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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGCTGGGGGGTGGAAGGACCGGACCACGGTGGAGGACATGGATCTGGCCATCCGGGCCAGCCTCAAGGGCTGGAAGTTCGTCTACCTCGGTGACGTCCAGgtacggttgataccaacaatcatgggcatccagaaatttcagatggaatgcgatgcaactttctagcaccgctatcattgaatcgaagacatttttggtc...

Basic information

species Zea mays
transcript GRMZM2G105631_T05
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G105631_T05 (Zea mays), 5'ss of exon 1
lower sequence: LOC_Os02g09930.2 (Oryza sativa), 5'ss of exon 5
GGCTGGGGGGTGGAAGGACCGGACCACGGTGGAGGACATGGATCTGGCCATCCGGGCCAGCCTCAAGGGCTGGAAGTTCGTCTACCTCGGTGACGTCCAGgtacg-gttgataccaacaatcatgggcatccagaaatttcagatggaatgcgatgcaactttctagcaccgctatcattgaatcg--aagacatttttggtc-----------------------------------------------------------------------------------------
||| || || ||||||||||||||||| |||||||||||||||||||| ||| |||| || || ||||| |||||||| |||||||| || || || |||||||      ||       ||| |   |||  |  |  || |||| | || | ||||| | || |  ||  ||| |   | | | |  |   |||||    ||                                                                                         
GGCGGGAGGATGGAAGGACCGGACCACAGTGGAGGACATGGATCTGGCAATCAGGGCGAGTCTTAAGGGATGGAAGTTTGTCTACCTTGGAGATGTTCAGgtacacaccaatcatggatatcctacacatg-atcagcttgagatagcatccaatgcatcctt-tgtcattgctcttgctaagttgctattgcatttcccttctttttctttttcttgaggaaatagtacattgattcatgttgcctaagagagaaaaaaaatgagtttaacaagaattgcgtcgttttcag

upper sequence: GRMZM2G105631_T05 (Zea mays), 5'ss of exon 1
lower sequence: GLYMA17G05350.1 (Glycine max), 5'ss of exon 5
GGCTGGGGGGTGGAAGGACCGGACCACGGTGGAGGACATGGATCTGGCCATCCGGGCCAGCCTCAAGGGCTGGAAGTTCGTCTACCTCGGTGACGTCCAGgtacggttgataccaacaatcatgggcatccagaaatttcagatggaatgcg-atgcaactttctagcaccgctatcat-tgaatcgaagacatttttggtc------------------------------------------------------------------------------------
 ||||| |||||||| ||| | || |||||||||||||||||||| ||  | || |||||||| | ||||||||||||  | |||||||| ||| | ||||||    |  |    | |   | | |     |  |||| || ||  | ||   || | || | ||   |  |  || || |||| |   |   | ||   ||                                                                                    
AGCTGGAGGGTGGAAAGACAGAACAACGGTGGAGGACATGGATCTTGCTGTTCGTGCCAGCCTTAGGGGCTGGAAGTTTTTGTACCTCGGAGACCTTCAGgtatacattttttttataccaacgcgaccttattaattcca-atcaattgtatatactacatgcttataatgg-atgatatgaagcatggttttgttaattctatcggcaatatttatctttacattttgtgtattagtaatgttctgtttctcattagtcatttacaaaaccaaactatgtatag

upper sequence: GRMZM2G105631_T05 (Zea mays), 5'ss of exon 1
lower sequence: Vv06s0061g01230.t01 (Vitis vinifera), 5'ss of exon 5
GGCTGGGGGGTGGAAGGACCGGACCACGGTGGAGGACATGGATCTGGCCATCCGGGCCAGCCTCAAGGGCTGGAAGTTCGTCTACCTCGGTGACGTCCAGgtacggttgataccaacaatcatgggcatccagaaatttcagatggaatgcgatgcaactttctagcaccgctatcattgaatcgaagacatttttggtc
|||||| |||||||||||| | || || ||||||||||||||||| ||| |||| || || |||||||||||||| ||||| || || |||||  | |||||||  || | |  ||      |  |         ||||||  |  | ||      | |||  |||    | | | |  |  ||    | |         
GGCTGGTGGGTGGAAGGACAGAACAACCGTGGAGGACATGGATCTTGCCGTCCGTGCTAGTCTCAAGGGCTGGAAATTCGTTTATCTTGGTGATCTTCAGgtacatttaa-ataaatgtctttaagttggggaccatttcatttaaattg----atagcttcttag--ttgatttaacggcttcatcaatag--------

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|9794218|gb|BE552526.1|BE552526
EST:     GGCCAGCCTC-AGGGCTGGAAGTTCGTCTACCTCGGTGACGTCCAG                         GTGAAAAGCGAGCTGCCGAGTACCTTCAAGGCCTTCCGGTTCCAGCAGCAC
genomic: GGCCAGCCTCAAGGGCTGGAAGTTCGTCTACCTCGGTGACGTCCAGgtacggttga ... attcctgcagGTGAAAAGCGAGCTGCCGAGTACCTTCAAGGCCTTCCGGTTCCAGCAGCAC
EST: gi|93284005|gb|EB676269.1|EB676269
EST:     TCCGGGCCAGCCTCAAGGGCTGGAAGTTCGTCTACCTCGGTGACGTCCAG                         GTGAAAAGCGAGCTGCCGAGTACCTTCAAGGCCTTCCGGTTCCAGCAGCAC
genomic: TCCGGGCCAGCCTCAAGGGCTGGAAGTTCGTCTACCTCGGTGACGTCCAGgtacggttga ... attcctgcagGTGAAAAGCGAGCTGCCGAGTACCTTCAAGGCCTTCCGGTTCCAGCAGCAC
EST: gi|71448756|gb|DR829806.1|DR829806
EST:     CTGGAAGTTCGTCTACCTCGGTGACGTCCAG                         GTGAAAAGCGAGCTGCCGAGTACCTTCAAGGCCTTCCGGTTCCAGCAGCAC
genomic: CTGGAAGTTCGTCTACCTCGGTGACGTCCAGgtacggttga ... attcctgcagGTGAAAAGCGAGCTGCCGAGTACCTTCAAGGCCTTCCGGTTCCAGCAGCAC
EST: gi|29167909|gb|CB411169.1|CB411169
EST:     GGGCTGGAAGTTCGTCTACCTCGG-GACGTCCAG                         GTG-AAAGCGAGCTGCCGAGTACCTTCAAGGCCTTCCGGTTCCAGCAGCAC
genomic: GGGCTGGAAGTTCGTCTACCTCGGTGACGTCCAGgtacggttga ... attcctgcagGTGAAAAGCGAGCTGCCGAGTACCTTCAAGGCCTTCCGGTTCCAGCAGCAC
EST: gi|76018154|gb|DT945324.1|DT945324
EST:     TCCGGGCCAGCCTCAAGGGCTGGAAGTTCGTCTACCTCGGTGACGTCCAG                         GTGAAAAGCGAGCTGCCGAGTACCTTCAAGGCCTTCCGGTTCCAGCAGCAC
genomic: TCCGGGCCAGCCTCAAGGGCTGGAAGTTCGTCTACCTCGGTGACGTCCAGgtacggttga ... attcctgcagGTGAAAAGCGAGCTGCCGAGTACCTTCAAGGCCTTCCGGTTCCAGCAGCAC
EST: gi|116829022|gb|EC863362.1|EC863362
EST:     TCGTCTACCTCGGTGACGTCCAG                         GTGAAAAGCGAGCTGCCGAGTA-CTTCAAGGCCTTCCGGGTTCCAGCAGCA
genomic: TCGTCTACCTCGGTGACGTCCAGgtacggttga ... attcctgcagGTGAAAAGCGAGCTGCCGAGTACCTTCAAGGCCTTCC-GGTTCCAGCAGCA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGCTGGGGGGTGGAAGGACCGGACCACGGTGGAGGACATGGATCTGGCCATCCGGGCCAGCCTCAAGGGCTGGAAGTTCGTCTACCTCGGTGACGTCCAGgtacggttgataccaacaatcatgggcatccagaaatttcagatggaatgcgatgcaactttctagcaccgctatcattgaatcgaagacatttttggtc

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG