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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AATTGGCCTCCTTTTCTGCCACTCATCCATCATGATATCACCAATGAGATACCGAGTCACCTTCAAAGAATGCAATATGTTGCATTTGCGTCGTTTCTTGgtatgctgcctctgattctcaatgtcatgaaacctttcactctgatgaataatcttcaatattctcttttatttaatgttgcaatggacatgttttccat...

Basic information

species Zea mays
transcript GRMZM2G041181_T01
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G041181_T01 (Zea mays), 5'ss of exon 6
lower sequence: LOC_Os07g37740.1 (Oryza sativa), 5'ss of exon 6
AATTGGCCTCCTTTTCTGCCACTCATCCATCATGATATCACCAATGAGATACCGAGTCACCTTCAAAGAATGCAATATGTTGCATTTGCGTCGTTTCTTGgtatgctgcctctgattctcaatgtcatgaaacctttcactctgatgaataatcttcaatattctctt--ttatttaatgttgcaatggacatgttttccat------
|| |||||||| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| || ||||||||||||||   ||||||| |||   ||   ||| |||  |  ||  || |    ||||  ||   | ||   |   |||||    |        || ||| |       
AACTGGCCTCCATTTCTGCCACTCATCCATCATGATATCACCAATGAGATACCGAGTCACCTTCAAAGAATGCAATATGTTGCATTTGCATCATTTCTTGgtatgct---tctgattgtcagattcccaaaatcttg-atgctcttgca----cttcggtaacgttttaactgcataatggacaagcattttagtcttctacaaagtt

upper sequence: GRMZM2G041181_T01 (Zea mays), 5'ss of exon 6
lower sequence: GLYMA15G07480.2 (Glycine max), 5'ss of exon 6
AATTGGCCTCCTTTTCTGCCACTCATCCATCATGATATCACCAATGAGATACCGAGTCACCTTCAAAGAATGCAATATGTTGCATTTGCGTCGTTTCTTGgtatgctgcctctgattct-caatgtcatgaaacctttcactctgatgaataatcttcaatattctcttt----tatttaatgttgcaatggacatgttttccat
|||||||| || ||| | ||| | ||||||||||||||  | ||||| ||||| | ||| ||||||||| |||| |||||||||||| | || ||  | |||| | |  | |   || | |    |    | |  |||        ||| |  | || ||     ||||       | | |||  ||| ||   || |  |    
AATTGGCCGCCATTTTTCCCAATTATCCATCATGATATTGCTAATGAAATACCAATTCATCTTCAAAGATTGCAGTATGTTGCATTTACTTCATTGTTAGgtaagttatcccatcttttgctccattgcaatatgttttgtatcattgagttgtttttaagccattcttgagggcgtctcatgc-gcattgattatttcat----

upper sequence: GRMZM2G041181_T01 (Zea mays), 5'ss of exon 6
lower sequence: GLYMA13G31830.1 (Glycine max), 5'ss of exon 6
AATTGGCCTCCTTTTCTGCCACTCATCCATCATGATATCACCAATGAGATACCGAGTCACCTTCAAAGAATGCAATATGTTGCATTTGCGTCGTTTCTTGgtatgctgcctctgattct-caatgtcatgaaacctttcactctgatgaataatcttcaatattctcttttatttaatgttgcaatggacatgttttccat
    |||| || ||| | ||| | ||||||||||||||| | ||||| || || | ||| ||||||||| |||| |||||||||||| | || ||  | |||| | |  | |   || |      |    | |   ||  |     ||| |  | || ||     ||||                                
----GGCCGCCATTTTTCCCAATTATCCATCATGATATCGCTAATGAAATTCCAATTCATCTTCAAAGATTGCAGTATGTTGCATTTACTTCATTGTTAGGTAAgttatcccatcttttgttccattgcaatatggtttgcatcattgagttgtttttaagccattcttaag-----------------------------

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|76929603|gb|DV172080.1|DV172080
EST:     ACCGAGTCACCTTCAAAGAATGCAATATGTTGCATTTGCGTCGTTTCTTG                         GGTTGGTTTGCTGCCTCTTCTGGAATGTCATAGCAGTTACTACAGCTTGGA
genomic: ACCGAGTCACCTTCAAAGAATGCAATATGTTGCATTTGCGTCGTTTCTTGgtatgctgcc ... tattgaatagGGTTGGTTTGCTGCCTCTTCTGGAATGTCATAGCAGTTACTACAGCTTGGA
EST: gi|71301449|gb|DR786760.1|DR786760
EST:     ACCGAGTCACCTTCAAAGAATGCAATATGTTGCATTTGCGTCGTTTCTTG                         GGTTGGTTTGCTGCCTCTTCTGGAATGTCATAGCAGTTACTACAGCTTGGA
genomic: ACCGAGTCACCTTCAAAGAATGCAATATGTTGCATTTGCGTCGTTTCTTGgtatgctgcc ... tattgaatagGGTTGGTTTGCTGCCTCTTCTGGAATGTCATAGCAGTTACTACAGCTTGGA
EST: gi|32906331|gb|CF011144.1|CF011144
EST:     ACCGAGTCACCTTCAAAGAATGCAATATGTTGCATTTGCGTCGTTTCTTG                         GGTTGGTTTGCTGCCTCTTCTGGAATGTCATAGCAGTTACTACAGCTTGGA
genomic: ACCGAGTCACCTTCAAAGAATGCAATATGTTGCATTTGCGTCGTTTCTTGgtatgctgcc ... tattgaatagGGTTGGTTTGCTGCCTCTTCTGGAATGTCATAGCAGTTACTACAGCTTGGA
EST: gi|76018527|gb|DT945697.1|DT945697
EST:     ACCGAGTCACCTTCAAAGAATGCAATATGTTGCATTTGCGTCGTTTCTTG                         GGTTGGTTTGCTGCCTCTTCTGGAATGTCATAGCAGTTACTACAGCTTGGA
genomic: ACCGAGTCACCTTCAAAGAATGCAATATGTTGCATTTGCGTCGTTTCTTGgtatgctgcc ... tattgaatagGGTTGGTTTGCTGCCTCTTCTGGAATGTCATAGCAGTTACTACAGCTTGGA
EST: gi|22819595|gb|BU499685.1|BU499685
EST:     ACCGAGTCACCTTCAAAGAATGCAATATGTTGCATTTGCGTCGTTTCTTG                         GGTTGGTTTGCTGCCTCTTCTGGAATGTCATAGCAGTTACTACAGCTTGGA
genomic: ACCGAGTCACCTTCAAAGAATGCAATATGTTGCATTTGCGTCGTTTCTTGgtatgctgcc ... tattgaatagGGTTGGTTTGCTGCCTCTTCTGGAATGTCATAGCAGTTACTACAGCTTGGA
EST: gi|37621887|gb|CF674940.1|CF674940
EST:     ACCGAGTCACCTTCAAAGAATGCAATATGTTGCATTTGCGTCGTTTCTTG                         GGTTGGTTTGCTGCCTCTTCTGGAATGTCATAGCAGTTACTACAGCTTGGA
genomic: ACCGAGTCACCTTCAAAGAATGCAATATGTTGCATTTGCGTCGTTTCTTGgtatgctgcc ... tattgaatagGGTTGGTTTGCTGCCTCTTCTGGAATGTCATAGCAGTTACTACAGCTTGGA
EST: gi|28566548|gb|CB278196.1|CB278196
EST:     ACCGAGTCACCTTCAAAGAATGCAATATGTTGCATTTGCGTCGTTTCTTG                         GGTTGGTTTGCTGCCTCTTCTGGAATGTCATAGCAGTTACTACAGCTTGGA
genomic: ACCGAGTCACCTTCAAAGAATGCAATATGTTGCATTTGCGTCGTTTCTTGgtatgctgcc ... tattgaatagGGTTGGTTTGCTGCCTCTTCTGGAATGTCATAGCAGTTACTACAGCTTGGA
EST: gi|74239804|gb|DT647718.1|DT647718
EST:     ACCGAGTCACCTTCAAAGAATGCAATATGTTGCATTTGCGTCGTTTCTTG                         GGTTGGTTTGCTGCCTCTTCTGGAATGTCATAGCAGTTACTACAGCTTGGA
genomic: ACCGAGTCACCTTCAAAGAATGCAATATGTTGCATTTGCGTCGTTTCTTGgtatgctgcc ... tattgaatagGGTTGGTTTGCTGCCTCTTCTGGAATGTCATAGCAGTTACTACAGCTTGGA
EST: gi|42491841|gb|CK700887.1|CK700887
EST:     ACCGAGTCACCTTCAAAGAATGCAATATGTTGCATTTGCGTCGTTTCTTG                         GGTTGGTTTGCTGCCTCTTCTGGAATCTCATAGCAGTTACTACAGCTTGGA
genomic: ACCGAGTCACCTTCAAAGAATGCAATATGTTGCATTTGCGTCGTTTCTTGgtatgctgcc ... tattgaatagGGTTGGTTTGCTGCCTCTTCTGGAATGTCATAGCAGTTACTACAGCTTGGA
EST: gi|149076171|gb|EE164763.2|EE164763
EST:     ACCGAGTCACCTTCAAAGAATGCAATATGTTGCATTTGCGTCGTTTCTTG                         GGTTGGTTTGCTGCCTCTTCTGGAATGTCATAGCAGTTACTACAGCTTGGA
genomic: ACCGAGTCACCTTCAAAGAATGCAATATGTTGCATTTGCGTCGTTTCTTGgtatgctgcc ... tattgaatagGGTTGGTTTGCTGCCTCTTCTGGAATGTCATAGCAGTTACTACAGCTTGGA
EST: gi|50322749|gb|CO517875.1|CO517875
EST:     ACCGAGTCACCTTCAAAGAATGCAATATGTTGCATTTGCGTCGTTTCTTG                         GGTTGGTTTGCTGCCTCTTCTGGAATGTCATAGCAGTTACTACAGCTTGGA
genomic: ACCGAGTCACCTTCAAAGAATGCAATATGTTGCATTTGCGTCGTTTCTTGgtatgctgcc ... tattgaatagGGTTGGTTTGCTGCCTCTTCTGGAATGTCATAGCAGTTACTACAGCTTGGA
EST: gi|37622034|gb|CF675087.1|CF675087
EST:     ACCGAGTCACCTTCAAAGAATGCAATATGTTGCATTTGCGTCGTTTCTTG                         GGTTGGTTTGCTGCCTCTTCTGGAATGTCATAGCAGTTACTACAGCTTGGA
genomic: ACCGAGTCACCTTCAAAGAATGCAATATGTTGCATTTGCGTCGTTTCTTGgtatgctgcc ... tattgaatagGGTTGGTTTGCTGCCTCTTCTGGAATGTCATAGCAGTTACTACAGCTTGGA
EST: gi|67033086|gb|CO461835.1|CO461835
EST:     ACCGAGTCACCTTCAAAGAATGCAATATGTTGCATTTGCGTCGTTTCTTG                         GGTTGGTTTGCTGCCTCTTCTGGAATGTCATAGCAGTTACTACAGCTTGGA
genomic: ACCGAGTCACCTTCAAAGAATGCAATATGTTGCATTTGCGTCGTTTCTTGgtatgctgcc ... tattgaatagGGTTGGTTTGCTGCCTCTTCTGGAATGTCATAGCAGTTACTACAGCTTGGA
EST: gi|94472178|gb|EB701136.1|EB701136
EST:     ACCGAGTCACCTTCAAAGAATGCAATATGTTGCATTTGCGTCGTTTCTTG                         GGTTGGTTTGCTGCCTCTTCTGGAATGTCATAGCAGTTACTACAGCTTGGA
genomic: ACCGAGTCACCTTCAAAGAATGCAATATGTTGCATTTGCGTCGTTTCTTGgtatgctgcc ... tattgaatagGGTTGGTTTGCTGCCTCTTCTGGAATGTCATAGCAGTTACTACAGCTTGGA
EST: gi|110944605|gb|EE164762.1|EE164762
EST:     TCACCTTCAAAGAATGCAATATGTTGCATTTGCGTCGTTTCTTG                         GGTTGGTTTGCTGCCTCTTCTGGAATGTCATAGCAGTTACTACAGCTTGGA
genomic: TCACCTTCAAAGAATGCAATATGTTGCATTTGCGTCGTTTCTTGgtatgctgcc ... tattgaatagGGTTGGTTTGCTGCCTCTTCTGGAATGTCATAGCAGTTACTACAGCTTGGA
EST: gi|38568932|gb|CF974817.1|CF974817
EST:     ACCGAGTCACCTTCAAAGAATGCAATATGTTGCATTTGCGTCGTTTCTTG                         GGTTGGTTTGCTGCCTCTTCTGGAATGTCATAGCAGTTACTACAGCTTGGA
genomic: ACCGAGTCACCTTCAAAGAATGCAATATGTTGCATTTGCGTCGTTTCTTGgtatgctgcc ... tattgaatagGGTTGGTTTGCTGCCTCTTCTGGAATGTCATAGCAGTTACTACAGCTTGGA
EST: gi|50325032|gb|CO520158.1|CO520158
EST:     ACCGAGTCACCTTCAAAGAATGCAATATGTTGCATTTGCGTCGTTTCTTG                         GGTTGGTTTGCTGCCTCTTCTGGAATGTCATAGCAGTTACTACAGCTTGGA
genomic: ACCGAGTCACCTTCAAAGAATGCAATATGTTGCATTTGCGTCGTTTCTTGgtatgctgcc ... tattgaatagGGTTGGTTTGCTGCCTCTTCTGGAATGTCATAGCAGTTACTACAGCTTGGA
EST: gi|37361385|gb|CF602674.1|CF602674
EST:     ACCGAGTCACCTTCAAAGAATGCAATATGTTGCATTTGCGTCGTTTCTTG                         GGTTGGTTTGCTGCCTCTTCTGGAATGTCATAGCAGTTACTACAGCTTGGA
genomic: ACCGAGTCACCTTCAAAGAATGCAATATGTTGCATTTGCGTCGTTTCTTGgtatgctgcc ... tattgaatagGGTTGGTTTGCTGCCTCTTCTGGAATGTCATAGCAGTTACTACAGCTTGGA

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), 49 (downstream exon)
Score: 131

AATTGGCCTCCTTTTCTGCCACTCATCCATCATGATATCACCAATGAGATACCGAGTCACCTTCAAAGAATGCAATATGTTGCATTTGCGTCGTTTCTTGgtatgctgcc ... tattgaatagGGTTGGTTTGCTGCCTCTTCTGGAATGTCATAGCAGTTACTACAGCTTGGATCAAGGGGGAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 193

AATTGGCCTCCTTTTCTGCCACTCATCCATCATGATATCACCAATGAGATACCGAGTCACCTTCAAAGAATGCAATATGTTGCATTTGCGTCGTTTCTTGgtatgctgcc ... tattgaatagGGTTGGTTTGCTGCCTCTTCTGGAATGTCATAGCAGTTACTACAGCTTGGATCAAGGGGGAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 143

AATTGGCCTCCTTTTCTGCCACTCATCCATCATGATATCACCAATGAGATACCGAGTCACCTTCAAAGAATGCAATATGTTGCATTTGCGTCGTTTCTTGgtatgctgcc ... tattgaatagGGTTGGTTTGCTGCCTCTTCTGGAATGTCATAGCAGTTACTACAGCTTGGATCAAGGGGGAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 294

AATTGGCCTCCTTTTCTGCCACTCATCCATCATGATATCACCAATGAGATACCGAGTCACCTTCAAAGAATGCAATATGTTGCATTTGCGTCGTTTCTTGgtatgctgcc ... tattgaatagGGTTGGTTTGCTGCCTCTTCTGGAATGTCATAGCAGTTACTACAGCTTGGATCAAGGGGGAAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AATTGGCCTCCTTTTCTGCCACTCATCCATCATGATATCACCAATGAGATACCGAGTCACCTTCAAAGAATGCAATATGTTGCATTTGCGTCGTTTCTTGgtatgctgcctctgattctcaatgtcatgaaacctttcactctgatgaataatcttcaatattctcttttatttaatgttgcaatggacatgttttccat

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA