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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGGAAAATGGCTGATATGTACACCTCATTGCAGTCATCAAGgtaagaccttgctcaatattttccttacaagtttagacatcttatcactacaacttcatttttccatcag

Basic information

species Zea mays
transcript GRMZM2G052630_T01
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G052630_T01 (Zea mays), 5'ss of exon 10
lower sequence: LOC_Os05g03480.2 (Oryza sativa), 5'ss of exon 11
GGGAAAATGGCTGATATGTACACCTCATTGCAGTCATCAAGgtaag---accttgctcaatattt-tccttacaagtttagacatcttatcactacaacttcatttttccatcag
|||||| |||| |||||||||||||| ||||||||||||||||| |   | ||| ||||| | || | || ||| |||||  ||| |  | |||  | |||  ||| |   | ||
GGGAAATTGGCAGATATGTACACCTCCTTGCAGTCATCAAGgtatgcatatctt-ctcaagacttatactgacaggtttaagcatatccttactgaagctttctttgttgtttag
















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|24769404|gb|CA404533.1|CA404533
EST:     GGGAAAATGGCTGATATGTACACCTCATTGCAGTCATCAAG                         ATCATTTGTATACTCGGTTGCTAGGGACTGCGATAATGGCAAAGTTGATCG
genomic: GGGAAAATGGCTGATATGTACACCTCATTGCAGTCATCAAGgtaagacctt ... tttccatcagATCATTTGTATACTCGGTTGCTAGGGACTGCGATAATGGCAAAGTTGATCG
EST: gi|110190881|gb|EC872779.1|EC872779
EST:     GGGAAAATGGCTGATATGTACACCTCATTGCAGTCATCAAG                         ATCATTTGTATACTCGGTTGCTAGGGACTGCGATAATGGCAAAGTTGATCG
genomic: GGGAAAATGGCTGATATGTACACCTCATTGCAGTCATCAAGgtaagacctt ... tttccatcagATCATTTGTATACTCGGTTGCTAGGGACTGCGATAATGGCAAAGTTGATCG
EST: gi|31354622|gb|CD438979.1|CD438979
EST:     GGGAAAATGGCTGATATGTACACCTCATTGCAGTCATCAAG                         ATCATTTGTATACTCGGTTGCTAGGGACTGCGATAATGGCAAAGTTGAT
genomic: GGGAAAATGGCTGATATGTACACCTCATTGCAGTCATCAAGgtaagacctt ... tttccatcagATCATTTGTATACTCGGTTGCTAGGGACTGCGATAATGGCAAAGTTGAT
EST: gi|78105056|gb|DV523474.1|DV523474
EST:     GGGAAAATGGCTGATATGTACACCTCATTGCAGTCATCAAG                         ATCATTTGTATACTCGGTTGCTAGGGACTGCGATAATGGCAAAGTTGATCG
genomic: GGGAAAATGGCTGATATGTACACCTCATTGCAGTCATCAAGgtaagacctt ... tttccatcagATCATTTGTATACTCGGTTGCTAGGGACTGCGATAATGGCAAAGTTGATCG
EST: gi|31360769|gb|CD445126.1|CD445126
EST:     GGGAAAATGGCTGATATGTACACCTCATTGCAGTCATCAAG                         ATCATTTGTATACTCGGCTGCTAGGGACTGCGATAATGGCAAAGTTGATCG
genomic: GGGAAAATGGCTGATATGTACACCTCATTGCAGTCATCAAGgtaagacctt ... tttccatcagATCATTTGTATACTCGGTTGCTAGGGACTGCGATAATGGCAAAGTTGATCG
EST: gi|60347547|gb|DN214520.1|DN214520
EST:     GGGAAAATGGCTGATATGTACACCTCATTGCAGTCATCAAG                         ATCATTTGTATACTCGGTTGCTAGGGACTGCGATAATGGCAAAGTTGATCG
genomic: GGGAAAATGGCTGATATGTACACCTCATTGCAGTCATCAAGgtaagacctt ... tttccatcagATCATTTGTATACTCGGTTGCTAGGGACTGCGATAATGGCAAAGTTGATCG
EST: gi|78027006|gb|DV495393.1|DV495393
EST:     GGGAAAATGGCTGATATGTACACCTCATTGCAGTCATCAAG                         ATCATTTGTATACTCGGTTGCTAGGGACTGCGATAATGGCAAAGTTGATCG
genomic: GGGAAAATGGCTGATATGTACACCTCATTGCAGTCATCAAGgtaagacctt ... tttccatcagATCATTTGTATACTCGGTTGCTAGGGACTGCGATAATGGCAAAGTTGATCG
EST: gi|5108421|gb|AI740134.1|AI740134
EST:     GGGAAAATGGCTGATATGTACACCTCATTGCAGTCATCAAG                         ATCATTTGTATACTCGGTTGCTAGGGACTGCGATAATGGCAAAGTTGATCG
genomic: GGGAAAATGGCTGATATGTACACCTCATTGCAGTCATCAAGgtaagacctt ... tttccatcagATCATTTGTATACTCGGTTGCTAGGGACTGCGATAATGGCAAAGTTGATCG
EST: gi|74240406|gb|DT648320.1|DT648320
EST:     GGGAAAATGGCTGATATGTACACCTCATTGCAGTCATCAAG                         ATCATTTGTATACTCGGTTGCTAGGGACTGCGATAATGGCAAAGTTGATCG
genomic: GGGAAAATGGCTGATATGTACACCTCATTGCAGTCATCAAGgtaagacctt ... tttccatcagATCATTTGTATACTCGGTTGCTAGGGACTGCGATAATGGCAAAGTTGATCG
EST: gi|76936507|gb|DV174755.1|DV174755
EST:     GGGAAAATGGCTGATATGTACACCTCATTGCAGTCATCAAG                         ATCATTTGTATACTCGGTTGCTAGGGACTGCGATAATGGCAAAGTTGATCG
genomic: GGGAAAATGGCTGATATGTACACCTCATTGCAGTCATCAAGgtaagacctt ... tttccatcagATCATTTGTATACTCGGTTGCTAGGGACTGCGATAATGGCAAAGTTGATCG
EST: gi|50336352|gb|CO531478.1|CO531478
EST:     GGGAAAATGGCTGATATGTACACCTCATTGCAGTCATCAAG                         ATCATTTGTATACTCGGTTGCTAGGGACTGCGATAATGGCAAAGTTGATCG
genomic: GGGAAAATGGCTGATATGTACACCTCATTGCAGTCATCAAGgtaagacctt ... tttccatcagATCATTTGTATACTCGGTTGCTAGGGACTGCGATAATGGCAAAGTTGATCG
EST: gi|78124549|gb|DV542933.1|DV542933
EST:     GGGAAAATGGCTGATATGTACACCTCATTGCAGTCATCAAG                         ATCATTTGTATACTCGGTTGCTAGGGACTGCGATAATGGCAAAGTTGATCG
genomic: GGGAAAATGGCTGATATGTACACCTCATTGCAGTCATCAAGgtaagacctt ... tttccatcagATCATTTGTATACTCGGTTGCTAGGGACTGCGATAATGGCAAAGTTGATCG
EST: gi|110195625|gb|EC877522.1|EC877522
EST:     ATTGCAGTCATCAAG                         ATCATTTGTATACTCGGTTGCTAGGGACTGCGATAATGGCAAAGTTGATCG
genomic: ATTGCAGTCATCAAGgtaagacctt ... tttccatcagATCATTTGTATACTCGGTTGCTAGGGACTGCGATAATGGCAAAGTTGATCG
EST: gi|110525230|gb|EE029414.1|EE029414
EST:     GGGAAAATGGCTGATATGTACACCTCATTGCAGTCATCAAG                         ATCATTTGTATACTCGGTTGCTAGGGACTGCGATAATGGCAAAGTTGATCG
genomic: GGGAAAATGGCTGATATGTACACCTCATTGCAGTCATCAAGgtaagacctt ... tttccatcagATCATTTGTATACTCGGTTGCTAGGGACTGCGATAATGGCAAAGTTGATCG
EST: gi|149076167|gb|EE164757.2|EE164757
EST:     GGGAAAATGGCTGATATGTACACCTCATTGCAGTCATCAAG                         ATCATTTGTATACTCGGTTGCTAGGGACTGCGATAATGGCAAAGTTGATCG
genomic: GGGAAAATGGCTGATATGTACACCTCATTGCAGTCATCAAGgtaagacctt ... tttccatcagATCATTTGTATACTCGGTTGCTAGGGACTGCGATAATGGCAAAGTTGATCG

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: 41 (upstream exon), 49 (downstream exon)
Score: 75

GGGAAAATGGCTGATATGTACACCTCATTGCAGTCATCAAGgtaagacctt ... tttccatcagATCATTTGTATACTCGGTTGCTAGGGACTGCGATAATGGCAAAGTTGATCGCAAG


Block sizes: 41 (upstream exon), 49 (downstream exon)
Score: 555

GGGAAAATGGCTGATATGTACACCTCATTGCAGTCATCAAGgtaagacctt ... tttccatcagATCATTTGTATACTCGGTTGCTAGGGACTGCGATAATGGCAAAGTTGATCGCAAG


Block sizes: 41 (upstream exon), 49 (downstream exon)
Score: 441

GGGAAAATGGCTGATATGTACACCTCATTGCAGTCATCAAGgtaagacctt ... tttccatcagATCATTTGTATACTCGGTTGCTAGGGACTGCGATAATGGCAAAGTTGATCGCAAG


Block sizes: 41 (upstream exon), 49 (downstream exon)
Score: 82

GGGAAAATGGCTGATATGTACACCTCATTGCAGTCATCAAGgtaagacctt ... tttccatcagATCATTTGTATACTCGGTTGCTAGGGACTGCGATAATGGCAAAGTTGATCGCAAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGGAAAATGGCTGATATGTACACCTCATTGCAGTCATCAAGgtaagaccttgctcaatattttccttacaagtttagacatcttatcactacaacttcatttttccatcag

- - - -  GCTGAT