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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtaattggggctagcccttgcattttgagagcatctgaattattttatgttcattaattacattcatatgtaaatgcatttttccttttcctttttccagGGTGGACTTTTTGTGTATGACATTTTCTGGGTGTTCTTCACTCCAGTTATGGTCAGTGTGGCTAAATCTTTCGATGCTCCAATAAAG

Basic information

species Zea mays
transcript GRMZM2G044348_T03
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G044348_T04 (Zea mays), 3'ss of exon 7
lower sequence: GLYMA14G21190.1 (Glycine max), 3'ss of exon 2
---gtaattggggctagcccttgcattttgaga-gcatctgaattattttatgttcattaattacattcatatgtaaatgcatttttccttttcctttttccagGGTGGACTTTTTGTGTATGACATTTTCTGGGTGTTCTTCACTCCAGTTATGGTCAGTGTGGCTAAATCTTTCGATGCTCCAATAAAG
     |||   |  |     |||  || | |   |  | | | | ||||| |  || || ||    ||    | | ||| | |||    | |    |||| |||| |||||| ||||| ||||||||||||||||| |||||||||||||| |||||||| || || ||||| || |||||||||||||||
gctacaat-aagattcatatttgttttgtaatttgtttttcattcattttttcatc-ttcatggtctttgctt-tgaat-cttttccaatctcatgttttgcagGCTGGACTCTTTGTTTATGACATTTTCTGGGTTTTCTTCACTCCAGTGATGGTCAGCGTTGCAAAATCATTTGATGCTCCAATAAAG

upper sequence: GRMZM2G044348_T04 (Zea mays), 3'ss of exon 7
lower sequence: GLYMA04G08510.1 (Glycine max), 3'ss of exon 7
gtaattggggctagcccttgcattttgagagcatctgaattattttatg-ttcattaattacattcatatg----taaatgcatttttccttttcctttttccagGGTGGACTTTTTGTGTATGACATTTTCTGGGTGTTCTTCACTCCAGTTATGGTCAGTGTGGCTAAATCTTTCGATGCTCCAATAAAG
     |  | |      |   |  || ||   ||     | ||| |||   || ||  ||   |  |||||    |  |  |  ||    |  |   |||| |||| ||| || ||||||||||||||||||||||| |||||||| ||||| |||||||| || || ||||| || |||||||||||||||
-----ttagtcagttattaaaagattaagcatatgcttttcattgtataactccttttttttttcaatatgatctttgactctcttacattcatgtattttacagGCTGGTCTATTTGTGTATGACATTTTCTGGGTTTTCTTCACCCCAGTGATGGTCAGCGTTGCAAAATCATTTGATGCTCCAATAAAG

upper sequence: GRMZM2G044348_T04 (Zea mays), 3'ss of exon 7
lower sequence: GLYMA06G08620.2 (Glycine max), 3'ss of exon 7
--gtaattggggctagcccttgcattttgagagcatctgaattattttatgttcattaattacattcatatgtaaatgcatttttccttttcctttttccagGGTGGACTTTTTGTGTATGACATTTTCTGGGTGTTCTTCACTCCAGTTATGGTCAGTGTGGCTAAATCTTTCGATGCTCCAATAAAG
    | ||      ||  |   ||| |      ||| || || ||| | | ||  ||  ||  ||       |  |  |  ||    |  |   |||| |||| ||| || ||||||||||||||||||||||| |||||||||||||| ||||| || || || ||||| || |||||||||||||||
agtcagttattaaaagatcaaacatatgcttttcat-tgtataattctctcttt-ttgtttcaatatggtctttgactctcttacattcatgtattttacagGCTGGTCTATTTGTGTATGACATTTTCTGGGTTTTCTTCACTCCAGTGATGGTTAGCGTTGCAAAATCATTTGATGCTCCAATAAAG

upper sequence: GRMZM2G044348_T04 (Zea mays), 3'ss of exon 7
lower sequence: AT2G03120.1 (Arabidopsis thaliana), 3'ss of exon 6
---gtaattggggctagcccttgcattttgagagcatctgaattattttatgttcattaattacattcatatgtaaatg-------cattt----ttccttttcctt--tttccagGGTGGACTTTTTGTGTATGACATTTTCTGGGTGTTCTTCACTCCAGTTATGGTCAGTGTGGCTAAATCTTTCGATGCTCCAATAAAG
     || ||   ||      |||  ||   ||  |  ||  |    || |       ||  | |||| | || |||||       ||||     ||  || | |||   || ||||  ||||| ||| | ||||| || |||||||| ||||| |||||||||||||| ||||| || ||||| |||||||||||||| |||
gtaagaactgcatcttttgaatgctattcttgaaaacttgtttggacttctagatgaaaagaaaattcgtttgaaaatgactcaatcattcggtgtttgttatgcttgacttgcagGCAGGACTATTTTTCTATGATATCTTCTGGGTTTTCTTTACTCCAGTTATGGTTAGTGTTGCCAAATCCTTCGATGCTCCAATTAAG

upper sequence: GRMZM2G044348_T04 (Zea mays), 3'ss of exon 7
lower sequence: Vv06s0009g03520.t01 (Vitis vinifera), 3'ss of exon 7
gtaattggggctagcccttgcattttgagagcatctgaattattttatgttca--ttaattacattcatatgtaaatgc--atttttccttttcctttttccagGGTGGACTTTTTGTGTATGACATTTTCTGGGTGTTCTTCACTCCAGTTATGGTCAGTGTGGCTAAATCTTTCGATGCTCCAATAAAG
    |||  || ||   ||   |          | ||  |  |  |   ||||  ||  ||  | |  || || | |    |  |      || |   || ||||  ||||||||||| ||||| ||||||||||| |||||||||||||| ||||||||||| || || || ||||||||||| || |||
----ttgatgccagtatttttgtccctcatatctatgcctgttcctgcattcagtttgtttgtacttctaagtgatttttgacatgggtacttgcgaattgcagGCAGGACTTTTTGTTTATGATATTTTCTGGGTCTTCTTCACTCCAGTGATGGTCAGTGTTGCAAAGTCCTTCGATGCTCCTATTAAG

upper sequence: GRMZM2G044348_T04 (Zea mays), 3'ss of exon 7
lower sequence: PP1S47_5V6.2 (Physcomitrella patens), 3'ss of exon 7
-gtaattggggctagcccttgcattttgagagcatctgaattattttatgttcattaattacattcatatgtaaatgcatttttccttttcctttttccagGGTGGACTTTTTGTGTATGACATTTTCTGGGTGTTCTTCACTCCAGTTATGGTCAGTGTGGCTAAATCTTTCGATGCTCCAATAAAG
 ||   || |   ||       | | |  |||  |  | ||| |    ||   |||||||         | | |     |  |             | ||||  ||||| ||  | || ||||| ||||||||||||||||| || || ||||| || ||||| || || ||||||||||| || |||
ggtttgtgtgaaaaggtgcaagagtgtt-gagttttgggattgtaaattggcaattaattggggaggagtttgagatgttggtggtcacgatggagtgcagGCAGGACTGTTCATATACGACATCTTCTGGGTGTTCTTCACGCCTGTAATGGTGAGCGTGGCAAAGTCGTTCGATGCTCCCATCAAG

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|149027787|gb|EE154597.2|EE154597
EST:     GGATTGAGATGCTGTCATTGGGATCATTTAAAACTGGAGCCATTCTCTTG                         GGTGGACTTTTTGTGTATGACATTTTCTGGGTGTTCTTCACTCCAGTTATG
genomic: GGATTGAGATGCTGTCATTGGGATCATTTAAAACTGGAGCCATTCTCTTGgtaagggttt ... ctttttccagGGTGGACTTTTTGTGTATGACATTTTCTGGGTGTTCTTCACTCCAGTTATG
EST: gi|94475589|gb|EB704547.1|EB704547
EST:     GGATTGAGATGCTGTCATTGGGATCATTTAAAACGGGAGCCATTCTCTTG                         GGTGGACTTTTTGTGTATGACATTTTCTGGGTGTTCTTCACTCCAGTTATG
genomic: GGATTGAGATGCTGTCATTGGGATCATTTAAAACTGGAGCCATTCTCTTGgtaagggttt ... ctttttccagGGTGGACTTTTTGTGTATGACATTTTCTGGGTGTTCTTCACTCCAGTTATG
EST: gi|7137682|gb|AW499217.1|AW499217
EST:     GGATTGAGATGCTGTCATTGGGATCATTTAAAACTGGAGCCATTCTCTTG                         GGTGGACTTTTTGTGTATGACATTTTCTGGGTGTTCTTCACTCCAGTTATG
genomic: GGATTGAGATGCTGTCATTGGGATCATTTAAAACTGGAGCCATTCTCTTGgtaagggttt ... ctttttccagGGTGGACTTTTTGTGTATGACATTTTCTGGGTGTTCTTCACTCCAGTTATG
EST: gi|67018214|gb|CO446963.1|CO446963
EST:     GGATTGAGATGCTGTCATTGGGATCATTTAAAACTGGAGCCATTCTCTTG                         GGTGGACTTTTTGTGTATGACATTTTCTGGGTGTTCTTCACTCCAGTTATG
genomic: GGATTGAGATGCTGTCATTGGGATCATTTAAAACTGGAGCCATTCTCTTGgtaagggttt ... ctttttccagGGTGGACTTTTTGTGTATGACATTTTCTGGGTGTTCTTCACTCCAGTTATG
EST: gi|148944600|gb|EC889730.2|EC889730
EST:     GGATTGAGATGCTGTCATTGGGATCATTTAAAACTGGAGCCATTCTCTTG                         GGTGGACTTTTTGTGTATGACATTTTCTGGGTGTTCTTCACTCCAGTTATG
genomic: GGATTGAGATGCTGTCATTGGGATCATTTAAAACTGGAGCCATTCTCTTGgtaagggttt ... ctttttccagGGTGGACTTTTTGTGTATGACATTTTCTGGGTGTTCTTCACTCCAGTTATG
EST: gi|149100816|gb|EE186910.2|EE186910
EST:     AGATTGAGATGCTGTCATTGGGATCATTTAAAACTGGAGCCATTCTCTTG                         GGTGGACTTTTTGTGTATGACATTTTCTGGGTGTTCTTCACTCCAGTTATG
genomic: GGATTGAGATGCTGTCATTGGGATCATTTAAAACTGGAGCCATTCTCTTGgtaagggttt ... ctttttccagGGTGGACTTTTTGTGTATGACATTTTCTGGGTGTTCTTCACTCCAGTTATG
EST: gi|148943972|gb|EC889053.2|EC889053
EST:     GGATTGAGATGCTGTCATTGGGATCATTTAAAACTGGAGCCATTCTCTTG                         GGTGGACTTTTTGTGTATGACATTTTCTGGGTGTTCTTCACTCCAGTTATG
genomic: GGATTGAGATGCTGTCATTGGGATCATTTAAAACTGGAGCCATTCTCTTGgtaagggttt ... ctttttccagGGTGGACTTTTTGTGTATGACATTTTCTGGGTGTTCTTCACTCCAGTTATG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatgttcattaattacattcatatgtaaatgcatttttccttttcctttttccagGGTGGACTTTTTGTGTATGACATTTTCTGGGTGTTCTTCACTCCAGTTATGGTCAGTGTGGCTAAATCTTTCGATGCTCCAATAAAG
      cattaat  putative branch site (score: 3)
                             tgcatttttccttttc  putative PPT
       attaattacattcata  TA-rich tract