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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaaactctagctgttagtgtttggacatgtaatgtgcatttgatttgatacaaggctaaatgttcacaactaacatacatagtacacgattgatttgcacagcatttgtttattccatagctattttgggctttggctcttggaaaacctaaacatatacacttttctttttgcagGTGATAGAAGCCCAACCTGACATGCCAGTTGTTGGAGCCATAACTCTATATGTATCACTTCTGACCTTTACTCTCCGTGTACATCCTGATCGGCTTGATT

Basic information

species Zea mays
transcript GRMZM5G844195_T03
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G844195_T02 (Zea mays), 3'ss of exon 11
lower sequence: LOC_Os03g58700.1 (Oryza sativa), 3'ss of exon 10
gtaaaactctagctgttagtgtttggacatgtaatgtgcatttgatttgatacaaggctaaatgttcacaactaacatacatagtacacgattgatttgcacagcatttgtttattccatagctattttgggctttggctcttggaaaacctaaacatatacacttttctttttgcagGTGATAGAAGCCCAACCTGACATGCCAGTTGTTGGAGCCATAACTCTATATGTATCACTTCTGACCTTTACTCTCCGTGTACATCCTGATCGGCTTGATT
                                                                        |    | | |  | |  | |  | ||  ||||   |||  |  |  ||     | ||   || |      || ||   |||   || || | ||  | ||| |||||||||||| ||||||  |||||||||||||||||| ||  ||||| |||||||||||||| |||| |||||||||||||| ||||| |||||||||||||
-----------------------------------------------------------------------ttttttttcttgctccttgctcaaattatacagttgttgcgtgctgtattatggtatta--ctgtcaaaactgaaa---ctagtgatctataatt--catttggcagGTGATAGAGGCCCAAGTTGACATGCCAGTTGTTGGTGCAGTAACTTTATATGTATCACTTTTGACATTTACTCTCCGTGTGCATCCGGATCGGCTTGATT

upper sequence: GRMZM5G844195_T02 (Zea mays), 3'ss of exon 11
lower sequence: GLYMA14G40270.1 (Glycine max), 3'ss of exon 10
gtaaaactctagctgttagtgtttggacatgtaatgtgcatttgatttgatacaaggctaaatgttcacaactaacatacatagtacacgattgatttgcac-agcatttgtttattccatagctattttgggctttggctcttggaaaacctaaacatatacacttttctttttgcagGTGATAGAAGCCCAACCTGACATGCCAGTTGTTGGAGCCATAACTCTATATGTATCACTTCTGACCTTTACTCTCCGTGTACATCCTGATCGGCTTGATT
                                                                            || | |  |    |  |  |    || ||   |   |||||  || |  | | |||   |    ||    |  |  |||||   | || ||   |  ||||||||||||||||| |||  |||||||||  |||| ||||| ||| || |  |||| || ||||| || |||||||||||||| ||||| ||||| |||||||
--------------------------------------------------------------------------ttatcccttctttgtgccttctaaatactagttataccttattgtatgg--actatggagctgcaatccaataccatataaac---tgcatttggttggttgcagGTGATAGAAGCACAAGTTGACATGCCTATTGTGGGAGCAATAGCTTTGCATGTTTCTCTTCTTACATTTACTCTCCGTGTTCATCCAGATCGACTTGATT

upper sequence: GRMZM5G844195_T02 (Zea mays), 3'ss of exon 11
lower sequence: AT1G75850.1 (Arabidopsis thaliana), 3'ss of exon 10
gtaaaactctagctgttagtgtttggacatgtaatgtgcatttgatttgatacaaggctaaatgttcacaactaacatacatagtacacgattgatttgcacagcatttgtttattccatagc-tattttgggctttggctcttggaaaaccta-----aacatatacacttttcttt--ttgcagGTGATAGAAGCCCAACCTGACATGCCAGTTGTTGGAGCCATAACTCTATATGTATCACTTCTGACCTTTACTCTCCGTGTACATCCTGATCGGCTTGATT
                                                                                      | | |||  ||    |     ||    |  |    || |||  ||   | |   ||||| || || ||      || |||  ||||    |    | |||||||||||  | || | ||| |||||  |||| ||||| || ||||| | ||| || ||| |||| ||||||||||| || ||||||||||||||||| |
--------------------------------------------------------------------------------------ctcaattctttgagtctttgctttcccagcctcctgcatataatgcaatatttttcttgaaatacatatatttgacttatggacttggtgtgggctacagGTGATAGATACACAGCTTGAGATGCCTATTGTCGGAGCTATGACTCTGTTTGTCTCTCTTTTGACTTTTACTCTCCGAGTTCATCCTGATCGGCTTGACT

upper sequence: GRMZM5G844195_T02 (Zea mays), 3'ss of exon 11
lower sequence: Vv04s0023g03870.t01 (Vitis vinifera), 3'ss of exon 10
gtaaaactctagctgttagtgtttggacatgtaatgtgcatttgatttgatacaaggctaaatgttcacaactaacatacatagtacacgattgatttgcacagcatttgtttattccat-agctattttg--ggctttggctcttggaaaacctaaacatatacacttttctttttgcagGTGATAGAAGCCCAACCTGACATGCCAGTTGTTGGAGCCATAACTCTATATGTATCACTTCTGACCTTTACTCTCCGTGTACATCCTGATCGGCTTGATT
                                                                             | | |         |  ||||   |   |   |||| | | || || ||| |    ||  |    |    |||||  |||  |  ||  || ||| ||   ||||| || ||||| ||   |||||||||  || |||||||  |||||||||||  ||| ||||| || |||||||| | ||| || ||||||||||||||||
-----------------------------------------------------------------------------ttcttccctttatgtctatttcttcgttacacgtttgtgcaattaggtatataaatggactaaagtaggagaaaatgtaa-tacttaatctgttcatt---cagGTCATCGAAGCACAGGTTGACATGCCTATTTTTGGAGCTGTAACTCTATATTCATCTCTTCTCACTTTTACTCTGCATGTGCACCCTGATCGGCTTGATT

upper sequence: GRMZM5G844195_T02 (Zea mays), 3'ss of exon 11
lower sequence: Vv18s0001g14680.t01 (Vitis vinifera), 3'ss of exon 10
gtaaaactctagctgttagtgtttggacatgtaatgtgcatttgatttgatacaaggctaaatgttcacaactaacatacatagtacacgattgatttgcacagca--tttgtttattccatagctattttgggctttggctcttggaaaacctaaacatatacacttttctttttgcagGTGATAGAAGCCCAACCTGACATGCCAGTTGTTGGAGCCATAACTCTATATGTATCACTTCTGACCTTTACTCTCCGTGTACATCCTGATCGGCTTGATT
                                                                             |     ||| | |  ||   |  |||     ||| || |||    |  |   || |  ||       |    ||  | |   | || | |||  | |   |||||||||||||| ||   ||||||||| ||| ||||||| |||||| ||||||| || ||||| || |||||||| ||||| |||||||||||||||||||
-----------------------------------------------------------------------------ttttctgtatatgtatgtccttaacaatgactttcttaatttagaatatggatttgttttcactaagtattgaagttcattgtttataatttaatgt---cagGTGATAGAAGCACAGGTTGACATGCCTGTTTTTGGAGCAATAACTTTATATGTCTCTCTTCTTACATTTACTCTTCGTGTTCATCCTGATCGGCTTGATT

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|19058370|gb|BM737037.1|BM737037
EST:     AGTTCTTGCAAGTTGAAGCTTTTGCTAAGTTCAGTAATGCTATTGGAAAG                         GTGATAGAAGCCCAACCTGACATGCCAGTTGTTGGAGCCATAACTCTATAT
genomic: AGTTCTTGCAAGTTGAAGCTTTTGCTAAGTTCAGTAATGCTATTGGAAAGgtaaaactct ... ctttttgcagGTGATAGAAGCCCAACCTGACATGCCAGTTGTTGGAGCCATAACTCTATAT
EST: gi|18963630|gb|BM660543.1|BM660543
EST:     AGTTCTTGCAAGTTGAAGCTTTTGCTAAGTTCAGTAATGCTATTGGAAAG                         GTGATAGAAGCCCAACCTGACATGCCAGTTGTTGGAGCCATAACTCTATAT
genomic: AGTTCTTGCAAGTTGAAGCTTTTGCTAAGTTCAGTAATGCTATTGGAAAGgtaaaactct ... ctttttgcagGTGATAGAAGCCCAACCTGACATGCCAGTTGTTGGAGCCATAACTCTATAT
EST: gi|19058197|gb|BM736864.1|BM736864
EST:     AGTTCTTGCAAGGTGAAGCTTTTGCTAAGTTCAGTAATGCTATTGGAAAG                         GTGATAGAAGCCCAACCTGACATGCCAGTTGTTGGAGCCATAACTCTATAT
genomic: AGTTCTTGCAAGTTGAAGCTTTTGCTAAGTTCAGTAATGCTATTGGAAAGgtaaaactct ... ctttttgcagGTGATAGAAGCCCAACCTGACATGCCAGTTGTTGGAGCCATAACTCTATAT
EST: gi|18963632|gb|BM660544.1|BM660544
EST:     AGTTCTTGCAAGTTGAAGCTTTTGCTAAGTTCAGTAATGCTATTGGAAAG                         GTGATAGAAGCCCAACCTGACATGCCAGTTGTTGGAGCCATAACTCTATAT
genomic: AGTTCTTGCAAGTTGAAGCTTTTGCTAAGTTCAGTAATGCTATTGGAAAGgtaaaactct ... ctttttgcagGTGATAGAAGCCCAACCTGACATGCCAGTTGTTGGAGCCATAACTCTATAT
EST: gi|19057727|gb|BM736394.1|BM736394
EST:     AGTTCTTGCAAGTTGAAGCTTTTGCTAAGTTCAGTAATGCTATTGGAAAG                         GTGATAGAAGCCCAACCTGACATGCCAGTTGTTGGAGCCATAACTCTATAT
genomic: AGTTCTTGCAAGTTGAAGCTTTTGCTAAGTTCAGTAATGCTATTGGAAAGgtaaaactct ... ctttttgcagGTGATAGAAGCCCAACCTGACATGCCAGTTGTTGGAGCCATAACTCTATAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tattttgggctttggctcttggaaaacctaaacatatacacttttctttttgcagGTGATAGAAGCCCAACCTGACATGCCAGTTGTTGGAGCCATAACTCTATATGTATCACTTCTGACCTTTACTCTCCGTGTACATCCTGATCGGCTTGATT
                         acctaaa  putative branch site (score: 3)
                                    tacacttttcttttt  putative PPT
                            taaacatata  TA-rich tract