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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aatgcttggtatgtgaagggttacagtttcaccatttacccactgatgctatatctatttaggtttccttgttgacttataatctcaatttccatgatagGACTGCTTTGGCCGGCCGATTGCTAGTGCACCAGATGCTTGGTTCGATGTGGTTGAGCGCTACTCAAATGACTGCAACAAGACACTCCA

Basic information

species Zea mays
transcript GRMZM2G010202_T02
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G010202_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os01g70380.1 (Oryza sativa), 3'ss of exon 2
aatgcttggtatgtgaagggttacagtttcaccatttacccactgatgctatatctatttaggtttccttgttgactt-ataatctcaatttccatgatagGACTGCTTTGGCCGGCCGATTGCTAGTGCACCAGATGCTTGGTTCGATGTGGTTGAGCGCTACTCAAATGACTGCAACAAGACACTCCA
| ||  | ||| ||  |  | |  |  |  |  ||  |   | | ||  |   | | |||  || || || |||||||  |  | ||||||  || |  ||||||| ||||||||||| |||||||| ||||||||||||||||| || ||||||||||| |||||||||||| | ||||||||||| ||
actgtatcgtaagttcactgcttaaactctagaatg-atgtattaatcttccttttgtttgtgtgtcgttattgactttgtgctgtcaattatcacggcagGACTGTTTTGGCCGGCCAATTGCTAGCGCACCAGATGCTTGGTTTGACGTGGTTGAGCGTTACTCAAATGACAGTAACAAGACACTGCA

upper sequence: GRMZM2G010202_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os01g70370.1 (Oryza sativa), 3'ss of exon 2
aatgcttgg-tatgtgaagggttacagtttcaccatttacccactgatgctatatctatttaggtttccttgttgacttataatctcaatttccatgatagGACTGCTTTGGCCGGCCGATTGCTAGTGCACCAGATGCTTGGTTCGATGTGGTTGAGCGCTACTCAAATGACTGCAACAAGACACTCCA
 ||  || | ||| |  |   ||| | | | |    ||       |||      | || || | ||   ||  | |  ||||       | ||      ||||||||||| | || || || || ||    || || || ||||||||||||||||||||||||||||||||| ||||||||||||||||
-ataattagctatttagacttttaaattattagatgttttattgagatttgtgttttaattggcttatgtttatcaactatatatatgttgtcacatgcagGACTGCTTTTGGCGACCAATAGCCAGCAAGCCGGACGCATGGTTCGATGTGGTTGAGCGCTACTCAAATGACAGCAACAAGACACTCCA

upper sequence: GRMZM2G010202_T01 (Zea mays), 3'ss of exon 2
lower sequence: AT5G23670.1 (Arabidopsis thaliana), 3'ss of exon 2
---------------------------------------------aatgcttggtatgtgaagggttacag--tttcaccatt-tacccactgatgctatatctatttag-gtttccttgttgacttataatctcaatttccatgat------agGACTGCTTTGGCCGGCCGATTGCTAGTGCACCAGATGCTTGGTTCGATGTGGTTGAGCGCTACTCAAATGACTGCAACAAGACACTCCA
                                              ||  |||| || || ||   | ||   ||| | | || |      |     |||   | | | | |||| ||  ||||    |||| |  || ||| |  |      |||| || ||||  || || ||  | |||||||| ||||||||||| |||||||||||||||||||| ||||||  ||||||||| ||  |
gtaaattcattatcaaatctatgattctgttaacaaaatcgaattgattattggcat-tgtagttatgcaagctttaagcgttgtgaatgtttggcttatgagtttctcgtgtttactgcttgatgactaatgtttatctccgttttgcttcaagGATTGTTTTGAACGACCTATATCGAGTGCACCTGATGCTTGGTTTGATGTGGTTGAGCGCTACTCTAATGACAACAACAAGACGCTTAA

upper sequence: GRMZM2G010202_T01 (Zea mays), 3'ss of exon 2
lower sequence: Vv17s0000g00500.t01 (Vitis vinifera), 3'ss of exon 2
aatgcttggtatgtgaagggtta--cagtttcaccatttacccactg-atgctatatctatttaggtttccttgttgacttataatctcaatttccatga-----tagGACTGCTTTGGCCGGCCGATTGCTAGTGCACCAGATGCTTGGTTCGATGTGGTTGAGCGCTACTCAAATGACTGCAACAAGACACTCCA
     || || | |||  | | |     | |    ||| | |   || ||| |  | |   | |  |||      | ||| ||| ||   || |  ||||      ||||||| ||||||||||| ||  | ||||| |||||||||||||| ||||| |||||  | | ||| ||||||   |||||||||||  |
---ttttcgtgtttgactgctaaattgatgttttgattgatcggatgcatgattcagcagctcaaatttg-----taactaatattccatatgttgatgaatatccagGACTGTTTTGGCCGGCCAATATCGAGTGCTCCAGATGCTTGGTTTGATGTAGTTGAAAGGTTCTCCAATGACAATAACAAGACACTAAA

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|19821837|gb|BQ047861.1|BQ047861
EST:     GCTTGGGACTCGAGGATTTCTACACGCGACGCCTCTACCTCCGCATCCAG                         GACTGCTTTGGCCGGCCGATTGCTAGTGCACCAGATGCTTGGTTCGATGTG
genomic: GCTTGGGACTCGAGGATTTCTACACGCGACGCCTCTACCTCCGCATCCAGgtgaggcgac ... tccatgatagGACTGCTTTGGCCGGCCGATTGCTAGTGCACCAGATGCTTGGTTCGATGTG
EST: gi|87151662|gb|DY396451.1|DY396451
EST:     GCTTGGGACTCGAGGATTTCTACACGCGACGCCTCTACCTCCGCATCCAG                         GACTGCTTTGGCCGGCCGATTGCTAGTGCACCAGATGCTTGGTTCGATGTG
genomic: GCTTGGGACTCGAGGATTTCTACACGCGACGCCTCTACCTCCGCATCCAGgtgaggcgac ... tccatgatagGACTGCTTTGGCCGGCCGATTGCTAGTGCACCAGATGCTTGGTTCGATGTG
EST: gi|18964841|gb|BM661241.1|BM661241
EST:     GCTTGGGACTCGAGGATTTCTACACGCGACGCCTCTACCTCCGCATCCAG                         GACTGCTTTGGCCGGCCGATTGCTAGTGCACCAGATGCTTGGTTCGATGTG
genomic: GCTTGGGACTCGAGGATTTCTACACGCGACGCCTCTACCTCCGCATCCAGgtgaggcgac ... tccatgatagGACTGCTTTGGCCGGCCGATTGCTAGTGCACCAGATGCTTGGTTCGATGTG
EST: gi|87152364|gb|DY397153.1|DY397153
EST:     GCTTGGGACTCGAGGATTTCTACACGCGACGCCTCTACCTCCGCATCCAG                         GACTGCTTTGGCCGGCCGATTGCTAGTGCACCAGATGCTTGGTTCGATGTG
genomic: GCTTGGGACTCGAGGATTTCTACACGCGACGCCTCTACCTCCGCATCCAGgtgaggcgac ... tccatgatagGACTGCTTTGGCCGGCCGATTGCTAGTGCACCAGATGCTTGGTTCGATGTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atgctatatctatttaggtttccttgttgacttataatctcaatttccatgatagGACTGCTTTGGCCGGCCGATTGCTAGTGCACCAGATGCTTGGTTCGATGTGGTTGAGCGCTACTCAAATGACTGCAACAAGACACTCCA
                        tgttgac  putative branch site (score: 3)
                                           tttccat  putative PPT
                               ttataatctcaattt  TA-rich tract