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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtttccctgcttctttgtaattcatttgtaggtttcgtaagtttatttggatgtttctaatgttgtgttttgcagTTTCTTGAGATCATGGCAGAATTTACTCCTGAGCAGCAACATGCTTTCTGCCAGTTTGTGACCGGTGCTCCTCGGCTTCCACCTGGGGGTTTGGCTGCTC

Basic information

species Zea mays
transcript GRMZM2G049141_T02
intron # 14
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G049141_T02 (Zea mays), 3'ss of exon 14
lower sequence: Vv04s0023g03830.t01 (Vitis vinifera), 3'ss of exon 14
------------------------------------gtaagtttccctgcttctttgtaattcatttgtaggtttcgtaagtttatttggatgtttctaatgttgtgttttgcagTTTCTTGAGATCATGGCAGAATTTACTCCTGAGCAGCAACATGCTTTCTGCCAGTTTGTGACCGGTGCTCCTCGGCTTCCACCTGGGGGTTTGGCTGCTC
                                    ||  |   |   |  |  |  ||| || | | ||   ||       | |||||  | ||   |    | || |||  |||| ||||| ||||||| |||||| |||||||||||||| ||||| |||||||| ||  | || ||||| ||| ||||||| ||||| ||| ||||     
gtaagattcttcctatatttggggcatttggatttagtgggaaacagggtgtaatgataactcttatata---ttgactgcatgatttgtttattgtaatgcctttgctttctagTTACTTGAAATCATGGGAGAATTCACTCCTGAGCAGCAGCATGCATTCTGCCAATTCATTACTGGTGCACCTAGGCTTCCTCCTGGAGGTCTGGCAATGT
















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|18659233|gb|BM500228.1|BM500228
EST:     ATATAAAATTCGACCATGGTTATACCTCTAAGAGTCCTGCAATTATTAAT                         TTTCTTGAGATCATGGCAGAATTTACTCCTGAGCAGCAACATGCTTTCTGC
genomic: ATATAAAATTCGACCATGGTTATACCTCTAAGAGTCCTGCAATTATTAATgtaagtttcc ... tgttttgcagTTTCTTGAGATCATGGCAGAATTTACTCCTGAGCAGCAACATGCTTTCTGC
EST: gi|211174646|gb|FL281696.1|FL281696
EST:     ATATAAAATTCGACCATGGTTATACCTCTAAGAGTCCTGCAATTATTAAN                         TTTCTTGAGATCATGGCAGAA
genomic: ATATAAAATTCGACCATGGTTATACCTCTAAGAGTCCTGCAATTATTAATgtaagtttcc ... tgttttgcagTTTCTTGAGATCATGGCAGAA
EST: gi|211176315|gb|FL281701.1|FL281701
EST:     ATATAADATTCGACCATGGTTATACCTCTAAGAGTCCTGCAATTGTTAAT                         TTTCTTGAGATCATGGCAGAATTTACTCCTGAGCA
genomic: ATATAAAATTCGACCATGGTTATACCTCTAAGAGTCCTGCAATTATTAATgtaagtttcc ... tgttttgcagTTTCTTGAGATCATGGCAGAATTTACTCCTGAGCA
EST: gi|20301115|gb|BQ164058.1|BQ164058
EST:     ATATAAAATTCGACCATGGTTATACCTCTAAGAGTCCTGCAATTATTAAT                         TTTCTTGAGATCATGGCAGAATTTACTCCTGAGCAGCAACATGCTTTCTGC
genomic: ATATAAAATTCGACCATGGTTATACCTCTAAGAGTCCTGCAATTATTAATgtaagtttcc ... tgttttgcagTTTCTTGAGATCATGGCAGAATTTACTCCTGAGCAGCAACATGCTTTCTGC
EST: gi|67039619|gb|CO465874.1|CO465874
EST:     ATATAAAATTCGACCATGGTTATACCTCTAAGAGTCCTGCAATTGGTAAT                         TTTCTTGAGATCATGGCAGAATTTACTCCTGAGCAGCA-CATGCTTTCTGC
genomic: ATATAAAATTCGACCATGGTTATACCTCTAAGAGTCCTGCAATTATTAATgtaagtttcc ... tgttttgcagTTTCTTGAGATCATGGCAGAATTTACTCCTGAGCAGCAACATGCTTTCTGC
EST: gi|20299937|gb|BQ162880.1|BQ162880
EST:     ATATAAAATTCGACCATGGTTATACCTCTAAGAGTCCTGCAATTATTAAT                         TTTCTTGAGATCATGGCAGAATTTACTCCTGAGCAGCAACATGCTTTCTGC
genomic: ATATAAAATTCGACCATGGTTATACCTCTAAGAGTCCTGCAATTATTAATgtaagtttcc ... tgttttgcagTTTCTTGAGATCATGGCAGAATTTACTCCTGAGCAGCAACATGCTTTCTGC
EST: gi|67021475|gb|CO450224.1|CO450224
EST:     TATAAAATTCGACCATGGTTATACCTCTAAGAGTCCTAGCA-TTGTTAAT                         TGTCTTGAGATCATGGCAGAATNTACTNCTGAGCAGCAACATGCTTTTCTG
genomic: TATAAAATTCGACCATGGTTATACCTCTAAGAGTCCT-GCAATTATTAATgtaagtttcc ... tgttttgcagTTTCTTGAGATCATGGCAGAATTTACTCCTGAGCAGCAACATGCTTT-CTG
EST: gi|211176314|gb|FL281700.1|FL281700
EST:     ATATAAAATTCGACCATGGTTATACCTCTAAGAGTCCTGCAATTGTTAAT                         TTTCTTGAGATCATGGCAGAATTTACTCCTGAGCAGCAACATGCTTTCTGC
genomic: ATATAAAATTCGACCATGGTTATACCTCTAAGAGTCCTGCAATTATTAATgtaagtttcc ... tgttttgcagTTTCTTGAGATCATGGCAGAATTTACTCCTGAGCAGCAACATGCTTTCTGC
EST: gi|211174647|gb|FL281697.1|FL281697
EST:     ATATAAAATTCGACCATGGTTATACCTCTAAGAGTCCTGCAATTGTTAAT                         TTTCTTGAGATCATGGCAGAATTTACTCCTGAGCAGCAACATGCTTTCTGC
genomic: ATATAAAATTCGACCATGGTTATACCTCTAAGAGTCCTGCAATTATTAATgtaagtttcc ... tgttttgcagTTTCTTGAGATCATGGCAGAATTTACTCCTGAGCAGCAACATGCTTTCTGC

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: 47 (upstream exon), 48 (downstream exon)
Score: 83

CCGGAAACACTGCCTGAACATATAAAATTCGACCATGGTTATACCTCTAAGAGTCCTGCAATTATTAATgtaagtttcc ... tgttttgcagTTTCTTGAGATCATGGCAGAATTTACTCCTGAGCAGCAACATGCTTTCTGCCAGTTTGTGACCGGTGCTCCTCGGCTTCCACCTGGGGGTTTGGCTGCTC


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 29

CCGGAAACACTGCCTGAACATATAAAATTCGACCATGGTTATACCTCTAAGAGTCCTGCAATTATTAATgtaagtttcc ... tgttttgcagTTTCTTGAGATCATGGCAGAATTTACTCCTGAGCAGCAACATGCTTTCTGCCAGTTTGTGACCGGTGCTCCTCGGCTTCCACCTGGGGGTTTGGCTGCTC


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 24

CCGGAAACACTGCCTGAACATATAAAATTCGACCATGGTTATACCTCTAAGAGTCCTGCAATTATTAATgtaagtttcc ... tgttttgcagTTTCTTGAGATCATGGCAGAATTTACTCCTGAGCAGCAACATGCTTTCTGCCAGTTTGTGACCGGTGCTCCTCGGCTTCCACCTGGGGGTTTGGCTGCTC


Block sizes: 47 (upstream exon), 48 (downstream exon)
Score: 84

CCGGAAACACTGCCTGAACATATAAAATTCGACCATGGTTATACCTCTAAGAGTCCTGCAATTATTAATgtaagtttcc ... tgttttgcagTTTCTTGAGATCATGGCAGAATTTACTCCTGAGCAGCAACATGCTTTCTGCCAGTTTGTGACCGGTGCTCCTCGGCTTCCACCTGGGGGTTTGGCTGCTC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcatttgtaggtttcgtaagtttatttggatgtttctaatgttgtgttttgcagTTTCTTGAGATCATGGCAGAATTTACTCCTGAGCAGCAACATGCTTTCTGCCAGTTTGTGACCGGTGCTCCTCGGCTTCCACCTGGGGGTTTGGCTGCTC
                                  ttctaat  putative branch site (score: 84)
                 taagtttattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtttccctgcttctttgtaattcatttgtaggtttcgtaagtttatttggatgtttctaatgttgtgttttgcagTTTCTTGAGATCATGGCAGAATTTACTCCTGAGCAGCAACATGCTTTCTGCCAGTTTGTGACCGGTGCTCCTCGGCTTCCACCTGGGGGTTTGGCTGCTC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT