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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgctcacccaactttctgtgtgcttcttgtccgtgaggtttacttcatgctaatattcaataacaatttcagTTCGTTCGGCTAAATTTATTGCACGTAAGCAATGGGTTGTTGCTGGTGCCGATGATATGTTCATCCGTGTGTACAACTATAACACAATGGACAAGGTCAA

Basic information

species Zea mays
transcript GRMZM2G124886_T01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G124886_T04 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os02g11830.2 (Oryza sativa), 3'ss of exon 5
gtatgctcacccaactttctgtgtgcttcttgtccgtgaggtttact-tcatgctaatatt-caataacaatttcagTTCGTTCGGCTAAATTTATTGCACGTAAGCAATGGGTTGTTGCTGGTGCCGATGATATGTTCATCCGTGTGTACAACTATAACACAATGGACAAGGTCAA
|||||||  |||| ||    |  | |||||     ||  | | |||  || |||||||||    ||  | ||||||||||| ||  ||||||||||  |||| || |||||||| |||||||||||||| ||||||||||| ||||||||||| || || || ||||| ||||||||
gtatgctttcccacctcatcgcttacttct-----gtttgatataccatcttgctaatataatcatccccatttcagTTCGGTCATCTAAATTTATCACACGGAAACAATGGGTAGTTGCTGGTGCCGACGATATGTTCATACGTGTGTACAATTACAATACGATGGATAAGGTCAA

upper sequence: GRMZM2G124886_T04 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA07G03890.1 (Glycine max), 3'ss of exon 5
------------------------------------------gtatgctcacccaactttctgtgtgcttcttgtccgtgaggtttacttcatg---ctaatattcaataacaattt-cagTTCGTTCGGCTAAATTTATTGCACGTAAGCAATGGGTTGTTGCTGGTGCCGATGATATGTTCATCCGTGTGTACAACTATAACACAATGGACAAGGTCAA
                                          |  |  | |  ||  |   ||    | | || |   |  | | || ||||||   || |||| ||  |  | ||| ||||| | || || || ||||||||||| || || ||||||||||| || || ||||||||||| || ||||| || || || ||||||||||| || || ||
gtgggtgaacgttttatagtctatttcattggttgtgtatctgccttttgattcatttgcttgaagtcattttttttctttg-tatatttcatgggtctcatatacagcatgattttgcagTTAGGTCAGCCAAGTTTATTGCACGCAAACAGTGGGTTGTTGCAGGGGCAGATGATATGTTTATTCGTGTATATAATTACAACACAATGGATAAAGTTAA

upper sequence: GRMZM2G124886_T04 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA13G43680.2 (Glycine max), 3'ss of exon 5
--------------------------------------------------------------gtatgctcacccaactttctgtgtgcttcttg--tccgt-----gaggtttacttcatgctaatattcaataacaattt-cagTTCGTTCGGCTAAATTTATTGCACGTAAGCAATGGGTTGTTGCTGGTGCCGATGATATGTTCATCCGTGTGTACAACTATAACACAATGGACAAGGTCAA
                                                              |  ||   || |   | | ||| |  ||| ||  | | |     || |   |||  | |||  ||| ||| |  | ||| ||||| | ||||| || ||||||||||| || || |||||||||||||| || ||||||||||| || ||||| || || || ||||||||||| || |||||
gtacatgaagtcatgaaccttttctggtccatttgtttgtctatatatctcttgatgcatttgcttgaagacacttttctttgtatatttcatgatttcttacttagaagaccactg-aagctcttatacaacatgattttgcagTTAGATCGGCCAAGTTTATTGCACGCAAACAGTGGGTTGTTGCTGGAGCAGATGATATGTTTATTCGTGTATATAATTACAACACAATGGATAAAGTCAA

upper sequence: GRMZM2G124886_T04 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA08G22140.1 (Glycine max), 3'ss of exon 5
----------------------------------gtatgctcacccaactttctgtgtgcttcttgtccgtgaggtt-------tacttcatg----ctaatattcaataacaattt-cagTTCGTTCGGCTAAATTTATTGCACGTAAGCAATGGGTTGTTGCTGGTGCCGATGATATGTTCATCCGTGTGTACAACTATAACACAATGGACAAGGTCAA
                                  ||||     ||      |   | |||||  ||||  |    ||       || ||||||    || |||| ||  |  | ||| ||||| | || || || ||||||||||| || || ||||||||||| || || ||||||||||| || ||||| || || || ||||||||||| || || ||
gtgggtggacgttttttagtctatttcattgatcgtatatctgcctcttgattcatttgcttgatgtcattttctttctttatatatttcatggggtctcatatgcagcatgattttgcagTTAGGTCAGCCAAGTTTATTGCACGCAAACAGTGGGTTGTTGCAGGGGCAGATGATATGTTTATTCGTGTATATAATTACAACACAATGGATAAAGTTAA

upper sequence: GRMZM2G124886_T04 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA15G01680.1 (Glycine max), 3'ss of exon 5
------------------------------------------------------------------gtatgctcacccaactttctgtgt-----gcttcttgtccgtgaggtttact-------tcatgctaatattcaataacaattt-cagTTCGTTCGGCTAAATTTATTGCACGTAAGCAATGGGTTGTTGCTGGTGCCGATGATATGTTCATCCGTGTGTACAACTATAACACAATGGACAAGGTCAA
                                                                  | |  | |||    |||| | | |     | ||  |  |   || | | |||       | || | | ||| ||| |  | ||| ||||| | ||||| || ||||||||||| || || |||||||||||||| || ||||||||||| |||||||| || || || ||||||||||| || |||||
gtacttgaagacgtgaaccttttttggtccatttgtttgtatatctacctcttgatgcatttgcttgaagacacacttttctttgtatatttcatgatttcttacttagaagatcactggagctcttatacaagtatacaacatgattttgcagTTAGATCGGCCAAGTTTATTGCACGCAAACAGTGGGTTGTTGCTGGAGCAGATGATATGTTTATCCGTGTATATAATTACAACACAATGGATAAAGTCAA

upper sequence: GRMZM2G124886_T04 (Zea mays), 3'ss of exon 5
lower sequence: AT1G52360.1 (Arabidopsis thaliana), 3'ss of exon 5
-------------------------------gtatgctcacccaactttc----tgtgtgcttcttgtccgtga--ggtttact--tcatgctaatattcaata--acaattt--cagTTCGTTCGGCTAAATTTATTGCACGTAAGCAATGGGTTGTTGCTGGTGCCGATGATATGTTCATCCGTGTGTACAACTATAACACAATGGACAAGGTCAA
                                |||  |   | |  |||     | ||| ||   |   ||||    ||||  |  | || ||  | ||  |||  |  | ||  ||||||| || || || ||| | ||||| |||||||||||||| || || || ||||||||||  |||||||| ||||| || ||||| ||||||||||| ||
gtatacggcttttgttcttttgtgtcttttgttatattgttcaagtttttgttgtatgtactaagtactcgtgtctagtttgttacttattctgcttttttatattatgactttgcagTTCGGTCAGCCAAGTTTGTAGCACGAAAGCAATGGGTTGTCGCAGGAGCTGATGATATGTATATCCGTGTATACAATTACAACACCATGGACAAGGTTAA

upper sequence: GRMZM2G124886_T04 (Zea mays), 3'ss of exon 5
lower sequence: AT3G15980.2 (Arabidopsis thaliana), 3'ss of exon 5
------------------------------------gtatgctcacccaactttctgtgtgcttcttgtccgtgaggtttacttcatgctaatattcaataacaattt--cagTTCGTTCGGCTAAATTTATTGCACGTAAGCAATGGGTTGTTGCTGGTGCCGATGATATGTTCATCCGTGTGTACAACTATAACACAATGGACAAGGTCAA
                                     |||         |||| |||| |  | | | |   |    | |   |  | || | ||| |   |  | ||  ||||| | ||||| || |||||| | || |||||||||||||| ||||| || |||||||||| ||||||||| ||||| || || |||||||||||||||||
gtataacaagtttatgagcatcttctgatttcattgttatagatttttcacttgctgtatattgcct-tgtatagtctgtcgctgttactgaaatttatatatgactttgcagTTAGGTCGGCCAAGTTTATTCCGCGCAAGCAATGGGTTGTGGCTGGAGCGGATGATATGTACATCCGTGTATACAATTACAATACAATGGACAAGGTCAA

upper sequence: GRMZM2G124886_T04 (Zea mays), 3'ss of exon 5
lower sequence: Vv09s0002g04810.t01 (Vitis vinifera), 3'ss of exon 5
----------------------------------------------------gtatgctcacccaacttt---ctgtgtgcttcttgtccgtgaggtttacttcatgct--aatattcaataacaatttcagTTCGTTCGGCTAAATTTATTGCACGTAAGCAATGGGTTGTTGCTGGTGCCGATGATATGTTCATCCGTGTGTACAACTATAACACAATGGACAAGGTCAA
                                                     |    | | |||  |||   |  | |   |||| |  || ||||| | | |||| |  ||| ||  || |  ||| ||||| | || || || ||||| ||||| |||||||||||||||||||| || ||||||||||| || ||||| ||||| |||||||||||||| ||||| ||
gtatgtacatgtactttatctgtttccatatgctctatttggtgtgattgaattcccttgatccatttttactcaatttctctcttattggtaaggtt-attacatgtttcaattttacattatcattgcagTTAGGTCAGCGAAGTTTATAGCACGCAAGCAATGGGTTGTTGCTGGAGCTGATGATATGTTTATTCGTGTATACAATTATAACACAATGGATAAGGTTAA

upper sequence: GRMZM2G124886_T04 (Zea mays), 3'ss of exon 5
lower sequence: PP1S79_180V6.1 (Physcomitrella patens), 3'ss of exon 5
-------------------------------------------------------------------------------------gtatgctcacc-caactttctgtgtgc-----ttcttgtccgtgaggt--ttacttca---tgctaa--------tattcaataacaatttc---agTTCGTTCGGCTAAATTTATTGCACGTAAGCAATGGGTTGTTGCTGGTGCCGATGATATGTTCATCCGTGTGTACAACTATAACACAATGGACAAGGTCAA
                                                                                       |  | ||   || ||||||||||       ||||      |||     | |||| |   |||| |         ||    |     ||||   ||| || || || || |||||  | |||||||| |||||||| ||| |  | ||||| ||||||||||| ||||| ||||||||||| |||||||| || ||
gtacgttgtttgagaccatgtttatccgtccgttccatggttcagctgtcattgtagtagtcactcgcgagttttattacagtcgtcactcacagtgcatctttctgtgtttagctgttctctattttgaaaccatcacttgaaagtgctgagaggagttcatctcgttctgttttctgcagTGCGATCAGCGAAGTTTATCCCCCGTAAGCAGTGGGTTGTGGCTTGCTCTGATGACATGTTCATCCGAGTGTATAACTATAACACGATGGACAAAGTGAA

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|32825347|gb|CD965069.1|CD965069
EST:     ACAATGGTGAAATCATTTGAAGTCACGGATTTACCAG                         TTCGTTCGGCTAAATTTATTGCACGTAAGCAATGGGTTGTTGCTGGTGCCG
genomic: ACAATGGTGAAATCATTTGAAGTCACGGATTTACCAGgtatgctcac ... acaatttcagTTCGTTCGGCTAAATTTATTGCACGTAAGCAATGGGTTGTTGCTGGTGCCG
EST: gi|78107583|gb|DV526001.1|DV526001
EST:     ACAATGGTGAAATCATTTGAAGTCACAGATTTACCAG                         TTCGTTCGGCTAAATTTATTGCACGTAAGCAATGGGTTGTTGCTGGTGCCG
genomic: ACAATGGTGAAATCATTTGAAGTCACGGATTTACCAGgtatgctcac ... acaatttcagTTCGTTCGGCTAAATTTATTGCACGTAAGCAATGGGTTGTTGCTGGTGCCG
EST: gi|50325003|gb|CO520129.1|CO520129
EST:     ATCATTTGAAGTCACGGGATTTACCAG                         TTCGTTCGGCTAAATTTTATTGCACGTAAGCAATGGGTTGTTGCTGGTGCC
genomic: ATCATTTGAAGTCAC-GGATTTACCAGgtatgctcac ... acaatttcagTTCGTTCGGCTAAA-TTTATTGCACGTAAGCAATGGGTTGTTGCTGGTGCC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtgtgcttcttgtccgtgaggtttacttcatgctaatattcaataacaatttcagTTCGTTCGGCTAAATTTATTGCACGTAAGCAATGGGTTGTTGCTGGTGCCGATGATATGTTCATCCGTGTGTACAACTATAACACAATGGACAAGGTCAA
                                        caataac  putative branch site (score: 2)
                                 taatattcaataacaa  TA-rich tract