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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacaaaccagaactactcagctcagttgccgttttcttaaacatctgtctgcctgcctatatggcacggtgttatatcattgtcttgtcgatttgattgtctgtccccatgttccgtttccagGTACAAGGTTTTCATAAACCCAAGCATCAGCGACGTCCTCTGCACCGCGACCGCGGAGGCGCTAGCGATGGGCAAGTTCGTGGTGTGCGCCGACCACCCG

Basic information

species Zea mays
transcript GRMZM2G175453_T02
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G175453_T02 (Zea mays), 3'ss of exon 7
lower sequence: LOC_Os11g05990.1 (Oryza sativa), 3'ss of exon 6
gtacaaaccagaactactcagctcagttgccgttttcttaaacatctgtctgcctgcctatatggcacggtgttatatcatt--gtcttgtcgatttgattgtctgtccccatgttccgtt--tccagGTACAAGGTTTTCATAAACCCAAGCATCAGCGACGTCCTCTGCACCGCGACCGCGGAGGCGCTAGCGATGGGCAAGTTCGTGGTGTGCGCCGACCACCCG
                                      ||||   | |     ||  ||   || ||   |  || ||| ||   | | ||  |||||| ||| | |||   | ||   ||  | ||||||||||||||| ||||| |||||||| || || ||||| ||||| |||||||| |||||  |||| ||||| ||||| || || ||||| |||||||| 
-------------------------------------gtaaaagacagagcctctcactgcctgacatcttcctacatctttagatatagttaatttgaatgtttttcctgttttttttttctttcagGTACAAGGTTTTTATAAATCCAAGCATTAGTGATGTCCTTTGCACTGCGACCGCTGAGGCATTAGCAATGGGTAAGTTTGTTGTCTGCGCAGACCACCCA

upper sequence: GRMZM2G175453_T02 (Zea mays), 3'ss of exon 7
lower sequence: AT3G11670.1 (Arabidopsis thaliana), 3'ss of exon 6
gtacaaaccagaactactcagctcagttgccgttttcttaaacatctgtctgcctgcctatatggcacggtgttatatcattgtcttgtcgatttgattgtctgtccccatgttccgtttccagGTACAAGGTTTTCATAAACCCAAGCATCAGCGACGTCCTCTGCACCGCGACCGCGGAGGCGCTAGCGATGGGCAAGTTCGTGGTGTGCGCCGACCACCCG
                                  |||| ||| || ||  |   ||| | ||             | | |  || | |    ||||||||||| | ||||  |   | |   |||||||| || ||||||||||| ||||||||||| || || ||||| || ||||| || || ||||| ||||| ||||| |||||||| || || ||||| 
-----------------------------gtaagttctgaaaaatgtgctt---tgctttta-------aaaacttgttaaggtttcgctc-tttgattgtct-ttcccacatcttgatga-agGTACAAAGTGTTCATAAACCCCAGCATCAGCGATGTTCTATGCACAGCAACCGCAGAAGCACTAGCCATGGGGAAGTTTGTGGTGTGTGCAGATCACCCT

upper sequence: GRMZM2G175453_T02 (Zea mays), 3'ss of exon 7
lower sequence: EDP08851 (Chlamydomonas reinhardtii), 3'ss of exon 8
-------------------gtacaaaccagaactactcagctcagttgccgttttcttaaacatctgtctgcctgcctatatggcacggtgttatatcattg----tcttgtcgatttgattgtctgtccccatgttccgtttccagGTACAAGGTTTTCATAAACCCAAGCATCAGCGACGTCCTCTGCACCGCGACCGCGGAGGCGCTAGCGATGGGCAAGTTCGTGGTGTGCGCCGACCACCCG-------
                   |      | |     ||| | | |    ||      |  | |||||   | |  |     | |  |    ||||       ||    || ||||    |   | |   |  | |    || ||  | |   | |||| || || ||||| ||| |    |||||  |    ||| | ||||| |||||||| || ||||||||||||||  ||||||| ||||||||        
gtgcgtgtggggcactggggactgggcaatgggcactgaacacgtacgcaa---cccaagacatccacccgattcatcgtgtaaccgtttgttcacgggctggagctcatgtcaccct--cttttcattgcaacccgcccttcaccgcccccagGTGTTTATCAACCCCAGCCTGTCGGACGTGGTGGCGACCACCACCGCCGAGGCGCTGGCCATGGGCAAGTTCGTACTGTGCGCGGACCACCCCTCCAACA

upper sequence: GRMZM2G175453_T02 (Zea mays), 3'ss of exon 7
lower sequence: PP1S152_62V6.1 (Physcomitrella patens), 3'ss of exon 6
----------------gtacaaaccagaactactcagctcagttgccgttttc-----ttaaacatctgtctgcctgcctatatggcacggtgttatatcattgtcttgtcgatttgattgtctgtccccatgttccgtt-tccagGTACAAGGTTTTCATAAACCCAAGCATCAGCGACGTCCTCTGCACCGCGACCGCGGAGGCGCTAGCGATGGGCAAGTTCGTGGTGTGCGCCGACCACCCG
                  |||   |   | | |||   |   || |  |  ||     ||  |||||| |      | || |    |   || |||  ||||||| || ||  |||||     | | | | | ||   || | ||| |||||| |||||||||| |||||  | ||||| ||  | |||||| | ||||| ||||| ||||||||||||||  | |||||||| || |||||||||
gtatgaccttcactttagacagtgcttgaatgctcttttatattccaatcatcatgtattttacatctatacaatagtctttgcatcggagt-ttagttcattgttttttc--tttgacgagttctgcaccttttgtcttgtgcagTTACAAGATTTTCATAAATCCAAGTTTGAGCGATGTTGTATGCACCACTACCGCAGAGGCTCTAGCGATGGGCAAAATAGTGGTGTGTGCAGACCACCCG

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|116818177|gb|EC861159.1|EC861159
EST:     TCTCTTCATGG                         GTACAA-GTTTTCATAAACCCAAGCATCAGCGACGT-CTCTGCACCGCGAC
genomic: TCTCTTCATGGgtacaaacca ... ccgtttccagGTACAAGGTTTTCATAAACCCAAGCATCAGCGACGTCCTCTGCACCGCGAC
EST: gi|91872681|gb|EB402638.1|EB402638
EST:     AACCTCAACTTTCATAAGGGCCGGGACCATGCGGATGATTCTCTTCATGG                         GTACAAGGTTTTCATAAACCCAAGCATCAGCGACGTCCTCTGCACCGCGAC
genomic: AACCTCAACTTTCATAAGGGCCGGGACCATGCGGATGATTCTCTTCATGGgtacaaacca ... ccgtttccagGTACAAGGTTTTCATAAACCCAAGCATCAGCGACGTCCTCTGCACCGCGAC
EST: gi|149072357|gb|EE160627.2|EE160627
EST:     AACCTCAACTTTCATAAGGGCCGGGACCATGCGGATGATTCTCTTCATGG                         GTACAAGGTTTTCATAAACCCAAGCATCAGCGACGTCCTCTGCACCGCGAC
genomic: AACCTCAACTTTCATAAGGGCCGGGACCATGCGGATGATTCTCTTCATGGgtacaaacca ... ccgtttccagGTACAAGGTTTTCATAAACCCAAGCATCAGCGACGTCCTCTGCACCGCGAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtgttatatcattgtcttgtcgatttgattgtctgtccccatgttccgtttccagGTACAAGGTTTTCATAAACCCAAGCATCAGCGACGTCCTCTGCACCGCGACCGCGGAGGCGCTAGCGATGGGCAAGTTCGTGGTGTGCGCCGACCACCCG
                      atttgat  putative branch site (score: 5)
                                           ttccgtttcc  putative PPT
     atatcatt  TA-rich tract