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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgagtgacatttattggtataaaaggagttttagttgctagaactgctttgtcatgaatagatccatattagatgtaacctttgggcttacttgatgcagGTCAAGTACTGGAAGTGTCCATGGCCAAACCATTGGCAGATAAGAAACCTGATCATTCACACAGGCCTGGAGGAGGCCCTAATTATCCCCTTCCTCCCTA

Basic information

species Zea mays
transcript GRMZM2G103430_T05
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G103430_T04 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os10g06130.2 (Oryza sativa), 3'ss of exon 6
-------tgagtgacatttattggtataaaaggagttttagttgctagaactgctttgtcatgaatagatccatattagatgtaacctttgggcttacttgat-gcagGTCAAGTACTGGAAGTGTCCATGGCCAAACCATTGGCAGATAAGAAACCTGATCATTCACACAGGCCTGGAGGAGGCCCTAATTATCCCCTTCCTCCCTA
       |  | ||| |||   | ||  |       | |   |  ||| |   ||| |  ||  || | |    ||||||  ||| ||| | ||| |||  ||  |||| ||||| |||||||| ||||||||||| ||||||| ||| ||||| |||||||| ||   || |||||||||||  || |||| ||| |||||||| ||
atgattttatgggacctttgcagttaccaccactactctgtatattagta--acttcgaaat--atggttg---attagaaataatctt-gtgctaactgaatcacagGGCAAGTGCTGGAAGTATCCATGGCCAAGCCATTGGGAGACAAGAAGCCTGATCACTCGTTCAAGCCTGGAGGAGCTCCAAATTTTCCTCTTCCTCCTTA

upper sequence: GRMZM2G103430_T04 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os11g14430.2 (Oryza sativa), 3'ss of exon 6
-tgagtgacatttattggtataaaaggagttttagttgctaga-actgctttgtcatgaatagatccatattagatgtaacctttgggcttacttga-tgcagGTCAAGTACTGGAAGTGTCCATGGCCAAACCATTGGCAGATAAGAAACCTGATCATTCACACAGGCCTGGAGGAGGCCCTAATTATCCCCTTCCTCCCTA
 |       |   | ||| ||       |  |  ||   | |  ||| ||   |  ||  |  |||   | ||||  ||| ||| |  || |||  |   |||| ||||| |||||||| |||||||||||||| ||||  || |||||||||||||| ||   || ||| | |||||  || |||| ||| |||||||| ||
atatcaaggaaccactggcattgccaaggactatgtgaatggctacttctaaattttg--ttcatcagaactagagttaatctt-gctctgactgaaacacagGGCAAGTGCTGGAAGTATCCATGGCCAAACCTTTGGGTGACAAGAAACCTGATCACTCGTTCAAGCCAGCAGGAGCTCCAAATTTTCCACTTCCTCCTTA
















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|211350822|gb|FL045986.1|FL045986
EST:     ATCAAGTGCATTGAAGGCAGTTAAAGGAAGTGAAAAATATGAAATCGATG                         GTCAAGTACTGGAAGTGTCCATGGCCAAACCATTGGCAGATAAGAAACCTG
genomic: ATCAAGTGCATTGAAGGCAGTTAAAGGAAGTGAAAAATATGAAATCGATGgtaaacttct ... cttgatgcagGTCAAGTACTGGAAGTGTCCATGGCCAAACCATTGGCAGATAAGAAACCTG
EST: gi|20811268|gb|BQ295746.1|BQ295746
EST:     ATCAAGTGCATTGAAGGCAGTTAAAGGAAGTGAAAAATATGAAATCGATG                         GTCAAGTACTGGAAGTGTCCATGGCCAAACCATTGGCAGATAAGAAACCTG
genomic: ATCAAGTGCATTGAAGGCAGTTAAAGGAAGTGAAAAATATGAAATCGATGgtaaacttct ... cttgatgcagGTCAAGTACTGGAAGTGTCCATGGCCAAACCATTGGCAGATAAGAAACCTG
EST: gi|32808288|gb|CD960522.1|CD960522
EST:     TAAAGGAAGTGAAAAATATGAAATCGATG                         GTCAAGTACTGGAAGTGTCCATGGCCAAACCATTGGCAGATAAGAAACCTG
genomic: TAAAGGAAGTGAAAAATATGAAATCGATGgtaaacttct ... cttgatgcagGTCAAGTACTGGAAGTGTCCATGGCCAAACCATTGGCAGATAAGAAACCTG
EST: gi|40336436|gb|CK370506.1|CK370506
EST:     ATCAAGTGCATTGAAGGCAGTTAAAGGAAGTGAAAAATATGAAATCGATG                         GTCAAGTACTGGAAGTGTCCATGGCCAAACCATTGGCAGATAAGAAACCTG
genomic: ATCAAGTGCATTGAAGGCAGTTAAAGGAAGTGAAAAATATGAAATCGATGgtaaacttct ... cttgatgcagGTCAAGTACTGGAAGTGTCCATGGCCAAACCATTGGCAGATAAGAAACCTG
EST: gi|211353220|gb|FL045989.1|FL045989
EST:     ATCAAGTGCATTGAAGGCAGTTAAAGGAAGTGAAAAATATGAAATCGATG                         GTCAAGTACTGGAAGTGTCCATGGCCAAACCATTGGCAGATAAGAAACCTG
genomic: ATCAAGTGCATTGAAGGCAGTTAAAGGAAGTGAAAAATATGAAATCGATGgtaaacttct ... cttgatgcagGTCAAGTACTGGAAGTGTCCATGGCCAAACCATTGGCAGATAAGAAACCTG
EST: gi|211350823|gb|FL045987.1|FL045987
EST:     ATCAAGTGCATTGAAGGCAGTTAAAGGAAGTGAAAAATATGAAATCGATG                         GTCAAGTACTGGAAGTGTCCATGGCCAAACCATTGGCAGATAAGAAACCTG
genomic: ATCAAGTGCATTGAAGGCAGTTAAAGGAAGTGAAAAATATGAAATCGATGgtaaacttct ... cttgatgcagGTCAAGTACTGGAAGTGTCCATGGCCAAACCATTGGCAGATAAGAAACCTG
EST: gi|211353219|gb|FL045988.1|FL045988
EST:     ATCAAGTGCATTGAAGGCAGTTAAAGGAAGTGAAAAATATGAAATCGATG                         GTCAAGTACTGGAAGTGTCCATGGCCAAACCATTGGCAGATAAGAAACCTG
genomic: ATCAAGTGCATTGAAGGCAGTTAAAGGAAGTGAAAAATATGAAATCGATGgtaaacttct ... cttgatgcagGTCAAGTACTGGAAGTGTCCATGGCCAAACCATTGGCAGATAAGAAACCTG
EST: gi|211078934|gb|FL257757.1|FL257757
EST:     ATCAAGTGCATTGAAGGCAGTTAAAGGAAGTGAAAAATATGAAATCGATG                         GTCAAGTACTGGAAGTGTCCATGGCCAAACCATTGGCAGATAAGAAACCTG
genomic: ATCAAGTGCATTGAAGGCAGTTAAAGGAAGTGAAAAATATGAAATCGATGgtaaacttct ... cttgatgcagGTCAAGTACTGGAAGTGTCCATGGCCAAACCATTGGCAGATAAGAAACCTG
EST: gi|67033789|gb|CO462538.1|CO462538
EST:     ATCAAGTGCATTGAAGGCAGTTAAAGGAAGTGAAAAATATGAAATTGATG                         GTCAAGTACTGGAAGTGTCCATGGCCAAACCATTGGCAGATAAGAAACCTG
genomic: ATCAAGTGCATTGAAGGCAGTTAAAGGAAGTGAAAAATATGAAATCGATGgtaaacttct ... cttgatgcagGTCAAGTACTGGAAGTGTCCATGGCCAAACCATTGGCAGATAAGAAACCTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gctttgtcatgaatagatccatattagatgtaacctttgggcttacttgatgcagGTCAAGTACTGGAAGTGTCCATGGCCAAACCATTGGCAGATAAGAAACCTGATCATTCACACAGGCCTGGAGGAGGCCCTAATTATCCCCTTCCTCCCTA
                                         cttactt  CT-rich tract
                    atattagat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgagtgacatttattggtataaaaggagttttagttgctagaactgctttgtcatgaatagatccatattagatgtaacctttgggcttacttgatgcagGTCAAGTACTGGAAGTGTCCATGGCCAAACCATTGGCAGATAAGAAACCTGATCATTCACACAGGCCTGGAGGAGGCCCTAATTATCCCCTTCCTCCCTA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG