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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtattttttccatggaaataatgtataaattgcatattatattttaatgtatttatatattctctaaatcaacacccatcttgtagCCTACTGCACTGGCCTTCTGTTGGCTCGCCGTGTGCTCAAGATCCGTGGTTTGGATCAGGAGTACGAGGGCAATGTTGAG

Basic information

species Zea mays
transcript GRMZM2G163081_T05
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G163081_T03 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os01g67134.1 (Oryza sativa), 3'ss of exon 4
gta-ttttttccatggaaataatgtataaattgcatattatattttaatgtatttatatattct-----ctaaatcaacacccatcttgtagCCTACTGCACTGGCCTTCTGTTGGCTCGCCGTGTGCTCAAGATCCGTGGTTTGGATCAGGAGTACGAGGGCAATGTTGAG
||| |||  ||  | |||  |||    | | |||   || | | ||  |||||  ||  | | |     ||   |    |  |||  |||||| || ||||||||| | || ||||||||||||||||||||| ||||||||||||| |||||||||||||||||| |||||
gtagtttcctcagttgaatgaatacgcagaatgctggtt-tgtgttgctgtatgaatgcaatttaattcctctgttttgatgcattgtgtagCTTATTGCACTGGCTTGCTTTTGGCTCGCCGTGTGCTCAAGCTCCGTGGTTTGGACCAGGAGTACGAGGGCAATATTGAG

upper sequence: GRMZM2G163081_T03 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os01g67126.1 (Oryza sativa), 3'ss of exon 4
gta-ttttttccatggaaataatgtataaattgcatattatattttaatgtatttatatattct-----ctaaatcaacacccatcttgtagCCTACTGCACTGGCCTTCTGTTGGCTCGCCGTGTGCTCAAGATCCGTGGTTTGGATCAGGAGTACGAGGGCAATGTTGAG
||| |||  ||    |||  ||| |  | | |||   || | | ||  |||||  ||| | | |     ||   |    |  |||  |||||| |||||||||||| | ||  ||||||| |||||||||| | ||||||||||||| ||||||||||||||||||||||||
gtagtttcctcagctgaatgaatatgcagaatgctggtt-tgtcttgctgtatgcatacaatttaattcctctgttttgatgcattgtgtagCTTACTGCACTGGCTTGCTTCTGGCTCGTCGTGTGCTCACGCTCCGTGGTTTGGACCAGGAGTACGAGGGCAATGTTGAG

upper sequence: GRMZM2G163081_T03 (Zea mays), 3'ss of exon 4
lower sequence: AT3G25520.2 (Arabidopsis thaliana), 3'ss of exon 2
gtattttttccatggaaataatgtataaattgcatattatattttaatgtatttatatattctctaaatcaacacccatcttgtagCCTACTGCACTGGCCTTCTGTTGGCTCGCCGTGTGCTCAAGATCCGTGGTTTGGATCAGGAGTACGAGGGCAATGTTGAG
                          | || |   ||| | | || |||   |||  |||  | ||| |         |    |||| ||||| ||||||||||| ||||||||||||||  | |||||    |   ||||| | ||||| ||||| || ||||||
-------------------------aatatggttgattctgtctttatg-gcttacttatg-tgtaatttttttttgttgaactagcttactgtactggccttcttttggctcgccgtgttttaaagATGTTGGAAATGGATGACGAGTATGAGGGAAACGTTGAG

upper sequence: GRMZM2G163081_T03 (Zea mays), 3'ss of exon 4
lower sequence: AT3G25520.1 (Arabidopsis thaliana), 3'ss of exon 3
-----gtattttttccatggaaataatgtataaattgcatattatattttaatgtatttatatattctctaaatcaacacccatcttgt------agCCTACTGCACTGGCCTTCTGTTGGCTCGCCGTGTGCTCAAGATCCGTGGTTTGGATCAGGAGTACGAGGGCAATGTTGAG
     | || | |    ||| | |  | |  || ||  ||||  | |  |  ||| |||||   ||   ||  |  |      | ||||      ||| ||||| ||||||||||| ||||||||||||||  | |||||    |   ||||| | ||||| ||||| || ||||||
gtattgaatgtgtcatctggtattgttttccaattta-atatggt-tgattctgtctttatggcttacttatgtgtaatttttttttgttgaactagCTTACTGTACTGGCCTTCTTTTGGCTCGCCGTGTTTTAAAGATGTTGGAAATGGATGACGAGTATGAGGGAAACGTTGAG

upper sequence: GRMZM2G163081_T03 (Zea mays), 3'ss of exon 4
lower sequence: Vv05s0094g00870.t01 (Vitis vinifera), 3'ss of exon 4
--------------------------------------------------------gtattttttccatggaaataatgtataaattgcatattatattttaatgtatttatatattctc-taaatcaacacccatcttgtagCCTACTGCACTGGCCTTCTGTTGGCTCGCCGTGTGCTCAAGATCCGTGGTTTGGATCAGGAGTACGAGGGCAATGTTGAG
                                                         |   ||||   | |      | | |||    ||||  || | | | | | ||     |||  | |  |  ||  ||  |   ||||| ||||||||||| ||||| ||||||||||||||  | || || | ||   |||||   || || || |||||||| |||
gtatatttatcagaaattggttcattgttcctatttatttaaaatttgtcatgtttatgaatttttacttgtgcctctttgtaaga-acataccatgtgtaacttttttgtggcattaacatggactaattccttttgagtagCTTACTGCACTGGGCTTCTCTTGGCTCGCCGTGTCTTGAAAATGCTTGAGATGGATGGTGAATATGAAGGCAATGTGGAG

upper sequence: GRMZM2G163081_T03 (Zea mays), 3'ss of exon 4
lower sequence: PP1S364_3V6.1 (Physcomitrella patens), 3'ss of exon 4
---------------------------gtatt--ttttccatggaaataatgtataaattgcatattatattttaatgt---atttatatattctctaaatcaacacccatctt-----gtagCCTACTGCACTGGCCTTCTGTTGGCTCGCCGTGTGCTCAAGATCCGTGGTTTGGATCAGGAGTACGAGGGCAATGTTGAG
                           |||||    |  || |  | |  | | |    |    ||  | | || |      ||||||  ||  |    ||     |  || ||       ||||||||||||||||||||| ||||| ||||||   || ||||     |   ||||| | |||||||  |||||||   ||
gttagttccaggactttctctaattcagtattgacctatcaagtcatttttctttcttctcaggatgctttctttacccgaaatttattgatgttgacgattttttcttatgtttctgcacagCCTACTGCACTGGCCTTCTCTTGGCCCGCCGTCACCTGAAGAATTACGACCTGGATGATGAGTACGTCGGCAATGAGCAG

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|26559987|gb|CA832222.1|CA832222
EST:     TGAGTTGCCACGATATGGTCTTGAAGTTGGTCTGACCAACTATGCAGCTG                         CCTACTGCACTGGCCTTCTGTTGGCTCGCCGTGTGCTCAAGATCCGTGGTT
genomic: TGAGTTGCCACGATATGGTCTTGAAGTTGGTCTGACCAACTATGCAGCTGgtattttttc ... catcttgtagCCTACTGCACTGGCCTTCTGTTGGCTCGCCGTGTGCTCAAGATCCGTGGTT
EST: gi|5917501|gb|AW054304.1|AW054304
EST:     TGAGTTGCCACGATATGGTCTTGAAGTTGGTCTGACCAACTATGCAGCTG                         CCTACTGCACTGGCCTTCTGTTGGCTCGCCGTGTGCTCAAGATCCGTGGTT
genomic: TGAGTTGCCACGATATGGTCTTGAAGTTGGTCTGACCAACTATGCAGCTGgtattttttc ... catcttgtagCCTACTGCACTGGCCTTCTGTTGGCTCGCCGTGTGCTCAAGATCCGTGGTT
EST: gi|67038759|gb|CO465014.1|CO465014
EST:     TGAGTTGCCACGATATGGTCTTGAAGTTGGTCTGACCAACTATGCAGCTG                         CCTACTGCACTGGCCTTCTGTTGGCTCGCCGTGTGCTCAAGATCCGTGGTT
genomic: TGAGTTGCCACGATATGGTCTTGAAGTTGGTCTGACCAACTATGCAGCTGgtattttttc ... catcttgtagCCTACTGCACTGGCCTTCTGTTGGCTCGCCGTGTGCTCAAGATCCGTGGTT
EST: gi|31356600|gb|CD440957.1|CD440957
EST:     TGAGTTGCCACGATATGGTCTTGAAGTTGGTCTGACCAACTATGCATCTG                         CCTACTGCACTGGCCTTCTGTTGGCTCGCCGTGTGCTCAAGATCCGTGGTT
genomic: TGAGTTGCCACGATATGGTCTTGAAGTTGGTCTGACCAACTATGCAGCTGgtattttttc ... catcttgtagCCTACTGCACTGGCCTTCTGTTGGCTCGCCGTGTGCTCAAGATCCGTGGTT
EST: gi|31612123|gb|CD568745.1|CD568745
EST:     TGAGTTGCCACGATATGGTCTTGAAGTTGGTCTGACCAACTATGCAGCTG                         CCTACTGCACTGGCCTTCTGTTGGCTCGCCGTGTGCTCAAGATCCGTGGTT
genomic: TGAGTTGCCACGATATGGTCTTGAAGTTGGTCTGACCAACTATGCAGCTGgtattttttc ... catcttgtagCCTACTGCACTGGCCTTCTGTTGGCTCGCCGTGTGCTCAAGATCCGTGGTT
EST: gi|26557726|gb|CA829961.1|CA829961
EST:     CTGACCAACTATGCAGCTG                         CCTACTGCACTGGCCTTCTGTTGGCTCGCCGTGTGCTCAAGATCCGTGGCT
genomic: CTGACCAACTATGCAGCTGgtattttttc ... catcttgtagCCTACTGCACTGGCCTTCTGTTGGCTCGCCGTGTGCTCAAGATCCGTGGTT
EST: gi|31357768|gb|CD442125.1|CD442125
EST:     TGAGTTGCCACGATATGGTCTTGAAGTTGGTCTGACCAACTATGCAGCTG                         CCTACTGCACTGGCCTTCTGTTGGCTCGCCGTGTGCTCAAGATCCGTGGTT
genomic: TGAGTTGCCACGATATGGTCTTGAAGTTGGTCTGACCAACTATGCAGCTGgtattttttc ... catcttgtagCCTACTGCACTGGCCTTCTGTTGGCTCGCCGTGTGCTCAAGATCCGTGGTT
EST: gi|24773952|gb|CA409206.1|CA409206
EST:     TGAGTTGCCACCATATGGTCTTGAAGTTGGTCTGACCAACTATGCAGCTG                         CCTACTGCACTGGCCTTCTGTTGGCTCGCCGTGTGCTCAAGATCCGTGGTT
genomic: TGAGTTGCCACGATATGGTCTTGAAGTTGGTCTGACCAACTATGCAGCTGgtattttttc ... catcttgtagCCTACTGCACTGGCCTTCTGTTGGCTCGCCGTGTGCTCAAGATCCGTGGTT
EST: gi|21809868|gb|BQ668186.1|BQ668186
EST:     TGAGTTGCCACGATATGGTCTTGAAGTTGGTCTGACCAACTATGCAGCTG                         CCTACTGCACTGGCCTTCTGTTGGCTCGCCGNGTGCTCAAGATCCGTGGTT
genomic: TGAGTTGCCACGATATGGTCTTGAAGTTGGTCTGACCAACTATGCAGCTGgtattttttc ... catcttgtagCCTACTGCACTGGCCTTCTGTTGGCTCGCCGTGTGCTCAAGATCCGTGGTT
EST: gi|60341012|gb|DN207985.1|DN207985
EST:     TGAGTTGCCACGATATGGTCTTGAAGTTGGTCTGACCAACTATGCAGCTG                         CCTACTGCACTGGCCTTCTGTTGGCTCGCCGTGTGCTCAAGATCCGTGGTT
genomic: TGAGTTGCCACGATATGGTCTTGAAGTTGGTCTGACCAACTATGCAGCTGgtattttttc ... catcttgtagCCTACTGCACTGGCCTTCTGTTGGCTCGCCGTGTGCTCAAGATCCGTGGTT
EST: gi|31360177|gb|CD444534.1|CD444534
EST:     TGAGTTGCCACGATATGGTCTTGAAGTTGGTCTGACCAACTATGCAGCTG                         CCTACTGCACTGGCCTTCTGTTGGCTCGCCGTGTGCTCAAGATCCGTGGTT
genomic: TGAGTTGCCACGATATGGTCTTGAAGTTGGTCTGACCAACTATGCAGCTGgtattttttc ... catcttgtagCCTACTGCACTGGCCTTCTGTTGGCTCGCCGTGTGCTCAAGATCCGTGGTT
EST: gi|6012680|gb|AW062117.1|AW062117
EST:     TGAGTTGCCACGATATGGTCTTGAAGTTGGTCTGACCAACTATGCAGCTG                         CCTACTGCACTGGCCTTCTGTTGGCTCGCCGTGTGCTCAAGATCCGTGGTT
genomic: TGAGTTGCCACGATATGGTCTTGAAGTTGGTCTGACCAACTATGCAGCTGgtattttttc ... catcttgtagCCTACTGCACTGGCCTTCTGTTGGCTCGCCGTGTGCTCAAGATCCGTGGTT
EST: gi|32929950|gb|CF034762.1|CF034762
EST:     TGAGTTGCCACGATATGGTCTTGAAGTTGGTCTGACCAACTATGCAGCTG                         CCTACTGCACTGGACTTCTGTTGGCTCGCCGTGTGCTAAAGATCCGTGGTT
genomic: TGAGTTGCCACGATATGGTCTTGAAGTTGGTCTGACCAACTATGCAGCTGgtattttttc ... catcttgtagCCTACTGCACTGGCCTTCTGTTGGCTCGCCGTGTGCTCAAGATCCGTGGTT
EST: gi|67042510|gb|CO468765.1|CO468765
EST:     TGAGTTGCCACGATATGGTCTTGAAGTTGGTCTGACCAACTATGCAGCTG                         CCTACTGCACTGGCCTTCTGTTGGCTCGCCGTGTGCTCAAGATCCGTGGTT
genomic: TGAGTTGCCACGATATGGTCTTGAAGTTGGTCTGACCAACTATGCAGCTGgtattttttc ... catcttgtagCCTACTGCACTGGCCTTCTGTTGGCTCGCCGTGTGCTCAAGATCCGTGGTT
EST: gi|31441038|gb|CD510469.1|CD510469
EST:     TGAGTTGCCACGATATGGTCTTGAAGTTGGTCTGACCAACTATGCAGCTG                         CCTACTGCACTGGCCTTCTGTTGGCTCGCCGTGTGCTCAAGATCCGTGGTT
genomic: TGAGTTGCCACGATATGGTCTTGAAGTTGGTCTGACCAACTATGCAGCTGgtattttttc ... catcttgtagCCTACTGCACTGGCCTTCTGTTGGCTCGCCGTGTGCTCAAGATCCGTGGTT
EST: gi|211413275|gb|FL046453.1|FL046453
EST:     TGAGTTGCCACGATATGGTCTTGAAGTTGGTCTGACCAACTATGCAGCTG                         CCTACTGCACTGGACTTCTGTTGGCTCGCCGTGTGCTAAAGATCCGTGGTT
genomic: TGAGTTGCCACGATATGGTCTTGAAGTTGGTCTGACCAACTATGCAGCTGgtattttttc ... catcttgtagCCTACTGCACTGGCCTTCTGTTGGCTCGCCGTGTGCTCAAGATCCGTGGTT
EST: gi|67011087|gb|CO439836.1|CO439836
EST:     CTTGAAGTTGGTCTGACCAACTATGCAGCTG                         CCTACTGCACTGGCCTTCTGTTGGCTCGCCGTGTGCTCAAGATCCGTGGTT
genomic: CTTGAAGTTGGTCTGACCAACTATGCAGCTGgtattttttc ... catcttgtagCCTACTGCACTGGCCTTCTGTTGGCTCGCCGTGTGCTCAAGATCCGTGGTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcatattatattttaatgtatttatatattctctaaatcaacacccatcttgtagCCTACTGCACTGGCCTTCTGTTGGCTCGCCGTGTGCTCAAGATCCGTGGTTTGGATCAGGAGTACGAGGGCAATGTTGAG
                              ctctaaa  putative branch site (score: 3)
                                           cccatctt  putative PPT
     ttatattttaatgtat  TA-rich tract