCACAGAATgtaatgtctg ... catgatccagGCATCTATTCACCAAATGCATACCGTGGTTTTGCTC
EST: gi|91877954|gb|EB407911.1|EB407911
EST:     GTATGCATACTTCAAAAAGCTGGATTACTTTTCCACAGAAT                         GCATCTATTCACCAAATGCATACGGTGGTTTTGTTCGTGAATTTATTAAAG
genomic: GTATGCATACTTCAAAAAGCTGGATTACTTTTCCACAGAATgtaatgtctg ... catgatccagGCATCTATTCACCAAATGCATACCGTGGTTTTGCTCGTGAATTTATTAAAG
EST: gi|71761950|gb|DR959887.1|DR959887
EST:     GTATGCATACTTCAAAAAGCTGGATTACTTTTCCACAGAAT                         GCATCTATTCACCAAATGCATACCGTGGTTTTGCTCGTGAATTTATTAAAG
genomic: GTATGCATACTTCAAAAAGCTGGATTACTTTTCCACAGAATgtaatgtctg ... catgatccagGCATCTATTCACCAAATGCATACCGTGGTTTTGCTCGTGAATTTATTAAAG
EST: gi|67014256|gb|CO443005.1|CO443005
EST:     GTATGCATACTTCAAAAAGCTGGATTACTTTTCCACAGAAT                         GCATCTATTCACCAAATGCATACCGTGGTTTTGCTCGTGAATTTATTAAAG
genomic: GTATGCATACTTCAAAAAGCTGGATTACTTTTCCACAGAATgtaatgtctg ... catgatccagGCATCTATTCACCAAATGCATACCGTGGTTTTGCTCGTGAATTTATTAAAG
EST: gi|50323940|gb|CO519066.1|CO519066
EST:     GTATGCATACTTCAAAAAGCTGGATTACTTTTCCACAGAAT                         GCATCTATTCACCAAATGCATACC
genomic: GTATGCATACTTCAAAAAGCTGGATTACTTTTCCACAGAATgtaatgtctg ... catgatccagGCATCTATTCACCAAATGCATACC
EST: gi|91872706|gb|EB402663.1|EB402663
EST:     GTATGCATACTTCAAAAAGCTGGATTACTTTTCCACAGAAT                         GCATCTATTCACCAAATGCATACCGTGGTTTTGCTCGTGAATTTATTAAAG
genomic: GTATGCATACTTCAAAAAGCTGGATTACTTTTCCACAGAATgtaatgtctg ... catgatccagGCATCTATTCACCAAATGCATACCGTGGTTTTGCTCGTGAATTTATTAAAG
EST: gi|60350684|gb|DN217657.1|DN217657
EST:     GTATGCATACTTCAAAAAGCTGGATTACTTTTCCACAGAAT                         GCATCTATTCACCAAATGCATACCGTGGTTTTGCTCGTGAATTTATTAAAG
genomic: GTATGCATACTTCAAAAAGCTGGATTACTTTTCCACAGAATgtaatgtctg ... catgatccagGCATCTATTCACCAAATGCATACCGTGGTTTTGCTCGTGAATTTATTAAAG
EST: gi|91878573|gb|EB408530.1|EB408530
EST:     GTATGCATACTTCAAAAAGCTGGATTACTTTTCCACAGAAT                         GCATCTATTCACCAAATGCATACCGGGGTTTTGCTGGGGAATTTATTAAAG
genomic: GTATGCATACTTCAAAAAGCTGGATTACTTTTCCACAGAATgtaatgtctg ... catgatccagGCATCTATTCACCAAATGCATACCGTGGTTTTGCTCGTGAATTTATTAAAG
EST: gi|71770543|gb|DR968480.1|DR968480
EST:     GTATGCATACTTCAAAAAGCTGGATTACTTTTCCACAGAAT                         GCATCTATTCACCAAATGCATACCGTGGTTTTGCTCGTGAATTTATTA
genomic: GTATGCATACTTCAAAAAGCTGGATTACTTTTCCACAGAATgtaatgtctg ... catgatccagGCATCTATTCACCAAATGCATACCGTGGTTTTGCTCGTGAATTTATTA
EST: gi|50323939|gb|CO519065.1|CO519065
EST:     GTATGCATACTTCAAAAAGCTGGATTACTTTTCCACAGAAT                         GCATCTATTCACCAAATGCATACCGTGGTTTTGCTCGTGAATTTATTAAAG
genomic: GTATGCATACTTCAAAAAGCTGGATTACTTTTCCACAGAATgtaatgtctg ... catgatccagGCATCTATTCACCAAATGCATACCGTGGTTTTGCTCGTGAATTTATTAAAG
EST: gi|71770542|gb|DR968479.1|DR968479
EST:     GTATGCATACTTCAAAAAGCTGGATTACTTTTCCACAGAAT                         GCATCTATTCACCAAATGCATACCGTGGTTTTGCTCGTGAATTTATTAAAG
genomic: GTATGCATACTTCAAAAAGCTGGATTACTTTTCCACAGAATgtaatgtctg ... catgatccagGCATCTATTCACCAAATGCATACCGTGGTTTTGCTCGTGAATTTATTAAAG

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: 36

GTATGCATACTTCAAAAAGCTGGATTACTTTTCCACAGAATgtaatgtctg ... catgatccagGCATCTATTCACCAAATGCATACCGTGGTTTTGCTCGTGAATTTATTAAAGATTTAGAAAGAATGAG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 34

GTATGCATACTTCAAAAAGCTGGATTACTTTTCCACAGAATgtaatgtctg ... catgatccagGCATCTATTCACCAAATGCATACCGTGGTTTTGCTCGTGAATTTATTAAAGATTTAGAAAGAATGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 46

GTATGCATACTTCAAAAAGCTGGATTACTTTTCCACAGAATgtaatgtctg ... catgatccagGCATCTATTCACCAAATGCATACCGTGGTTTTGCTCGTGAATTTATTAAAGATTTAGAAAGAATGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 33

GTATGCATACTTCAAAAAGCTGGATTACTTTTCCACAGAATgtaatgtctg ... catgatccagGCATCTATTCACCAAATGCATACCGTGGTTTTGCTCGTGAATTTATTAAAGATTTAGAAAGAATGAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTATGCATACTTCAAAAAGCTGGATTACTTTTCCACAGAATgtaatgtctggatcttttttctgttcagttcttttcattttttcccgcattgaaggagaccactttattccaatatcagaaaatgctaggatgtcacttg

- - - - - - - - AAGCTG
- - - - - - - - - GCTGGA