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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CGACCCCGCGCCGCCGCACCTCGCCGGGCGCATCTCATTCCACCGCCTTAACATAAAAAACGACTCCAGGCTAGAGGGGCTCATCAAGATGGCCGATCTGgtcagttagtgcctattcttccacctatcttccttttttctttctcgattgcttactactacttggaatgcatttcgaattgactcacggatttcctcatcctctcctgccatgctgctgctgcttggatctgatctgcgcgccaag

Basic information

species Zea mays
transcript GRMZM2G063949_T01
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G063949_T01 (Zea mays), 5'ss of exon 1
lower sequence: LOC_Os01g73790.1 (Oryza sativa), 5'ss of exon 1
CGACCCCGCGCCGCCGCACCTCGCCGGGCGCATCTCATTCCACCGCCTTAACATAAAAAACGACTCCAGGCTAGAGGGGCTCATCAAGATGGCCGATCTGgtcagttagtgcctattcttccacctatcttccttttttctttctcgattgcttactactacttggaatgcatttcgaattgactcacggatttcctcatcctctcctgccatgctgctgctgcttggatctgatctgcgcgccaag
||||||||| || || ||||||   || |||||||| ||||||||||| ||||| || |||||||||||||| ||||| ||||||||||||||||||||||||  |   |  || | | |||     |  ||    ||||  ||||  ||  || ||  ||    |  |  ||| || ||   |  |                                                            
CGACCCCGCCCCTCCCCACCTCCATGGCCGCATCTCCTTCCACCGCCTCAACATCAAGAACGACTCCAGGCTCGAGGGCCTCATCAAGATGGCCGATCTGgtctctccctctctctccctcc-----tgctctcaatttcaatctcatttcatttctgataacacgccttgattccggatctgcgtag-----------------------------------------------------------

upper sequence: GRMZM2G063949_T01 (Zea mays), 5'ss of exon 1
lower sequence: GLYMA12G08930.1 (Glycine max), 5'ss of exon 1
CGACCCCGCGCCGCCGCACCTCGCCGGGCGCATCTCATTCCACCGCCTTAACATAAAAAACGACTCCAGGCTAGAGGGGCTCATCAAGATGGCCGATCTGgtcagttagtgcctattcttccacctatcttccttttttctttctcgattgcttactactacttggaatgcatttcgaattgactcacggatttcctcatcctctcctgccatgctgctgctgcttggatctgatctgcgcgccaag
||| ||| |     | | |   ||||| |||||| | ||||||||||| ||||| ||| |||||||  | || || || |||||||||||||| ||||| || |  || | |||  | |||    | | ||||| |||  ||| |   || |||   |     | |  |   | ||   || |                                                                
CGAACCCTCCGATTCCCCCTGGGCCGGCCGCATCACCTTCCACCGCCTCAACATCAAACACGACTCTCGCCTCGAAGGCCTCATCAAGATGGCAGATCTCgtaa--taataccttcttttctctttcttttcctctttgttttat---tttctttacatcgtatcgtttctttctccgtttcag---------------------------------------------------------------
















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|149113013|gb|EE295788.2|EE295788
EST:     ACATAAAAAACGACTCCAGGCTAGAGGGGCTCATCAAGATGGCCGATCTG                         ACCATAAACCTGGCCGCGATCTGCACGCCGGCCGACTACAACACTCGCCCA
genomic: ACATAAAAAACGACTCCAGGCTAGAGGGGCTCATCAAGATGGCCGATCTGgtcagttagt ... gcgcgccaagACCATAAACCTGGCCGCGATCTGCACGCCGGCCGACTACAACACTCGCCCA
EST: gi|149080206|gb|EE169228.2|EE169228
EST:     ACATAAAAAACGACTCCAGGCTAGAGGGGCTCATCAAGATGGCCGATCTG                         ACCATAAACCTGGCCGCGATCTGCACGCCGGCCGACTACAACACTCGCCCA
genomic: ACATAAAAAACGACTCCAGGCTAGAGGGGCTCATCAAGATGGCCGATCTGgtcagttagt ... gcgcgccaagACCATAAACCTGGCCGCGATCTGCACGCCGGCCGACTACAACACTCGCCCA
EST: gi|211213921|gb|FL245928.1|FL245928
EST:     ACATAAAAAACGACTCCAGGCTAGAGGGGCTCATCAAGATGGCCGATCTG                         ACCATAAACCTGGCCGCGATCTGCACGCCGGCCGACTACAACACTCGCCCA
genomic: ACATAAAAAACGACTCCAGGCTAGAGGGGCTCATCAAGATGGCCGATCTGgtcagttagt ... gcgcgccaagACCATAAACCTGGCCGCGATCTGCACGCCGGCCGACTACAACACTCGCCCA
EST: gi|21809590|gb|BQ667908.1|BQ667908
EST:     ACATAAAAAACGACTCCAGGCTAGAGGGGCTCATCAAGATGGCCGATCTG                         ACCATAAACCTGGCCGCGATCTGCACGCCGGCCGACTACAACACTCGCCCA
genomic: ACATAAAAAACGACTCCAGGCTAGAGGGGCTCATCAAGATGGCCGATCTGgtcagttagt ... gcgcgccaagACCATAAACCTGGCCGCGATCTGCACGCCGGCCGACTACAACACTCGCCCA
EST: gi|67020065|gb|CO448814.1|CO448814
EST:     ACATAAAAAACGACTCCAGGCTAGAGGGGCTCATCAAGATGGCCGATCTG                         ACCATAAACCTGGCCGCGATCTGCACGCCGGCCGACTACAACACTCGCCCA
genomic: ACATAAAAAACGACTCCAGGCTAGAGGGGCTCATCAAGATGGCCGATCTGgtcagttagt ... gcgcgccaagACCATAAACCTGGCCGCGATCTGCACGCCGGCCGACTACAACACTCGCCCA
EST: gi|109637685|gb|EC591230.1|EC591230
EST:     ACATAAAAAACGACTCCAGGCTAGAGGGGCTCATCAAGATGGCCGATCTG                         ACCATAAACCTGGCCGCGATCTGCACGCCGGCCGACTACAACACTCGCCCA
genomic: ACATAAAAAACGACTCCAGGCTAGAGGGGCTCATCAAGATGGCCGATCTGgtcagttagt ... gcgcgccaagACCATAAACCTGGCCGCGATCTGCACGCCGGCCGACTACAACACTCGCCCA
EST: gi|149086197|gb|EE175737.2|EE175737
EST:     ACATAAAAAACGACTCCAGGCTAGAGGGGCTCATCAAGATGGCCGATCTG                         ACCATAAACCTGGCCGCGATCTGCACGCCGGCCGACTACAACACTCGCCCA
genomic: ACATAAAAAACGACTCCAGGCTAGAGGGGCTCATCAAGATGGCCGATCTGgtcagttagt ... gcgcgccaagACCATAAACCTGGCCGCGATCTGCACGCCGGCCGACTACAACACTCGCCCA
EST: gi|101398997|gb|EB821371.1|EB821371
EST:     ACATAAAAAACGACTCCAGGCTAGAGGGGCTCATCAAGATGGCCGATCTG                         ACCATAAACCTGGCCGCGATCTGCACGCCGGCCGACTACAACACTCGCCCA
genomic: ACATAAAAAACGACTCCAGGCTAGAGGGGCTCATCAAGATGGCCGATCTGgtcagttagt ... gcgcgccaagACCATAAACCTGGCCGCGATCTGCACGCCGGCCGACTACAACACTCGCCCA
EST: gi|211216493|gb|FL245943.1|FL245943
EST:     ACATCAAAAACGACTCCAGGCTAGAGGGGCTCATCAAGATGGCCGATCTG                         ACCATAAACCTGGCCGCGATCTGCACGCCGGCCGACTACAACACTCGCCCA
genomic: ACATAAAAAACGACTCCAGGCTAGAGGGGCTCATCAAGATGGCCGATCTGgtcagttagt ... gcgcgccaagACCATAAACCTGGCCGCGATCTGCACGCCGGCCGACTACAACACTCGCCCA
EST: gi|116817633|gb|EC860508.1|EC860508
EST:     ACATAAAAAACGACTCCAGGCTAGAGGGGCTCATCAAGATGGCCGATCTG                         ACCATAAACCTGGCCGCGATCTGCACGCCGGCCGACTACAACACTCGCCCA
genomic: ACATAAAAAACGACTCCAGGCTAGAGGGGCTCATCAAGATGGCCGATCTGgtcagttagt ... gcgcgccaagACCATAAACCTGGCCGCGATCTGCACGCCGGCCGACTACAACACTCGCCCA
EST: gi|211216498|gb|FL245948.1|FL245948
EST:     ACATCAAAAACGACTCCAGGCTAGAGGGGCTCATCAAGATGGCCGATCTG                         ACCATAAACCTGGCCGCGATCTGCACGCCGGCCGACTACAACACTCGCCCA
genomic: ACATAAAAAACGACTCCAGGCTAGAGGGGCTCATCAAGATGGCCGATCTGgtcagttagt ... gcgcgccaagACCATAAACCTGGCCGCGATCTGCACGCCGGCCGACTACAACACTCGCCCA
EST: gi|211213924|gb|FL245931.1|FL245931
EST:     ACATCAAAAACGACTCCAGGCTAGAGGGGCTCATCAAGATGGCCGATCTG                         ACCATAAACCTGGCCGCGATCTGCACGCCGGCCGACTACAACACTCGCCCA
genomic: ACATAAAAAACGACTCCAGGCTAGAGGGGCTCATCAAGATGGCCGATCTGgtcagttagt ... gcgcgccaagACCATAAACCTGGCCGCGATCTGCACGCCGGCCGACTACAACACTCGCCCA
EST: gi|22472630|gb|BU037110.1|BU037110
EST:     ACATAAAAAACGACTCCAGGCTAGAGGGGCTCATCAAGATGGCCGATCTG                         ACCATAAACCTGGCCGCGATCTGCACGCCGGCCGACTACAACACTCGCCCA
genomic: ACATAAAAAACGACTCCAGGCTAGAGGGGCTCATCAAGATGGCCGATCTGgtcagttagt ... gcgcgccaagACCATAAACCTGGCCGCGATCTGCACGCCGGCCGACTACAACACTCGCCCA
EST: gi|67020590|gb|CO449339.1|CO449339
EST:     ACATAAAAAACGACTCCAGGCTAGAGGGGCTCATCAAGATGGCCGATCTG                         ACCATAAACCTGGCCGCGATCTGCACGCCGGCCGACTACAACACTCGCCCA
genomic: ACATAAAAAACGACTCCAGGCTAGAGGGGCTCATCAAGATGGCCGATCTGgtcagttagt ... gcgcgccaagACCATAAACCTGGCCGCGATCTGCACGCCGGCCGACTACAACACTCGCCCA
EST: gi|67011006|gb|CO439755.1|CO439755
EST:     ACATAAAAAACGACTCCAGGCTAGAGGGGCTCATCAAGATGGCCGATCTG                         ACCATAAACCTGGCCGCGATCTGCACGCCGGCCGACTACAACACTCGCCCA
genomic: ACATAAAAAACGACTCCAGGCTAGAGGGGCTCATCAAGATGGCCGATCTGgtcagttagt ... gcgcgccaagACCATAAACCTGGCCGCGATCTGCACGCCGGCCGACTACAACACTCGCCCA
EST: gi|211216491|gb|FL245941.1|FL245941
EST:     ACATAAAAAACGACTCCAGGCTAGAGGGGCTCATCAAGATGGCCGATCTG                         ACCATAAACCTGGCCGCGATCTGCACGCCGGCCGACTACAACACTCGCCCA
genomic: ACATAAAAAACGACTCCAGGCTAGAGGGGCTCATCAAGATGGCCGATCTGgtcagttagt ... gcgcgccaagACCATAAACCTGGCCGCGATCTGCACGCCGGCCGACTACAACACTCGCCCA
EST: gi|211216495|gb|FL245945.1|FL245945
EST:     ACATCAAAAACGACTCCAGGCTAGAGGGGCTCATCAAGATGGCCGATCTG                         ACCATAAACCTGGCCGCGATCTGCACGCCGGC-GACTACAACACTCGCCCA
genomic: ACATAAAAAACGACTCCAGGCTAGAGGGGCTCATCAAGATGGCCGATCTGgtcagttagt ... gcgcgccaagACCATAAACCTGGCCGCGATCTGCACGCCGGCCGACTACAACACTCGCCCA
EST: gi|211216489|gb|FL245939.1|FL245939
EST:     ACATCAAAAACGACTCCAGGCTAGAGGGGCTCATCAAGATGGCCGATCTG                         ACCATAAACCTGGCCGCGATCTGCACGCCGGCCGACTACAACACTCG
genomic: ACATAAAAAACGACTCCAGGCTAGAGGGGCTCATCAAGATGGCCGATCTGgtcagttagt ... gcgcgccaagACCATAAACCTGGCCGCGATCTGCACGCCGGCCGACTACAACACTCG
EST: gi|211216488|gb|FL245938.1|FL245938
EST:     ACATCAAAAACGACTCCAGGCTAGAGGGGCTCATCAAGATGGCCGATCTG                         ACCATAAACCTGGCCGCGATCTGCACG
genomic: ACATAAAAAACGACTCCAGGCTAGAGGGGCTCATCAAGATGGCCGATCTGgtcagttagt ... gcgcgccaagACCATAAACCTGGCCGCGATCTGCACG
EST: gi|31356398|gb|CD440755.1|CD440755
EST:     ACATAAAAAACGACTCCAGGCTAGAGGGGCTCATCAAGATGGCCGATCTG                         ACCATAAACCTGGCCGCGATCTGCACGCCGGCCGACTACAACACTCGCCCA
genomic: ACATAAAAAACGACTCCAGGCTAGAGGGGCTCATCAAGATGGCCGATCTGgtcagttagt ... gcgcgccaagACCATAAACCTGGCCGCGATCTGCACGCCGGCCGACTACAACACTCGCCCA
EST: gi|37418845|gb|CF647095.1|CF647095
EST:     ACATAAAAAACGACTCCAGGCTAGAGGGGCTCATCAAGATGGCCGATCTG                         ACCATAAACCTGGCCGCGATCTGCACGCCGGCCGACTACAACACTCGCCCA
genomic: ACATAAAAAACGACTCCAGGCTAGAGGGGCTCATCAAGATGGCCGATCTGgtcagttagt ... gcgcgccaagACCATAAACCTGGCCGCGATCTGCACGCCGGCCGACTACAACACTCGCCCA
EST: gi|211213923|gb|FL245930.1|FL245930
EST:     ACATAAAAAACGACTCCAGGCTAGAGGGGCTCATCAAGATGGCCGATCTG                         ACCATAAACCTGGCCGCGATCTGCACGCCGGCCGACTACAACACTCGCCCA
genomic: ACATAAAAAACGACTCCAGGCTAGAGGGGCTCATCAAGATGGCCGATCTGgtcagttagt ... gcgcgccaagACCATAAACCTGGCCGCGATCTGCACGCCGGCCGACTACAACACTCGCCCA
EST: gi|93281901|gb|EB674165.1|EB674165
EST:     ACATAAAAAACGACTCCAGGCTAGAGGGGCTCATCAAGATGGCCGATCTG                         ACCATAAACCTGGCCGCGATCTGCACGCCGGCCGACTACAACACTCGCCCA
genomic: ACATAAAAAACGACTCCAGGCTAGAGGGGCTCATCAAGATGGCCGATCTGgtcagttagt ... gcgcgccaagACCATAAACCTGGCCGCGATCTGCACGCCGGCCGACTACAACACTCGCCCA
EST: gi|31355714|gb|CD440071.1|CD440071
EST:     ACATAAAAAACGACTCCAGGCTAGAGGGGCTCATCAAGATGGCCGATCTG                         ACCATAAACCTGGCCGCGATCTGCACGCCGGCCGACTACAACACTCGCCCA
genomic: ACATAAAAAACGACTCCAGGCTAGAGGGGCTCATCAAGATGGCCGATCTGgtcagttagt ... gcgcgccaagACCATAAACCTGGCCGCGATCTGCACGCCGGCCGACTACAACACTCGCCCA
EST: gi|211213920|gb|FL245927.1|FL245927
EST:     ACATCAAAAACGACTCCAGGCTAGAGGGGCTCATCAAGATGGCCGATTTG                         ACCATAAACCTGGCCGCGATCTGCACGCCGGCCGACTACAACACTCGCCCA
genomic: ACATAAAAAACGACTCCAGGCTAGAGGGGCTCATCAAGATGGCCGATCTGgtcagttagt ... gcgcgccaagACCATAAACCTGGCCGCGATCTGCACGCCGGCCGACTACAACACTCGCCCA
EST: gi|61118012|gb|DN558973.1|DN558973
EST:     ACATAAAAAACGACTCCAGGCTAGAGGGGCTCATCAAGATGGCCGATCTG                         ACCATAAACCTGGCCGCGATCTGCACGCCGGCCGACTACAACACTCGCCCA
genomic: ACATAAAAAACGACTCCAGGCTAGAGGGGCTCATCAAGATGGCCGATCTGgtcagttagt ... gcgcgccaagACCATAAACCTGGCCGCGATCTGCACGCCGGCCGACTACAACACTCGCCCA
EST: gi|149098034|gb|EE183981.2|EE183981
EST:     ACATAAAAAACGACTCCAGGCTAGAGGGGCTCATCAAGATGGCCGATCTG                         ACCATAAACCTGGCCGCGATCTGCACGCCGGCCGACTACAACACTCGCCCA
genomic: ACATAAAAAACGACTCCAGGCTAGAGGGGCTCATCAAGATGGCCGATCTGgtcagttagt ... gcgcgccaagACCATAAACCTGGCCGCGATCTGCACGCCGGCCGACTACAACACTCGCCCA
EST: gi|211216496|gb|FL245946.1|FL245946
EST:     ACATAAAAAACGACTCCAGGCTAGAGGGGCTCATCAAGATGGCCGATCTG                         ACCATAAACCTGGCCGCGATCTGCACGCCGGCCGACTACAACACTCGCCCA
genomic: ACATAAAAAACGACTCCAGGCTAGAGGGGCTCATCAAGATGGCCGATCTGgtcagttagt ... gcgcgccaagACCATAAACCTGGCCGCGATCTGCACGCCGGCCGACTACAACACTCGCCCA
EST: gi|211213922|gb|FL245929.1|FL245929
EST:     ACATCAAAAACGACTCCAGGCTAGAGGGGCTCATCAAGATGGCCGATCTG                         ACCATAAACCTGGCCGCGATCTGCACGCCGGCCGACTACAACACTCGCCCA
genomic: ACATAAAAAACGACTCCAGGCTAGAGGGGCTCATCAAGATGGCCGATCTGgtcagttagt ... gcgcgccaagACCATAAACCTGGCCGCGATCTGCACGCCGGCCGACTACAACACTCGCCCA

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: 428

CGACCCCGCGCCGCCGCACCTCGCCGGGCGCATCTCATTCCACCGCCTTAACATAAAAAACGACTCCAGGCTAGAGGGGCTCATCAAGATGGCCGATCTGgtcagttagt ... gcgcgccaagACCATAAACCTGGCCGCGATCTGCACGCCGGCCGACTACAACACTCGCCCACTTGACACCATCTACAGCAACTTCATCGACGCACTCCCAGTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 136

CGACCCCGCGCCGCCGCACCTCGCCGGGCGCATCTCATTCCACCGCCTTAACATAAAAAACGACTCCAGGCTAGAGGGGCTCATCAAGATGGCCGATCTGgtcagttagt ... gcgcgccaagACCATAAACCTGGCCGCGATCTGCACGCCGGCCGACTACAACACTCGCCCACTTGACACCATCTACAGCAACTTCATCGACGCACTCCCAGTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 125

CGACCCCGCGCCGCCGCACCTCGCCGGGCGCATCTCATTCCACCGCCTTAACATAAAAAACGACTCCAGGCTAGAGGGGCTCATCAAGATGGCCGATCTGgtcagttagt ... gcgcgccaagACCATAAACCTGGCCGCGATCTGCACGCCGGCCGACTACAACACTCGCCCACTTGACACCATCTACAGCAACTTCATCGACGCACTCCCAGTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 288

CGACCCCGCGCCGCCGCACCTCGCCGGGCGCATCTCATTCCACCGCCTTAACATAAAAAACGACTCCAGGCTAGAGGGGCTCATCAAGATGGCCGATCTGgtcagttagt ... gcgcgccaagACCATAAACCTGGCCGCGATCTGCACGCCGGCCGACTACAACACTCGCCCACTTGACACCATCTACAGCAACTTCATCGACGCACTCCCAGTG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CGACCCCGCGCCGCCGCACCTCGCCGGGCGCATCTCATTCCACCGCCTTAACATAAAAAACGACTCCAGGCTAGAGGGGCTCATCAAGATGGCCGATCTGgtcagttagtgcctattcttccacctatcttccttttttctttctcgattgcttactactacttggaatgcatttcgaattgactcacggatttcctcatcctctcctgccatgctgctgctgcttggatctgatctgcgcgccaag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG