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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCTGTGCCACGGCTTTTGCCTACTACGCACAAGCAACTGCAGCTCAAGAGATATTTGGCCACACTTTGCAATCCCTTCGTGGAATTAAGTATCTTTACAAgttagtctcccaaatgaagagcagatttagttgctctgttttacaggtgttgtagacattattaaatttcgactgtattctgatcctttaccacaaaacatgcag

Basic information

species Zea mays
transcript GRMZM2G012284_T01
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G012284_T01 (Zea mays), 5'ss of exon 10
lower sequence: LOC_Os06g03760.2 (Oryza sativa), 5'ss of exon 12
TCTGTGCCACGGCTTTTGCCTACTACGCACAAGCAACTGCAGCTCAAGAGATATTTGGCCACACTTTGCAATCCCTTCGTGGAATTAAGTATCTTTACAAgttagtctcc------caaatgaagagcagattta--gttgctctgttttacagg-------------tgttgtagacatt-----attaaa-tttcgactgtattctgatcctttaccacaaaacatgcag
|||||||||| |||||||| || || || ||||||||||||||||| ||||| |||||||||||  ||||||| || ||||||||||||||||| |||||||  || ||       |||||  | ||    ||||  |||| |   |   | | |             ||| || || |||     || ||| ||| ||   | |||||||  || ||  |  || ||||||
TCTGTGCCACAGCTTTTGCTTATTATGCGCAAGCAACTGCAGCTCAGGAGATCTTTGGCCACACACTGCAATCTCTCCGTGGAATTAAGTATCTCTACAAgtatgtatctagcatgcaaatccatagtcagtttacagttgtttgctcgaataagctggatatatccatgtggtggatattggagcatcaaacttttgaaaatgttctgatt-ttaacatctgaatatgcag

upper sequence: GRMZM2G012284_T01 (Zea mays), 5'ss of exon 10
lower sequence: GLYMA07G18160.1 (Glycine max), 5'ss of exon 12
TCTGTGCCACGGCTTTTGCCTACTACGCACAAGCAACTGCAGCTCAAGAGATATTTGGCCACACTTTGCAATCCCTTCGTGGAATTAAGTATCTTTACAAgttagtctcccaaatgaagagcagatttagttgctctgttttacag-gtgttgtagacattattaaatttcgactgtattctgatcctttaccacaaaacatgcag
||||  |||| || ||||||||||| || |||||||||||||| || || |||||||||||||||||| | || ||||| |||||||| ||| | ||||||| ||||   |          | |  |   ||||||||  ||| |  | |    | |   |       ||   ||   || |    ||  | |||| ||       
TCTGCTCCACAGCATTTGCCTACTATGCTCAAGCAACTGCAGCCCAGGAAATATTTGGCCACACTTTGGAGTCTCTTCGAGGAATTAAATATTTGTACAAgtgagtcaatcgggatttcttctgcctctcttgctctgccttatactggggcaaaaatggtcccttccttttgctaagttgtagatctagagcacacaat------

upper sequence: GRMZM2G012284_T01 (Zea mays), 5'ss of exon 10
lower sequence: GLYMA03G07890.1 (Glycine max), 5'ss of exon 12
TCTGTGCCACGGCTTTTGCCTACTACGCACAAGCAACTGCAGCTCAAGAGATATTTGGCCACACTTTGCAATCCCTTCGTGGAATTAAGTATCTTTACAAgttagtctcccaaatgaagagcagatttagttgctctgttttacaggtgttgtagacattattaaatttcgactgtattctgatcctttacc-acaaaacatgcag
||||  |||| || ||||||||||| || |||||||||||||| || || |||||||||||||| ||| | || |||||||||||||| ||| | ||||||| ||||   |      |        | | |  | |       | | |   ||  | ||  | || | | ||   ||  ||  || |||||   ||||   |    
TCTGCTCCACAGCATTTGCCTACTATGCTCAAGCAACTGCAGCACAGGAAATATTTGGCCACACCTTGGAGTCTCTTCGTGGAATTAAATATTTGTACAAgtaagtcaagctgg-atatttttccctcactctccccaaccctctgattgggtgaagat-gtgaagtatagaacctaaacttttcgtttacttgcaaattgt----

upper sequence: GRMZM2G012284_T01 (Zea mays), 5'ss of exon 10
lower sequence: GLYMA16G19230.1 (Glycine max), 5'ss of exon 11
TCTGTGCCACGGCTTTTGCCTACTACGCACAAGCAACTGCAGCTCAAGAGATATTTGGCCACACTTTGCAATCCCTTCGTGGAATTAAGTATCTTTACAAgttagtctcccaaatgaagagcagatttagttgctctgttttacag-gtgttgtagacattattaaatttcgactgtattctgatcctttaccacaaaacatgcag
||||  |||| || ||||||||||| || |||||||||||||| || || |||||||||||||||||| | || ||||| |||||||| ||| | ||||||| ||||   |          | |  |   ||||||||  ||| |  | |    | |   |       ||   ||   || |    ||  | |||| ||       
TCTGCTCCACAGCATTTGCCTACTATGCTCAAGCAACTGCAGCCCAGGAAATATTTGGCCACACTTTGGAGTCTCTTCGAGGAATTAAATATTTGTACAAgtgagtcaatctggatttcttctgcctctcttgctctgccttatactggggcaaaaatggtcccttccttttgctaagttgtagatctagagcacacaat------

upper sequence: GRMZM2G012284_T01 (Zea mays), 5'ss of exon 10
lower sequence: GLYMA01G30400.1 (Glycine max), 5'ss of exon 12
TCTGTGCCACGGCTTTTGCCTACTACGCACAAGCAACTGCAGCTCAAGAGATATTTGGCCACACTTTGCAATCCCTTCGTGGAATTAAGTATCTTTACAAgttagtctc-ccaaatgaagagcagatttagttgctctgttttacaggtgttgtagacattattaaatttcgactgtattctgatcctttaccacaaaacatgcag
||||  |||| || ||||||||||| || |||||||||||||| || || |||||||||||||| ||| |||| |||||||||||||| ||| | ||||||| ||||   |   ||      |        || | |     |   | |   ||  | |   | || | | ||   ||  ||  || || ||    |||  |    
TCTGCTCCACAGCATTTGCCTACTATGCTCAAGCAACTGCAGCACAGGAAATATTTGGCCACACCTTGGAATCTCTTCGTGGAATTAAATATTTGTACAAgtaagtcaagctggatatttttcccgcgctcttccccaaccct-tggattgggtgaagac-gtgaagtatagaacctacacttttcgttaacttgcaaattt----

upper sequence: GRMZM2G012284_T01 (Zea mays), 5'ss of exon 10
lower sequence: GLYMA18G43020.1 (Glycine max), 5'ss of exon 12
TCTGTGCCACGGCTTTTGCCTACTACGCACAAGCAACTGCAGCTCAAGAGATATTTGGCCACACTTTGCAATCCCTTCGTGGAATTAAGTATCTTTACAAgttagtctcccaaatgaagagcagatttagttgctctgttttacaggtgttgtagacattattaaat--ttcgactgtattctgatcctttaccacaaaacatgcag
||||  |||| || ||||||||||| || |||||||||||||| || || |||||||| ||||||||| | || ||||| |||||||| ||| | ||||||| ||||   |          | |  |    |||||||  || | ||||  | | | ||  |    |  ||  ||| | || | |  ||  | |||| ||       
TCTGCTCCACAGCATTTGCCTACTATGCTCAAGCAACTGCAGCCCAGGAAATATTTGGTCACACTTTGGAGTCTCTTCGAGGAATTAAATATTTGTACAAgtgagtcagtctgg-attcttctgcctctcctgctctgcctt-ctggtggggcaaaaatggtcccttcttttcactatgttgtaaatctagagcacacaatg-----

upper sequence: GRMZM2G012284_T01 (Zea mays), 5'ss of exon 10
lower sequence: AT5G01460.1 (Arabidopsis thaliana), 5'ss of exon 12
TCTGTGCCACGGCTTTTGCCTACTACGCACAAGCAACTGCAGCTCAAGAGATATTTGGCCACACTTTGCAATCCCTTCGTGGAATTAAGTATCTTTACAAgttagtctcccaaatgaagagcagatttagttgctctgttttacaggtgttgtagacattattaaatttcgactgtattctgatcctttaccacaaaacatgcag
|||| ||||| || ||||  || || || ||||| || || ||||| ||||||||||||||||||||||| |||||||| || |||||||| || ||||||| |||              ||| ||  || | |||  || |  |  |      ||   || |   |  |     |||    ||| || |               
TCTGCGCCACTGCATTTGGATATTATGCTCAAGCCACCGCCGCTCAGGAGATATTTGGCCACACTTTGCAGTCCCTTCGCGGTATTAAGTACCTCTACAAgtaagtaatatcgggtttttgcaaataaaggt-ctcacttgtgtacataagactgatgataatct-tccctttcttatcggtatctttcag--------------

upper sequence: GRMZM2G012284_T01 (Zea mays), 5'ss of exon 10
lower sequence: AT3G08930.1 (Arabidopsis thaliana), 5'ss of exon 12
TCTGTGCCACGGCTTTTGCCTACTACGCACAAGCAACTGCAGCTCAAGAGATATTTGGCCACACTTTGCAATCCCTTCGTGGAATTAAGTATCTTTACAAgttagtctcccaaatgaagagcagatttagttgctctgttttacaggtgttgtagacattattaaatttcgactgtattctgatcctttaccacaaaacatgcag
| |||||||| || ||||  || ||||| ||||| ||||| || || ||||||||||||||||| ||||| |||||| | ||||||||||| |||||||||| |||      ||     |  | || |||  |   | |  || |   ||  |     ||||| |  ||    | ||||                          
TTTGTGCCACTGCATTTGGATATTACGCTCAAGCCACTGCTGCCCAGGAGATATTTGGCCACACATTGCAGTCCCTTAGAGGAATTAAGTACCTTTACAAgtaagta----gaagtggtataacatatagcagtcatatgctatatccgtgatgcgtcttattgaggtt---ttatatttcag----------------------

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|76288405|gb|DV027973.1|DV027973
EST:     ATATTTGGCCACACTTTGCAATCCCTTCGTGGAATTAAGTATCTTTACAA                         GTACAATGTTTTCCAGTATGGCTTTGTTGCTCTTGCCATCCTCACTCTCTT
genomic: ATATTTGGCCACACTTTGCAATCCCTTCGTGGAATTAAGTATCTTTACAAgttagtctcc ... aaacatgcagGTACAATGTTTTCCAGTATGGCTTTGTTGCTCTTGCCATCCTCACTCTCTT
EST: gi|67039856|gb|CO466111.1|CO466111
EST:     ATATTTGGCCACACTTTGCAATCCCTTCGTGGAATTAAGTATCTTTACAA                         GTACAATGTTTTCCAGTATGGCTTTGTTGCTCTTGCCATCCTCACTCTCTT
genomic: ATATTTGGCCACACTTTGCAATCCCTTCGTGGAATTAAGTATCTTTACAAgttagtctcc ... aaacatgcagGTACAATGTTTTCCAGTATGGCTTTGTTGCTCTTGCCATCCTCACTCTCTT
EST: gi|76288406|gb|DV027974.1|DV027974
EST:     ATATTTGGCCACACTTTGCAATCCCTTCGTGGAATTAAGTATCTTTACAA                         GTACAATGTTTTTCAGTATGGCTTTGTTGCTCTTGCCATCCTCACTCTCTT
genomic: ATATTTGGCCACACTTTGCAATCCCTTCGTGGAATTAAGTATCTTTACAAgttagtctcc ... aaacatgcagGTACAATGTTTTCCAGTATGGCTTTGTTGCTCTTGCCATCCTCACTCTCTT
EST: gi|91872772|gb|EB402729.1|EB402729
EST:     ATATTTGGCCACACTTTGCAATCCCTTCGTGGAATTAAGTATCTTTACAA                         GTACAATGTTTTCCAGTATGGCTTTGTTGCTCTTGCCATCCTCACTCTCTT
genomic: ATATTTGGCCACACTTTGCAATCCCTTCGTGGAATTAAGTATCTTTACAAgttagtctcc ... aaacatgcagGTACAATGTTTTCCAGTATGGCTTTGTTGCTCTTGCCATCCTCACTCTCTT
EST: gi|67024981|gb|CO453730.1|CO453730
EST:     ATATTTGGCCACACTTTGCAATCCCTTCGTGGAATTAAGTATCTTTACAA                         GTACAATGTTTTCCAGTATGGCTTTGTTGCTCTTGCCATCCTCACTCTCTT
genomic: ATATTTGGCCACACTTTGCAATCCCTTCGTGGAATTAAGTATCTTTACAAgttagtctcc ... aaacatgcagGTACAATGTTTTCCAGTATGGCTTTGTTGCTCTTGCCATCCTCACTCTCTT
EST: gi|71763789|gb|DR961726.1|DR961726
EST:     ATATTTGGCCACACTTTGCAATCCCTTCGTGGAATTAAGTATCTTTACAA                         GTACAATGTTTTCCAGTATGGCTTTGTTGCTCTTGCCATCCTCACTCTCTT
genomic: ATATTTGGCCACACTTTGCAATCCCTTCGTGGAATTAAGTATCTTTACAAgttagtctcc ... aaacatgcagGTACAATGTTTTCCAGTATGGCTTTGTTGCTCTTGCCATCCTCACTCTCTT
EST: gi|6952443|gb|AW424511.1|AW424511
EST:     ATTAAGTATCTTTACAA                         GTACAATGTTTTCCAGTATGGCTTTGTTGCTCTTGCCATCCTCACTCTCTT
genomic: ATTAAGTATCTTTACAAgttagtctcc ... aaacatgcagGTACAATGTTTTCCAGTATGGCTTTGTTGCTCTTGCCATCCTCACTCTCTT
EST: gi|71449543|gb|DR830593.1|DR830593
EST:     ATATTTGGCCACACTTTGCAATCCCTTCGTGGAATTAAGTATCTTTACAA                         GTACAATGTTTTCCAGTATGGCTTTGTTGCTCTTGCCATCCTCACTCTCTT
genomic: ATATTTGGCCACACTTTGCAATCCCTTCGTGGAATTAAGTATCTTTACAAgttagtctcc ... aaacatgcagGTACAATGTTTTCCAGTATGGCTTTGTTGCTCTTGCCATCCTCACTCTCTT
EST: gi|148962661|gb|EE013558.2|EE013558
EST:     TTGCAATCCCTTCGTGGAATTAAGTATCTTTACAA                         GTACAATGTTTTCCAGTATGGCTTTGTTGCTCTTGCCATCCTCACTCTCTT
genomic: TTGCAATCCCTTCGTGGAATTAAGTATCTTTACAAgttagtctcc ... aaacatgcagGTACAATGTTTTCCAGTATGGCTTTGTTGCTCTTGCCATCCTCACTCTCTT
EST: gi|33942467|gb|CF349067.1|CF349067
EST:     ATATTTGGCCACACTTTGCAATCCCTTCGTGGAATTAAGTATCTTTACAA                         GTACAATGTTTTCCAGTATGGCTTTGTTGCTCTTGCCATCCTCACTCTCTT
genomic: ATATTTGGCCACACTTTGCAATCCCTTCGTGGAATTAAGTATCTTTACAAgttagtctcc ... aaacatgcagGTACAATGTTTTCCAGTATGGCTTTGTTGCTCTTGCCATCCTCACTCTCTT

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: 49 (upstream exon), 48 (downstream exon)
Score: 306

TCTGTGCCACGGCTTTTGCCTACTACGCACAAGCAACTGCAGCTCAAGAGATATTTGGCCACACTTTGCAATCCCTTCGTGGAATTAAGTATCTTTACAAgttagtctcc ... aaacatgcagGTACAATGTTTTCCAGTATGGCTTTGTTGCTCTTGCCATCCTCACTCTCTTCTACTATGCTATATTT


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 257

TCTGTGCCACGGCTTTTGCCTACTACGCACAAGCAACTGCAGCTCAAGAGATATTTGGCCACACTTTGCAATCCCTTCGTGGAATTAAGTATCTTTACAAgttagtctcc ... aaacatgcagGTACAATGTTTTCCAGTATGGCTTTGTTGCTCTTGCCATCCTCACTCTCTTCTACTATGCTATATTT


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 269

TCTGTGCCACGGCTTTTGCCTACTACGCACAAGCAACTGCAGCTCAAGAGATATTTGGCCACACTTTGCAATCCCTTCGTGGAATTAAGTATCTTTACAAgttagtctcc ... aaacatgcagGTACAATGTTTTCCAGTATGGCTTTGTTGCTCTTGCCATCCTCACTCTCTTCTACTATGCTATATTT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 355

TCTGTGCCACGGCTTTTGCCTACTACGCACAAGCAACTGCAGCTCAAGAGATATTTGGCCACACTTTGCAATCCCTTCGTGGAATTAAGTATCTTTACAAgttagtctcc ... aaacatgcagGTACAATGTTTTCCAGTATGGCTTTGTTGCTCTTGCCATCCTCACTCTCTTCTACTATGCTATATTT