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

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtcagtagctagccaatctctcctgctttctctctctctctcaagtctgaatcgactattctccgtcattttcttgagcatttctgcctgcagGTCTCGCTGTGTGTCAAGAGGCTCATCTACACCAACGATGCCGGAGAGATCGTCAAAGGAGTCTGCTCCAACTTCTTATGTACGTCTACGTCTCTTCACA

Basic information

species Zea mays
transcript GRMZM2G168143_T02
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G168143_T02 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os06g01850.1 (Oryza sativa), 3'ss of exon 2
gtcagtagctagccaatct-ctcctgctttctctctctc---tctcaagtctgaatcgactattctccgtca-------ttttcttgagcatttctgcctgcagGTCTCGCTGTGTGTCAAGAGGCTCATCTACACCAACGATGCCGGAGAGATCGTCAAAGGAGTCTGCTCCAACTTCTTATGTACGTCTACGTCTCTTCACA
||||||  |   |   ||| ||||| |||  ||  ||||    ||       | |||||      | | |||       |  || |   || || | |||  |||| || || || |||||||||||| | |||||||||||    |||||||| |||||||||||||||||||||||| | |                     
gtcagtccccctcttctcttctcctccttattcaatctcattccttctcatcggatcgatctcctttcttcacaccagataatcatcttcacttgtacctctagGTTTCACTCTGCGTCAAGAGGCTCGTTTACACCAACGACCAGGGAGAGATTGTCAAAGGAGTCTGCTCCAACTTCCTCT---------------------

upper sequence: GRMZM2G168143_T02 (Zea mays), 3'ss of exon 2
lower sequence: AT5G66190.2 (Arabidopsis thaliana), 3'ss of exon 3
gtcagtagctagccaatctctcctgctttctctctctctctcaagtctgaatcgactattctccgtcattttcttgagcatttctgcctgcagGTCTCGCTGTGTGTCAAGAGGCTCATCTACACCAACGATGCCGGAGAGATCGTCAAAGGAGTCTGCTCCAACTTCTTATGTACGTCTACGTCTCTTCACA
    |||   |   |||| |||   |     ||  ||   | | |  | |    |  ||  ||  | || |     |     ||    ||||||| || || ||||||||||| ||  | ||||| || |||| ||||||||| || || || ||||||||||||||||| |                     
----gtaagcaaataatccctctaaca---actaactaaataatgatttacaaaatgatcttctcttatctgg--aaatggatccttttgcagGTTTCTCTCTGTGTCAAGAGACTAGTTTACACAAATGATGGCGGAGAGATTGTTAAGGGGGTCTGCTCCAACTTCTTGT---------------------
















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|71441572|gb|DR822622.1|DR822622
EST:     TCTACTCCATCGCCAGCAGCGCGATCGGCGACTTCGGCGACTCCAAGACA                         GTCTCGCTGTGTGTCAAGAGGCTCATCTACACCAACGATGCCGGAGAGATC
genomic: TCTACTCCATCGCCAGCAGCGCGATCGGCGACTTCGGCGACTCCAAGACAgtcagtagct ... ctgcctgcagGTCTCGCTGTGTGTCAAGAGGCTCATCTACACCAACGATGCCGGAGAGATC
EST: gi|93015751|gb|EB641271.1|EB641271
EST:     TCTACTCCATCGCCAGCAGCGCGATCGGCGACTTCGGCGACTCCAAGACA                         GTCTCGCTGTGTGTCAAGAGGCTCATCTACACCAACGATGCCGGAGAGATC
genomic: TCTACTCCATCGCCAGCAGCGCGATCGGCGACTTCGGCGACTCCAAGACAgtcagtagct ... ctgcctgcagGTCTCGCTGTGTGTCAAGAGGCTCATCTACACCAACGATGCCGGAGAGATC
EST: gi|148932036|gb|EC875356.2|EC875356
EST:     TCTACTCCATCGCCAGCAGCGCGATCGGCGAATTCGGCGACTTCAAGACA                         GTCTCGCTGTGTGTCAAGAGGCTCATCTACCCCAA-GAATGCCGGAGAGAT
genomic: TCTACTCCATCGCCAGCAGCGCGATCGGCGACTTCGGCGACTCCAAGACAgtcagtagct ... ctgcctgcagGTCTCGCTGTGTGTCAAGAGGCTCATCTACACCAACGA-TGCCGGAGAGAT
EST: gi|74242655|gb|DT650569.1|DT650569
EST:     TCTACTCCATCGCCAGCAGCGCGATCGGCGACTTCGGCGACTCCAAGACA                         GTCTCGCTGTGTGTCAAGAGGCTCATCTACACCAACGATGCCGGAGAGATC
genomic: TCTACTCCATCGCCAGCAGCGCGATCGGCGACTTCGGCGACTCCAAGACAgtcagtagct ... ctgcctgcagGTCTCGCTGTGTGTCAAGAGGCTCATCTACACCAACGATGCCGGAGAGATC
EST: gi|50327429|gb|CO522555.1|CO522555
EST:     TCTACTCCATCGCCAGCAGCGCGATCGGCGACTTCGGCGACTCCAAGACA                         GTCTCGCTGTGTGTCAAGAGGCTCATCTACACCAACGATGCCGGAGAGATC
genomic: TCTACTCCATCGCCAGCAGCGCGATCGGCGACTTCGGCGACTCCAAGACAgtcagtagct ... ctgcctgcagGTCTCGCTGTGTGTCAAGAGGCTCATCTACACCAACGATGCCGGAGAGATC
EST: gi|94475152|gb|EB704110.1|EB704110
EST:     TCTACTCCATCGCCAGCAGCGCGATCGGCGACTTCGGCGACTCCAAGACA                         GTCTCGCTGTGTGTCAAGAGGCTCATCTACACCAACGATGCCGGAGAGATC
genomic: TCTACTCCATCGCCAGCAGCGCGATCGGCGACTTCGGCGACTCCAAGACAgtcagtagct ... ctgcctgcagGTCTCGCTGTGTGTCAAGAGGCTCATCTACACCAACGATGCCGGAGAGATC
EST: gi|91047927|gb|EB158345.1|EB158345
EST:     TCTACTCCATCGCCAGCAGCGCGATCGGCGACTTCGGCGACTCCAAGACA                         GTCTCGCTGTGTGTCAAGAGGCTCATCTA
genomic: TCTACTCCATCGCCAGCAGCGCGATCGGCGACTTCGGCGACTCCAAGACAgtcagtagct ... ctgcctgcagGTCTCGCTGTGTGTCAAGAGGCTCATCTA

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), 44 (downstream exon)
Score: 14

CGTCATCGCCGATGGCGTCGACAAGAACGGCAAGCCGCACAAGGTCAGGCTCTACTCCATCGCCAGCAGCGCGATCGGCGACTTCGGCGACTCCAAGACAgtcagtagct ... ctgcctgcagGTCTCGCTGTGTGTCAAGAGGCTCATCTACACCAACGATGCCGGAGAGATCGTCAAAGGAGTCTGCTCCAACTTCTTATGTACGTCTACGTCTCTTCACA


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 70

CGTCATCGCCGATGGCGTCGACAAGAACGGCAAGCCGCACAAGGTCAGGCTCTACTCCATCGCCAGCAGCGCGATCGGCGACTTCGGCGACTCCAAGACAgtcagtagct ... ctgcctgcagGTCTCGCTGTGTGTCAAGAGGCTCATCTACACCAACGATGCCGGAGAGATCGTCAAAGGAGTCTGCTCCAACTTCTTATGTACGTCTACGTCTCTTCACA


Block sizes: 46 (upstream exon), 44 (downstream exon)
Score: 5

CGTCATCGCCGATGGCGTCGACAAGAACGGCAAGCCGCACAAGGTCAGGCTCTACTCCATCGCCAGCAGCGCGATCGGCGACTTCGGCGACTCCAAGACAgtcagtagct ... ctgcctgcagGTCTCGCTGTGTGTCAAGAGGCTCATCTACACCAACGATGCCGGAGAGATCGTCAAAGGAGTCTGCTCCAACTTCTTATGTACGTCTACGTCTCTTCACA


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 83

CGTCATCGCCGATGGCGTCGACAAGAACGGCAAGCCGCACAAGGTCAGGCTCTACTCCATCGCCAGCAGCGCGATCGGCGACTTCGGCGACTCCAAGACAgtcagtagct ... ctgcctgcagGTCTCGCTGTGTGTCAAGAGGCTCATCTACACCAACGATGCCGGAGAGATCGTCAAAGGAGTCTGCTCCAACTTCTTATGTACGTCTACGTCTCTTCACA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctcaagtctgaatcgactattctccgtcattttcttgagcatttctgcctgcagGTCTCGCTGTGTGTCAAGAGGCTCATCTACACCAACGATGCCGGAGAGATCGTCAAAGGAGTCTGCTCCAACTTCTTATGTACGTCTACGTCTCTTCACA
                                          tttctgcct  CT-rich tract
                             attttctt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtcagtagctagccaatctctcctgctttctctctctctctcaagtctgaatcgactattctccgtcattttcttgagcatttctgcctgcagGTCTCGCTGTGTGTCAAGAGGCTCATCTACACCAACGATGCCGGAGAGATCGTCAAAGGAGTCTGCTCCAACTTCTTATGTACGTCTACGTCTCTTCACA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG