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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgttaatgggaccttggcttcatttggcatgtacaagtaccaggggatctgagttaccaaggttgtgcagGGTGAGGCGTTATTCCAGACTCACGAAAACTTGGAACATCTGGCTATGATGGAGAGAGTTCTTGGACCTTTGCCGTACCATATGCTTAAGAGGGCAGA

Basic information

species Zea mays
transcript GRMZM2G063792_T05
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G063792_T06 (Zea mays), 3'ss of exon 7
lower sequence: LOC_Os12g27520.1 (Oryza sativa), 3'ss of exon 9
gtatgttaatggg----accttggcttcatttggcat-gtacaagtaccaggggatctgagttaccaaggttgt-gcagGGTGAGGCGTTATTCCAGACTCACGAAAACTTGGAACATCTGGCTATGATGGAGAGAGTTCTTGGACCTTTGCCGTACCATATGCTTAAGAGGGCAGA
|||||||  ||||    |  || | ||  | |   ||   |  |  | ||||   | |||||||| || | |   |||||| || || || || ||||| || ||||||||||| ||||| |||||||||||||| ||  |||| |||||||| |  || ||||| || ||||||||
gtatgttgttgggtgcaatatttggtttgtattctatcacaacaacagcaggatttttgagttacgaaagctaccgcagGGAGAAGCATTGTTTCAGACCCATGAAAACTTGGAGCATCTTGCTATGATGGAGAGGGTATTTGGTCCTTTGCCATGTCACATGCTCAAAAGGGCAGA

upper sequence: GRMZM2G063792_T06 (Zea mays), 3'ss of exon 7
lower sequence: GLYMA04G36360.1 (Glycine max), 3'ss of exon 8
gtatgttaatgggaccttggcttcattt--ggcatgtacaagta--ccaggggatctgagttacc--aagg-----ttgtgcagGGTGAGGCGTTATTCCAGACTCACGAAAACTTGGAACATCTGGCTATGATGGAGAGAGTTCTTGGACCTTTGCCGTACCATATGCTTAAGAGGGCAGA
||| |||  |||  |  ||| | | |||  ||||  |  |   |     |    | | | | | |  | ||     |  |||||||||| || || || |||||||| ||||| || || |||||||||||||||||||| || ||||| ||| | ||  | || ||| | ||||| |  ||
gtaagtt--tggctctctggatactttttaggcaattttatccagttttgtttgtttaaatcagcttatgggcttctattgcagGGTGAAGCTTTGTTTCAGACTCATGAAAATTTAGAGCATCTGGCTATGATGGAGAGGGTGCTTGGTCCTATACCACAGCAGATGTTAAAGAGAGTTGA

upper sequence: GRMZM2G063792_T06 (Zea mays), 3'ss of exon 7
lower sequence: GLYMA06G18530.1 (Glycine max), 3'ss of exon 8
gtatgttaatgggaccttggcttcatttggcatgtacaagtaccag-----gggatctgagttacc----aaggttgt---gcagGGTGAGGCGTTATTCCAGACTCACGAAAACTTGGAACATCTGGCTATGATGGAGAGAGTTCTTGGACCTTTGCCGTACCATATGCTTAAGAGGGCAGA
||| |||  |||  |  ||| | | ||||   |  | |    ||||     |   | | | | | |     || || |   ||||||||| || || || |||||||| ||||| || || |||||||| ||||||||||| || ||||| ||| | ||  | || ||| | ||||| |  ||
gtaagtt--tggctctctggatacttttgaggttaatattatccagtttttgttgtttaaatcagcttatgagtttctattgcagGGTGAAGCTTTGTTTCAGACTCATGAAAATTTAGAGCATCTGGCCATGATGGAGAGGGTGCTTGGTCCTATACCACAGCAGATGTTAAAGAGAGTTGA

upper sequence: GRMZM2G063792_T06 (Zea mays), 3'ss of exon 7
lower sequence: PP1S132_58V6.1 (Physcomitrella patens), 3'ss of exon 9
------------------------------------------------------------------------------------------gtatgttaatgggaccttggcttcatttg-gcatgtacaagtaccaggggatctgagttaccaaggttgt-------------gcagGGTGAGGCGTTATTCCAGACTCACGAAAACTTGGAACATCTGGCTATGATGGAGAGAGTTCTTGGACCTTTGCCGTACCATATGCTTAAGAGGGCAGA
                                                                                          | |  |   ||    | | | ||    || | |  |      ||||  | |  ||  || |   ||||               ||||||||| || || || ||||||||||| || ||||| ||| |||||||||||||  ||||  | || ||| | ||    || ||| | |||||||||||
gtatgggattcctatcgccttcctttctcttttatattcctctattatccagtaattccctatactttctcttcaaacttgtaaatttgagaaaatctttgatgtcatagtttttcatgcgaagatgttgaaaccaatgtaaatgtttttcagtggttacagtatttgctatggcagGGTGATGCATTGTTTCAGACTCACGAGAATTTGGAGCATTTGGCTATGATGGAACGAGTCTTAGGTCCTATTCCTGTACACATGATCAAGAGGGCAGA

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|32804365|gb|CD956601.1|CD956601
EST:     ACCCATGTGATATCTGGAGTGTTGGTTGTATTCTTGTTGAGCTTTGCACG                         GGTGAGGCGTTATTCCAGACTCACGAAAACTTGGAACATCTGGCTATGATG
genomic: ACCCATGTGATATCTGGAGTGTTGGTTGTATTCTTGTTGAGCTTTGCACGgtatgttaat ... ggttgtgcagGGTGAGGCGTTATTCCAGACTCACGAAAACTTGGAACATCTGGCTATGATG
EST: gi|32845985|gb|CD985666.1|CD985666
EST:     ACCCATGTGATATCTGGAGTGTTGGTTGTATTCTTGTTGAGCTTTGCACG                         GGTGAGGCGTTATTCCAGACTCACGAAAACTTGGAACATCTGGCTATGATG
genomic: ACCCATGTGATATCTGGAGTGTTGGTTGTATTCTTGTTGAGCTTTGCACGgtatgttaat ... ggttgtgcagGGTGAGGCGTTATTCCAGACTCACGAAAACTTGGAACATCTGGCTATGATG
EST: gi|113698224|gb|DW851180.1|DW851180
EST:     GTTGGTTGTATTCTTGTTGAGCTTTGCACG                         GGTGAGGCGTTATTCCAGACTCACGAAAACTTGGAACATCTGGCTATGATG
genomic: GTTGGTTGTATTCTTGTTGAGCTTTGCACGgtatgttaat ... ggttgtgcagGGTGAGGCGTTATTCCAGACTCACGAAAACTTGGAACATCTGGCTATGATG
EST: gi|32802406|gb|CD954642.1|CD954642
EST:     ACCCATGTGATATCTGGAGTGTTGGTTGTATTCTTGTTGAGCTTTGCACG                         GGTGAGGCGTTATTCCAGACTCACGAAAACTTGGAACATCTGGCTATGATG
genomic: ACCCATGTGATATCTGGAGTGTTGGTTGTATTCTTGTTGAGCTTTGCACGgtatgttaat ... ggttgtgcagGGTGAGGCGTTATTCCAGACTCACGAAAACTTGGAACATCTGGCTATGATG
EST: gi|32804851|gb|CD957087.1|CD957087
EST:     ACCCATGTGATATCTGGAGTGTTGGTTGTATTCTTGTTGAGCTTTGCACG                         GGTGAGGCGTTATTCCAGACTCACGAAAACTTGGAACATCTGGCTATGATG
genomic: ACCCATGTGATATCTGGAGTGTTGGTTGTATTCTTGTTGAGCTTTGCACGgtatgttaat ... ggttgtgcagGGTGAGGCGTTATTCCAGACTCACGAAAACTTGGAACATCTGGCTATGATG
EST: gi|32794020|gb|CD946256.1|CD946256
EST:     ACCCATGTGATATCTGGAGTGTTGGTTGTATTCTTGTTGAGCTTTGCACG                         GGTGAGGCGTTATTCCAGACTCACGAAAACTTGGAACATCTGGCTATGATG
genomic: ACCCATGTGATATCTGGAGTGTTGGTTGTATTCTTGTTGAGCTTTGCACGgtatgttaat ... ggttgtgcagGGTGAGGCGTTATTCCAGACTCACGAAAACTTGGAACATCTGGCTATGATG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgttaatgggaccttggcttcatttggcatgtacaagtaccaggggatctgagttaccaaggttgtgcagGGTGAGGCGTTATTCCAGACTCACGAAAACTTGGAACATCTGGCTATGATGGAGAGAGTTCTTGGACCTTTGCCGTACCATATGCTTAAGAGGGCAGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG