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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...catcagtaggtatgcacgatgtgatctagttgtttacttgtattaatcacattgatcacagcaaaatactgaagtagtcttgtgcctcaatttgttgcagTGTTCCTGGGGAAGCAAGCCGACTCCACAAGGGACAGCATCCTTGCCTCTGCCTCCTCCAGCACTGGCACCATTCTCCACTGGAGTGTCGGCCACCGACT

Basic information

species Zea mays
transcript GRMZM5G835213_T02
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G835213_T02 (Zea mays), 3'ss of exon 11
lower sequence: LOC_Os11g40510.2 (Oryza sativa), 3'ss of exon 11
-----------catcagtaggtatgcacgatgtgatctagttgtttacttgtattaatcacattgatcacagcaaaatactgaagtagtcttgtgcctcaatttgttgcagTGTTCCTGGGGAAGCAAGCCGACTCCACAAGGGACAGCATCCTTGCCTCTGCCTCCTCCAGCACTGGCACCATTCTCCACTGGAGTGTCGGCCACCGACT
             |||    || |  |   |  |     | |||   || ||  |  |       ||  |||| |||   | |     |||||| |||       |||||||||||||||||||||||||| ||||||| |||||||||||||  ||| || || ||||||||||  |||||||||    ||||  ||||||| |||||| 
gcaagttatgttttcaccgagtttttatcgtaaggagaggatgtagtctagttatggttcttgcaatt-cagctaaactttaa-----tcttgttcctac-----ttgcagTGTTCCTGGGGAAGCAAGCCAACTCCACCAGGGACAGCATCCGCGCCCCTACCCCCTCCAGCACCAGCACCATTCAATCCTGGCATGTCGGCGACCGACC
















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|110519364|gb|EE023825.1|EE023825
EST:     GATGGGTAATGGCCAACTTATTGGCGGGAGGCAGATAAAAG                         TGTTCCTGGGGAAGCAAGCCGACTCCACAAGGGACAAGCATCCTTGCGTC
genomic: GATGGGTAATGGCCAACTTATTGGCGGGAGGCAGAT-AAAGgtatctttgg ... tttgttgcagTGTTCCTGGGGAAGCAAGCCGACTCCACAAGGGAC-AGCATCCTTGCCTC
EST: gi|31361403|gb|CD445760.1|CD445760
EST:     GCAATTCAGATGGGGTA-TGGCCAACTTATTGGCGGGAGGCAGAATAA-G                         TGTTCCTGGGGAAGCAAGCCGACTCCACA-GGGACAGCATCCTTGCCTCT
genomic: GCAATTCAGATGGG-TAATGGCCAACTTATTGGCGGGAGGCAGA-TAAAGgtatctttgg ... tttgttgcagTGTTCCTGGGGAAGCAAGCCGACTCCACAAGGGACAGCATCCTTGCCTCT
EST: gi|149098620|gb|EE184625.2|EE184625
EST:     TGGCAATTCAGATGGGTAATGGCCAACTTATTGGCGGGAGGCAGATAAAG                         TGTTCCTGGGGAAGCAAGCCGACTCCACAAGGGACAGCATCCTTGCCTCTG
genomic: TGGCAATTCAGATGGGTAATGGCCAACTTATTGGCGGGAGGCAGATAAAGgtatctttgg ... tttgttgcagTGTTCCTGGGGAAGCAAGCCGACTCCACAAGGGACAGCATCCTTGCCTCTG
EST: gi|4827563|gb|AI668255.1|AI668255
EST:     TGGCAATTCAGATGGGTAATGGCCAACTTATTGGCGGGAGGCAGATAAAG                         TGTTCCTGGGGAAGCAAGCCGACTCCACAAGGGACAGCATCCTTGCCTCTG
genomic: TGGCAATTCAGATGGGTAATGGCCAACTTATTGGCGGGAGGCAGATAAAGgtatctttgg ... tttgttgcagTGTTCCTGGGGAAGCAAGCCGACTCCACAAGGGACAGCATCCTTGCCTCTG
EST: gi|78024764|gb|DV493151.1|DV493151
EST:     TGGCAATTCAGATGGGTAATGGCCAACTTATTGGCGGGAGGCAGATAAAG                         TGTTCCTGGGGAAGCAAGCCGACTCCACAAGGGACAGCATCCTTGCCTCTG
genomic: TGGCAATTCAGATGGGTAATGGCCAACTTATTGGCGGGAGGCAGATAAAGgtatctttgg ... tttgttgcagTGTTCCTGGGGAAGCAAGCCGACTCCACAAGGGACAGCATCCTTGCCTCTG
EST: gi|7135994|gb|AW498371.1|AW498371
EST:     TGGCAATTCAGATGGGTAATGGCCAACTTATTGGCGGGAGGCAGATAAAG                         TGTTCCTGGGGAAGCAAGCCGACTCCACAAGGGACAGCATCCTTGCCTCTG
genomic: TGGCAATTCAGATGGGTAATGGCCAACTTATTGGCGGGAGGCAGATAAAGgtatctttgg ... tttgttgcagTGTTCCTGGGGAAGCAAGCCGACTCCACAAGGGACAGCATCCTTGCCTCTG
EST: gi|26456718|gb|CA828301.1|CA828301
EST:     TGGCAATTCAGATGGGTAATGGCCAACTTATTGGCGGGAGGCAGATAAAG                         TGTTCCTGGGGAAGCAAGCCGACTCCACAAGGGACAGCATCCTTGCCTCTG
genomic: TGGCAATTCAGATGGGTAATGGCCAACTTATTGGCGGGAGGCAGATAAAGgtatctttgg ... tttgttgcagTGTTCCTGGGGAAGCAAGCCGACTCCACAAGGGACAGCATCCTTGCCTCTG
EST: gi|93012834|gb|EB638354.1|EB638354
EST:     TGGCAATTCAGATGGGTAATGGCCAACTTATTGGCGGGAGGCAGATAAAG                         TGTTCCTGGGGAAGCAAGCCGACTCCACAAGGGACAGCATCCTTGCCTCTG
genomic: TGGCAATTCAGATGGGTAATGGCCAACTTATTGGCGGGAGGCAGATAAAGgtatctttgg ... tttgttgcagTGTTCCTGGGGAAGCAAGCCGACTCCACAAGGGACAGCATCCTTGCCTCTG
EST: gi|31362301|gb|CD446658.1|CD446658
EST:     TGGCAATTCAGATGGGTAATGGCCAACTTATTGGCGGGAGGCAGATAAAG                         TGTTCCTGGGGAAGCAAGCCGACTCCACAAGGGACAGCATCCTTGCCTCTG
genomic: TGGCAATTCAGATGGGTAATGGCCAACTTATTGGCGGGAGGCAGATAAAGgtatctttgg ... tttgttgcagTGTTCCTGGGGAAGCAAGCCGACTCCACAAGGGACAGCATCCTTGCCTCTG
EST: gi|211492468|gb|FL234470.1|FL234470
EST:     TGGCAATTCAGATGGGTAATGGCCAACTTATTGGCGGGAGGCAGATAAAG                         TGTTCCTGGGGAAGCAAGCCGACTCCACAAGG-ACAGCATCCTTGCCTCTG
genomic: TGGCAATTCAGATGGGTAATGGCCAACTTATTGGCGGGAGGCAGATAAAGgtatctttgg ... tttgttgcagTGTTCCTGGGGAAGCAAGCCGACTCCACAAGGGACAGCATCCTTGCCTCTG
EST: gi|211492467|gb|FL234469.1|FL234469
EST:     TGGCAATTCAGATGGGTAATGGCCAACTTATTGGCGGGAGGCAGATAAAG                         TGTTCCTGGGGAAGCAAGCCGACTCCACAAGGGACAGCATCCTTGCCTCTG
genomic: TGGCAATTCAGATGGGTAATGGCCAACTTATTGGCGGGAGGCAGATAAAGgtatctttgg ... tttgttgcagTGTTCCTGGGGAAGCAAGCCGACTCCACAAGGGACAGCATCCTTGCCTCTG
EST: gi|31361559|gb|CD445916.1|CD445916
EST:     TGGCAATTCAGATGGGTAATGGCCAACTTATTGGCGGGAGGCAGATAAAG                         TGTTCCTGGGGAAGCAAGCCGACTCCACAAGGGACAGCATCCTTGCCTCTG
genomic: TGGCAATTCAGATGGGTAATGGCCAACTTATTGGCGGGAGGCAGATAAAGgtatctttgg ... tttgttgcagTGTTCCTGGGGAAGCAAGCCGACTCCACAAGGGACAGCATCCTTGCCTCTG
EST: gi|149104834|gb|EE290298.2|EE290298
EST:     TGGCAATTCAGATGGGTAATGGCCAACTTATTGGCGGGAGGCAGATAAAG                         TGTTCCTGGGGAAGCAAGCCGACTCCACAAGGGACAGCATCCTTGCCTCTG
genomic: TGGCAATTCAGATGGGTAATGGCCAACTTATTGGCGGGAGGCAGATAAAGgtatctttgg ... tttgttgcagTGTTCCTGGGGAAGCAAGCCGACTCCACAAGGGACAGCATCCTTGCCTCTG
EST: gi|71439176|gb|DR820226.1|DR820226
EST:     TGGCAATTCAGATGGGTAATGGCCAACTTATTGGCGGGAGGCAGATAAAG                         TGTTCCTGGGGAAGCAAGCCGACTCCACAAGGGACAGCATCCTTGCCTCTG
genomic: TGGCAATTCAGATGGGTAATGGCCAACTTATTGGCGGGAGGCAGATAAAGgtatctttgg ... tttgttgcagTGTTCCTGGGGAAGCAAGCCGACTCCACAAGGGACAGCATCCTTGCCTCTG
EST: gi|148944553|gb|EC889677.2|EC889677
EST:     TGGCAATTCAGATGGGTAATGGCCAACTTATTGGCGGGAGGCAGATAAAG                         TGTTCCTGGGGAAGCAAGCCGACTCCACAAGGGACAGCATCCTTGCCTTTG
genomic: TGGCAATTCAGATGGGTAATGGCCAACTTATTGGCGGGAGGCAGATAAAGgtatctttgg ... tttgttgcagTGTTCCTGGGGAAGCAAGCCGACTCCACAAGGGACAGCATCCTTGCCTCTG
EST: gi|71431559|gb|DR812609.1|DR812609
EST:     TGGCAATTCAGATGGGTAATGGCCAACTTATTGGCGGGAGGCAGATAAAG                         TGTTCCTGGGGAAGCAAGCCGACTCCACAAGGGACAGCATCCTTGCCTCTG
genomic: TGGCAATTCAGATGGGTAATGGCCAACTTATTGGCGGGAGGCAGATAAAGgtatctttgg ... tttgttgcagTGTTCCTGGGGAAGCAAGCCGACTCCACAAGGGACAGCATCCTTGCCTCTG

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: 437

TGATAAAGGCTTTGGCTTTGTGAGGTACAGCACCCATGAGGAGGCTGCATTGGCAATTCAGATGGGTAATGGCCAACTTATTGGCGGGAGGCAGATAAAGgtatctttgg ... tttgttgcagTGTTCCTGGGGAAGCAAGCCGACTCCACAAGGGACAGCATCCTTGCCTCTGCCTCCTCCAGCACTGGCACCATTCTCCACTGGAGTGTCGGCCACCGACT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 213

TGATAAAGGCTTTGGCTTTGTGAGGTACAGCACCCATGAGGAGGCTGCATTGGCAATTCAGATGGGTAATGGCCAACTTATTGGCGGGAGGCAGATAAAGgtatctttgg ... tttgttgcagTGTTCCTGGGGAAGCAAGCCGACTCCACAAGGGACAGCATCCTTGCCTCTGCCTCCTCCAGCACTGGCACCATTCTCCACTGGAGTGTCGGCCACCGACT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 234

TGATAAAGGCTTTGGCTTTGTGAGGTACAGCACCCATGAGGAGGCTGCATTGGCAATTCAGATGGGTAATGGCCAACTTATTGGCGGGAGGCAGATAAAGgtatctttgg ... tttgttgcagTGTTCCTGGGGAAGCAAGCCGACTCCACAAGGGACAGCATCCTTGCCTCTGCCTCCTCCAGCACTGGCACCATTCTCCACTGGAGTGTCGGCCACCGACT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 479

TGATAAAGGCTTTGGCTTTGTGAGGTACAGCACCCATGAGGAGGCTGCATTGGCAATTCAGATGGGTAATGGCCAACTTATTGGCGGGAGGCAGATAAAGgtatctttgg ... tttgttgcagTGTTCCTGGGGAAGCAAGCCGACTCCACAAGGGACAGCATCCTTGCCTCTGCCTCCTCCAGCACTGGCACCATTCTCCACTGGAGTGTCGGCCACCGACT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atcacattgatcacagcaaaatactgaagtagtcttgtgcctcaatttgttgcagTGTTCCTGGGGAAGCAAGCCGACTCCACAAGGGACAGCATCCTTGCCTCTGCCTCCTCCAGCACTGGCACCATTCTCCACTGGAGTGTCGGCCACCGACT
                 aaaatact  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
catcagtaggtatgcacgatgtgatctagttgtttacttgtattaatcacattgatcacagcaaaatactgaagtagtcttgtgcctcaatttgttgcagTGTTCCTGGGGAAGCAAGCCGACTCCACAAGGGACAGCATCCTTGCCTCTGCCTCCTCCAGCACTGGCACCATTCTCCACTGGAGTGTCGGCCACCGACT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC
- - - - -gtatgca
- - - - - - - - cgatgtg
- - - - - - - - - - - - - - - - -ttacttg
- - - - - - - - - - - - - - - - - - - - - - aatcaca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - cagcaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cttgtgc