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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cagtcattttgttcattgtcaatgcgatgcagccctttctgcattgtaaactcctgcagttaacttacagaaaagtttcatttattcgttttggtcccagCTGGTTGAGCACTTCTTCCAATCTGTGGTGAACACATCTGGGATGACTCTTCACATCCGTCAG

Basic information

species Zea mays
transcript GRMZM2G094255_T01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G094255_T01 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os04g52710.1 (Oryza sativa), 3'ss of exon 5
cagtcattttgttcattgtcaatgcgatgcagccctttctgcattgtaaactcctgcagttaacttacagaaaagtttcatttattcgttttggtc-ccagCTGGTTGAGCACTTCTTCCAATCTGTGGTGAACACATCTGGGATGACTCTTCACATCCGTCAG
|     |||| || ||  || |||| ||||   | |||| |   |||| ||||||||  | | |||| | |    ||  ||||||||  |||| |  |||||| ||||||||||| ||||||||| | ||||| |||||||||||||| |||||||||||||||
cttcttttttttttatcatcgatgccatgctatcttttcagtcatgtatactcctgctatcatcttagacagctattg-atttattcactttgatgaccagCTAGTTGAGCACTTTTTCCAATCTCTTGTGAATACATCTGGGATGACACTTCACATCCGTCAG

upper sequence: GRMZM2G094255_T01 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA20G28420.2 (Glycine max), 3'ss of exon 5
------------------------------------------------------------------cagtcattttgttcattgtcaat-gcgatgcagccctttctgcattgtaaactcctgcagt----taacttacagaaaagtttcatttattcgttttggtcccagCTGGTTGAGCACTTCTTCCAATCTGTGGTGAACACATCTGGGATGACTCTTCACATCCGTCAG
                                                                  ||   ||||| || | ||| |||     | ||  | | |     ||||     |||  | |    | | ||||  |  |   |   |   |    |   |   || |||| ||||| |||||||||||  |||||||||| ||||| ||||| |||||||| |  |||
gtagtgtatgctgtttaattacttcattaaagtttagaattttgcctattgagcttctgatgtttccaaatatttt-tttaatgtgaatcatctttcatgcttgttccttttgtctttccctttattcttattatttactaatgaacct-gctggatatcctcatttatagTTGGTGGAGCATTTCTTCCAATCCCTGGTGAACACGTCTGGTATGACACTTCACATTCAGCAG

upper sequence: GRMZM2G094255_T01 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA10G39370.1 (Glycine max), 3'ss of exon 5
-----------------------------------------------------------------cagtcattttgttcattgtcaatgcgatgcagccctttctgca----ttgtaaactcctgcagttaacttac-agaaaagtttcatttattcgttttggtcc-cagCTGGTTGAGCACTTCTTCCAATCTGTGGTGAACACATCTGGGATGACTCTTCACATCCGTCAG
                                                                 ||   | | | || | ||| |||    |      |||  ||      ||||     |||  | |    |||  |  || |   | | |     |  |  |    || |||| ||||| |||||||||||  |||||||||| ||||| ||||| |||||||| |  |||
gtagtgtatgttgtttaattacttcattaaactttggaattttgctattgagcctctgatgtttccaaatactctttttaatgtgaatcatctatcatgcttcttgttccttttgtctttccctttattcttattattactaatgaaccctctggatatcctcatttatagTTGGTGGAGCATTTCTTCCAATCCCTGGTGAACACGTCTGGTATGACACTTCACATTCAGCAG

upper sequence: GRMZM2G094255_T01 (Zea mays), 3'ss of exon 5
lower sequence: AT3G22425.2 (Arabidopsis thaliana), 3'ss of exon 5
-cagtcattttgttcattg--tcaatgcgatgcagccctttctgcattgtaaactcctg------cagttaacttacagaaaagtttcatttattcgttttggtcccagCTGGTTGAGCACTTCTTCCAATCTGTGGTGAACACATCTGGGATGACTCTTCACATCCGTCAG
    ||  |||| || | |  |        |   |   | ||||  || |    |  |       || | ||  |   |  ||   |  ||||  | ||    |   || |||| |||||||| ||||| ||  ||||||| || ||||| ||||||||||||||||| |||
gttctctctttgctcctggaattgtcttcttttgggtttatctgtgttattcgttgtttagtaatcattgaaagtgttgccaaaaattgtttaacctttcgatttgtagTTGGTGGAGCACTTTTTCCAGTCGTTGGTGAATACTTCTGGTATGACTCTTCACATCCGGCAG

upper sequence: GRMZM2G094255_T01 (Zea mays), 3'ss of exon 5
lower sequence: AT4G14910.1 (Arabidopsis thaliana), 3'ss of exon 5
cagtcattttgttcattgtcaatgcgatgcagccctttctgcattgtaaactcctgcagttaacttacagaaaagtttcatttattcgttttggtcccagCTGGTTGAGCACTTCTTCCAATCTGTGGTGAACACATCTGGGATGACTCTTCACATCCGTCAG
   || |    || | | |    |  || |||   |||| |  ||   |     | |  ||   ||    |||    | | | | || |||       || |||| || ||||||||||| ||  ||||||| || ||||| ||||||||||||||||| |||
-gttcttcacatttagtattttagt-atccagtt-tttcggtttttctagtgttttc--tttgtttgttaaaatcactaaatgactcttttcccatttagTTGGTGGAACACTTCTTCCAGTCATTGGTGAATACTTCTGGTATGACTCTTCACATCCGACAG

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|76010862|gb|DT938032.1|DT938032
EST:     GCTGTGGCTTAGATATTCCTACTCAAAGAGTTGGCACATATGATACACAG                         CTGGTTGAGCACTTCTTCCAATCTGTGGTGAACACATCTGGGATGACTCTT
genomic: GCTGTGGCTTAGATATTCCTACTCAAAGAGTTGGCACATATGATACACAGgtaaattgtg ... ttggtcccagCTGGTTGAGCACTTCTTCCAATCTGTGGTGAACACATCTGGGATGACTCTT
EST: gi|31355338|gb|CD439695.1|CD439695
EST:     GCTGTGGCTTAGATATTCCTACTCAAAGAGTTGGCACATATGATACACAG                         CTGGTTGAGCACTTCTTCCAATCTGTGGTGAACACATCTGGGATGACTCTT
genomic: GCTGTGGCTTAGATATTCCTACTCAAAGAGTTGGCACATATGATACACAGgtaaattgtg ... ttggtcccagCTGGTTGAGCACTTCTTCCAATCTGTGGTGAACACATCTGGGATGACTCTT
EST: gi|12970168|gb|BG266848.1|BG266848
EST:     CTCAAAGAGTTGGCACATACGATACACAG                         CTGGTTGAGCACTTCTTCCAATCTGTGGTGAACACATCTGGGATGACTCTT
genomic: CTCAAAGAGTTGGCACATATGATACACAGgtaaattgtg ... ttggtcccagCTGGTTGAGCACTTCTTCCAATCTGTGGTGAACACATCTGGGATGACTCTT
EST: gi|50323498|gb|CO518624.1|CO518624
EST:     GCTGTGGCTTAGATATTCCTACTCAAAGAGTTGGCACATATGATACACAG                         CTGGTTGAGCACTTCTTCCAATCTGTGGTGAACACATCTGGGATGACTCTT
genomic: GCTGTGGCTTAGATATTCCTACTCAAAGAGTTGGCACATATGATACACAGgtaaattgtg ... ttggtcccagCTGGTTGAGCACTTCTTCCAATCTGTGGTGAACACATCTGGGATGACTCTT
EST: gi|76284483|gb|DV024051.1|DV024051
EST:     CAAAGAGTTGGCACATATGATACACAG                         CTGGTTGAGCACTTCTTCCAATCTGTGGTGAACACATCTGGGATGACTCTT
genomic: CAAAGAGTTGGCACATATGATACACAGgtaaattgtg ... ttggtcccagCTGGTTGAGCACTTCTTCCAATCTGTGGTGAACACATCTGGGATGACTCTT
EST: gi|94478728|gb|EB707686.1|EB707686
EST:     GCTGTGGCTTAGATATTCCTACTCAAAGAGTTGGCACATATGATACACAG                         CTGGTTGAGCACTTCTTCCAATCTGTGGTGAACACATCTGGGATGACTCTT
genomic: GCTGTGGCTTAGATATTCCTACTCAAAGAGTTGGCACATATGATACACAGgtaaattgtg ... ttggtcccagCTGGTTGAGCACTTCTTCCAATCTGTGGTGAACACATCTGGGATGACTCTT
EST: gi|78107718|gb|DV526136.1|DV526136
EST:     GCTGTGGCTTAGATATTCCTACTCAAAGAGTTGGCACATATGATACACAG                         CTGGTTGAGCACTTCTTCCAATCTGTGGTGAACACATCTGGGATGACTCTT
genomic: GCTGTGGCTTAGATATTCCTACTCAAAGAGTTGGCACATATGATACACAGgtaaattgtg ... ttggtcccagCTGGTTGAGCACTTCTTCCAATCTGTGGTGAACACATCTGGGATGACTCTT
EST: gi|71327961|gb|DR800622.1|DR800622
EST:     GCTGTGGCTTAGATATTCCTACTCAAAGAGTTGGCACATACGATACACAG                         CTGGTTGAGCACTTCTTCCAATCTGTGGTGAACACATCTGGGATGACTCTT
genomic: GCTGTGGCTTAGATATTCCTACTCAAAGAGTTGGCACATATGATACACAGgtaaattgtg ... ttggtcccagCTGGTTGAGCACTTCTTCCAATCTGTGGTGAACACATCTGGGATGACTCTT
EST: gi|60349510|gb|DN216483.1|DN216483
EST:     GCTGTGGCTTAGATATTCCTACTCAAAGAGTTGGCACATATGATACACAG                         CTGGTTGAGCACTTCTTCCAATCTGTGGTGAACACATCTGGGATGACTCTT
genomic: GCTGTGGCTTAGATATTCCTACTCAAAGAGTTGGCACATATGATACACAGgtaaattgtg ... ttggtcccagCTGGTTGAGCACTTCTTCCAATCTGTGGTGAACACATCTGGGATGACTCTT
EST: gi|76289085|gb|DV028653.1|DV028653
EST:     GCTGTGGCTTAGATATTCCTACTCAAAGAGTTGGCACATATGATACACAG                         CTGGTTGAGCACTTCTTCCAATCTGTGGTGAACACATCTGGGATGACTCTT
genomic: GCTGTGGCTTAGATATTCCTACTCAAAGAGTTGGCACATATGATACACAGgtaaattgtg ... ttggtcccagCTGGTTGAGCACTTCTTCCAATCTGTGGTGAACACATCTGGGATGACTCTT
EST: gi|76010863|gb|DT938033.1|DT938033
EST:     GCTGTGGCTTAGATATTCCTACTCAAAGAGTTGGCACATATGATACACAG                         CTGGTTGAGCACTTCTTCCAATCTGTGGTGAACACATCTGGGATGACTCTT
genomic: GCTGTGGCTTAGATATTCCTACTCAAAGAGTTGGCACATATGATACACAGgtaaattgtg ... ttggtcccagCTGGTTGAGCACTTCTTCCAATCTGTGGTGAACACATCTGGGATGACTCTT
EST: gi|74232835|gb|DT640749.1|DT640749
EST:     CTCAAAGAGTTGGCACATATGATACACAG                         CTGGTTGAGCACTTCTTCCAATCTGTGGTGAACACATCTGGGATGACTCTT
genomic: CTCAAAGAGTTGGCACATATGATACACAGgtaaattgtg ... ttggtcccagCTGGTTGAGCACTTCTTCCAATCTGTGGTGAACACATCTGGGATGACTCTT
EST: gi|76293135|gb|DV032703.1|DV032703
EST:     GCTGTGGCTTAGATATTCCTACTCAAAGAGTTGGCACATATGATACACAG                         CTGGTTGAGCACTTCTTCCAATCTGTGGTGAACACATCTGGGATGACTCTT
genomic: GCTGTGGCTTAGATATTCCTACTCAAAGAGTTGGCACATATGATACACAGgtaaattgtg ... ttggtcccagCTGGTTGAGCACTTCTTCCAATCTGTGGTGAACACATCTGGGATGACTCTT
EST: gi|74232836|gb|DT640750.1|DT640750
EST:     GCTGTGGCTTAGATATTCCTACTCAAAGAGTTGGCACATATGATACACAG                         CTGGTTGAGCACTTCTTCCAATCTGTGGTGAACACATCTGGGATGACTCTT
genomic: GCTGTGGCTTAGATATTCCTACTCAAAGAGTTGGCACATATGATACACAGgtaaattgtg ... ttggtcccagCTGGTTGAGCACTTCTTCCAATCTGTGGTGAACACATCTGGGATGACTCTT
EST: gi|76284484|gb|DV024052.1|DV024052
EST:     GCTGTGGCTTAGATATTCCTACTCAAAGAGTTGGCACATATGATACACAG                         CTGGTTGAGCACTTCTTCCAATCTGTGGTGAACACATCTGGGATGACTCTT
genomic: GCTGTGGCTTAGATATTCCTACTCAAAGAGTTGGCACATATGATACACAGgtaaattgtg ... ttggtcccagCTGGTTGAGCACTTCTTCCAATCTGTGGTGAACACATCTGGGATGACTCTT
EST: gi|31664107|gb|CD573287.1|CD573287
EST:     GCTGTGGCTTAGATATTCCTACTCAAAGAGTTGGCACATATGATACACAG                         CTGGTTGAGCACTTCTTCCAATCTGTGGTGAACACATCTGGGATGACTCTT
genomic: GCTGTGGCTTAGATATTCCTACTCAAAGAGTTGGCACATATGATACACAGgtaaattgtg ... ttggtcccagCTGGTTGAGCACTTCTTCCAATCTGTGGTGAACACATCTGGGATGACTCTT
EST: gi|78107717|gb|DV526135.1|DV526135
EST:     GCTGTGGCTTAGATATTCCTACTCAAAGAGTTGGCACATATGATACACAG                         CTGGTTGAGCACTTCTTCCAATCTGTGGTGAACACATCTGGGATGACTCTT
genomic: GCTGTGGCTTAGATATTCCTACTCAAAGAGTTGGCACATATGATACACAGgtaaattgtg ... ttggtcccagCTGGTTGAGCACTTCTTCCAATCTGTGGTGAACACATCTGGGATGACTCTT
EST: gi|78112492|gb|DV530886.1|DV530886
EST:     GCTGTGGCTTAGATATTCCTACTCAAAGAGTTGGCACATATGATACACAG                         CTGGTTGAGCACTTCTTCCAATCTGTGGGGAACACATCTGGGATGACTCTT
genomic: GCTGTGGCTTAGATATTCCTACTCAAAGAGTTGGCACATATGATACACAGgtaaattgtg ... ttggtcccagCTGGTTGAGCACTTCTTCCAATCTGTGGTGAACACATCTGGGATGACTCTT
EST: gi|78086465|gb|DV514858.1|DV514858
EST:     GCTGTGGCTTAGATATTCCTACTCAAAGAGTTGGCACATATGATACACAG                         CTGGTTGAGCACTTCTTCCAATCTGTGGTGAACACATCTGGGATGACTCTT
genomic: GCTGTGGCTTAGATATTCCTACTCAAAGAGTTGGCACATATGATACACAGgtaaattgtg ... ttggtcccagCTGGTTGAGCACTTCTTCCAATCTGTGGTGAACACATCTGGGATGACTCTT

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), 48 (downstream exon)
Score: 79

GATCTGTCTGGTCGCCCTCATTTAAGCTGTGGCTTAGATATTCCTACTCAAAGAGTTGGCACATATGATACACAGgtaaattgtg ... ttggtcccagCTGGTTGAGCACTTCTTCCAATCTGTGGTGAACACATCTGGGATGACTCTTCACATCCGTCAG


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 90

GATCTGTCTGGTCGCCCTCATTTAAGCTGTGGCTTAGATATTCCTACTCAAAGAGTTGGCACATATGATACACAGgtaaattgtg ... ttggtcccagCTGGTTGAGCACTTCTTCCAATCTGTGGTGAACACATCTGGGATGACTCTTCACATCCGTCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 70

GATCTGTCTGGTCGCCCTCATTTAAGCTGTGGCTTAGATATTCCTACTCAAAGAGTTGGCACATATGATACACAGgtaaattgtg ... ttggtcccagCTGGTTGAGCACTTCTTCCAATCTGTGGTGAACACATCTGGGATGACTCTTCACATCCGTCAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 89

GATCTGTCTGGTCGCCCTCATTTAAGCTGTGGCTTAGATATTCCTACTCAAAGAGTTGGCACATATGATACACAGgtaaattgtg ... ttggtcccagCTGGTTGAGCACTTCTTCCAATCTGTGGTGAACACATCTGGGATGACTCTTCACATCCGTCAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtaaactcctgcagttaacttacagaaaagtttcatttattcgttttggtcccagCTGGTTGAGCACTTCTTCCAATCTGTGGTGAACACATCTGGGATGACTCTTCACATCCGTCAG
                aacttac  putative branch site (score: 89)
                                       ttcgtttt  putative PPT
                         aaaagtttcatttatt  TA-rich tract