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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacgtccaagccgcttccccgtttccgttgtctccttcaattcttcgtccgtagtaccgtgatcgattgtcttccgtttgtcttactgcctcgtctgcgtctaaaactttacctgcagTTAGCGTGAGCGAGGTCGAGGCATTGTATGAACTGTTCAAGAAGATCAGCAGTGCTGTGATTGATGATGGGCTGATCAACAAG

Basic information

species Zea mays
transcript GRMZM2G112672_T01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G112672_T02 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os03g42840.1 (Oryza sativa), 3'ss of exon 1
gtacgtccaagc-cgcttccccgtttcc----gttgtctccttcaattc----ttcgtccgtagtaccgtgatcgattgtcttccgtt--tgtcttactgcctcgtctgcgtctaaaac---------------tttacctgcagTTAGCGTGAGCGAGGTCGAGGCATTGTATGAACTGTTCAAGAAGATCAGCAGTGCTGTGATTGATGATGGGCTGATCAACAAG
||||||||   | | ||  | || || |    |  || | ||| | |      |   ||  | | || |  ||  ||||| |||| ||  ||| |  | ||       || |                      | | | ||||||||| ||||||||||| ||||| |||||||| |||||||||||||||||||| || ||||| ||||| || ||||||||||||
gtacgtcctctctctctctctcgcttgctcgtgcagtgtacttgagtgtcgattgtttcacttgaactgaaattaattgtgttccctttttgtttcgcggcgcatgtggcattgggggtggtggtctgctcgtttgtgcgtgcagTTAGTGTGAGCGAGGTTGAGGCGTTGTATGAGCTGTTCAAGAAGATCAGCAGCGCGGTGATCGATGACGGACTGATCAACAAG

upper sequence: GRMZM2G112672_T02 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA07G39940.1 (Glycine max), 3'ss of exon 2
gtacgtccaagccgcttccccgtttccgttgtctccttcaattcttcgtccgtagtaccgtgatcgattgtcttccgtttgtcttactgcctcgtctgcgtctaaaactttacctgcagTTAGCGTGAGCGAGGTCGAGGCATTGTATGAACTGTTCAAGAAGATCAGCAGTGCTGTGATTGATGATGGGCTGATCAACAAG
                   | ||||    | ||   ||    |  |  |    |  | | | |   || |        ||  |  | |      | |  || |   | | |     ||||||| || || ||| | || ||| |||||||| |||||||||||||||||||||| ||||||||||| || || || || |||
-----------------atctgtttttactctcaatttt--cttctttttatcaaaatcataaaaaataggaaagaaattaacaaaataagatatttatgtgttttattgttgacacagTTAGTGTAAGTGAGATTGAAGCACTGTATGAATTGTTCAAGAAGATCAGCAGTGCAGTGATTGATGACGGACTAATTAATAAG

upper sequence: GRMZM2G112672_T02 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA17G00830.1 (Glycine max), 3'ss of exon 2
gtacgtccaagccgcttccccgtttccgttgtctccttcaatt--cttcgtccgt-agtaccgtgatcgattgtcttccgtt--tgtcttactgcctcgtctgcgtctaaaactttacctgcagTTAGCGTGAGCGAGGTCGAGGCATTGTATGAACTGTTCAAGAAGATCAGCAGTGCTGTGATTGATGATGGGCTGATCAACAAG
                        || ||| | ||  ||||||  |||| |  || |  | | | |   ||||        |  |  |  | |      | |  || |   | | |   ||||||||| || || ||| | || ||  | |||||| |||||||||||||||||||||| ||||||||||| || || || || |||
------------------------tctgttttttctctcaattttcttcttttgtcaaaagcataaaaaattggaaagaaatattaacaaaataagatatttatgtgttttattgttgatgcagTTAGTGTAAGTGAGATTGAAGCGCTATATGAATTGTTCAAGAAGATCAGCAGTGCAGTGATTGATGACGGACTAATTAATAAG

upper sequence: GRMZM2G112672_T02 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA09G01870.2 (Glycine max), 3'ss of exon 2
gtacgtccaagccgcttccccgtttccgttgtctccttcaattcttcgtccgtagtaccgtgatcgattgtcttccgtttgtcttactgcctcgtctgcgtctaaaactttacctgcagTTAGCGTGAGCGAGGTCGAGGCATTGTATGAACTGTTCAAGAAGATCAGCAGTGCTGTGATTGATGATGGGCTGATCAACAAG
        || | | |     ||     |        | | || | |   | |  | | || | | |   ||||   |  | |||    | |    ||  |     | |||  |||||||||| || || ||| | || ||| |||||||||| |||||||||||||||||||  || || ||  | ||  | || |  |||
--------aaactgttat---gtaggaatgaatctgcttagttttac---catttttcagttaccaaggctcttat-taagacttggaacataacttgtttt----attttcactgcagTTAGTGTAAGTGAGATTGAAGCACTGTATGAACTATTCAAGAAGATCAGCAGTGGAGTAATGGACAAAGGATTAATTACTAAG

upper sequence: GRMZM2G112672_T02 (Zea mays), 3'ss of exon 1
lower sequence: AT5G55990.1 (Arabidopsis thaliana), 3'ss of exon 3
gtacgtccaagccgcttccccgtttccgttgtctccttcaattcttcgtccgtagtaccg-tgatcgattgtcttccgtttgtcttactgcctcgtctgc-gtcta---------aaactttacct------gcagTTAGCGTGAGCGAGGTCGAGGCATTGTATGAACTGTTCAAGAAGATCAGCAGTGCTGTGATTGATGATGGGCTGATCAACAAG
||| | || | |  |||| |   |    || | |  ||   ||    ||    ||   || ||    |   | |   |  ||    | |   || ||||  | |||          || ||    |      |||||||| ||||| ||  | || ||  | ||||| || || ||||| ||||||||||| ||||||||||||||||| || ||||||
gtatgccctatcaccttctctactctttttttttttttttttttccggttataagattcgatgcaataccatttgaggaatgcaaaaatatttcttctgaagactattgatgattgaatttggttttggaatgcagTTAGTGTGAGTGAAATAGAAGCTCTTTATGAGCTTTTTAAGAAAATCAGCAGTGCCGTGATTGATGATGGGCTAATAAACAAG

upper sequence: GRMZM2G112672_T02 (Zea mays), 3'ss of exon 1
lower sequence: AT4G26570.2 (Arabidopsis thaliana), 3'ss of exon 3
------------------------------gtacgtccaagccgcttccccgtttccgttgtctccttcaattcttcgtccgt-agtaccgtgatcgattgtcttcc---------------gtttgtcttactgcctcgtctgcgtctaaaactttacctgcagTTAGCGTGAGCGAGGTCGAGGCATTGTATGAACTGTTCAAGAAGATCAGCAGTGCTGTGATTGATGATGGGCTGATCAACAAG
                               ||  | | |  | |||     || | ||| | |   | | |     |   |  | |||  |  | |||  |||                   | | |||| |||  |  |   | |  |    |||   ||||||||||||||| ||  | |||||  | ||||| ||||| ||||| ||||||||||||||||||||||||||||| || ||||||
gtatgctctcaacttcttttccatcttattttaacttccatgcactttttttttccagttatatgtatgattcaaaggcttgccattactctagttgatgctctctgttaagaggaatgcaaatctttctttctgtgttttgatcattgactcgtttgggtgcagTTAGCGTGAGTGAAATAGAGGCTCTCTATGAGCTGTTTAAGAAAATCAGCAGTGCTGTGATTGATGATGGGCTAATAAACAAG

upper sequence: GRMZM2G112672_T02 (Zea mays), 3'ss of exon 1
lower sequence: Vv00s1569g00020.t01 (Vitis vinifera), 3'ss of exon 1
gtacgtccaagccgcttccccgtttccgttgtctccttcaattcttcgtccgtagtaccgtgatcgattgtcttccgtttgtcttactgcctcgtctgcgtctaaaactttacctgcagTTAGCGTGAGCGAGGTCGAGGCATTGTATGAACTGTTCAAGAAGATCAGCAGTGCTGTGATTGATGATGGGCTGATCAACAAG
                                                                                                                       |||| || || ||  | || ||| | ||||||||||| |||||||||||||||||||| ||||||||||| || |||||||||
-----------------------------------------------------------------------------------------------------------------------ttAGTGTAAGTGAAATAGAAGCACTTTATGAACTGTTTAAGAAGATCAGCAGTGCTGTAATTGATGATGGCCTCATCAACAAG

upper sequence: GRMZM2G112672_T02 (Zea mays), 3'ss of exon 1
lower sequence: Vv19s0015g01070.t01 (Vitis vinifera), 3'ss of exon 1
gtacgtccaagccgcttccccgtttccgttgtctccttcaattcttcgtccgtagtaccgtgatcgattgtcttccgtttgtcttactgcctcgtctgcgtctaaaactttacctgcagTTAGCGTGAGCGAGGTCGAGGCATTGTATGAACTGTTCAAGAAGATCAGCAGTGCTGTGATTGATGATGGGCTGATCAACAAG
                    | || |       | ||   | | | | | |     ||  |  |       | |       |  |||||     | |   | |     ||    | ||||||| || || ||  |||||||| | || || ||||| |||||||||||||| |||||||||||||| || ||||||||||||
-------------------tcattcctacctaatgctaatagtttgctttctgccaactcttttaatgaaccattaaagcattgtactgaagattgtaatttttttctttccaatacagTTAGTGTAAGTGAAATCGAGGCACTATACGAGCTGTTTAAGAAGATCAGCAGCGCTGTGATTGATGACGGTCTGATCAACAAG

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|5325037|gb|AI783228.1|AI783228
EST:     GCTAGGGAGACCGTGT                         TTAGCGTGAGCGAGGTCGAGGCATTGTATGAGCTGTTCAAGAAGATCAGCA
genomic: GCTAGGGAGACCGTGTgtacgtccaa ... ttacctgcagTTAGCGTGAGCGAGGTCGAGGCATTGTATGAACTGTTCAAGAAGATCAGCA






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cgattgtcttccgtttgtcttactgcctcgtctgcgtctaaaactttacctgcagTTAGCGTGAGCGAGGTCGAGGCATTGTATGAACTGTTCAAGAAGATCAGCAGTGCTGTGATTGATGATGGGCTGATCAACAAG
                                   gtctaaa  putative branch site (score: 3)
                                           ctttacct  CT-rich tract
                                      taaaacttta  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacgtccaagccgcttccccgtttccgttgtctccttcaattcttcgtccgtagtaccgtgatcgattgtcttccgtttgtcttactgcctcgtctgcgtctaaaactttacctgcagTTAGCGTGAGCGAGGTCGAGGCATTGTATGAACTGTTCAAGAAGATCAGCAGTGCTGTGATTGATGATGGGCTGATCAACAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGATCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGAT