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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_T02
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|211542545|gb|FL409073.1|FL409073
EST:     CGCAGCTTGCTCGGAAGATCCCTGATACACTGTTCGGGATCTTCTTTGAG                         G
genomic: CGCAGCTTGCTCGGAAGATCCCTGATACACTGTTCGGGATCTTCTTTGAGgtgagacagt ... actgcaggag-
EST: gi|211542545|gb|FL409073.1|FL409073
EST:     CGCAGCTTGCTCGGAAGATCCCTGATACACTGTTCGGGATCTTCTTTGAG                         G
genomic: CGCAGCTTGCTCGGAAGATCCCTGATACACTGTTCGGGATCTTCTTTGAGgtgagacagt ... actgcaggag-
EST: gi|71769116|gb|DR967053.1|DR967053
EST:     CGCAGCTTGCTCGGAAGATCCCTGATACACTGTTCGGGATCTTCTTTGAGGAG                       
genomic: CGCAGCTTGCTCGGAAGATCCCTGATACACTGTTCGGGATCTTCTTT---GAGgtgagacagt ... actgcagg
EST: gi|6194981|gb|AW147085.1|AW147085
EST:     CGCAGCTTGCTCGGAAGATCCCTGATACACTGTTCGGGATCTTCTTTGAG                         G
genomic: CGCAGCTTGCTCGGAAGATCCCTGATACACTGTTCGGGATCTTCTTTGAGgtgagacagt ... actgcaggag-
EST: gi|6194981|gb|AW147085.1|AW147085
EST:     CGCAGCTTGCTCGGAAGATCCCTGATACACTGTTCGGGATCTTCTTTGAG                         G
genomic: CGCAGCTTGCTCGGAAGATCCCTGATACACTGTTCGGGATCTTCTTTGAGgtgagacagt ... actgcaggag-
EST: gi|211106638|gb|FL406855.1|FL406855
EST:     CGCAGCTTGCTCGGAAGATCCCTGATACACTGTTCGGGATCTTCTTTGAG                         G
genomic: CGCAGCTTGCTCGGAAGATCCCTGATACACTGTTCGGGATCTTCTTTGAGgtgagacagt ... actgcaggag-
EST: gi|211106638|gb|FL406855.1|FL406855
EST:     CGCAGCTTGCTCGGAAGATCCCTGATACACTGTTCGGGATCTTCTTTGAG                         G
genomic: CGCAGCTTGCTCGGAAGATCCCTGATACACTGTTCGGGATCTTCTTTGAGgtgagacagt ... actgcaggag-
EST: gi|211148949|gb|FL408684.1|FL408684
EST:     CGCAGCTTGCTCGGAAGATCCCTGATACACTGTTCGGGATCTTCTTTGAG                         G
genomic: CGCAGCTTGCTCGGAAGATCCCTGATACACTGTTCGGGATCTTCTTTGAGgtgagacagt ... actgcaggag-
EST: gi|211148949|gb|FL408684.1|FL408684
EST:     CGCAGCTTGCTCGGAAGATCCCTGATACACTGTTCGGGATCTTCTTTGAG                         G
genomic: CGCAGCTTGCTCGGAAGATCCCTGATACACTGTTCGGGATCTTCTTTGAGgtgagacagt ... actgcaggag-
EST: gi|71769433|gb|DR967370.1|DR967370
EST:     CGCAGCTTGCTCGGAAGATCCCTGATACACTGTTCGGGATCTTCTTTGAGGAG                       
genomic: CGCAGCTTGCTCGGAAGATCCCTGATACACTGTTCGGGATCTTCTTT---GAGgtgagacagt ... actgcagg
EST: gi|211024644|gb|FL381981.1|FL381981
EST:     CGCAGCTTGCTCGGAAGATCCCTGATACACTGTTCGGGATCTTCTTTGAG                         ATCAACCATGCAGGGGCTGGTGGCATATGGGCTGAACTTGTTAGTAACAGA
genomic: CGCAGCTTGCTCGGAAGATCCCTGATACACTGTTCGGGATCTTCTTTGAGgtgagacagt ... actgcaggagATCAACCATGCAGGGGCTGGTGGCATATGGGCTGAACTTGTTAGTAACAGA
EST: gi|211410871|gb|FL399291.1|FL399291
EST:     CGCAGCTTGCTCGGAAGATCCCTGATACACTGTTCGGGATCTTCTTTGAG                         G
genomic: CGCAGCTTGCTCGGAAGATCCCTGATACACTGTTCGGGATCTTCTTTGAGgtgagacagt ... actgcaggag-
EST: gi|211410871|gb|FL399291.1|FL399291
EST:     CGCAGCTTGCTCGGAAGATCCCTGATACACTGTTCGGGATCTTCTTTGAG                         G
genomic: CGCAGCTTGCTCGGAAGATCCCTGATACACTGTTCGGGATCTTCTTTGAGgtgagacagt ... actgcaggag-


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtccaaacacacttggtcgtgttctcagataaccaggttgctttcactgcaggagATCAACCATGCAGGGGCTGGTGGCATATGGGCTGAACTTGTTAGTAACAGAG
                          agataac  putative branch site (score: 3)
                                        ctttcact  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

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG