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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCATAGTTTAAAGGAAGTTTTGGACACACCAGGTGTGATGGCACTGATAAAAGATACAAAAGCAGCACAGGAGgtaagactgactataaatcacacacgtcactagatatactaatttatgtatgagctttctttaaaataacaacaacaaagtcttttaatcccaagtaagt...

Basic information

species Zea mays
transcript GRMZM2G044011_T02
intron # 11
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G044011_T02 (Zea mays), 5'ss of exon 11
lower sequence: LOC_Os04g56480.3 (Oryza sativa), 5'ss of exon 11
GCATAGTTTAAAGGAAGTTTTGGACACACCAGGTGTGATGGCACTGATAAAAGATACAAAAGCAGCACAGGAGgtaagactgactataaatcacacacgtcactagatatactaatttatgtatg-agctttctttaaaataacaacaacaaagtcttttaatcccaagtaagt----------------------------------------------------------------------------------------
||||||  | |||||||||||||| |  ||| |||||||| |||| |||||||||||||| || || ||||||||||| |  | |   ||  | | |  |||||| ||   ||||| ||    |   |   | | | ||| |    |  ||   |  | |||| |  | ||||                                                                                         
GCATAGCCTGAAGGAAGTTTTGGATAGCCCAAGTGTGATGACACTAATAAAAGATACAAAGGCGGCGCAGGAGgtaagccatattcagaacaagatatatcactaaatgccctaatgtacacctatggtgctttctcaaacagttcccccatgttgatataatacgcactaaggcactaagcacattcaaaacaatttctaagtacagacagcttctcatatttgttttctgacgctcttatatttcctttctaatttgcag

upper sequence: GRMZM2G044011_T02 (Zea mays), 5'ss of exon 11
lower sequence: Vv04s0023g00140.t01 (Vitis vinifera), 5'ss of exon 12
GCATAGTTTAAAGGAAGTTTTGGACACACCAGGTGTGATGGCACTGATAAAAGATACAAAAGCAGCACAGGAGgtaaga--ctgactataaatcacacacgtcactagatatactaatttatgtatgagctttctttaaaataacaacaaca----aagtcttttaatcccaagtaagt----------------------------------------------------
|||||||||||| || ||||||||  |||||  |||||||    ||||||| ||||||||||||||||| |||||| ||  |  |   |   |     || ||   |  | |     | |   | ||    |  |   || |        |     ||  || ||  |   |||  ||                                                     
GCATAGTTTAAAAGAGGTTTTGGATGCACCAAATGTGATGAACATGATAAAGGATACAAAAGCAGCACAAGAGgtaggatgcaaatccttcttggttaacatcttcatctgtctctttctgattttgtttctcttcctaactcttgttgtctgttcaaacctgtttgt--taagcgagctctgtccatctttgccttgaaataacaaatatctttctccccctttttgtag
















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|67018038|gb|CO446787.1|CO446787
EST:     AGCAGCACAGGAG                         GTCCGAGCTCTGCAGGATTTCTTCAATATGCTTACTAAT
genomic: AGCAGCACAGGAGgtaagactga ... tactttgcagGTCCGAGCTCTGCAGGATTTCTTCAATATGCTTACTAAT
EST: gi|211495349|gb|FL234479.1|FL234479
EST:     ATACACCAGGTGTGATGGCACTGATAAAAGATACAAAAGCAGCACAGGAG                         GTCCGAGCTCTGCAGGATTTCTTCAATATGCTTACTAAT
genomic: ACACACCAGGTGTGATGGCACTGATAAAAGATACAAAAGCAGCACAGGAGgtaagactga ... tactttgcagGTCCGAGCTCTGCAGGATTTCTTCAATATGCTTACTAAT
EST: gi|91048656|gb|EB159074.1|EB159074
EST:     ACACACCAGGTGTGATGGCACTGATAAAAGATACAAAAGCAGCACAGGAG                         GTCCGAGCTCTGCAGGATTTCTTCAATATGCTTACTAAT
genomic: ACACACCAGGTGTGATGGCACTGATAAAAGATACAAAAGCAGCACAGGAGgtaagactga ... tactttgcagGTCCGAGCTCTGCAGGATTTCTTCAATATGCTTACTAAT
EST: gi|67018605|gb|CO447354.1|CO447354
EST:     ATACACCAGGTGTGATGGCACTAATAAAAGATACAAAAGCAGCACAGGAG                         GTCCGAGCTCTGCAGGATTTCTTCAATATGCTTACTAAT
genomic: ACACACCAGGTGTGATGGCACTGATAAAAGATACAAAAGCAGCACAGGAGgtaagactga ... tactttgcagGTCCGAGCTCTGCAGGATTTCTTCAATATGCTTACTAAT
EST: gi|67024357|gb|CO453106.1|CO453106
EST:     ATACACCAGGTGTGATGGCACTAATAAAAGATACAAAAGCAGCACAGGAG                         GTCCGAGCTCTGCAGGATTTCTTCAATATGCTTACTAAT
genomic: ACACACCAGGTGTGATGGCACTGATAAAAGATACAAAAGCAGCACAGGAGgtaagactga ... tactttgcagGTCCGAGCTCTGCAGGATTTCTTCAATATGCTTACTAAT
EST: gi|40303701|gb|CK348088.1|CK348088
EST:     ACACACCAGGTGTGATGGCACTGATAAAAGATACAAAAGCAGCACAGGAG                         GTCCGAGCTCTGCAGGATTTCTTCAATATGCTTACTAAT
genomic: ACACACCAGGTGTGATGGCACTGATAAAAGATACAAAAGCAGCACAGGAGgtaagactga ... tactttgcagGTCCGAGCTCTGCAGGATTTCTTCAATATGCTTACTAAT
EST: gi|71763506|gb|DR961443.1|DR961443
EST:     ACACACCAGGTGTGATGGCACTGATAAAAGATACAAAAGCAGCACAGGAG                         GTCCGAGCTCTGCAGGATTTCTTCAATATGCTTACTAAT
genomic: ACACACCAGGTGTGATGGCACTGATAAAAGATACAAAAGCAGCACAGGAGgtaagactga ... tactttgcagGTCCGAGCTCTGCAGGATTTCTTCAATATGCTTACTAAT
EST: gi|74236267|gb|DT644181.1|DT644181
EST:     GCACACCAGGTGTGATGGCACTGATAAAAGATACAAAAGCAGCACAGGAG                         GTCCGAGCTCTGCAGGATTTCTTCAATATGCTTACTAAT
genomic: ACACACCAGGTGTGATGGCACTGATAAAAGATACAAAAGCAGCACAGGAGgtaagactga ... tactttgcagGTCCGAGCTCTGCAGGATTTCTTCAATATGCTTACTAAT
EST: gi|211359052|gb|FL430699.1|FL430699
EST:     ATACACCAGGTGTGATGGCACTGATAAAAGATACAAAASCAGCACAGGAG                         GTCCGAGCTCTGCAGGATTTCTTCAATATGCTTACTAAT
genomic: ACACACCAGGTGTGATGGCACTGATAAAAGATACAAAAGCAGCACAGGAGgtaagactga ... tactttgcagGTCCGAGCTCTGCAGGATTTCTTCAATATGCTTACTAAT
EST: gi|71442136|gb|DR823186.1|DR823186
EST:     ACACACCAGGTGTGATGGCACTGATAAAAGATACAAAAGCAGCACAGGAG                         GTCCGAGCTCTGCAGGATTTCTTCAATATGCTTACTAAT
genomic: ACACACCAGGTGTGATGGCACTGATAAAAGATACAAAAGCAGCACAGGAGgtaagactga ... tactttgcagGTCCGAGCTCTGCAGGATTTCTTCAATATGCTTACTAAT
EST: gi|50333168|gb|CO528294.1|CO528294
EST:     ACACACCAGGTGTGATGGCACTGATAAAAGATACAAAAGCAGCACAGGAG                         GTCCGAGCTCTGCAGGATTTCTTCAATATGCTTACTAAT
genomic: ACACACCAGGTGTGATGGCACTGATAAAAGATACAAAAGCAGCACAGGAGgtaagactga ... tactttgcagGTCCGAGCTCTGCAGGATTTCTTCAATATGCTTACTAAT
EST: gi|67021632|gb|CO450381.1|CO450381
EST:     ATACACCAGGTGTGATGGCACTAATAAAAGATACAAAAGCAGCACAGGAG                         GTCCGAGCTCTGCAGGATTTCTTCAATATGCTTACTAAT
genomic: ACACACCAGGTGTGATGGCACTGATAAAAGATACAAAAGCAGCACAGGAGgtaagactga ... tactttgcagGTCCGAGCTCTGCAGGATTTCTTCAATATGCTTACTAAT
EST: gi|71302744|gb|DR787484.1|DR787484
EST:     ACACACCAGGTGTGATGGCACTGATAAAAGATACAAAAGCAGCACAGGAG                         GTCCGAGCTCTGCAGGATTTCTTCAATATGCTTACTAAT
genomic: ACACACCAGGTGTGATGGCACTGATAAAAGATACAAAAGCAGCACAGGAGgtaagactga ... tactttgcagGTCCGAGCTCTGCAGGATTTCTTCAATATGCTTACTAAT
EST: gi|76016282|gb|DT943452.1|DT943452
EST:     ACACACCAGGTGTGATGGCACTGATAAAAGATACAAAAGCAGCACAGGAG                         GTCCGAGCTCTGCAGGATTTCTTCAATATGCTTACTAAT
genomic: ACACACCAGGTGTGATGGCACTGATAAAAGATACAAAAGCAGCACAGGAGgtaagactga ... tactttgcagGTCCGAGCTCTGCAGGATTTCTTCAATATGCTTACTAAT

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), 47 (downstream exon)
Score: 49

GCATAGTTTAAAGGAAGTTTTGGACACACCAGGTGTGATGGCACTGATAAAAGATACAAAAGCAGCACAGGAGgtaagactga ... tactttgcagGTCCGAGCTCTGCAGGATTTCTTCAATATGCTTACTAAT


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 137

GCATAGTTTAAAGGAAGTTTTGGACACACCAGGTGTGATGGCACTGATAAAAGATACAAAAGCAGCACAGGAGgtaagactga ... tactttgcagGTCCGAGCTCTGCAGGATTTCTTCAATATGCTTACTAAT


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 106

GCATAGTTTAAAGGAAGTTTTGGACACACCAGGTGTGATGGCACTGATAAAAGATACAAAAGCAGCACAGGAGgtaagactga ... tactttgcagGTCCGAGCTCTGCAGGATTTCTTCAATATGCTTACTAAT


Block sizes: 46 (upstream exon), 46 (downstream exon)
Score: 84

GCATAGTTTAAAGGAAGTTTTGGACACACCAGGTGTGATGGCACTGATAAAAGATACAAAAGCAGCACAGGAGgtaagactga ... tactttgcagGTCCGAGCTCTGCAGGATTTCTTCAATATGCTTACTAAT


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCATAGTTTAAAGGAAGTTTTGGACACACCAGGTGTGATGGCACTGATAAAAGATACAAAAGCAGCACAGGAGgtaagactgactataaatcacacacgtcactagatatactaatttatgtatgagctttctttaaaataacaacaacaaagtcttttaatcccaagtaagt

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaaataac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aacaacaa