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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtcaggtctgccgctacctgtctggtggtttgttacccgcaacatgtgtgtagctcaaaggctagcttgtttgtttgggtcgcgcgtgcctacctgcatgcagGTTCGTGTGGGATGAGGGCAAGTACCCCACAATGTCGTCGCTCAAGGAGATCGTCGGCAGCATCCAGTCGCAGGTCGCCAAGATCGAGGATGACATGAAG

Basic information

species Zea mays
transcript GRMZM2G177912_T02
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G177912_T02 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os05g51530.1 (Oryza sativa), 3'ss of exon 3
--------gtcaggtctgccgctacctgtctggtggtttgttacccgcaacatgtgtgtagctcaaaggctagcttgtttgtttgggtcgcgcgtgcctacctgcatgcagGTTCGTGTGGGATGAGGGCAAGTACCCCACAATGTCGTCGCTCAAGGAGATCGTCGGCAGCATCCAGTCGCAGGTCGCCAAGATCGAGGATGACATGAAG
         ||    ||||| || | || ||    | ||        ||||   | | | ||| ||   ||       ||  ||   | ||   | | |   | |    ||||| ||||||||||||||||| ||||| || |||||  ||||||||||||| |||||||||||||| || |||||| ||||||| || ||||||||||||
gtcgctcgctcgctcctgcccctgc-tgcctctcagcttagcgattccaac---tcttttgctaaagctctctacctcttccttcctttgcttcttcttcttttc---tagGTTTGTGTGGGATGAGGGCAAATACCCAACGATGTCACCGCTCAAGGAGATTGTCGGCAGCATCCAATCACAGGTCTCCAAGATTGAAGATGACATGAAG

upper sequence: GRMZM2G177912_T02 (Zea mays), 3'ss of exon 3
lower sequence: Vv17s0000g00460.t01 (Vitis vinifera), 3'ss of exon 3
gtcaggtctgccgctacctgtc-tggtggtttgttacccgcaacatgtgtgtagctcaaaggctagcttgtttgtttgggtcgcgcgtgcctacctgcatgcagGTTCGTGTGGGATGAGGGCAAGTACCCCACAATGTCGTCGCTCAAGGAGATCGTCGGCAGCATCCAGTCGCAGGTCGCCAAGATCGAGGATGACATGAAG
                   ||  ||  | ||   |   |   |  || |  |         ||||   || |  ||    |      ||  |       | ||||||||||||||||||||  |||||||| ||||||||  | |||| |||||| || |   |||| ||    || || || ||||| ||||||||  | |||
-------------------gtaatgcagattaagtgatcatgatttgaggattctgtctctgctactgtgataatt---attcaatttgaatgttcaattccagGTTCGTGTGGGATGAGGCGAAGTACCCTACAATGTCTCCTCTCAGGGAGATTGTGGATGGCATTCATGTACAAGTAGCTAAGATTGAGGATGATCTTAAG
















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|211359331|gb|FL325567.1|FL325567
EST:     AGCGGGGCCCTCACCGTCGATGGCGTTCCCGTCGACACCTACCTCACCAG                         GTTCGTGTGGGATGAGGGCAAGTACCCCACAATGTCGTCGCTCAAGGAGAT
genomic: AGCGGGGCCCTCACCGTCGATGGCGTTCCCGTCGACACCTACCTCACCAGgtcaggtctg ... ctgcatgcagGTTCGTGTGGGATGAGGGCAAGTACCCCACAATGTCGTCGCTCAAGGAGAT
EST: gi|9953349|gb|BE639932.1|BE639932
EST:     AGCGGGGCCCTCACCGTCGATGGCGTTCCCGTCGACACCTACCTCACCAG                         GTTCGTGTGGGATGAGGGCAGGTACCCCACAATGTCGTCGCTCAAGGAGAT
genomic: AGCGGGGCCCTCACCGTCGATGGCGTTCCCGTCGACACCTACCTCACCAGgtcaggtctg ... ctgcatgcagGTTCGTGTGGGATGAGGGCAAGTACCCCACAATGTCGTCGCTCAAGGAGAT
EST: gi|78120131|gb|DV538515.1|DV538515
EST:     AGCGGGGCCCTCACCGTCGATGGCGTTCCCGTCGACACCTACCTCACCAG                         GTTCGTGTGGGATGAGGGCAAGTACCCCACAATGTCGTCGCTCAAGGAGAT
genomic: AGCGGGGCCCTCACCGTCGATGGCGTTCCCGTCGACACCTACCTCACCAGgtcaggtctg ... ctgcatgcagGTTCGTGTGGGATGAGGGCAAGTACCCCACAATGTCGTCGCTCAAGGAGAT
EST: gi|211114226|gb|FL350275.1|FL350275
EST:     AGCGGGGCCCTCACCGTCGAWGGCGTTCCCGTCGACACCTAACTCACCAG                         GTTCGTGTGGGATGAGGGCAAGTACCCCACAATGTCGTCGC
genomic: AGCGGGGCCCTCACCGTCGATGGCGTTCCCGTCGACACCTACCTCACCAGgtcaggtctg ... ctgcatgcagGTTCGTGTGGGATGAGGGCAAGTACCCCACAATGTCGTCGC
EST: gi|211267792|gb|FL344631.1|FL344631
EST:     AGCGGGGCCCTCACCGTCGATGGCGTTCCCGTCGACACCTACCTCACCAG                         GTTCGTGTGGGATGAGGGCAAGTACCCCACAATGTCGTCGCTCAAGGAGAT
genomic: AGCGGGGCCCTCACCGTCGATGGCGTTCCCGTCGACACCTACCTCACCAGgtcaggtctg ... ctgcatgcagGTTCGTGTGGGATGAGGGCAAGTACCCCACAATGTCGTCGCTCAAGGAGAT
EST: gi|211217973|gb|FL307283.1|FL307283
EST:     AGCGGGGCCCTCACCGTCGATGGCGTTCCCGTCGACACCTACCTCACCAG                         GTTCGTGTGGGATGAGGGCAAGTACCCCACAATGTCGTCGCTCAAGGAGAT
genomic: AGCGGGGCCCTCACCGTCGATGGCGTTCCCGTCGACACCTACCTCACCAGgtcaggtctg ... ctgcatgcagGTTCGTGTGGGATGAGGGCAAGTACCCCACAATGTCGTCGCTCAAGGAGAT
EST: gi|71303539|gb|DR787880.1|DR787880
EST:     AGCGGGGCCCTCACCGTCGATGGCGTTCCCGTCGACACCTACCTCACCAG                         GTTCGTGTGGGATGAGGGCAAGTACCCCACAATGTCGTCGCTCAAGGAGAT
genomic: AGCGGGGCCCTCACCGTCGATGGCGTTCCCGTCGACACCTACCTCACCAGgtcaggtctg ... ctgcatgcagGTTCGTGTGGGATGAGGGCAAGTACCCCACAATGTCGTCGCTCAAGGAGAT
EST: gi|211362192|gb|FL333555.1|FL333555
EST:     AGCGGGTCCCTCACCGTCGATGGCGTTCCCGTCGACACCTACCTCACCAG                         GTTCGTGTGGGATGAGGGCAAGTACCCCACAATGTCGTCGCTCAAGGAGAT
genomic: AGCGGGGCCCTCACCGTCGATGGCGTTCCCGTCGACACCTACCTCACCAGgtcaggtctg ... ctgcatgcagGTTCGTGTGGGATGAGGGCAAGTACCCCACAATGTCGTCGCTCAAGGAGAT
EST: gi|148969238|gb|EE019992.2|EE019992
EST:     AGCGGGGCCCTCACCGTCGATGGCGTTCCCGTCGACACCTACCTCACCAG                         GTTCGTGTGGGATGAGGGCAAGTACCCCACAATGTCGTCGCTCAAGGAGAT
genomic: AGCGGGGCCCTCACCGTCGATGGCGTTCCCGTCGACACCTACCTCACCAGgtcaggtctg ... ctgcatgcagGTTCGTGTGGGATGAGGGCAAGTACCCCACAATGTCGTCGCTCAAGGAGAT
EST: gi|149104624|gb|EE290073.2|EE290073
EST:     AGCGGGGCCCTCACCGTCGATGGCGTTCCCGTCGACACCTACCTCACCAG                         GTTCGTGTGGGATGAGGGCAAGTACCCCACAATGTCGTCGCTCAAGGAGAT
genomic: AGCGGGGCCCTCACCGTCGATGGCGTTCCCGTCGACACCTACCTCACCAGgtcaggtctg ... ctgcatgcagGTTCGTGTGGGATGAGGGCAAGTACCCCACAATGTCGTCGCTCAAGGAGAT
EST: gi|211316704|gb|FL359227.1|FL359227
EST:     AGCGGGGCCCTCACCGTCGATGGCGTTCCCGTCGACACCTACCTCACCAG                         GTTCGTGTGGGATGAGGGCAAGTACCCCACAATGTCGTCGCTCAAGGAGAT
genomic: AGCGGGGCCCTCACCGTCGATGGCGTTCCCGTCGACACCTACCTCACCAGgtcaggtctg ... ctgcatgcagGTTCGTGTGGGATGAGGGCAAGTACCCCACAATGTCGTCGCTCAAGGAGAT
EST: gi|67016433|gb|CO445182.1|CO445182
EST:     AGCGGGGCCCTCACCGTCGATGGCGTTCCCGTCGACACCTACCTCACCAG                         GTTCGTGTGGGATGAGGGCAAGTACCCCACAATGTCGTCGCTCAAGGAGAT
genomic: AGCGGGGCCCTCACCGTCGATGGCGTTCCCGTCGACACCTACCTCACCAGgtcaggtctg ... ctgcatgcagGTTCGTGTGGGATGAGGGCAAGTACCCCACAATGTCGTCGCTCAAGGAGAT
EST: gi|211105804|gb|FL320712.1|FL320712
EST:     AGCGGGGCCCTCACCGTCGATGGCGTTCCCGTCGACACCTACCTCACCAG                         GTTCGTGTGGGATGAGGGCAAGTACCCCACAATGTCGTCGCTCAAGGAGAT
genomic: AGCGGGGCCCTCACCGTCGATGGCGTTCCCGTCGACACCTACCTCACCAGgtcaggtctg ... ctgcatgcagGTTCGTGTGGGATGAGGGCAAGTACCCCACAATGTCGTCGCTCAAGGAGAT
EST: gi|211283545|gb|FL347777.1|FL347777
EST:     AGCGGGGCCCTCACCGTCGATGGCGTTCCCGTCGACACCTACCTCACCAG                         GTTCGTGTGGGATGAGGGCAAGTACCCCACAATGTC
genomic: AGCGGGGCCCTCACCGTCGATGGCGTTCCCGTCGACACCTACCTCACCAGgtcaggtctg ... ctgcatgcagGTTCGTGTGGGATGAGGGCAAGTACCCCACAATGTC
EST: gi|211064773|gb|FL350726.1|FL350726
EST:     AGCGGGGCCCTCACCGTCGATGGCGTTCCCGTCGACACCTACCTCACCAG                         GTTCGTGTGGGATGAGGGCAAGTAC
genomic: AGCGGGGCCCTCACCGTCGATGGCGTTCCCGTCGACACCTACCTCACCAGgtcaggtctg ... ctgcatgcagGTTCGTGTGGGATGAGGGCAAGTAC
EST: gi|211460898|gb|FL364621.1|FL364621
EST:     AGCGGGGCCCTCACCGTCGATGGCGTTCCCGTCGACACCTACCTCACCAG                         GTTCGTGTGGGATGAGGGCAAGTACCCCACAATGTCGTCGCTCAAGGAGAT
genomic: AGCGGGGCCCTCACCGTCGATGGCGTTCCCGTCGACACCTACCTCACCAGgtcaggtctg ... ctgcatgcagGTTCGTGTGGGATGAGGGCAAGTACCCCACAATGTCGTCGCTCAAGGAGAT
EST: gi|211078718|gb|FL360383.1|FL360383
EST:     AGCGGGGCCCTCACCGTCGATGGCGTTCCCGTCGACACCTACCTCACCAG                         GTTCGTGTGGGATGAGGGCAAGTACCCCACAATGTCGTCGCTCAAGGAGAT
genomic: AGCGGGGCCCTCACCGTCGATGGCGTTCCCGTCGACACCTACCTCACCAGgtcaggtctg ... ctgcatgcagGTTCGTGTGGGATGAGGGCAAGTACCCCACAATGTCGTCGCTCAAGGAGAT
EST: gi|76288290|gb|DV027858.1|DV027858
EST:     AGCGGGGCCCTCACCGTCGATGGCGTTCCCGTCGACACCTACCTCACCAG                         GTTCGTGTGGGATGAGGGCAAGTACCCCACAATGTCGTCGCTCAAGGAGAT
genomic: AGCGGGGCCCTCACCGTCGATGGCGTTCCCGTCGACACCTACCTCACCAGgtcaggtctg ... ctgcatgcagGTTCGTGTGGGATGAGGGCAAGTACCCCACAATGTCGTCGCTCAAGGAGAT
EST: gi|211414492|gb|FL334083.1|FL334083
EST:     AGCGGGGCCCTCACCGTCGATGGCGTTCCCGTCGACACCTACCTCACCAG                         GTTCGTGTGGGATGAGGGCAAGTACCCCACAATGTCGTCGCTCAAGGAGAA
genomic: AGCGGGGCCCTCACCGTCGATGGCGTTCCCGTCGACACCTACCTCACCAGgtcaggtctg ... ctgcatgcagGTTCGTGTGGGATGAGGGCAAGTACCCCACAATGTCGTCGCTCAAGGAGA-
EST: gi|211381249|gb|FL356117.1|FL356117
EST:     AGCGGGGCCCTCACCGTCGATGGCGTTCCCGTCGACACCTACCTCACCAG                         GTTCGTGTGGGATGAGGGCAAGTACCCCACAATGTCGTCGCTCAAGGAGAT
genomic: AGCGGGGCCCTCACCGTCGATGGCGTTCCCGTCGACACCTACCTCACCAGgtcaggtctg ... ctgcatgcagGTTCGTGTGGGATGAGGGCAAGTACCCCACAATGTCGTCGCTCAAGGAGAT
EST: gi|211467481|gb|FL327941.1|FL327941
EST:     AGCGGGGCCCTCACCGTCGATGGCGTTCCCGTCGACACCTACCTCACCAG                         GTTCGTGTGGGATGAGGGCAAGT
genomic: AGCGGGGCCCTCACCGTCGATGGCGTTCCCGTCGACACCTACCTCACCAGgtcaggtctg ... ctgcatgcagGTTCGTGTGGGATGAGGGCAAGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtagctcaaaggctagcttgtttgtttgggtcgcgcgtgcctacctgcatgcagGTTCGTGTGGGATGAGGGCAAGTACCCCACAATGTCGTCGCTCAAGGAGATCGTCGGCAGCATCCAGTCGCAGGTCGCCAAGATCGAGGATGACATGAAG
                                        cctacct  CT-rich tract
                     tttgttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtcaggtctgccgctacctgtctggtggtttgttacccgcaacatgtgtgtagctcaaaggctagcttgtttgtttgggtcgcgcgtgcctacctgcatgcagGTTCGTGTGGGATGAGGGCAAGTACCCCACAATGTCGTCGCTCAAGGAGATCGTCGGCAGCATCCAGTCGCAGGTCGCCAAGATCGAGGATGACATGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGATG