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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTGATGCTGCTCTTGATCTGAGCCACACTCAAAACATTGGTAGAATGATCAAGGCTCATTTTCCGCACTCTCAGgtaatatattcctgcttagtaaggaggtagtacattttaatatgtagcagatacaattaactaaatactgaaagtttgagctattgatttgtttttttgcag

Basic information

species Zea mays
transcript GRMZM2G006452_T02
intron # 13
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G006452_T01 (Zea mays), 5'ss of exon 13
lower sequence: LOC_Os01g67740.1 (Oryza sativa), 5'ss of exon 19
GTTGATGCTGCTCTTGATCTGAGCCACACTCAAAACATTGGTAGAATGATCAAGGCTCATTTTCCGCACTCTCAGgtaatatattcctgcttagt--aaggaggtagt-acattttaatatgtagcagatacaatt--aactaaatactgaaagtttgagcta--ttgatttgtttttttgcag----------------------------------------
||||||||||| || ||||||||||| || |||||||||||||||||||||||||| |||||||||||||| |||||| | |   || ||||  |  || || | | | |  |   | |    |    | |   ||  |   || |    || |  |   |||     |||| |||  |    |                                        
GTTGATGCTGCCCTAGATCTGAGCCATACACAAAACATTGGTAGAATGATCAAGGCGCATTTTCCGCACTCCCAGgta-tgtgc-ccagcttgctccaaagatgcaatcatgtgacagttcacaattcacatccttgcacacaatttacaaatgcatatactaggcaaatttatttcatcattggagttcagggttctgaaaattggtgctactacattttcag

upper sequence: GRMZM2G006452_T01 (Zea mays), 5'ss of exon 13
lower sequence: GLYMA13G27210.1 (Glycine max), 5'ss of exon 20
GTTGATGCTGCTCTTGATCTGAGCCACACTCAAAACATTGGTAGAATGATCAAGGCTCATTTTCCGCACTCTCAGgtaatatattcctgcttagtaaggaggtagtacattttaatatgtagcagatacaattaactaaatactgaaagtt-tgagctattgatttgtttttttgcag
|||||||| ||||||||| |||||||||| |||||||| || |||||||| |||||||| ||||||||||||||||||    ||   || | | |   |  ||   |  | ||   || | |    | |||||    ||| | | | ||     | |   | |||     || |  | 
GTTGATGCAGCTCTTGATTTGAGCCACACACAAAACATAGGGAGAATGATAAAGGCTCACTTTCCGCACTCTCAGgtagaggataattgttca-tgttgtcgtgtgatttcttgcaatcttgtctttccaattc-taaaaaattaatagccacaaacctcttattgtaggttataaa-

upper sequence: GRMZM2G006452_T01 (Zea mays), 5'ss of exon 13
lower sequence: GLYMA12G36520.1 (Glycine max), 5'ss of exon 20
GTTGATGCTGCTCTTGATCTGAGCCACACTCAAAACATTGGTAGAATGATCAAGGCTCATTTTCCGCACTCTCAGgtaatatattcctgctta-gtaaggaggtagtacattttaatatgtagcagatacaattaactaaatactgaaa--gtttgagctatt--gatttgtttttttgcag-----------------------------------------------------------------------
|||||||| ||||||||| |||||||||| |||||||| || |||||||| |||||||| ||||||||||||||||||    ||   || | | ||      ||  |   ||||  | | | | | |     |    |   | |||  |  |||  |   |||  ||  |||  ||||  |                                                                        
GTTGATGCAGCTCTTGATTTGAGCCACACACAAAACATAGGGAGAATGATAAAGGCTCACTTTCCGCACTCTCAGgtagaggataattgttgatgttgtcgtgtgat-ttttttggtttcttgtatacttc-tccttttggttctgctattgttaaattcattctgacatgtcattttcaaagttcctgctagtgacagttcagcatccaataagttgaataacctcatttctttggttcttttgatttgcag

upper sequence: GRMZM2G006452_T01 (Zea mays), 5'ss of exon 13
lower sequence: AT5G62410.1 (Arabidopsis thaliana), 5'ss of exon 19
GTTGATGCTGCTCTTGATCTGAGCCACACTCAAAACATTGGTAGAATGATCAAGGCTCATTTTCCGCACTCTCAGgtaatatattcctgcttagtaaggaggtagtacattttaatatgtagcagatacaattaact--aaatactgaa-agtttgagctattga---tttgtttttttgcag
|||||||| ||||||||||| || ||||| || ||||| || |||||||| |  |||||||| || ||||| |||||  || ||  ||  ||          || || | | |  ||||||     |  |   || |       || || | |||  ||| || |   |   |  ||   |||
GTTGATGCAGCTCTTGATCTCAGTCACACACAGAACATAGGAAGAATGATAAGAGCTCATTTCCCTCACTCGCAGgtc-taaatctctatttcaagccttactaatatactcttctatgtatttacttaatccaattttggtctctaaacattttctgctttttaaactcgatgcttaaacag

upper sequence: GRMZM2G006452_T01 (Zea mays), 5'ss of exon 13
lower sequence: AT3G47460.1 (Arabidopsis thaliana), 5'ss of exon 19
GTTGATGCTGCTCTTGATCTGAGCCACACTCAAAACATTGGTAGAATGATCAAGGCTCATTTTCCGCACTCTCAGgtaatatattcctg-------cttagtaaggaggtagtacattttaatatgtagcagatacaattaactaaatactgaaagtttgagctat-tgatttg--tttttttgcag
|||||||| ||||||||||| |||||||| || ||||| || |||||||| ||  ||||||| || || || ||||| |||  ||   |       || | |  | ||  |  |   || || | |    || ||    ||  || ||    ||  ||   ||| | |||| ||  || | || |||
GTTGATGCAGCTCTTGATCTAAGCCACACACAGAACATAGGAAGAATGATAAAATCTCATTTCCCACATTCACAGgtcataattttacggatttctctgattgtgtagtcaccatgattcaaaaagctttagttat--ctatttatatctcaaacattactgctgtctgatatgatttctcttacag

upper sequence: GRMZM2G006452_T01 (Zea mays), 5'ss of exon 13
lower sequence: Vv16s0022g00060.t01 (Vitis vinifera), 5'ss of exon 19
GTTGATGCTGCTCTTGATCTGAGCCACACTCAAAACATTGGTAGAATGATCAAGGCTCATTTTCCGCACTCTCAGgt-aatatattcctgcttagtaaggaggtagtacattttaatatgtagcagatacaattaactaaatactg--aaagtttgagctattgatttgtttttttgcag
|| |||||||| |||||| | || ||||||||||||||||| |||||||| ||  | ||||| || || || ||||| | || ||   |  ||  ||      | || |   | |  |||| | |   ||  ||   |  || ||   ||| |||  | ||||  ||||    ||     
GTCGATGCTGCCCTTGATTTAAGTCACACTCAAAACATTGGAAGAATGATTAAATCCCATTTCCCACATTCCCAGgttagtaaatatatattt--tattttatttgttctcatcagcatgttg-attcacttttctttttatcctcctaaactttaggatatttttttgccaattgaa--

upper sequence: GRMZM2G006452_T01 (Zea mays), 5'ss of exon 13
lower sequence: PP1S52_57V6.1 (Physcomitrella patens), 5'ss of exon 20
GTTGATGCTGCTCTTGATCTGAGCCACACTCAAAACATTGGTAGAATGATCAAGGCTCATTTTCCGCACTCTCAGgtaatatattcc--tgcttagtaaggaggt-agtacattttaatatgtagcagatacaattaa--ctaaatactgaaagtttgagctattgatttgtttttttgcag----------------------------------------
|| || |||||||||||| |||| ||||| || ||||| |||||||||||||| |  || ||||| ||||| ||||||  | | |    ||    || |   |   |||   |  | |||      ||   || ||||  |||  |||| ||     || || |||    ||| |     |                                         
GTGGACGCTGCTCTTGATTTGAGTCACACACAGAACATAGGTAGAATGATCAAAGAACACTTTCCACACTCGCAGgtacgaaagttaaatgtcctgtcatttgtcgagtttttagtgatagtcttgagtagcagttaatcctatctacttaactcgcgaccttttgtgaagttataagatatcaaggcacttacattgtgcctgtgttgtaattttggtcag

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|60343263|gb|DN210236.1|DN210236
EST:     ACACTCAAAACATTGGTAGAATGATCAAGGCTCATTTTCCGCACTCTCAG                         TTCATAGTTGTCTCTTTAAAAGAGGGTATGTTCAACAACGCCAATGTGATA
genomic: ACACTCAAAACATTGGTAGAATGATCAAGGCTCATTTTCCGCACTCTCAGgtaatatatt ... ttttttgcagTTCATAGTTGTCTCTTTAAAAGAGGGTATGTTCAACAACGCCAATGTGATA
EST: gi|211376362|gb|FL264047.1|FL264047
EST:     ACACTCAAAACATTGGTAGAATGATCAAGGCTCATTTTCCGCACTCTCAG                         TTCATAGTTGTCTCTTTAAAAGAGGGTATGTTCAACAACGCCAATGTGAT
genomic: ACACTCAAAACATTGGTAGAATGATCAAGGCTCATTTTCCGCACTCTCAGgtaatatatt ... ttttttgcagTTCATAGTTGTCTCTTTAAAAGAGGGTATGTTCAACAACGCCAATGTGAT
EST: gi|22473074|gb|BU037554.1|BU037554
EST:     ACACTCAAAACATTGGTAGAATGATCAAGGCTCATTTTCCGCACTCTCAG                         TTCATAGTTGTCTCTTTAAAAGAGGGTATGTTCAACAACGCCAATGTGATA
genomic: ACACTCAAAACATTGGTAGAATGATCAAGGCTCATTTTCCGCACTCTCAGgtaatatatt ... ttttttgcagTTCATAGTTGTCTCTTTAAAAGAGGGTATGTTCAACAACGCCAATGTGATA
EST: gi|60342521|gb|DN209494.1|DN209494
EST:     ACACTCAAAACATTGGTAGAATGATCAAGGCTCATTTTCCGCACTCTCAG                         TTCATAGTTGTCTCTTTAAAAGAGGGTATGTTCAACAACGCCAATGTGATA
genomic: ACACTCAAAACATTGGTAGAATGATCAAGGCTCATTTTCCGCACTCTCAGgtaatatatt ... ttttttgcagTTCATAGTTGTCTCTTTAAAAGAGGGTATGTTCAACAACGCCAATGTGATA
EST: gi|5525454|gb|AI861347.1|AI861347
EST:     TTGGTAGAATGATCAAGGCTCATTTTCCGCACTCTCAG                         TTCATAGTTGTCTCTTTAAAAGAGGGTATGTTCAACAACGCCAATGTGATA
genomic: TTGGTAGAATGATCAAGGCTCATTTTCCGCACTCTCAGgtaatatatt ... ttttttgcagTTCATAGTTGTCTCTTTAAAAGAGGGTATGTTCAACAACGCCAATGTGATA
EST: gi|6031321|gb|AW076178.1|AW076178
EST:     ACACTCAAAACATTGGTAGAATGATCAAGGCTCATTTTCCGCACTCTCAG                         TTCATAGTTGTCTCTTTAAAAGAGGGTATGTTCAACAACGC
genomic: ACACTCAAAACATTGGTAGAATGATCAAGGCTCATTTTCCGCACTCTCAGgtaatatatt ... ttttttgcagTTCATAGTTGTCTCTTTAAAAGAGGGTATGTTCAACAACGC

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 4 RNA-Seq libraries.


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 175

GTTGATGCTGCTCTTGATCTGAGCCACACTCAAAACATTGGTAGAATGATCAAGGCTCATTTTCCGCACTCTCAGgtaatatatt ... ttttttgcagTTCATAGTTGTCTCTTTAAAAGAGGGTATGTTCAACAACGCCAATGTGATATTTCGAACAAAATTTGTTGATGGTGTGTCCACCGTGACACGAACAGTGC


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 14

GTTGATGCTGCTCTTGATCTGAGCCACACTCAAAACATTGGTAGAATGATCAAGGCTCATTTTCCGCACTCTCAGgtaatatatt ... ttttttgcagTTCATAGTTGTCTCTTTAAAAGAGGGTATGTTCAACAACGCCAATGTGATATTTCGAACAAAATTTGTTGATGGTGTGTCCACCGTGACACGAACAGTGC


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 47

GTTGATGCTGCTCTTGATCTGAGCCACACTCAAAACATTGGTAGAATGATCAAGGCTCATTTTCCGCACTCTCAGgtaatatatt ... ttttttgcagTTCATAGTTGTCTCTTTAAAAGAGGGTATGTTCAACAACGCCAATGTGATATTTCGAACAAAATTTGTTGATGGTGTGTCCACCGTGACACGAACAGTGC


Block sizes: 47 (upstream exon), 48 (downstream exon)
Score: 19

GTTGATGCTGCTCTTGATCTGAGCCACACTCAAAACATTGGTAGAATGATCAAGGCTCATTTTCCGCACTCTCAGgtaatatatt ... ttttttgcagTTCATAGTTGTCTCTTTAAAAGAGGGTATGTTCAACAACGCCAATGTGATATTTCGAACAAAATTTGTTGATGGTGTGTCCACCGTGACACGAACAGTGC