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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttacaacggtcagattaaatcttgcattcatataactactctatgttttcctgttatgatccatttgttttaattgtggctttgtattgcacttttcaagGTCCGTGACGCAGGAAACCTTTTGACAAGGGCAGGCTTTACCCTTCCAGGAGTTGATGTTGATCAGTATACCGTTAGATACAATAATG

Basic information

species Zea mays
transcript GRMZM2G087692_T01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G087692_T01 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os12g10200.1 (Oryza sativa), 3'ss of exon 5
ttacaacggtcagattaa-atcttgcattcatataactactctatgttttcctgttatgatccatttgttttaattgtggctttgtattgcacttttcaagGTCCGTGACGCAGGAAACCTTTTGACAAGGGCAGGCTTTACCCTTCCAGGAGTTGATGTTGATCAGTATACCGTTAGATACAATAATG------------
|| ||||      |     |  |||||| || || | | || ||| ||  | | ||    |  |||   | | || |||   |||  |||||||||||||||||||||| |||||||||||||||||||| |||||||| ||||||||||||||||| ||||| |  || || || | |||||||| ||            
ttgcaaccacttaacagctagattgcat-cacattattgctttatcttgacatattggtgtttattcagtctgatggtgatattgggttgcacttttcaagGTCCGTGATGCAGGAAACCTTTTGACAAGAGCAGGCTTCACCCTTCCAGGAGTTGACGTTGACCGTTACACTGTGAAATACAATAGTGGTTTGTAAACAA

upper sequence: GRMZM2G087692_T01 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA12G37130.2 (Glycine max), 3'ss of exon 7
---ttacaacggtcagat-taaatcttgcattcatataactactctatgttttcctgttatgatccatttgttttaattgtggctttgtattgcacttttcaagGTCCGTGACGCAGGAAACCTTTTGACAAGGGCAGGCTTTACCCTTCCAGGAGTTGATGTTGATCAGTATACCGTTAGATACAATAATG
   |||    ||   | | ||  | |     |  |||        | | ||||  ||| |  ||   | |     |  ||    | |||  | || |||   |||| || || || || || |||||||| |||||||| || ||||||||||| |||||||||||| | |||   |||| |||  | | ||
tagttaatctggcttgttgtagctttaatggttgtattgaagacttgtattttt-tgtcaaaata-gtataagaaagctgacattctgtcctccattttc--agGTTCGAGATGCTGGGAATCTTTTGACTAGGGCAGGTTTCACCCTTCCAGGTGTTGATGTTGATGATTATGTAGTTAAATATGAAAGTG

upper sequence: GRMZM2G087692_T01 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA04G43650.1 (Glycine max), 3'ss of exon 6
ttacaacggtcagattaaatcttgcattcat-ataactactctatgttttcctgttatgatccatttgttttaattgtggctttgtattgcacttttcaagGTCCGTGACGCAGGAAACCTTTTGACAAGGGCAGGCTTTACCCTTCCAGGAGTTGATGTTGATCAGTATACCGTTAGATACAATAATG
        ||    ||||   ||| ||| |  |    || | | |||     |  ||| |   |  ||          | | || | |    | |||  |||| || || || || || |||||||| |||||||| || ||||||||||| |||||||||||| |||||   |||| |||  | | ||
-gcttgttgtagctttaatggttgtattgaagacttgtattttttgtcaaaatagtataagaaagctggaactgagcagacattctgtcctccattttcagGTTCGAGATGCTGGGAATCTTTTGACTAGGGCAGGTTTCACCCTTCCAGGGGTTGATGTTGATGAGTATGTAGTTAAATATGAAAGTG

upper sequence: GRMZM2G087692_T01 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA04G43530.1 (Glycine max), 3'ss of exon 4
ttacaacggtcagattaaatcttgcattcatataactactctatgttttcctgttatgatccatttgttttaattgtggctttgtattgcacttttcaagGTCCGTGACGCAG-GAAACCTTTTGACAAGGGCAGGCTTTACCCTTCCAGGAGTTGATGTTGATCAGTATACCGTTAGATACAATAATG
                               | |  |    | | || ||    ||  ||      | |  || |  | | || | |    | |||  |||| || || || | ||| | ||||||| |||||||| || ||||||||||| |||||||||||| |||||   |||| |||  | |   
------------------------------aagacttgtatttttttgtcaaaatagtataagaaagctggaactaagaccttctgtcctccattttcaggttcgagatgctgtgaatctttttgactagGGCAGGTTTCACCCTTCCAGGTGTTGATGTTGATGAGTATGTAGTTAAATATGAAAGC-

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|78078319|gb|DV506734.1|DV506734
EST:     AAATGGAACGCGAAGGGGGCATCAGTCCTCGAATGTCCCCTTTAGCGCAA                         GTCCGTGACGCANGAAACCTTTTGACAAGGGCAGGCTTTACCCTTCCAGGA
genomic: AAATGGAACGCGAAGGGGGCATCAGTCCTCGAATGTCCCCTTTAGCGCAAgtatggctat ... acttttcaagGTCCGTGACGCAGGAAACCTTTTGACAAGGGCAGGCTTTACCCTTCCAGGA
EST: gi|50328095|gb|CO523221.1|CO523221
EST:     AAATGGAACGCGAAGGGGGCATCAGTCCTCGAATGTCCCCTTTAGCGCAA                         GTCCGTGACGCAGGAAACCTTTTGACAAGGGCAGGCTTTACCCT
genomic: AAATGGAACGCGAAGGGGGCATCAGTCCTCGAATGTCCCCTTTAGCGCAAgtatggctat ... acttttcaagGTCCGTGACGCAGGAAACCTTTTGACAAGGGCAGGCTTTACCCT
EST: gi|93282992|gb|EB675256.1|EB675256
EST:     AAATGGAACGCGAAGGGGGCATCAGTCCTCGAATGTCCCCTTTAGCGCAA                         GTCCGTGACGCAGGAAACCTTTTGACAAGGGCAGGCTTTACCCTTCCAGGA
genomic: AAATGGAACGCGAAGGGGGCATCAGTCCTCGAATGTCCCCTTTAGCGCAAgtatggctat ... acttttcaagGTCCGTGACGCAGGAAACCTTTTGACAAGGGCAGGCTTTACCCTTCCAGGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttcctgttatgatccatttgttttaattgtggctttgtattgcacttttcaagGTCCGTGACGCAGGAAACCTTTTGACAAGGGCAGGCTTTACCCTTCCAGGAGTTGATGTTGATCAGTATACCGTTAGATACAATAATG
                      ttttaat  putative branch site (score: 3)
                                            cacttttc  putative PPT
                 atttgttttaattgt  TA-rich tract