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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ACTGGCAAGATTTCTGTAACCGACTATGTCAGAGTGACAAGCACAGAATGgtactatacattaaatctgctcaaaccagggtttagtttagaagtaaccagattgtcatatcaaaatgcattgttcaactagcaaaaaaaaaaaaaacaatggtacaaattactcaaccattttcag

Basic information

species Zea mays
transcript GRMZM2G020002_T01
intron # 11
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G020002_T01 (Zea mays), 5'ss of exon 11
lower sequence: LOC_Os01g59340.2 (Oryza sativa), 5'ss of exon 14
---ACTGGCAAGATTTCTGTAACCGACTATGTCAGAGTGACAAGCACAGAATGgtactatacattaaatctgctcaaaccagggtttagtttagaagtaaccagattgtcatatcaaaatgcattgttcaactagcaaaaaaaaaaaaaacaatggtacaaattactcaaccattttcag
   ||||||   |||||||| |  || ||||| ||||||||||||||||||||||| |||  |  ||||   ||  | | |    | | |||| |    | || |||  |           || | ||||||             ||  |||||| | ||||||||||||   |||||||
GAGACTGGCCGAATTTCTGTCAGTGATTATGTGAGAGTGACAAGCACAGAATGgta-tattgaagaaattcact--agcta----tcattttaaac---aacaaattccc-----------cactattcaac------------gaagtacaatgat-caaattactcaaatcttttcag
















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|74240936|gb|DT648850.1|DT648850
EST:     ACTGGCAAGATTTCTGTAACCGACTATGTCAGAGTGACAAGCACAGAATG                         CGCCAAGACCTTCAACATATTCCCTCGGAAAGGAGCAATCCTGGAAGGATC
genomic: ACTGGCAAGATTTCTGTAACCGACTATGTCAGAGTGACAAGCACAGAATGgtactataca ... ccattttcagCGCCAAGACCTTCAACATATTCCCTCGGAAAGGAGCAATCCTGGAAGGATC
EST: gi|113703820|gb|EE681324.1|EE681324
EST:     ACTGGCAAGATTTCTGTAACCGACTATGTCAGAGTGACAAGCACAGAATG                         CGCCAAGACCTTCAACATATTCCCTCGGAAAGGAGCAATCCTGGAAGGATC
genomic: ACTGGCAAGATTTCTGTAACCGACTATGTCAGAGTGACAAGCACAGAATGgtactataca ... ccattttcagCGCCAAGACCTTCAACATATTCCCTCGGAAAGGAGCAATCCTGGAAGGATC
EST: gi|211361841|gb|FL432810.1|FL432810
EST:     ACTGGCAAGATTTCTGTAACCGACTATGTCAGAGTGACAAGCACAGAATG                         CGCCAAGACCTTCAACATATTCCCTCGGAAAGGAGCAATCCTGGAAGGATC
genomic: ACTGGCAAGATTTCTGTAACCGACTATGTCAGAGTGACAAGCACAGAATGgtactataca ... ccattttcagCGCCAAGACCTTCAACATATTCCCTCGGAAAGGAGCAATCCTGGAAGGATC
EST: gi|148990302|gb|EE031901.2|EE031901
EST:     CAAGATTTCTGTAACCGACTATGTCAGAGTGACAAGCACAGAATG                         CGCCAAGACCTTCAACATATTCCCTCGGAAAGGAGCAATCCTGGAAGGATC
genomic: CAAGATTTCTGTAACCGACTATGTCAGAGTGACAAGCACAGAATGgtactataca ... ccattttcagCGCCAAGACCTTCAACATATTCCCTCGGAAAGGAGCAATCCTGGAAGGATC
EST: gi|78079711|gb|DV508123.1|DV508123
EST:     ACTGGCAAGATTTCTGTAACCGACTATGTCAGAGTGACAAGCACAGAATG                         CGCCAAGACCTTCAACATATTCCCTCGGAAAGGAGCAATCCTGGAAGGATC
genomic: ACTGGCAAGATTTCTGTAACCGACTATGTCAGAGTGACAAGCACAGAATGgtactataca ... ccattttcagCGCCAAGACCTTCAACATATTCCCTCGGAAAGGAGCAATCCTGGAAGGATC
EST: gi|148929734|gb|EC876616.2|EC876616
EST:     ACTGGCAAGATTTCTGTATCCGACTATGTCAGAGTGACAAGCACAGAATG                         CGCCAAGACCTTCAACATATTCCCTCGGAAAGGAGCAATCCTGGAAGGATC
genomic: ACTGGCAAGATTTCTGTAACCGACTATGTCAGAGTGACAAGCACAGAATGgtactataca ... ccattttcagCGCCAAGACCTTCAACATATTCCCTCGGAAAGGAGCAATCCTGGAAGGATC
EST: gi|149082367|gb|EE171551.2|EE171551
EST:     TAACCGACTATGTCAGAGTGACAAGCACAGAATG                         CGCCAAGACCTTCAACATATTCCCTCGGAAAGGAGCAATCCTGGAAGGATC
genomic: TAACCGACTATGTCAGAGTGACAAGCACAGAATGgtactataca ... ccattttcagCGCCAAGACCTTCAACATATTCCCTCGGAAAGGAGCAATCCTGGAAGGATC

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: 27

ACTGGCAAGATTTCTGTAACCGACTATGTCAGAGTGACAAGCACAGAATGgtactataca ... ccattttcagCGCCAAGACCTTCAACATATTCCCTCGGAAAGGAGCAATCCTGGAAGGATCTGACGCAGATATCATAATCCTGAACCCTGAAAGGAGCTTTGTGATGGGT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 108

ACTGGCAAGATTTCTGTAACCGACTATGTCAGAGTGACAAGCACAGAATGgtactataca ... ccattttcagCGCCAAGACCTTCAACATATTCCCTCGGAAAGGAGCAATCCTGGAAGGATCTGACGCAGATATCATAATCCTGAACCCTGAAAGGAGCTTTGTGATGGGT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 52

ACTGGCAAGATTTCTGTAACCGACTATGTCAGAGTGACAAGCACAGAATGgtactataca ... ccattttcagCGCCAAGACCTTCAACATATTCCCTCGGAAAGGAGCAATCCTGGAAGGATCTGACGCAGATATCATAATCCTGAACCCTGAAAGGAGCTTTGTGATGGGT


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 38

ACTGGCAAGATTTCTGTAACCGACTATGTCAGAGTGACAAGCACAGAATGgtactataca ... ccattttcagCGCCAAGACCTTCAACATATTCCCTCGGAAAGGAGCAATCCTGGAAGGATCTGACGCAGATATCATAATCCTGAACCCTGAAAGGAGCTTTGTGATGGGT


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ACTGGCAAGATTTCTGTAACCGACTATGTCAGAGTGACAAGCACAGAATGgtactatacattaaatctgctcaaaccagggtttagtttagaagtaaccagattgtcatatcaaaatgcattgttcaactagcaaaaaaaaaaaaaacaatggtacaaattactcaaccattttcag

- - GCAAGA