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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...caagttcaaacaagtcatcagtagtcatgcttcatggctatatatatgttccgatagtcctgtatttagtcactgacaagtgttttctacaatttctcagGGACAACCAAAATCAAGAATCTAGATTCCAACATTGACTCCTTGAAGGTGAAACTGACAGACGAAGATCTGAAAGAAATGGGCAGCCAGATACGGGAAGA

Basic information

species Zea mays
transcript GRMZM2G024315_T01
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G024315_T01 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os01g43090.1 (Oryza sativa), 3'ss of exon 6
caagttcaaaca-agtcatcagtagtcatgcttcatggctatatatatgttccgatagtcctgtattta---gtcactgacaagtg-ttttctacaatttctcagGGACAACCAAAATCAAGAATCTAGATTCCAACATTGACTCCTTGAAGGTGAAACTGACAGACGAAGATCTGAAAGAAATGGGCAGCCAGATACGGGAAGA
 |    ||| ||  | ||| || ||  | |||     | | | | |||| ||  |||  ||   ||| |    ||||||| ||    ||   |||| ||||||||| |||||||| || || || |||||| |||||||||||||||| |||||||| || || || || || |||||||| ||    |||||| |||| |||||
-agtcccaagcacggacataagcagcaaagctc----gttgtttgtatgctctaatatgccgtgattgatccatcactgagaaacaattcgttacattttctcagGAACAACCAAGATAAAAAACCTAGATGCCAACATTGACTCCTTAAAGGTGAACCTCACGGATGATGACCTGAAAGAGATCTCTAGCCAGGTACGCGAAGA
















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|14244154|gb|BG842002.2|BG842002
EST:     AGCTTTAGCATGGGTTCTGCATCAAGGAGATGATGTGGCTCCTATACCAG                         GGACAACCAAAATCAAGAATCTAGATTCCAACATTGACTGCTTGAAGGTGA
genomic: AGCTTTAGCATGGGTTCTGCATCAAGGAGATGATGTGGTTCCTATACCAGgtgttacctt ... aatttctcagGGACAACCAAAATCAAGAATCTAGATTCCAACATTGACTCCTTGAAGGTGA
EST: gi|91878930|gb|EB408887.1|EB408887
EST:     AGCTTTAGCATGGGTTCTGCCTCAAGGAGATGATGTGGTTCCTATACCAG                         GGACAACCAAAATCAAGAATCTAGATTCCCACATTGACTCCTTGAAGGTGA
genomic: AGCTTTAGCATGGGTTCTGCATCAAGGAGATGATGTGGTTCCTATACCAGgtgttacctt ... aatttctcagGGACAACCAAAATCAAGAATCTAGATTCCAACATTGACTCCTTGAAGGTGA
EST: gi|93011652|gb|EB637172.1|EB637172
EST:     AGCTTTAGCATGGGTTCTGCATCAAGGAGATGATGTGGTTCCTATACCAG                         GGACAACCAAAATCAAGAATCTAGATTCCAACATTGACTCCTTGAAGGTGA
genomic: AGCTTTAGCATGGGTTCTGCATCAAGGAGATGATGTGGTTCCTATACCAGgtgttacctt ... aatttctcagGGACAACCAAAATCAAGAATCTAGATTCCAACATTGACTCCTTGAAGGTGA
EST: gi|78090110|gb|DV518484.1|DV518484
EST:     AGCTTTAGCATGGGTTTTGCATCAAGGAGATGATGTGGTTCCTATACCAG                         GGACAACCAAAATCAAGAATTTAGATTCCAACATTGACTCCTTGAAGGTGA
genomic: AGCTTTAGCATGGGTTCTGCATCAAGGAGATGATGTGGTTCCTATACCAGgtgttacctt ... aatttctcagGGACAACCAAAATCAAGAATCTAGATTCCAACATTGACTCCTTGAAGGTGA
EST: gi|71327902|gb|DR800585.1|DR800585
EST:     AGCTTTAGCATGGGTTCTGCATCAAGGAGATGATGTGGTTCCTATACCAG                         GGACAACCAAAATCAAGAATCTAGATTCCAACATTGACTCCTTGAAGGTGA
genomic: AGCTTTAGCATGGGTTCTGCATCAAGGAGATGATGTGGTTCCTATACCAGgtgttacctt ... aatttctcagGGACAACCAAAATCAAGAATCTAGATTCCAACATTGACTCCTTGAAGGTGA
EST: gi|148929206|gb|EC874773.2|EC874773
EST:     AGCTTTAGCATGGGTTTTGCATCAAGGAGATGATGTGGTTCCTATACCAG                         GGACAACCAAAATCAAGAATCTAGATTCCAACATTGACTCCTTGAAGGTGA
genomic: AGCTTTAGCATGGGTTCTGCATCAAGGAGATGATGTGGTTCCTATACCAGgtgttacctt ... aatttctcagGGACAACCAAAATCAAGAATCTAGATTCCAACATTGACTCCTTGAAGGTGA
EST: gi|71759316|gb|DR957253.1|DR957253
EST:     AGCTTTAGCATGGGTTCTGCATCAAGGAGATGATGTGGTTCCTATACCAG                         GGACAACCAAAATCAAGAATCTAGATTCCAACATTGACTCCTTGAAGGTGA
genomic: AGCTTTAGCATGGGTTCTGCATCAAGGAGATGATGTGGTTCCTATACCAGgtgttacctt ... aatttctcagGGACAACCAAAATCAAGAATCTAGATTCCAACATTGACTCCTTGAAGGTGA
EST: gi|37386431|gb|CF630401.1|CF630401
EST:     AGCTTTAGCATGGGTTCTGCATCAAGGAGATGATGTGGTTCCTATACCAG                         GGACAACCAAAATCAAGAATCTAGATTCCAACATTGACTCCTTGAAGGTGA
genomic: AGCTTTAGCATGGGTTCTGCATCAAGGAGATGATGTGGTTCCTATACCAGgtgttacctt ... aatttctcagGGACAACCAAAATCAAGAATCTAGATTCCAACATTGACTCCTTGAAGGTGA
EST: gi|60399433|gb|DN232245.1|DN232245
EST:     AGCTTTAGCATGGGTTCTGCATCAAGGAGATGATGTGGTTCCTATACCAG                         GGACAACCAAAATCAAGAATCTAGATTCCAACATTGACTCCTTGAAGGTGA
genomic: AGCTTTAGCATGGGTTCTGCATCAAGGAGATGATGTGGTTCCTATACCAGgtgttacctt ... aatttctcagGGACAACCAAAATCAAGAATCTAGATTCCAACATTGACTCCTTGAAGGTGA
EST: gi|37382589|gb|CF628250.1|CF628250
EST:     AGCTTTAGCATGGGTTCTGCATCAAGGAGATGATGTGGTTCCTATACCAG                         GGACAACCAAAATCAAGAATCTAGATTCCAACATTGACTCCTTGAAGGTGA
genomic: AGCTTTAGCATGGGTTCTGCATCAAGGAGATGATGTGGTTCCTATACCAGgtgttacctt ... aatttctcagGGACAACCAAAATCAAGAATCTAGATTCCAACATTGACTCCTTGAAGGTGA
EST: gi|71430217|gb|DR811267.1|DR811267
EST:     AGCTTTAGCATGGGTTTTGCATCAAGGAGATGATGTGGTTCTTATACCAG                         GGACAACCAAAATCAAGAATCTAGATTCCAACATTGACTCCTTGAAGGTGA
genomic: AGCTTTAGCATGGGTTCTGCATCAAGGAGATGATGTGGTTCCTATACCAGgtgttacctt ... aatttctcagGGACAACCAAAATCAAGAATCTAGATTCCAACATTGACTCCTTGAAGGTGA
EST: gi|60396046|gb|DN228916.1|DN228916
EST:     AGCTTTAGCATGGGTTCTGCATCAAGGAGATGATGTGGTTCCTATACCAG                         GGACAACCAAAATCAAGAATCTAGATTCCAACATTGACTCCTTGAAGGTGA
genomic: AGCTTTAGCATGGGTTCTGCATCAAGGAGATGATGTGGTTCCTATACCAGgtgttacctt ... aatttctcagGGACAACCAAAATCAAGAATCTAGATTCCAACATTGACTCCTTGAAGGTGA
EST: gi|18181122|gb|BM382332.1|BM382332
EST:     AGCTTTAGCATGGGTTCTGCATCAAGGAGATGATGTGGTTCCTATACCAG                         GGACAACCAAAATCAAGAATCTAGATTCCAACATTGACTCCTTGAAGGTGA
genomic: AGCTTTAGCATGGGTTCTGCATCAAGGAGATGATGTGGTTCCTATACCAGgtgttacctt ... aatttctcagGGACAACCAAAATCAAGAATCTAGATTCCAACATTGACTCCTTGAAGGTGA
EST: gi|149014829|gb|EE044531.2|EE044531
EST:     AGCTTTAGCATGGGTTCTGCATCAAGGAGATGATGTGGTTCCTATACCAG                         GGACAACCAAAATCAAGAATCTAGATTCCAACATTGACTCCTTGAAGGTGA
genomic: AGCTTTAGCATGGGTTCTGCATCAAGGAGATGATGTGGTTCCTATACCAGgtgttacctt ... aatttctcagGGACAACCAAAATCAAGAATCTAGATTCCAACATTGACTCCTTGAAGGTGA
EST: gi|14204195|gb|BG837872.1|BG837872
EST:     AGCTTTAGCATGGGTTTTGCATCAAGGCGATGATGTGGTTCCTATACCAG                         GGACAACCAAAATCAAGAATCTAGATTCCAACATTGACTCCTTGAAGGTGA
genomic: AGCTTTAGCATGGGTTCTGCATCAAGGAGATGATGTGGTTCCTATACCAGgtgttacctt ... aatttctcagGGACAACCAAAATCAAGAATCTAGATTCCAACATTGACTCCTTGAAGGTGA

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), 48 (downstream exon)
Score: 50

TTGCGAATGGAAGAACTGGCCAATAAGCACCAGTGCAGCCCTGCTCAGCTAGCTTTAGCATGGGTTCTGCATCAAGGAGATGATGTGGTTCCTATACCAGgtgttacctt ... aatttctcagGGACAACCAAAATCAAGAATCTAGATTCCAACATTGACTCCTTGAAGGTGAAACTGACAGACGAAGATCTGAAAGAAATGGGCAGCCAGATACGGGAAGA


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 232

TTGCGAATGGAAGAACTGGCCAATAAGCACCAGTGCAGCCCTGCTCAGCTAGCTTTAGCATGGGTTCTGCATCAAGGAGATGATGTGGTTCCTATACCAGgtgttacctt ... aatttctcagGGACAACCAAAATCAAGAATCTAGATTCCAACATTGACTCCTTGAAGGTGAAACTGACAGACGAAGATCTGAAAGAAATGGGCAGCCAGATACGGGAAGA


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 104

TTGCGAATGGAAGAACTGGCCAATAAGCACCAGTGCAGCCCTGCTCAGCTAGCTTTAGCATGGGTTCTGCATCAAGGAGATGATGTGGTTCCTATACCAGgtgttacctt ... aatttctcagGGACAACCAAAATCAAGAATCTAGATTCCAACATTGACTCCTTGAAGGTGAAACTGACAGACGAAGATCTGAAAGAAATGGGCAGCCAGATACGGGAAGA


Block sizes: 46 (upstream exon), 48 (downstream exon)
Score: 85

TTGCGAATGGAAGAACTGGCCAATAAGCACCAGTGCAGCCCTGCTCAGCTAGCTTTAGCATGGGTTCTGCATCAAGGAGATGATGTGGTTCCTATACCAGgtgttacctt ... aatttctcagGGACAACCAAAATCAAGAATCTAGATTCCAACATTGACTCCTTGAAGGTGAAACTGACAGACGAAGATCTGAAAGAAATGGGCAGCCAGATACGGGAAGA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atgttccgatagtcctgtatttagtcactgacaagtgttttctacaatttctcagGGACAACCAAAATCAAGAATCTAGATTCCAACATTGACTCCTTGAAGGTGAAACTGACAGACGAAGATCTGAAAGAAATGGGCAGCCAGATACGGGAAGA
                         cactgac  putative branch site (score: 85)
                                               tttctc  putative PPT
               tgtattta  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
caagttcaaacaagtcatcagtagtcatgcttcatggctatatatatgttccgatagtcctgtatttagtcactgacaagtgttttctacaatttctcagGGACAACCAAAATCAAGAATCTAGATTCCAACATTGACTCCTTGAAGGTGAAACTGACAGACGAAGATCTGAAAGAAATGGGCAGCCAGATACGGGAAGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - -aaacaag
- - - - - - - - - - - - - - -cttcatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgtattt