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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagacagtgatttcttggtacacaccagccttattgatcttacaaggatttgtccatgtaagcggaatggtccaaacacacttggtcgtgttctcagataaccaggttgctttcactgcagGAGATCAACCATGCAGGGGCTGGTGGCATATGGGCTGAACTTGTTAGTAACAGAG

Basic information

species Zea mays
transcript GRMZM2G077299_T01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G077299_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os11g03730.2 (Oryza sativa), 3'ss of exon 2
-----------------------------------------------gtgagacagtgatttct----tggtacacaccagccttattgatc--ttacaaggatttgtccatg-taagcggaatggtccaaacacacttggtcgtgttctca-gataaccaggttg-ctttcactgcagGAGATCAACCATGCAGGGGCTGGTGGCATATGGGCTGAACTTGTTAGTAACAGAG
                                               ||   ||  |    | |    ||| ||      |      || ||   | ||      || |||   ||| |    | |   | |||   |    | ||| || | |||||  |  ||| ||   | || |||| ||||||||||||||||||||||| ||||||||||||||||||||||||||||
gtaagccgtgagacatatacagtaattctgtttttcacaattgcactgtatcactatatcctttcctctggcacttttttgttaggatgctcaagtgcattagcatgcccagaataatccaggtagattatacatgttccaccatgtcctgatgataatgatcttggctaatattgtagGAAATCAACCATGCAGGGGCTGGTGGAATATGGGCTGAACTTGTTAGTAACAGAG

upper sequence: GRMZM2G077299_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os12g03470.5 (Oryza sativa), 3'ss of exon 2
------------gtg-agacagtgatttcttggtacacaccagccttat-------tgatcttac----aaggatttgtccatgtaagcggaatggtccaa-------acacacttggtcgtgttctca-gataaccaggttgctttcactgcagGAGATCAACCATGCAGGGGCTGGTGGCATATGGGCTGAACTTGTTAGTAACAGAG
             |  | | ||| ||||  |  | ||||   || ||||       ||  ||| |         |||||     |     ||||    ||        |||   ||     ||| || | |  ||     | |||   | || |||| |||||||||||||| |||||||| ||||||||||||||||||||||||||||
gtaaaccgtaagatacatatagtaattttgttttgcacaattgcattatatcactttgtcctttcctctggcactttgttagcatgtctagaataagtcaggtagactacatgtttcactatgtcctgatggcaatttcttggctaatattgtagGAAATCAACCATGCAGGAGCTGGTGGAATATGGGCTGAACTTGTTAGTAACAGAG

upper sequence: GRMZM2G077299_T01 (Zea mays), 3'ss of exon 2
lower sequence: AT3G10740.1 (Arabidopsis thaliana), 3'ss of exon 2
gtgagacagtgatttcttggtacacaccagccttattgatcttacaaggatttgtcca-tgtaagcggaatggtccaaacacacttggtcgtgttctcagataaccaggttgctttcactgcagGAGATCAACCATGCAGGGGCTGGTGGCATATGGGCTGAACTTGTTAGTAACAGAG
                            |   |||  | ||| | |  ||| | | || |||| ||    || || || ||  | |   |      | | ||   |    |   |||| |  |||||||||||||||| || || |||||  ||||||| ||||||||||| |||||||
---------------------gtttgttaatgttac-ggtctcaaatagatctttgcaatgtacgcaatgtgttcaaatcaatcataaac-----tttatatgctc----tatgttcattatagGAGATCAACCATGCTGGTGCCGGTGGATTATGGGCCGAACTTGTTAGCAACAGAG

upper sequence: GRMZM2G077299_T01 (Zea mays), 3'ss of exon 2
lower sequence: Vv08s0040g00320.t01 (Vitis vinifera), 3'ss of exon 3
gtgagacagtgatttcttggtacacaccagccttattgatcttacaaggatttgtccatgtaagcggaatggtccaaacacacttggtcgtgttctcagataaccaggttgctttcactgcagGAGATCAACCATGCAGGGGCTGGTGGCATATGGGCTGAACTTGTTAGTAACAGAG
| |       || ||||  | |   | ||   ||| ||    |  ||    ||||  || |        || |    | | | |  |   ||||   |           ||  ||   || ||||||||||||||||||| ||||||||  | ||||| || ||||| || |||||||
gggttgtttcgaattctgagcaattagcaat-ttactgccactgtaa----ttgtgtatatgt------tgattttga-agattgagctttgtttgaaa----------tgtctttg-tgtagGAGATCAACCATGCAGGAGCTGGTGGACTGTGGGCAGAGCTTGTCAGCAACAGAG

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|71769116|gb|DR967053.1|DR967053
EST:     CGCAGCTTGCTCGGAAGATCCCTGATACACTGTTCGGGATCTTCTTTGAG                         GAGATCAACCATGCAGGGGCTGGTGGCATATGGGCTGAACTTGTTAGTAAC
genomic: CGCAGCTTGCTCGGAAGATCCCTGATACACTGTTCGGGATCTTCTTTGAGgtgagacagt ... ttcactgcagGAGATCAACCATGCAGGGGCTGGTGGCATATGGGCTGAACTTGTTAGTAAC
EST: gi|211315178|gb|FL384852.1|FL384852
EST:     CGCAGCTTGCTCGGAAGATCCCTGATACACTGTTCGGGATCTTCTTTGAG                         GAGATCAACCATGCAGGGGCTGGTGGCATATGGGCTGAACTTGTTAGTAAC
genomic: CGCAGCTTGCTCGGAAGATCCCTGATACACTGTTCGGGATCTTCTTTGAGgtgagacagt ... ttcactgcagGAGATCAACCATGCAGGGGCTGGTGGCATATGGGCTGAACTTGTTAGTAAC
EST: gi|211106638|gb|FL406855.1|FL406855
EST:     CGCAGCTTGCTCGGAAGATCCCTGATACACTGTTCGGGATCTTCTTTGAG                         GAGATCAACCATGCAGGGGCTGGTGGCATATGGGCTGAACTTGTTAGTAAC
genomic: CGCAGCTTGCTCGGAAGATCCCTGATACACTGTTCGGGATCTTCTTTGAGgtgagacagt ... ttcactgcagGAGATCAACCATGCAGGGGCTGGTGGCATATGGGCTGAACTTGTTAGTAAC
EST: gi|6194987|gb|AW147091.1|AW147091
EST:     CGCAGCTTGCTCGGAAGATCCCTGATACACTGTTCGGGATCTTCTTTGAG                         GAGATCAACCATGCAGGGGCTGGTGGCATATGGGCTGAACTTGTTAGTAAC
genomic: CGCAGCTTGCTCGGAAGATCCCTGATACACTGTTCGGGATCTTCTTTGAGgtgagacagt ... ttcactgcagGAGATCAACCATGCAGGGGCTGGTGGCATATGGGCTGAACTTGTTAGTAAC
EST: gi|211024644|gb|FL381981.1|FL381981
EST:     CGCAGCTTGCTCGGAAGATCCCTGATACACTGTTCGGGATCTTCTTTGAG                         -A--TCAACCATGCAGGGGCTGGTGGCATATGGGCTGAACTTGTTAGTAAC
genomic: CGCAGCTTGCTCGGAAGATCCCTGATACACTGTTCGGGATCTTCTTTGAGgtgagacagt ... ttcactgcagGAGATCAACCATGCAGGGGCTGGTGGCATATGGGCTGAACTTGTTAGTAAC
EST: gi|211518127|gb|FL378400.1|FL378400
EST:     CGCAGCTTGCTCGGAAGATCCCTGATACACTGTTCGGGATCTTCTTTGAG                         GAGATCAACCATGCAGGGGCTGGTGGCATATGGGCTGAACTTGTTAGTAAC
genomic: CGCAGCTTGCTCGGAAGATCCCTGATACACTGTTCGGGATCTTCTTTGAGgtgagacagt ... ttcactgcagGAGATCAACCATGCAGGGGCTGGTGGCATATGGGCTGAACTTGTTAGTAAC
EST: gi|71769433|gb|DR967370.1|DR967370
EST:     CGCAGCTTGCTCGGAAGATCCCTGATACACTGTTCGGGATCTTCTTTGAG                         GAGATCAACCATGCAGGGGCTGGTGGCATATGGGCTGAACTTGTTAGTAAC
genomic: CGCAGCTTGCTCGGAAGATCCCTGATACACTGTTCGGGATCTTCTTTGAGgtgagacagt ... ttcactgcagGAGATCAACCATGCAGGGGCTGGTGGCATATGGGCTGAACTTGTTAGTAAC
EST: gi|211410871|gb|FL399291.1|FL399291
EST:     CGCAGCTTGCTCGGAAGATCCCTGATACACTGTTCGGGATCTTCTTTGAG                         GAGATCAACCATGCAGGGGCTGGTGGCATATGGGCTGAACTTGTTAGTAAC
genomic: CGCAGCTTGCTCGGAAGATCCCTGATACACTGTTCGGGATCTTCTTTGAGgtgagacagt ... ttcactgcagGAGATCAACCATGCAGGGGCTGGTGGCATATGGGCTGAACTTGTTAGTAAC
EST: gi|6194981|gb|AW147085.1|AW147085
EST:     CGCAGCTTGCTCGGAAGATCCCTGATACACTGTTCGGGATCTTCTTTGAG                         GAGATCAACCATGCAGGGGCTGGTGGCATATGGGCTGAACTTGTTAGTAAC
genomic: CGCAGCTTGCTCGGAAGATCCCTGATACACTGTTCGGGATCTTCTTTGAGgtgagacagt ... ttcactgcagGAGATCAACCATGCAGGGGCTGGTGGCATATGGGCTGAACTTGTTAGTAAC
EST: gi|101399286|gb|EB821516.1|EB821516
EST:     CGCAGCTTGCTCGGAAGATCCCTGATACACTGTTCGGGATCTTCTTTGAG                         GAGATCAACCATGCAGGGGCTGGTGGCATATGGGCTGAACTTGTTAGTAAC
genomic: CGCAGCTTGCTCGGAAGATCCCTGATACACTGTTCGGGATCTTCTTTGAGgtgagacagt ... ttcactgcagGAGATCAACCATGCAGGGGCTGGTGGCATATGGGCTGAACTTGTTAGTAAC
EST: gi|211542545|gb|FL409073.1|FL409073
EST:     CGCAGCTTGCTCGGAAGATCCCTGATACACTGTTCGGGATCTTCTTTGAG                         GAGATCAACCATGCAGGGGCTGGTGGCATATGGGCTGAACTTGTTAGTAAC
genomic: CGCAGCTTGCTCGGAAGATCCCTGATACACTGTTCGGGATCTTCTTTGAGgtgagacagt ... ttcactgcagGAGATCAACCATGCAGGGGCTGGTGGCATATGGGCTGAACTTGTTAGTAAC
EST: gi|74232033|gb|DT639947.1|DT639947
EST:     CGCAGCTTGCTCGGAAGATCCCTGATACACTGTTCGGGATCTTCTTTGAG                         GAGATCACCCATGCAGGGGCTGGTGGCATATGGGCTGAACTTGTTAGTAAC
genomic: CGCAGCTTGCTCGGAAGATCCCTGATACACTGTTCGGGATCTTCTTTGAGgtgagacagt ... ttcactgcagGAGATCAACCATGCAGGGGCTGGTGGCATATGGGCTGAACTTGTTAGTAAC
EST: gi|211152046|gb|FL419672.1|FL419672
EST:     CGCAGCTTGCTCGGAAGATCCCTGATACACTGTTCGGGATCTTCTTTGAG                         GAGATCAACCATGCAGGGGCTGGTGGCATATGGGCTGAACTTGTTAGTAAC
genomic: CGCAGCTTGCTCGGAAGATCCCTGATACACTGTTCGGGATCTTCTTTGAGgtgagacagt ... ttcactgcagGAGATCAACCATGCAGGGGCTGGTGGCATATGGGCTGAACTTGTTAGTAAC
EST: gi|211148949|gb|FL408684.1|FL408684
EST:     CGCAGCTTGCTCGGAAGATCCCTGATACACTGTTCGGGATCTTCTTTGAG                         GAGATCAACCATGCAGGGGCTGGTGGCATATGGGCTGAACTTGTTAGTAAC
genomic: CGCAGCTTGCTCGGAAGATCCCTGATACACTGTTCGGGATCTTCTTTGAGgtgagacagt ... ttcactgcagGAGATCAACCATGCAGGGGCTGGTGGCATATGGGCTGAACTTGTTAGTAAC
EST: gi|211464409|gb|FL419840.1|FL419840
EST:     CGCAGCTTGCTCGGAAGATCCCTGATACACTGTTCGGGATCTTCTTTGAG                         GAGATCAACCATGCAGGGGCTGGTGGCATATNGGCTGAACTTGTTAGTAAC
genomic: CGCAGCTTGCTCGGAAGATCCCTGATACACTGTTCGGGATCTTCTTTGAGgtgagacagt ... ttcactgcagGAGATCAACCATGCAGGGGCTGGTGGCATATGGGCTGAACTTGTTAGTAAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atggtccaaacacacttggtcgtgttctcagataaccaggttgctttcactgcagGAGATCAACCATGCAGGGGCTGGTGGCATATGGGCTGAACTTGTTAGTAACAGAG
                             agataac  putative branch site (score: 3)
                                        ttgctttc  putative PPT
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagacagtgatttcttggtacacaccagccttattgatcttacaaggatttgtccatgtaagcggaatggtccaaacacacttggtcgtgttctcagataaccaggttgctttcactgcagGAGATCAACCATGCAGGGGCTGGTGGCATATGGGCTGAACTTGTTAGTAACAGAG

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