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'   		12  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGCAATGGCAGCACTTACAGAGGATAGAAAGAAGATGCTTACTCCTACAATTCGGTTGATGGTTCGGCTGGCACTCAAAAGGAAATTACAAAATGAGAAGgtattatctgctttgttcttgcccctttttagcttacctcggttcaaactatatgtggtgtctcatgtagtaatttcatttcacagttttcttgaaaatg...

Basic information

species Zea mays
transcript GRMZM2G457881_T03
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G457881_T03 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os03g49730.3 (Oryza sativa), 5'ss of exon 3
AGCAATGGCAGCACTTACAGAGGATAGAAAGAAGATGCTTACTCCTACAATTCGGTTGATGGTTCGGCTGGCACTCAAAAGGAAATTACAAAATGAGAAGgtattatctgctttgttcttgcccctttttagcttacctcggttcaaactatatgtg-----gtgtctcatgtagtaatttcat-ttcacagttttcttgaaaatg-------------
|||||| || || |||||||||||||||||||||||||||||||| |||||||| |||||||| ||||| | ||| | ||| ||| | ||  |||| |||||||| |||  ||  ||  ||      | ||    | |  |      |  |||| |         |  ||||| | | |||  |       | |  ||||| | ||             
AGCAATCGCCGCGCTTACAGAGGATAGAAAGAAGATGCTTACTCCCACAATTCGTTTGATGGTGCGGCTTGTACTTAGAAGAAAACTGCAGGATGACAAGgtattgtctagttgattgatgtaaaaatataatgcatcatgtcaatgatgatatttttgtatacatggcatgttgaagttttctgcatgttggtaacttgatattggttgttttgccag
















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|211471995|gb|FK962992.1|FK962992
EST:     TTCGGTTGATGGTTCGGCTGGCACTCAAAAGAAAATTACAAAATGAGAAG                         GTCATTCCATCCTCAAGTA
genomic: TTCGGTTGATGGTTCGGCTGGCACTCAAAAGGAAATTACAAAATGAGAAGgtattatctg ... ttattgccagGTCATTCCATCCTCAAGTA
EST: gi|211474518|gb|FK963007.1|FK963007
EST:     TTCGGTTGATGGTTCGGCTGGCACTCAAAAGGAAATTACAAAATGAGAAG                         GTCATTCCATCCTCAAGTATAGATAACTACAATCTGGTTGATGCCTTGGAG
genomic: T-CGGTTGATGGTTCGGCTGGCACTCAAAAGGAAATTACAAAATGAGAAGgtattatctg ... ttattgccagGTCATTCCATCCTCAAGTATAGATAACTACAATCTGGTTGATGGCTTGGAG
EST: gi|211477029|gb|FK963011.1|FK963011
EST:     TTCGGTTGATGGTTCGGCTGGCACTCAAAAGGAAATTACAAAATGAGAAG                         GTCATTCCATCCTCAAGTATAGATNACTACAATCTGGTTGATGCCTTGGA
genomic: TTCGGTTGATGGTTCGGCTGGCACTCAAAAGGAAATTACAAAATGAGAAGgtattatctg ... ttattgccagGTCATTCCATCCTCAAGTATAGATAACTACAATCTGGTTGATGGCTTGGA
EST: gi|211474509|gb|FK962998.1|FK962998
EST:     TTCGGTTGATGGTTCGGCTGGCACTCAAAAGGAAATTACAAAATGAGAAG                         GTCATTCCATCCTCAAGTATAGATAACTACAATCTGGTTGATGCCTTGGAG
genomic: TTCGGTTGATGGTTCGGCTGGCACTCAAAAGGAAATTACAAAATGAGAAGgtattatctg ... ttattgccagGTCATTCCATCCTCAAGTATAGATAACTACAATCTGGTTGATGGCTTGGAG
EST: gi|211474515|gb|FK963004.1|FK963004
EST:     TTCGGTTGATGGTTCGGCTGGCACTCAAAAGGAAATTACAAAATGAGAAG                         GTCATTCCATCCTCAAGTATAGATAACTACAATCTGGTTGATGCCTTGGAG
genomic: TTCGGTTGATGGTTCGGCTGGCACTCAAAAGGAAATTACAAAATGAGAAGgtattatctg ... ttattgccagGTCATTCCATCCTCAAGTATAGATAACTACAATCTGGTTGATGGCTTGGAG
EST: gi|211471996|gb|FK962993.1|FK962993
EST:     TTCGGTTGATGGTTCGGCTGGCACTCAAAAGAAAATTACAAAATGAGAAG                         GTCATTCCATCCTCAAGTA
genomic: TTCGGTTGATGGTTCGGCTGGCACTCAAAAGGAAATTACAAAATGAGAAGgtattatctg ... ttattgccagGTCATTCCATCCTCAAGTA
EST: gi|211474511|gb|FK963000.1|FK963000
EST:     TCCGGTTGATGGTTCGGCTGGCACTCAAAAGGAAATTACAAAATGAGAAG                         GTCATTCCATCCTCAAGTATAGATAACTACCATCTGGTTGATGNCTTGGAG
genomic: TC-GGTTGATGGTTCGGCTGGCACTCAAAAGGAAATTACAAAATGAGAAGgtattatctg ... ttattgccagGTCATTCCATCCTCAAGTATAGATAACTACAATCTGGTTGATGGCTTGGAG
EST: gi|211474516|gb|FK963005.1|FK963005
EST:     TTCGGTTGATGGTTCGGCTGGCACTCCAAAGGAAATTACAAAATGAGAAG                         GNCATTCCATCCTCAAGTATAGATAACTACAATCTGGTTGATGCCTTGGAG
genomic: TTCGGTTGATGGTTCGGCTGGCACTCAAAAGGAAATTACAAAATGAGAAGgtattatctg ... ttattgccagGTCATTCCATCCTCAAGTATAGATAACTACAATCTGGTTGATGGCTTGGAG
EST: gi|211474507|gb|FK962996.1|FK962996
EST:     TTCGGTTGATGGTTCGGCTGGCACTCAAAAGGAAATTACAAAATGAGAAG                         GTCATTCCATCCTCAAGTATAGATAACTACAATCTGGTTGATGCCTTGGAG
genomic: TTCGGTTGATGGTTCGGCTGGCACTCAAAAGGAAATTACAAAATGAGAAGgtattatctg ... ttattgccagGTCATTCCATCCTCAAGTATAGATAACTACAATCTGGTTGATGGCTTGGAG
EST: gi|211474508|gb|FK962997.1|FK962997
EST:     TTCGGTTGATGGTTCGGCTGGCACTCAAAAGGAAATYACAAAATGAGAAG                         GTCATTCCCATCCTCAAGTATAGATAACTACAATCTGGTTGATGGCTTGGA
genomic: TTCGGTTGATGGTTCGGCTGGCACTCAAAAGGAAATTACAAAATGAGAAGgtattatctg ... ttattgccagGTCATTCC-ATCCTCAAGTATAGATAACTACAATCTGGTTGATGGCTTGGA
EST: gi|211474510|gb|FK962999.1|FK962999
EST:     TTCGGTTGATGGTTCGGCTGGCACTCAAAAGGAAATTACAAAATGAGAAG                         GTCATTCCATCCTCAAGTATAGATAACTACAATCTGGTTGATGCCTTGGAG
genomic: TTCGGTTGATGGTTCGGCTGGCACTCAAAAGGAAATTACAAAATGAGAAGgtattatctg ... ttattgccagGTCATTCCATCCTCAAGTATAGATAACTACAATCTGGTTGATGGCTTGGAG
EST: gi|149023564|gb|EE045895.2|EE045895
EST:     TTCGGTTGATGGTTCGGCTGGCACTCAAAAGGAAATTACAAAATGAGAAG                         GTCATTCCATCCTCAAGTATAGATAACTACAATCTGGTTGATGGCTTGGAG
genomic: TTCGGTTGATGGTTCGGCTGGCACTCAAAAGGAAATTACAAAATGAGAAGgtattatctg ... ttattgccagGTCATTCCATCCTCAAGTATAGATAACTACAATCTGGTTGATGGCTTGGAG
EST: gi|211474517|gb|FK963006.1|FK963006
EST:     TTCGGTTGATGGTTCGGCTGGCACTCAAAAGGAAATTACAAAATGAGAAG                         GTCATTCCATCCTCAAGTATAGATAACTACAATCTGGTTGATGCCTTGGAG
genomic: TTCGGTTGATGGTTCGGCTGGCACTCAAAAGGAAATTACAAAATGAGAAGgtattatctg ... ttattgccagGTCATTCCATCCTCAAGTATAGATAACTACAATCTGGTTGATGGCTTGGAG
EST: gi|211474514|gb|FK963003.1|FK963003
EST:     TTCGGTTGATGGTTCGGCTGGCACTCAAAAGGAAATTACAAAATGAGAAG                         GTCATTCCATCCTCAAGTMTAGATAACTACAATCTGGTTGATGCCCTTGGA
genomic: TTCGGTTGATGGTTCGGCTGGCACTCAAAAGGAAATTACAAAATGAGAAGgtattatctg ... ttattgccagGTCATTCCATCCTCAAGTATAGATAACTACAATCTGGTTGATGGC-TTGGA
EST: gi|211474521|gb|FK963010.1|FK963010
EST:     TTCGGTTGATGGTTCGGCTGGCACTCAAAAGAAAATTACAAAATGAGAAG                         GTCATTCCATCCTCAAGTATAGATAACTACAATCTGGTTGATGGCTTGGAG
genomic: TTCGGTTGATGGTTCGGCTGGCACTCAAAAGGAAATTACAAAATGAGAAGgtattatctg ... ttattgccagGTCATTCCATCCTCAAGTATAGATAACTACAATCTGGTTGATGGCTTGGAG
EST: gi|71322965|gb|DR798157.1|DR798157
EST:     TTCGGTTGATGGTTCGGCTGGCACTCAAAAGGAAATTACAAAATGAGAAG                         GTCATTCCATCCTCAAGTATAGATAACTACAATCTGGTTGATGGCTTGGAG
genomic: TTCGGTTGATGGTTCGGCTGGCACTCAAAAGGAAATTACAAAATGAGAAGgtattatctg ... ttattgccagGTCATTCCATCCTCAAGTATAGATAACTACAATCTGGTTGATGGCTTGGAG
EST: gi|211471998|gb|FK962995.1|FK962995
EST:     TTCGGTTGATGGTTCGGCTGGCACTCAAAAGGAAATTACAAAATGAGAAG                         GTCATTCCATCCTCAAGTATAGATAACTACAATCTGGTTGA
genomic: TTCGGTTGATGGTTCGGCTGGCACTCAAAAGGAAATTACAAAATGAGAAGgtattatctg ... ttattgccagGTCATTCCATCCTCAAGTATAGATAACTACAATCTGGTTGA
EST: gi|211474513|gb|FK963002.1|FK963002
EST:     TTCGGTTGATGGTTCGGCTGGCACTCAAAAGGAAATTACAAAATGAGAAG                         GTCATTCCATCCTCAAGTAYAGATAACTACAATCTGGTTGATG
genomic: TTCGGTTGATGGTTCGGCTGGCACTCAAAAGGAAATTACAAAATGAGAAGgtattatctg ... ttattgccagGTCATTCCATCCTCAAGTATAGATAACTACAATCTGGTTGATG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGCAATGGCAGCACTTACAGAGGATAGAAAGAAGATGCTTACTCCTACAATTCGGTTGATGGTTCGGCTGGCACTCAAAAGGAAATTACAAAATGAGAAGgtattatctgctttgttcttgcccctttttagcttacctcggttcaaactatatgtggtgtctcatgtagtaatttcatttcacagttttcttgaaaatg

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA