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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaggaaactgttgtcagagcacatcacgttattgctgtgaacttcactattggtgcaccaccagacttttataaaatattcgatcttaattccagCGGACTATTGAGGTCCATTTTAGGGAATCTTGGGGCACCACGCCATGTTCGGCTTCTCACTTATGCAAGATGTGCTATACACGGTCTTGAGAAGCAGCAC

Basic information

species Zea mays
transcript GRMZM2G040720_T01
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G040720_T01 (Zea mays), 3'ss of exon 11
lower sequence: LOC_Os11g34750.1 (Oryza sativa), 3'ss of exon 14
gtaaggaa-actgttgtcagagcacat-cacgttattgctgtgaacttcactattggtgcaccaccagacttttataaaatattcgatcttaattccagCGGACTATTGAGGTCCATTTTAGGGAATCTTGGGGCACCACGCCATGTTCGGCTTCTCACTTATGCAAGATGTGCTATACACGGTCTTGAGAAGCAGCAC-------------
||||| || | | ||||||| ||| |  || ||||   |||    |||   | ||    ||          ||    | |  |  ||| || | | ||| |||||| ||||||| |||||||| ||||| || |||||||||||||| || ||||| || ||||||| ||| ||| |  |||| |||||  | |||| |             
gtaagcaatatttttgtcagtgcataagcatgttac-actg----ctttcgtctttacccatttttgctgctt----acacttgtgatatttacttcagtggactactgaggtcaattttagGTAATCTAGGTGCACCACGCCATGTGCGACTTCTTACCTATGCAAAATGCGCTTTGTACGGCCTTGAAGAACAGCCCAAATCACAGTCAG
















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|32931165|gb|CF035977.1|CF035977
EST:     TCATTTATGGAATCCTTGCCACCGGACCTCTATGTCATACTACGAACAGA                         CGGACTATTGAGGTCCATTTTAGGGAATCTTGGGGCACCACGCCATGTTCG
genomic: TCATTTATGGAATCCTTGCCACCGGACTTCTATGTCATACTACGAACAGAgtaaggaaac ... ttaattccagCGGACTATTGAGGTCCATTTTAGGGAATCTTGGGGCACCACGCCATGTTCG
EST: gi|60338335|gb|DN205308.1|DN205308
EST:     TCATTTATGGAATCCTTGCCACCGGACTTCTATGTCATACTACGAACAGA                         CGGACTATTGAGGTCCATTTTAGGGAATCTTGGGGCACCACGCCATGTTCG
genomic: TCATTTATGGAATCCTTGCCACCGGACTTCTATGTCATACTACGAACAGAgtaaggaaac ... ttaattccagCGGACTATTGAGGTCCATTTTAGGGAATCTTGGGGCACCACGCCATGTTCG
EST: gi|37381459|gb|CF627617.1|CF627617
EST:     TCATTTATGGAATCCTTGCCACCGGACTTCTATGTCATACTACGAACAGA                         CGGACTATTGAGGTCCATTTTAGGGAATCTTGGGGCACCACGCCATGTTCG
genomic: TCATTTATGGAATCCTTGCCACCGGACTTCTATGTCATACTACGAACAGAgtaaggaaac ... ttaattccagCGGACTATTGAGGTCCATTTTAGGGAATCTTGGGGCACCACGCCATGTTCG
EST: gi|37390531|gb|CF632497.1|CF632497
EST:     CCGGACTTTTATGTCATACTACGAACAGA                         CGGACTATTGAGGTCCATTTTAGGGAATCTTGGGGCACCACGCCATGTTCG
genomic: CCGGACTTCTATGTCATACTACGAACAGAgtaaggaaac ... ttaattccagCGGACTATTGAGGTCCATTTTAGGGAATCTTGGGGCACCACGCCATGTTCG
EST: gi|9824900|gb|BE574997.1|BE574997
EST:     TCATTTATGGAATCCTTGCCACCGGACTTCTATGTCATACTACGAACAGA                         CGGACTATTGAGGGCCATTTTA
genomic: TCATTTATGGAATCCTTGCCACCGGACTTCTATGTCATACTACGAACAGAgtaaggaaac ... ttaattccagCGGACTATTGAGGTCCATTTTA
EST: gi|60341736|gb|DN208709.1|DN208709
EST:     TCATTTATGGAATCCTTGCCACCGGACTTCTATGTCATACTACGAACAGA                         CGGACTATTGAGGTCCATTTTAGGGAATCTTGGGGCACCACGCCATGTTCG
genomic: TCATTTATGGAATCCTTGCCACCGGACTTCTATGTCATACTACGAACAGAgtaaggaaac ... ttaattccagCGGACTATTGAGGTCCATTTTAGGGAATCTTGGGGCACCACGCCATGTTCG
EST: gi|71305468|gb|DR788864.1|DR788864
EST:     ATCCTTGCCACCGGACTTCTATGTCATACTACGAACAGA                         CGGACTATTGAGGTCCATTTTAGGGAATCTTGGGGCACCACGCCATGTTCG
genomic: ATCCTTGCCACCGGACTTCTATGTCATACTACGAACAGAgtaaggaaac ... ttaattccagCGGACTATTGAGGTCCATTTTAGGGAATCTTGGGGCACCACGCCATGTTCG
EST: gi|60344633|gb|DN211606.1|DN211606
EST:     TCATTTATGGAATCCTTGCCACCGGACTTCTATGTCATACTACGAACAGA                         CGGACTATTGAGGTCCATTTTAGGGAATCTTGGGGCACCACGCCATGTTCG
genomic: TCATTTATGGAATCCTTGCCACCGGACTTCTATGTCATACTACGAACAGAgtaaggaaac ... ttaattccagCGGACTATTGAGGTCCATTTTAGGGAATCTTGGGGCACCACGCCATGTTCG
EST: gi|40336243|gb|CK370313.1|CK370313
EST:     TGCCACCGGACTTTTATGTCATACTACGAACAGA                         CGGACTATTGAGGTCCATTTTAGGGAATCTTGGGGCACCACGCCATGTTCG
genomic: TGCCACCGGACTTCTATGTCATACTACGAACAGAgtaaggaaac ... ttaattccagCGGACTATTGAGGTCCATTTTAGGGAATCTTGGGGCACCACGCCATGTTCG
EST: gi|86474242|gb|DY240612.1|DY240612
EST:     TCATTTATGGAATCCTTGCCACCGGACTTCTATGTCATACTACGAACAGA                         CGGACTATTGAGGTCCATTTTAGGGAATCTTGGGGCACCACGCCATGTTCG
genomic: TCATTTATGGAATCCTTGCCACCGGACTTCTATGTCATACTACGAACAGAgtaaggaaac ... ttaattccagCGGACTATTGAGGTCCATTTTAGGGAATCTTGGGGCACCACGCCATGTTCG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acttcactattggtgcaccaccagacttttataaaatattcgatcttaattccagCGGACTATTGAGGTCCATTTTAGGGAATCTTGGGGCACCACGCCATGTTCGGCTTCTCACTTATGCAAGATGTGCTATACACGGTCTTGAGAAGCAGCAC
                                           tcttaat  putative branch site (score: 3)
                        acttttataaaatatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaggaaactgttgtcagagcacatcacgttattgctgtgaacttcactattggtgcaccaccagacttttataaaatattcgatcttaattccagCGGACTATTGAGGTCCATTTTAGGGAATCTTGGGGCACCACGCCATGTTCGGCTTCTCACTTATGCAAGATGTGCTATACACGGTCTTGAGAAGCAGCAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC