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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtacctgatacactatttgctatttgtacaaccgcttatttcttcacatcgatttcgtattgtacatttaacagaaaacatttgctttctgctggtttgtttacgttatttattcatcaatgcaatacttgatttatacaagcaaccctaatttaaaactgtcgccagGTTAATCCTTCAGATGTTATTATTTTGGAAGGAATTCTAGTTTTTCATGATTCACGCCTCAGGGATTTGATGAACATGAAGATCTTCGTTGATACAG

Basic information

species Zea mays
transcript GRMZM2G034143_T03
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G034143_T03 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os02g17320.1 (Oryza sativa), 3'ss of exon 5
gtaagtacctgatacactatttgctatttgtacaaccgcttatttcttcacatcgatttcgtattgtacatttaacagaaaacatttgctttctgctggtttgtttacgttatttattcatcaatgcaatacttgatttatacaagcaaccctaat-ttaaaactgtcgccagGTTAATCCTTCAGATGTTATTATTTTGGAAGGAATTCTAGTTTTTCATGATTCACGCCTCAGGGATTTGATGAACATGAAGATCTTCGTTGATACAG
                                                                         || |    |    || || | | |  ||  | | | || ||||| |||   ||   ||||| || | |   || ||||||||| ||   |||   | ||||| |||||||||||||| |||||||||||||||||||| ||||| |||||||||||  || ||||||||||||||||||||||||| ||||| ||||
------------------------------------------------------------------------gaaaattggatcactgattacagtttattcttct-ctttgtttatccatatctgttttactttatgtttcagagaaaccctaatattttgacttctgtcagGTCAATCCTTCAGATGTAATTATTTTGGAAGGAATTCTGGTTTTCCATGATTCACGTGTCCGGGATTTGATGAACATGAAGATCTTTGTTGACACAG

upper sequence: GRMZM2G034143_T03 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os11g16370.1 (Oryza sativa), 3'ss of exon 5
gtaagtacctgatacactatttgctatttgtacaaccgcttatttcttcacatcgatttcgtattgtacatttaacagaaaacatttgctttctgctggtttgtttacgttatttattcatcaatgcaatacttgatttatacaagcaaccctaat-ttaaaactgtcgccagGTTAATCCTTCAGATGTTATTATTTTGGAAGGAATTCTAGTTTTTCATGATTCACGCCTCAGGGATTTGATGAACATGAAGATCTTCGTTGATACAG
                                                                         || |  | |    |||||   | | |||  || || ||||||||||||   ||   ||||| || | |   ||  |||||||| ||   ||||  | ||||| |||||||||||||| |||||||||||||| ||||| ||||| |||||||||||  || |||| ||||||||||||||||| || ||||||||||
----------------------------------------------------------------------aagaaaattagatcactgcttatagtttgttc-ttcactttatttattcatatttgttttactttatgtttcagag--accctaatattttgactgctgtcagGTCAATCCTTCAGATGTAATTATTTTGGAAGGTATTCTGGTTTTCCATGATTCACGTGTCCGGGACTTGATGAACATGAAGATATTTGTTGATACAG

upper sequence: GRMZM2G034143_T03 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA18G08180.1 (Glycine max), 3'ss of exon 5
gtaagtacctgatacactatttgctatttgtacaaccgcttatttcttcacatcgatttcgtattgtacatttaacagaaaacatttgctttctgctggtttgtttacgttatttattcatcaatgcaatacttgatttatacaagcaaccctaatttaaaactgtcgccagGTTAATCCTTCAGATGTTATTATTTTGGAAGGAATTCTAGTTTTTCATGATTCACGCCTCAGGGATTTGATGAACATGAAGATCTTCGTTGATACAG-
                                                                         | || | ||   |    |||     |  | |||  | | |   || || ||     |       | ||   |       |   || |   |||   ||||| || |||||||||||||| ||||| ||||| || || ||||| |||||| ||||  |  |||| |||||||| |||||||| || ||||| |||| 
------------------------------------------------------------------------aagcatagaatcatgatattccaaatgcatattttagct-tagttttatgaagttgctgtcattctcatttcattttgtgttgctttatcatgttttcaggTGAACCCTTCAGATGTTATAATTTTAGAAGGCATCCTTGTTTTCCATGATCCACGTGTTCGGGAGTTGATGAATATGAAGATATTTGTTGACACAGG

upper sequence: GRMZM2G034143_T03 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA02G47270.1 (Glycine max), 3'ss of exon 5
gtaagtacctgatacactatttgctatttgtacaaccgcttatttcttcacatcgatttcgtattgtacatttaacagaaaacatttgctttctgctggtttgtttacgttatttattcatcaatgcaatacttgattta--tacaagcaaccctaatttaaaactgtcgccagGTTAATCCTTCAGATGTTATTATTTTGGAAGGAATTCTAGTTTTTCATGATTCACGCCTCAGGGATTTGATGAACATGAAGATCTTCGTTGATACAG
                                                                    ||| |  |      | |||  | ||   | |  ||     |  ||||||     ||| ||||    | | ||  | |     |   |  |||||     |   ||||| || ||  | |||||||||||||||||||| || || |||||||||||| ||||  |  | |  |||||||| |||||||| || ||||| ||||
--------------------------------------------------------------------catgtttcttcttgcgttttatctccattagagtg-----gaaatttatatgg-aatacaatttcagctatacttcccttttatgttggtttaatctgttttgcagGTAAACCCAGCGGATGTTATTATTTTGGAAGGTATCCTTGTTTTTCATGATCCACGAGTGCGAGCATTGATGAATATGAAGATATTTGTTGACACAG

upper sequence: GRMZM2G034143_T03 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA08G45270.1 (Glycine max), 3'ss of exon 5
gtaagtacctgatacactatttgctatttgtacaaccgcttatttcttcacatcgatttcgtattgtacatttaacagaaaacatttgctttctgctggtttgtttacgttatttattcatcaatgcaatacttgatttatacaagcaaccctaattta----aaactgtcgccagGTTAATCCTTCAGATGTTATTATTTTGGAAGGAATTCTAGTTTTTCATGATTCACGCCTCAGGGATTTGATGAACATGAAGATCTTCGTTGATACAG
                                                                          | | || ||||||  |   || | ||     | | | |||| |   |  |   | |  |||   |   ||    |   |   ||     |   |||   ||||| || |||||||||||||| ||||||||||| || || ||||| |||||  ||||  |  |||| |||||||| |||||||| || ||||| ||||
--------------------------------------------------------------------------ataaaatacattt--tacatgatagtccaaatgcataatttttagttttacaaagttgttgtcattctcatttcattttgtgttgccttatcgtgttttcagGTGAACCCTTCAGATGTTATAATTTTGGAAGGCATCCTTGTTTTCCATGACCCACGTGTTCGGGAGTTGATGAATATGAAGATATTTGTTGACACAG

upper sequence: GRMZM2G034143_T03 (Zea mays), 3'ss of exon 6
lower sequence: Vv19s0015g01730.t01 (Vitis vinifera), 3'ss of exon 5
gtaagtacctgatacactatttgctatttgtacaaccgcttatttcttcacatcgatttcgtattgtacatttaacagaaaacatttgctttctgctggtttgtttacgttatttattcatcaatgcaatacttgatttat--acaagcaaccctaatttaaaactgtcgccagGTTAATCCTTCAGATGTTATTATTTTGGAAGGAATTCTAGTTTTTCATGATTCACGCCTCAGGGATTTGATGAACATGAAGATCTTCGTTGATACAG
                                                                          |  |    | |      | ||    | | |||  | || ||  |      | |     |  ||  ||  | || |  |  |  | | |||   | | ||||| || ||||||||||| || ||||||||||| || ||  |||||||||||   ||  || |||| ||||||||||||||||| || ||||||||||
--------------------------------------------------------------------------agggtggtcctgaatcctgtgagattatatttcaggtacttgatttctgttcccgggttacatgcattgagaaccctcattgctatgaaatatttggcagGTCAACCCTTCAGATGTGATAATTTTGGAAGGCATACTCATTTTTCATGATCTTCGTGTCCGGGAATTGATGAACATGAAGATATTTGTTGATACAG

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|60344955|gb|DN211928.1|DN211928
EST:     ANNNNNNNNGTGAAAAACTACAATTTATG                         GTTAATCCTTCAGATGTTATTATTTTGGAAGGAATTCTAGTTTTTCATGAT
genomic: ATTTTTTTTGTGAAAAACTACAATTTATGgtaagtacct ... ctgtcgccagGTTAATCCTTCAGATGTTATTATTTTGGAAGGAATTCTAGTTTTTCATGAT






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcatcaatgcaatacttgatttatacaagcaaccctaatttaaaactgtcgccagGTTAATCCTTCAGATGTTATTATTTTGGAAGGAATTCTAGTTTTTCATGATTCACGCCTCAGGGATTTGATGAACATGAAGATCTTCGTTGATACAG
                                ccctaat  putative branch site (score: 3)
          aatacttgatttata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtacctgatacactatttgctatttgtacaaccgcttatttcttcacatcgatttcgtattgtacatttaacagaaaacatttgctttctgctggtttgtttacgttatttattcatcaatgcaatacttgatttatacaagcaaccctaatttaaaactgtcgccagGTTAATCCTTCAGATGTTATTATTTTGGAAGGAATTCTAGTTTTTCATGATTCACGCCTCAGGGATTTGATGAACATGAAGATCTTCGTTGATACAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA