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

...aactagtggcataacttgtacacaaacccacgcctagagtaaagcctcaggttgctagcagcacatccttatatcttcacaatgcacattttactgacagATCTTCGAGATGACAAGCAGTTCTTTGTGGACCATCCTGGTGCTGTTCCTATCACTACTGCTCAG

Basic information

species Zea mays
transcript GRMZM5G803949_T03
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G803949_T02 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os02g02840.1 (Oryza sativa), 3'ss of exon 4
-aactag-tggcataacttgtacaca-aacccacgcctaga---gtaaagcctcaggttgctagcagcacatccttatatcttcacaatgcacattttactgacagATCTTCGAGATGACAAGCAGTTCTTTGTGGACCATCCTGGTGCTGTTCCTATCACTACTGCTCAG
 || ||  |  ||    || |||| | ||    | | | ||   ||||||   ||  |     | ||| ||     || | |||||| ||   |||  |||| ||||||||||||||||||||||||| |||||||||||||||||||||||||||||||| |||||||||
aaattaaattccaatcattctacagataatatccccttcgacctgtaaagatccaact-----gtagcccacttacat-ttttcacattgtttattgcactggcagATCTTCGAGATGACAAGCAGTTTTTTGTGGACCATCCTGGTGCTGTTCCTATCACCACTGCTCAG

upper sequence: GRMZM5G803949_T02 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA16G23340.1 (Glycine max), 3'ss of exon 4
-------aactagtggcataacttgtacacaaacccacgcctagagtaaagcctcaggttgctagcagcacatccttatatcttcacaatgcacattttactgacagATCTTCGAGATGACAAGCAGTTCTTTGTGGACCATCCTGGTGCTGTTCCTATCACTACTGCTCAG
       ||  |    | |  | | |||||| ||   | || |  ||    | |    ||   ||      ||  |   || ||   |||    | |     |||||| ||||||||||| |||||||||||  | ||||||||||||||||| || || || || | ||||
ttttgttaaaaatattcttggcctctacacatactatcaccaattgtt---ctttcaattaagagttagttatt-taccattttttgaatttgaaatga---gacagACCTTCGAGATGATAAGCAGTTCTTCATAGACCATCCTGGTGCTGTACCCATTACCACCGTTCAG

upper sequence: GRMZM5G803949_T02 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA11G11510.1 (Glycine max), 3'ss of exon 4
--aactagtggcataacttgtacacaaacccacgcctagagtaaagcctcaggttgctagcagcacatccttatatcttcacaa-tgcacattttactgacagATCTTCGAGATGACAAGCAGTTCTTTGTGGACCATCCTGGTGCTGTTCCTATCACTACTGCTCAG
     || | | ||  ||| |       ||   | | |   ||||||  |   |   |||     | |    || || | |||| |  |  |||  ||   ||||||||| ||||| ||||||||||||   |||||||||||||| || |||||||| || || |||
tagtttaattgtatg-cttttgatggttccattgaccatgataaagctgcca-tgattagtt-tgcttgggcatttcatgacaactaaatctttgtcttgtagATCTTCGGGATGATAAGCAGTTCTTTCAAGACCATCCTGGTGCAGTGCCTATCACCACAGCACAG

upper sequence: GRMZM5G803949_T02 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA04G02530.3 (Glycine max), 3'ss of exon 4
aactagtg-gcataacttgtacacaaacccacgcctagagtaaagcctcaggttgctagcagcacatccttatatcttcacaatgcacattttactgacagATCTTCGAGATGACAAGCAGTTCTTTGTGGACCATCCTGGTGCTGTTCCTATCACTACTGCTCAG
|| |  ||  | |      | |   |    ||   |   |   |                 | |     | | | ||  | ||||||   |||   | |||||||||| ||||| ||||| || ||| |||||||||||||||| || || || ||||| || |||
aattcctgtacgtggtcaatgctgcatgtaacagtttctggccaattcatatccaaagttggaatggtttgacaactcta-aatgcatgatttgtcggcagATCTTCGGGATGATAAGCAATTTTTTATGGACCATCCTGGTGCAGTGCCAATTACTACAGCACAG

upper sequence: GRMZM5G803949_T02 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA02G05160.1 (Glycine max), 3'ss of exon 4
aactagtggcataacttgtacacaaacccacgcctag--agtaaagcctcaggttgctagcagcacatccttatatcttcacaatgcacattttactgacagATCTTCGAGATGACAAGCAGTTCTTTGTGGACCATCCTGGTGCTGTTCCTATCACTACTGCTCAG
|  | ||   | || || |  ||     ||    |    |  ||    ||     | ||  ||   |||||| || | |     |        |   |||||| ||||||||||| ||||||||||| || || ||||||||||| || || || || |||| ||| 
attttgttaaaaaatttctcaacctctacatattttatcaccaattgttctttcagttaagagttaatcctt-taccgtttttttatttgaaatga-gacagACCTTCGAGATGATAAGCAGTTCTTCGTAGATCATCCTGGTGCCGTACCCATTACCACTGTTCAA

upper sequence: GRMZM5G803949_T02 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA12G03660.1 (Glycine max), 3'ss of exon 4
aactagtggcataacttgtacacaaacccac---gcctagagtaaagcctcaggttgctagcagcacatccttatatcttcacaatgcacatttta-ctgacagATCTTCGAGATGACAAGCAGTTCTTTGTGGACCATCCTGGTGCTGTTCCTATCACTACTGCTCAG
     ||    |      |  | |    |||   | | |   ||||||  |   |   |||     | |    || || | ||||   |   | |  ||   ||||||||| ||||| ||||||||||||   |||||||||||||| || |||||||| || || |||
--tctgtaaatttttccattaatagtttcactttgaccacgataaagctgcca-tgattagtt-tgcttgggcatttcatgacaaccaaatctctgtcttgtagATCTTCGGGATGATAAGCAGTTCTTTCAAGACCATCCTGGTGCAGTGCCTATCACCACAGCACAG

upper sequence: GRMZM5G803949_T02 (Zea mays), 3'ss of exon 4
lower sequence: AT2G17800.2 (Arabidopsis thaliana), 3'ss of exon 5
-----aactagtggcataacttgtacacaaacccacgcctagagtaaagcctcaggttgctagcagcacatccttatatcttcacaatgcacattttactgacagATCTTCGAGATGACAAGCAGTTCTTTGTGGACCATCCTGGTGCTGTTCCTATCACTACTGCTCAG
     ||||   ||| |    | |  |     | |  ||||   | ||   | | |    |  |  |   | ||||| | ||     | ||   | || || |||||||||| |||||||| ||||||||  | ||||| ||||| ||||| || || ||||||||||||
tgcttaactttcggcctgctgtctg-atccgtctagacctacttttaatagttatgagttt--cgtctggtgcttatgt-tttgtgtttcatcatata-tgccagATCTTCGGGATGACAAACAGTTCTTCATTGACCACCCTGGCGCTGTACCAATTACTACTGCTCAG

upper sequence: GRMZM5G803949_T02 (Zea mays), 3'ss of exon 4
lower sequence: AT4G35950.1 (Arabidopsis thaliana), 3'ss of exon 4
-------aactagtggcataacttgtacacaaacccacgcctagagtaaagcctcaggttgctagcagcacatccttatatcttcacaatgcacattttactgacagATCTTCGAGATGACAAGCAGTTCTTTGTGGACCATCCTGGTGCTGTTCCTATCACTACTGCTCAG
       | | ||||  ||| ||| || | ||    || | |  |  | | | ||||    ||       |   | | | |  |       |     ||  || ||||||||||||||||||| ||||| ||  | ||||||||||||||||| ||||| || |||| ||||
actgtatagcaagtg-tatacctt-tataaaag---acacttgca--agatcttcagtcaactcatgatcctggcctttttgattgtctaaccttggttgttgtcagATCTTCGAGATGACAAACAGTTTTTCATCGACCATCCTGGTGCTGTCCCTATTACCACTGTTCAG

upper sequence: GRMZM5G803949_T02 (Zea mays), 3'ss of exon 4
lower sequence: Vv04s0023g03860.t01 (Vitis vinifera), 3'ss of exon 5
---aactagtggcataacttgtacacaaacccacgcctagagtaaagcctcaggttgctagcagcacatccttatatc-ttcacaatgcacattttactgacagATCTTCGAGATGACAAGCAGTTCTTTGTGGACCATCCTGGTGCTGTTCCTATCACTACTGCTCAG
   || |||| | |  | || | ||  |      |  ||          |  | |   || ||     |  || | |  ||  |||||   |||   ||   ||||||||| || ||||||||||||||  | ||||||||||||||||| || ||| || | ||||||
ctaaattagtagaaggaatt-tgcagtaggagtaggttatttatggttttgtgataattaacaaattttttttgtctgattttcaatgttaattgagct---agATCTTCGGGAAGACAAGCAGTTCTTCATAGACCATCCTGGTGCTGTGCCCATCTCTGCAGCTCAG

upper sequence: GRMZM5G803949_T02 (Zea mays), 3'ss of exon 4
lower sequence: PP1S126_126V6.2 (Physcomitrella patens), 3'ss of exon 5
---------------------------------------------------------------------aactagtggcataacttgtacacaa-acccacgcctaga---gtaaagcctcaggttgctagcagcacatccttatatcttc---------acaatgcacatttta-ctgacagATCTTCGAGATGACAAGCAGTTCTTTGTGGACCATCCTGGTGCTGTTCCTATCACTACTGCTCAG
                                                                         | ||    || | | ||| || |  |  ||   ||   |    ||    | |||  |     |    |   ||| ||          |||     |   | |  || |||||||||||||||| || ||||||||||  ||||||||||| || | ||| || || ||  |||| 
gtataaaactccggcttcacttgtggtttgggaatgtgctactgacaagtttattcaatcggatgtaatccacaatgctgaaaatcgaacaaaacattctagcacggatgcgctgtgctcttgcttgtcatttttattctcaagtatttttcactctcttacagctggcgcgtcaattggcagATCTTCGAGATGATAAACAGTTCTTTGCTGACCATCCTGGAGCGGCTCCAATTACAACCTCTCAA

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|211356952|gb|FL222516.1|FL222516
EST:     GAAGCATTATGCACCTGGTGTGCCAATAATTCTCGTARGGACAAAGCTTG                         ATCTTCGAGATGACAAGCAGTTCTTTGTGGACCATCCTGGTGCTGTTCCCN
genomic: GAAGCATTATGCACCTGGTGTGCCAATAATTCTCGTAGGGACAAAGCTTGgtaagtatga ... ttactgacagATCTTCGAGATGACAAGCAGTTCTTTGTGGACCATCCTGGTGCTGTTCC--




















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: 48 (upstream exon), 49 (downstream exon)
Score: 368

TGGATACCTGAACTGAAGCATTATGCACCTGGTGTGCCAATAATTCTCGTAGGGACAAAGCTTGgtaagtatga ... ttactgacagATCTTCGAGATGACAAGCAGTTCTTTGTGGACCATCCTGGTGCTGTTCCTATCACTACTGCTCAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 216

TGGATACCTGAACTGAAGCATTATGCACCTGGTGTGCCAATAATTCTCGTAGGGACAAAGCTTGgtaagtatga ... ttactgacagATCTTCGAGATGACAAGCAGTTCTTTGTGGACCATCCTGGTGCTGTTCCTATCACTACTGCTCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 274

TGGATACCTGAACTGAAGCATTATGCACCTGGTGTGCCAATAATTCTCGTAGGGACAAAGCTTGgtaagtatga ... ttactgacagATCTTCGAGATGACAAGCAGTTCTTTGTGGACCATCCTGGTGCTGTTCCTATCACTACTGCTCAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 984

TGGATACCTGAACTGAAGCATTATGCACCTGGTGTGCCAATAATTCTCGTAGGGACAAAGCTTGgtaagtatga ... ttactgacagATCTTCGAGATGACAAGCAGTTCTTTGTGGACCATCCTGGTGCTGTTCCTATCACTACTGCTCAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctcaggttgctagcagcacatccttatatcttcacaatgcacattttactgacagATCTTCGAGATGACAAGCAGTTCTTTGTGGACCATCCTGGTGCTGTTCCTATCACTACTGCTCAG
                                           ttttact  CT-rich tract
                       ttatatctt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aactagtggcataacttgtacacaaacccacgcctagagtaaagcctcaggttgctagcagcacatccttatatcttcacaatgcacattttactgacagATCTTCGAGATGACAAGCAGTTCTTTGTGGACCATCCTGGTGCTGTTCCTATCACTACTGCTCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGTT
- - - - - - - - - -acacaaa
- - - - - - - - - - - - - -ccacgcc
- - - - - - - - - - - - - - - - - - - - - - - - - - tgctagc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aatgcac