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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtgcatacattttaaaccttaatttactgattgtcaatagcaaatccttaatgcttctcttttgaaaattttagCATGATTATCATGTTAAAGAGAAGATTCTCACGCTGATAGATACTTGGCAAGAAGTTTTTGGTGGTGCACGTGCAAGATATCCACAATATTATGCAGCAT

Basic information

species Zea mays
transcript GRMZM2G053925_T01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G053925_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os02g17350.2 (Oryza sativa), 3'ss of exon 3
gtatgtgcatacattttaaaccttaatttactgattgtc-----aatagcaaatcctt--------aatgc-ttctcttttgaaaattttagCATGATTATCATGTTAAAGAGAAGATTCTCACGCTGATAGATACTTGGCAAGAAGTTTTTGGTGGTGCACGTGCAAGATATCCACAATATTATGCAGCAT
||||||  |||  ||| || | | ||  |    ||||||     | | | |||  |||        || || || |  |||  |  ||||||| ||||| |||||| ||||||||||| ||||| |||||||| |||||||||||||||||||| || | ||||||||||||||||||||| || |||||||
gtatgtatataagtttaaaccttaaaagttaaaattgtctggttagttgtaaactctttaaattttaacgccttattcttttgagcttttagCCTGATTTTCATGTGAAAGAGAAGATCCTCACTCTGATAGACACTTGGCAAGAAGTTTTTGGCGGGGTACGTGCAAGATATCCACAATACTACGCAGCAT

upper sequence: GRMZM2G053925_T01 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA17G26440.1 (Glycine max), 3'ss of exon 3
----------gtatgtgcatacattttaaacctt---aatttactgattg-tcaatagcaaatcc-ttaatgct-tctcttttgaaaattttagCATGATTATCATGTTAAAGAGAAGATTCTCACGCTGATAGATACTTGGCAAGAAGTTTTTGGTGGTGCACGTGCAAGATATCCACAATATTATGCAGCAT
           |   || |||  |||  | | ||   |  || ||| ||  |  ||   ||||   || |||   | | |  ||  |||| |||| ||||| |||||| ||||| ||||| ||    ||  |||||||||||||||||| |||||| ||  || | ||||||||||||||||||||||| ||||
gtatacataatttcttgaatatttttgcagctttctgatgtttctgttttcttcatgtaaaatatgttgatgtgatttgtcatgccaattgtagCCTGATTTTCATGTCAAAGAAAAGATACTGGTTCTTGTAGATACTTGGCAAGAAGCTTTTGGAGGCCCAAGGGCAAGATATCCACAATATTATGCTGCAT

upper sequence: GRMZM2G053925_T01 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA06G08710.1 (Glycine max), 3'ss of exon 3
gtatgtgcatacattttaaaccttaattta---ctgatt--gtcaatagcaa-atccttaatgcttctcttttgaaaattttagCATGATTATCATGTTAAAGAGAAGATTCTCACGCTGATAGATACTTGGCAAGAAGTTTTTGGTGGTGCACGTGCAAGATATCCACAATATTATGCAGCAT
||||  |  | |||   |  ||| | ||||   ||||||   |||  |  |  ||  |||     | | |     ||||| |||| |||||| ||||| | |||||||||  | |  || ||||||||||||||||||| |||||| ||  || | |||||||||||||| |||||||||||||
gtattagttttcatggcattcct-attttatacctgatttcatcatgaaaagtatgtttatcatatttatcacacaaattgtagCCTGATTACCATGTCAGAGAGAAGATATTGATTCTTATAGATACTTGGCAAGAAGCTTTTGGAGGGCCAAGGGCAAGATATCCACAGTATTATGCAGCAT

upper sequence: GRMZM2G053925_T01 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA04G08600.1 (Glycine max), 3'ss of exon 3
-----------------gtatgtgcatacattttaaaccttaatttactgattgtcaatagcaa-atccttaatgcttctcttttgaaaattttagCATGATTATCATGTTAAAGAGAAGATTCTCACGCTGATAGATACTTGGCAAGAAGTTTTTGGTGGTGCACGTGCAAGATATCCACAATATTATGCAGCAT
                  | | | ||||   ||   |  |||         |  |||  |  || ||  |||     | | |   | ||||| |||| |||||||||||| | |||||||||  | |  || ||||||||||||||||||| |||||| ||  || | |||||||||||||| |||||||||||||
gtattgatatttcttggatgttttcatagccttcctattttatacctgatttcatcatgaaaaatatgtttatcatatttatcacgcaaattgtagCCTGATTATCATGTCAGAGAGAAGATATTGATTCTTATAGATACTTGGCAAGAAGCTTTTGGAGGGTCAAGGGCAAGATATCCACAGTATTATGCAGCAT

upper sequence: GRMZM2G053925_T01 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA14G21410.1 (Glycine max), 3'ss of exon 3
----------gtatgtgcatacattttaaacctt--aatttactgattgtca--atagcaaatccttaatgct-tctcttttgaaaattttagCATGATTATCATGTTAAAGAGAAGATTCTCACGCTGATAGATACTTGGCAAGAAGTTTTTGGTGGTGCACGTGCAAGATATCCACAATATTATGCAGCAT
           |   || |||  |||| |   ||  ||| |     || ||   |||   |    || |||   | | |  |   |||| |||| ||||| |||||| ||||||||||| || |  || ||||||||||||||||||| |||||| ||  |  | ||||||||||||||||||||||| || |
gtatacatagtttcttgaatattttttcagttttctaatgtctctgttttcttcatatatatatgttgatgtcatttgtcataccaattgtagCCTGATTTTCATGTCAAAGAGAAGATACTGATTCTTATAGATACTTGGCAAGAAGCTTTTGGAGGCCCGAGGGCAAGATATCCACAATATTATGCTGCTT

upper sequence: GRMZM2G053925_T01 (Zea mays), 3'ss of exon 3
lower sequence: Vv04s0008g03720.t01 (Vitis vinifera), 3'ss of exon 3
-----------------gtat-gtgcatacattttaaaccttaatttactgattgtcaatagcaaatccttaatgct-tctcttttg-aaaattttagCATGATTATCATGTTAAAGAGAAGATTCTCACGCTGATAGATACTTGGCAAGAAGTTTTTGGTGGTGCACGTGCAAGATATCCACAATATTATGCAGCAT
                 |||   |   |   ||    |  || ||||| | | |      || ||    || ||  | | | || || ||||||  ||| |||||  ||||| | |||||||||  | |  |||||||||||||||||||||| |||||| ||  || | ||||||||||||||||| ||||| ||||
gtcagactgtcattcaagtaccatttttttgttccctagtttcatttatttacttatccgagaaacctgttcatagtatttattctgcaaaattgcagCCTGATTTGCATGTCAGAGAGAAGATATTGATTCTGATAGATACTTGGCAAGAAGCTTTTGGAGGACCAAGGGCAAGATATCCACAATACTATGCTGCAT

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|6918389|gb|AW399919.1|AW399919
EST:     NTGCTGAGAGAGACATACTTCATGAGATGGTCAAGATAGTAAAGAAAAGG                         CATGATTATCATGTTAAAGAGAAGATTCTCACGCTGATAGATACTTGGCAA
genomic: TTGCTGAGAGAGACATACTTCATGAGATGGTCAAGATAGTAAAGAAAAGGgtatgtgcat ... aaaattttagCATGATTATCATGTTAAAGAGAAGATTCTCACGCTGATAGATACTTGGCAA
EST: gi|211196101|gb|FL010962.1|FL010962
EST:     TTGCTGAGAGAGACATACTTCATGAGATGGTCAAGATAGTAAAGAAAAGG                         CATGATTATCATGTTAAAGAG
genomic: TTGCTGAGAGAGACATACTTCATGAGATGGTCAAGATAGTAAAGAAAAGGgtatgtgcat ... aaaattttagCATGATTATCATGTTAAAGAG
EST: gi|89757177|gb|DY686889.1|DY686889
EST:     TTGCTGAGAGAGACATACTTCATGAGATGGTCAAGATAGTAAAGAAAAGG                         CATGATTATCATGTTAAAGAGAAGATTCTCACGCTGATAGATACTTGGCAA
genomic: TTGCTGAGAGAGACATACTTCATGAGATGGTCAAGATAGTAAAGAAAAGGgtatgtgcat ... aaaattttagCATGATTATCATGTTAAAGAGAAGATTCTCACGCTGATAGATACTTGGCAA
EST: gi|78088815|gb|DV517208.1|DV517208
EST:     TTGCTGAGAGAGACATACTTCATGAGATGGTCAAGATAGTAAAGAAAAGG                         CATGATTATCATGTTAAAGAGAAGATTCTCACGCTGATAGATACTTGGCAA
genomic: TTGCTGAGAGAGACATACTTCATGAGATGGTCAAGATAGTAAAGAAAAGGgtatgtgcat ... aaaattttagCATGATTATCATGTTAAAGAGAAGATTCTCACGCTGATAGATACTTGGCAA
EST: gi|12046215|gb|BF728354.1|BF728354
EST:     TTGCTGAGAGAGACATACTTCATGAGATGGTCAAGATAGTAAAGAAAAGG                         CATGATTATCATGTTAAAGAGAAGATTCTCACGCTGATAGATACTTGGCAA
genomic: TTGCTGAGAGAGACATACTTCATGAGATGGTCAAGATAGTAAAGAAAAGGgtatgtgcat ... aaaattttagCATGATTATCATGTTAAAGAGAAGATTCTCACGCTGATAGATACTTGGCAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taatttactgattgtcaatagcaaatccttaatgcttctcttttgaaaattttagCATGATTATCATGTTAAAGAGAAGATTCTCACGCTGATAGATACTTGGCAAGAAGTTTTTGGTGGTGCACGTGCAAGATATCCACAATATTATGCAGCAT
                                      tcttttgaaaatttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgtgcatacattttaaaccttaatttactgattgtcaatagcaaatccttaatgcttctcttttgaaaattttagCATGATTATCATGTTAAAGAGAAGATTCTCACGCTGATAGATACTTGGCAAGAAGTTTTTGGTGGTGCACGTGCAAGATATCCACAATATTATGCAGCAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA