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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaactgctcacagaattcctcaattaaatgttcctatccatcattgttagtgataatagtactgctttttgttcagAAATTTATTGAGACAACTCGAGAAACCAGCCCTACTTTCATCATTGGGAAGTTTGATGGAATTCTTGGTCTCGGATTTCCTGAAATTTCTGTAGGAGGAG

Basic information

species Zea mays
transcript GRMZM2G077233_T04
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G077233_T04 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os01g18630.1 (Oryza sativa), 3'ss of exon 4
gtaaactgctcacagaatt-cctcaattaaatgttcctatccatcattgttagtgataatagtactgctttttgttcagAAATTTATTGAGACAACTCGAGAAACCAGCCCTACTTTCATCATTGGGAAGTTTGATGGAATTCTTGGTCTCGGATTTCCTGAAATTTCTGTAGGAGGAG
|| |  |  || ||  |||  |||| | |||  ||   || ||||||||||  || |    || |   ||||  ||||||  || |||||||||||  | ||| | |||| |||||||||||| ||||||||||||||||||||||| || |||||||| || || ||||| |||||||
gtgactta-tcgcactattgtctcagtaaaacatttagatgcatcattgttgatgctgcaggt-ccatttttctttcagATGTTCATTGAGACAACCAGGGAACCGAGCCTTACTTTCATCATCGGGAAGTTTGATGGAATTCTTGGACTTGGATTTCCGGAGATCTCTGTGGGAGGAG
















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|8367213|gb|BE050158.1|BE050158
EST:     TCTTCAGTGAGGACAATGTGTTGGTTGGCAACCTTGTTGTGCAAAATCAG                         AAATTTATTGAGACAACTCGAGAAACCAGCCCTACTTTCATCATTGGGAAG
genomic: TCTTCAGTGAGGACAATGTGTTGGTTGGCAACCTTGTTGTGCAAAATCAGgtaaactgct ... ttttgttcagAAATTTATTGAGACAACTCGAGAAACCAGCCCTACTTTCATCATTGGGAAG
EST: gi|211429217|gb|FL412881.1|FL412881
EST:     TTCAGTGAGGACAATGTGTTTGTTGGCCACCTTTGTTGTGCAAAATTCAG                         AAATTTATTGAGACNACTCGAGAAACCAGCCCTACTTTCATCATTTGGAA
genomic: TTCAGTGAGGACAATGTGTTGGTTGGCAACCTT-GTTGTGCAAAAT-CAGgtaaactgct ... ttttgttcagAAATTTATTGAGACAACTCGAGAAACCAGCCCTACTTTCATCATTGGGAA
EST: gi|67034446|gb|CO462996.1|CO462996
EST:     TCTTCAGTGAGGACAATGTGTTGGTTGGTAACCTTGTTGTGCAAAATCAG                         AAATTTATTGAGACAACTCGAGAAACCAGCCCTACTTTCATCATTGGGAAG
genomic: TCTTCAGTGAGGACAATGTGTTGGTTGGCAACCTTGTTGTGCAAAATCAGgtaaactgct ... ttttgttcagAAATTTATTGAGACAACTCGAGAAACCAGCCCTACTTTCATCATTGGGAAG
EST: gi|211541914|gb|FL379334.1|FL379334
EST:     TCTTCAGTGAGGACAATGTGTTGGTTGGTAACCTTGTTGTGCAAAATCAG                         AAATTTATTGAGACAACTCGAGAAACCAGCCCTACTTTCATCATTGGGGAG
genomic: TCTTCAGTGAGGACAATGTGTTGGTTGGCAACCTTGTTGTGCAAAATCAGgtaaactgct ... ttttgttcagAAATTTATTGAGACAACTCGAGAAACCAGCCCTACTTTCATCATTGGGAAG
EST: gi|91876413|gb|EB406370.1|EB406370
EST:     TCTTCAGTGAGGACAATGTGTTGGTTGGCAACCTTGTTGTGCAAAATCAG                         AAATTTATTGGGACAACTCGAGAAACCAGCCCTACTTTCATCATTGGGGAG
genomic: TCTTCAGTGAGGACAATGTGTTGGTTGGCAACCTTGTTGTGCAAAATCAGgtaaactgct ... ttttgttcagAAATTTATTGAGACAACTCGAGAAACCAGCCCTACTTTCATCATTGGGAAG
EST: gi|60357617|gb|DN224590.1|DN224590
EST:     TCTTCAGTGAGGACAATGTGTTGGTTGGCAACCTTGTTGTGCAAAATCAG                         AAATTTATTGAGACAACTCGAGAAACCGGCCCTACTTTTC-TCATTGGGAA
genomic: TCTTCAGTGAGGACAATGTGTTGGTTGGCAACCTTGTTGTGCAAAATCAGgtaaactgct ... ttttgttcagAAATTTATTGAGACAACTCGAGAAACCAGCCCTACTTT-CATCATTGGGAA
EST: gi|76291015|gb|DV030583.1|DV030583
EST:     TCTTCAGTGAGGACAATGTGTTGGTTGGCAACCTTGTTGTGCAAAATCAG                         AAATTTATTGAGACAACTCGAGAAACCAGCCCTACTTTCATCATTGGGAAG
genomic: TCTTCAGTGAGGACAATGTGTTGGTTGGCAACCTTGTTGTGCAAAATCAGgtaaactgct ... ttttgttcagAAATTTATTGAGACAACTCGAGAAACCAGCCCTACTTTCATCATTGGGAAG
EST: gi|211068181|gb|FL270394.1|FL270394
EST:     TCTTCAGTGAGGACAATGTGTTGGTTGGTAACCTTGTTGTGCAAAATCAG                         AAATTTATTGAGACAACTCGAGAAAC-AGCCCTACTTTCATCATTGGGAAG
genomic: TCTTCAGTGAGGACAATGTGTTGGTTGGCAACCTTGTTGTGCAAAATCAGgtaaactgct ... ttttgttcagAAATTTATTGAGACAACTCGAGAAACCAGCCCTACTTTCATCATTGGGAAG
EST: gi|32851441|gb|CD991122.1|CD991122
EST:     TCTTCAGTGAGGACAATGTGTTGGTTGGCAACCTTGTTGTGCAAAATCAG                         AAATTTATTGAGACAACTCGAGAAACCAGCCCTACTTTCATCATTGGGAAG
genomic: TCTTCAGTGAGGACAATGTGTTGGTTGGCAACCTTGTTGTGCAAAATCAGgtaaactgct ... ttttgttcagAAATTTATTGAGACAACTCGAGAAACCAGCCCTACTTTCATCATTGGGAAG
EST: gi|211504863|gb|FL422036.1|FL422036
EST:     TCTTCAGTGAGGACAATGTGTTGGTTGGTAACCTTGTTGTGCAAAATCAG                         AAATTTATTGA
genomic: TCTTCAGTGAGGACAATGTGTTGGTTGGCAACCTTGTTGTGCAAAATCAGgtaaactgct ... ttttgttcagAAATTTATTGA
EST: gi|211384115|gb|FL248478.1|FL248478
EST:     TCTTCAGTGAGGACAATGTGTTGGTTGGCAACCTTGTTGTGCAAAATCAG                         AAATTTATTGAGACAACTCGAGAAACCAGCCCTACTTTCATCATTGGGAAG
genomic: TCTTCAGTGAGGACAATGTGTTGGTTGGCAACCTTGTTGTGCAAAATCAGgtaaactgct ... ttttgttcagAAATTTATTGAGACAACTCGAGAAACCAGCCCTACTTTCATCATTGGGAAG
EST: gi|76289740|gb|DV029308.1|DV029308
EST:     TCTTCAGTGAGGACAATGTGTTGGTTGGCAACCTTGTTGTGCAAAATCAG                         AAATTTATTGAGACAACTCGAGAAACCAGCCCTACTTTCATCATTGGGAAG
genomic: TCTTCAGTGAGGACAATGTGTTGGTTGGCAACCTTGTTGTGCAAAATCAGgtaaactgct ... ttttgttcagAAATTTATTGAGACAACTCGAGAAACCAGCCCTACTTTCATCATTGGGAAG
EST: gi|211373714|gb|FL377783.1|FL377783
EST:     TCTTCAGTGAGGACAATGTGTTGGTTGGCAACCTTGTTGTGCAAAATCAG                         AAATTTATTGAGACAACTCGAGAAACCAGCCCTACTTTCATCATTGGGAAG
genomic: TCTTCAGTGAGGACAATGTGTTGGTTGGCAACCTTGTTGTGCAAAATCAGgtaaactgct ... ttttgttcagAAATTTATTGAGACAACTCGAGAAACCAGCCCTACTTTCATCATTGGGAAG
EST: gi|101393193|gb|EB818527.1|EB818527
EST:     TCTTCAGTGAGGACAATGTGTTGGTTGGCAACCTTGTTGTGCAAAATCAG                         AAATTTATTGAGACAACTCGAGAAACCAGCCCTACTTTCATCATTGGGAAG
genomic: TCTTCAGTGAGGACAATGTGTTGGTTGGCAACCTTGTTGTGCAAAATCAGgtaaactgct ... ttttgttcagAAATTTATTGAGACAACTCGAGAAACCAGCCCTACTTTCATCATTGGGAAG
EST: gi|78179156|gb|DV549529.1|DV549529
EST:     TCTTCAGTGAGGACAATGTGTTGGTTGGCAACCTTGTTGTGCAAAATCAG                         AAATTTATTGAGACAACTCGAGAAACCAGCCCTACTTTCATCATTGGGAAG
genomic: TCTTCAGTGAGGACAATGTGTTGGTTGGCAACCTTGTTGTGCAAAATCAGgtaaactgct ... ttttgttcagAAATTTATTGAGACAACTCGAGAAACCAGCCCTACTTTCATCATTGGGAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aattaaatgttcctatccatcattgttagtgataatagtactgctttttgttcagAAATTTATTGAGACAACTCGAGAAACCAGCCCTACTTTCATCATTGGGAAGTTTGATGGAATTCTTGGTCTCGGATTTCCTGAAATTTCTGTAGGAGGAG
                                           ctttttgttc  CT-rich tract
                               ataatagta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaactgctcacagaattcctcaattaaatgttcctatccatcattgttagtgataatagtactgctttttgttcagAAATTTATTGAGACAACTCGAGAAACCAGCCCTACTTTCATCATTGGGAAGTTTGATGGAATTCTTGGTCTCGGATTTCCTGAAATTTCTGTAGGAGGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG