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

...caacttctatatactggaacttgtggttgcttgcagcattggtatgctaacttttgcagtgaatatttgttgttgattacagatttatgtttttttgcagCTAATGATAAACAGCAAGAAGGAAACGACTCCACCTTCGCAGCAAAAGATGGAGAGATTGCAAAGTTTTGAGGAGGAACACAAGAATGCTCTCCAGAGAG

Basic information

species Zea mays
transcript GRMZM2G174315_T01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G174315_T03 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os06g14490.2 (Oryza sativa), 3'ss of exon 5
-----caacttctatatactggaacttgtggttgcttgcagcattggtatgctaacttttgcagtgaatatttgttgttgattacagatttatgtttttttgcagCTAATGATAAACAGCAAGAAGGAAACGACTCCACCTTCGCAGCAAAAGATGGAGAGATTGCAAAGTTTTGAGGAGGAACACAAGAATGCTCTCCAGAGAG
       |    | |  | |||| |||    ||   ||| ||| |  | |||||| ||       ||||| |||||  | |||| ||    |   | |||||||||| |||| |   |   ||||   ||| ||||| ||| |||| ||||||||||| ||| |||| ||||||||||| |||||||||||||| ||| ||||||
aagaaagataaatgttcattggatcttaacatt---tgccgcactaatttgctaagttgcatgaagaatacttgtttataattatag--cgacactgttttgcagCTTATGAAAGGAAATGAGAAACCAACAACTCCGCCTGCGCAACAAAAGATGGAAAGACTGCAGAGTTTTGAGGAAGAACACAAGAATGCCCTCGAGAGAG
















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|18177115|gb|BM378325.1|BM378325
EST:     CTGATCATGGCATTTATTGGATTGAACGAGAATCACAAAAGGCTTTAGAG                         CTAATGATAAACAGCAAGAAGGAAACGACTCCACCTCCGCAGCAAAAGATG
genomic: CTGATCATGGCATTTATTGGATTGAACGAGAATCACAAAAGGCTTTAGAGgtataaactc ... ttttttgcagCTAATGATAAACAGCAAGAAGGAAACGACTCCACCTTCGCAGCAAAAGATG
EST: gi|78077830|gb|DV506259.1|DV506259
EST:     CTGATCATGGCATTTATTGGATTGAACGAGAATCACAAAAGGCTTTAGAG                         CTAATGATAAACAGCAAGAAGGAAACGACTCCCCCTTCGCAGCAAAAGATG
genomic: CTGATCATGGCATTTATTGGATTGAACGAGAATCACAAAAGGCTTTAGAGgtataaactc ... ttttttgcagCTAATGATAAACAGCAAGAAGGAAACGACTCCACCTTCGCAGCAAAAGATG
EST: gi|211451504|gb|FL478327.1|FL478327
EST:     CTGATCATGGCATTTATTGGATTGAACGAGAATCACAAAAGGCTTTAGAG                         CTAATGATAAACAGCAAGAAGGAAACGACTCCACCTTCGCAGCAAAAGATG
genomic: CTGATCATGGCATTTATTGGATTGAACGAGAATCACAAAAGGCTTTAGAGgtataaactc ... ttttttgcagCTAATGATAAACAGCAAGAAGGAAACGACTCCACCTTCGCAGCAAAAGATG
EST: gi|78125709|gb|DV544093.1|DV544093
EST:     CTGATCATGGCATTTATTGGATTGAACGAGAATCACAAAAGGCTTTAGAG                         CTAATGATAAACAGCAAGAAGGAAACGACTCCACCTTCGCAGCAAAAGATG
genomic: CTGATCATGGCATTTATTGGATTGAACGAGAATCACAAAAGGCTTTAGAGgtataaactc ... ttttttgcagCTAATGATAAACAGCAAGAAGGAAACGACTCCACCTTCGCAGCAAAAGATG
EST: gi|78025864|gb|DV494251.1|DV494251
EST:     CTGATCATGGCATTTATTGGATTGAACGAGAATCACAAAAGGCTTTAGAG                         CTAATGATAAACAGCAAGAAGGAAACGACTCCACCTCCGCAGCAAAAGATG
genomic: CTGATCATGGCATTTATTGGATTGAACGAGAATCACAAAAGGCTTTAGAGgtataaactc ... ttttttgcagCTAATGATAAACAGCAAGAAGGAAACGACTCCACCTTCGCAGCAAAAGATG
EST: gi|87154057|gb|DY398846.1|DY398846
EST:     CTGATCATGGCATTTATTGGATTGAACGAGAATCACAAAAGGCTTTAGAG                         CTAATGATAAACAGCAAGAAGGAAACGACTCCACCTTCGCAGCAAAAGATG
genomic: CTGATCATGGCATTTATTGGATTGAACGAGAATCACAAAAGGCTTTAGAGgtataaactc ... ttttttgcagCTAATGATAAACAGCAAGAAGGAAACGACTCCACCTTCGCAGCAAAAGATG
EST: gi|89247661|gb|DY619447.1|DY619447
EST:     CTGATCATGGCATTTATTGGATTGAACGAGAATCACAAAAGGCTTTAGAG                         CTAATGATAAACAGCAAGAAGGAAACGACTCCCCCTTCGCAGCAAAAGATG
genomic: CTGATCATGGCATTTATTGGATTGAACGAGAATCACAAAAGGCTTTAGAGgtataaactc ... ttttttgcagCTAATGATAAACAGCAAGAAGGAAACGACTCCACCTTCGCAGCAAAAGATG
EST: gi|19351885|gb|BM896417.1|BM896417
EST:     CTGATCATGGCATTTATTGGATTGAACGAGAATCACAAAAGGCTTTAGAG                         CTAATGATAAACAGCAAGAAGGAAACGACTCCACCTTCGCAGCAAAAGATG
genomic: CTGATCATGGCATTTATTGGATTGAACGAGAATCACAAAAGGCTTTAGAGgtataaactc ... ttttttgcagCTAATGATAAACAGCAAGAAGGAAACGACTCCACCTTCGCAGCAAAAGATG
EST: gi|4776055|gb|AI665058.1|AI665058
EST:     CTGATCATGGCATTTATTGGATTGAACGAGAATCACAAAAGGCTTTAGAG                         CTAATGATAAACAGCAAGAAGGAAACGACTCCACCTCCGCAGCAAAAGATG
genomic: CTGATCATGGCATTTATTGGATTGAACGAGAATCACAAAAGGCTTTAGAGgtataaactc ... ttttttgcagCTAATGATAAACAGCAAGAAGGAAACGACTCCACCTTCGCAGCAAAAGATG
EST: gi|78083300|gb|DV511693.1|DV511693
EST:     CTGATCATGGCATTTATTGGATTGAACGAGAATCACAAAAGGCTTTAGAG                         CTAATGATAAACAGCAAGAAGGAAACGACTCCCCCTTCGCAGCAAAAGATG
genomic: CTGATCATGGCATTTATTGGATTGAACGAGAATCACAAAAGGCTTTAGAGgtataaactc ... ttttttgcagCTAATGATAAACAGCAAGAAGGAAACGACTCCACCTTCGCAGCAAAAGATG
EST: gi|78080954|gb|DV509366.1|DV509366
EST:     CTGATCATGGCATTTATTGGATTGAACGAGAATCACAAAAGGCTTTAGAG                         CTAATGATAAACAGCAAGAAGGAAACGACTCCACCTTCGCAGCAAAAGATG
genomic: CTGATCATGGCATTTATTGGATTGAACGAGAATCACAAAAGGCTTTAGAGgtataaactc ... ttttttgcagCTAATGATAAACAGCAAGAAGGAAACGACTCCACCTTCGCAGCAAAAGATG
EST: gi|88755923|gb|DY540064.1|DY540064
EST:     CTGATCATGGCATTTATTGGATTGAACGAGAATCACAAAAGGCTTTAGAG                         CTAATGATAAACAGCAAGAAGGAAACGACTCCACCTTCGCAGCAAAAGATG
genomic: CTGATCATGGCATTTATTGGATTGAACGAGAATCACAAAAGGCTTTAGAGgtataaactc ... ttttttgcagCTAATGATAAACAGCAAGAAGGAAACGACTCCACCTTCGCAGCAAAAGATG
EST: gi|12970002|gb|BG266765.1|BG266765
EST:     CTGATCATGGCATTTATTGGATTGACCGAGAATCACAAAAGGCTTTAGAG                         CTAATGATAAACAGCAAGAAGGAAACGACTCCACCTCCGCAGCAAAAGATG
genomic: CTGATCATGGCATTTATTGGATTGAACGAGAATCACAAAAGGCTTTAGAGgtataaactc ... ttttttgcagCTAATGATAAACAGCAAGAAGGAAACGACTCCACCTTCGCAGCAAAAGATG
EST: gi|22491379|gb|BU051302.1|BU051302
EST:     CTGATCATGGCATTTATTGGATTGAACGAGAATCACAAAAGGCTTTAGAG                         CTAATGATAAACAGCAAGAAGGAAACGACTCCACCTTCGCAGCAAAAGATG
genomic: CTGATCATGGCATTTATTGGATTGAACGAGAATCACAAAAGGCTTTAGAGgtataaactc ... ttttttgcagCTAATGATAAACAGCAAGAAGGAAACGACTCCACCTTCGCAGCAAAAGATG
EST: gi|149095322|gb|EE180958.2|EE180958
EST:     CTGATCATGGCATTTATTGGATTGAACGAGAATCACAAAAGGCTTTAGAG                         CTAATGATAAACAGCAAGAAGGAAACGACTCCACCTTCGCAGCAAAAGATG
genomic: CTGATCATGGCATTTATTGGATTGAACGAGAATCACAAAAGGCTTTAGAGgtataaactc ... ttttttgcagCTAATGATAAACAGCAAGAAGGAAACGACTCCACCTTCGCAGCAAAAGATG
EST: gi|18660661|gb|BM500981.1|BM500981
EST:     CTGATCATGGCATTTATTGGATTGAACGAGAATCACAAAAGGCTTTAGAG                         CTAATGATAAACAGCAAGAAGGAAACGACTCCACCTTCGCAGCAAAAGATG
genomic: CTGATCATGGCATTTATTGGATTGAACGAGAATCACAAAAGGCTTTAGAGgtataaactc ... ttttttgcagCTAATGATAAACAGCAAGAAGGAAACGACTCCACCTTCGCAGCAAAAGATG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gctaacttttgcagtgaatatttgttgttgattacagatttatgtttttttgcagCTAATGATAAACAGCAAGAAGGAAACGACTCCACCTTCGCAGCAAAAGATGGAGAGATTGCAAAGTTTTGAGGAGGAACACAAGAATGCTCTCCAGAGAG
                                          tgttttttt  CT-rich tract
                              attacagatttatgtt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
caacttctatatactggaacttgtggttgcttgcagcattggtatgctaacttttgcagtgaatatttgttgttgattacagatttatgtttttttgcagCTAATGATAAACAGCAAGAAGGAAACGACTCCACCTTCGCAGCAAAAGATGGAGAGATTGCAAAGTTTTGAGGAGGAACACAAGAATGCTCTCCAGAGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGGA
- - - - - - - - - - - - - -tgcttgc
- - - - - - - - - - - - - - - - - - - - -gtatgct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgttgat