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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatacaaacttcttatggataattgctaggaaattcaagaaagaatctgacaagtttcttttacttgcactgtacagCAACTTTTGTTCTTCATCATCCGGAGCATGGTCATGCAGTTGTACATCCAATTCTTTCACCCATCATAGATGGGACACTGTGCTATGATAGGCATGGTCC

Basic information

species Zea mays
transcript GRMZM5G844173_T01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G844173_T01 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os01g08700.1 (Oryza sativa), 3'ss of exon 5
gtaatacaaacttcttatggataattgct----aggaaattcaagaaagaatctgacaagtttcttttacttgcactgtacagCAACTTTTGTTCTTCATCATCCGGAGCATGGTCATGCAGTTGTACATCCAATTCTTTCACCCATCATAGATGGGACACTGTGCTATGATAGGCATGGTCC
|||||   | |   | ||  |||  || |    |   |||| |||||||| | |||||  ||| | | |  |      | ||||||||||||||||||||||||| |||||||| ||||||||||| ||||| ||||| |||| ||||||||||||||||||  | ||||||||  |||||  
gtaatttgatccagtgatcaatacatgttccacaaacaattgaagaaagagtttgacatatttttctcatatt-----tccagCAACTTTTGTTCTTCATCATCCTGAGCATGGCCATGCAGTTGTGCATCCGATTCTGTCACGCATCATAGATGGGACACTCAGTTATGATAGAAATGGTTT

upper sequence: GRMZM5G844173_T01 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA10G36600.1 (Glycine max), 3'ss of exon 4
---------------------------------gtaatacaaacttcttatggataattgctagga---aattcaagaaagaatctgacaagtttcttttacttgcac-tgta----cagCAACTTTTGTTCTTCATCATCCGGAGCATGGTCATGCAGTTGTACATCCAATTCTTTCACCCATCATAGATGGGACACTGTGCTATGATAGGCATGGTCC
                                  | ||  |  |  | ||   ||  || | | ||   | ||| |       | | | || ||  || |  || ||| ||||     ||| || ||||| ||||||||||| |||||||| ||||||||||| | ||||||| |||||   || || ||||| |||||   |||||||| |  | ||||
gtatttatgctctatcccatgtcagtttaacttatgattgactcaacataaatatggttaccatgatttatttctattttatttgtaataacttctttatgttttcacatgtaaatctagCGACATTTGTCCTTCATCATCCAGAGCATGGGCATGCAGTTGTGCTTCCAATTATTTCATGTATTATTGATGGTACACTAGTCTATGATAAGGCTAGTCC

upper sequence: GRMZM5G844173_T01 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA09G07240.1 (Glycine max), 3'ss of exon 4
----------------------gtaatacaaacttc--ttatggataattgctaggaaattcaagaaagaatctga--caagt------ttcttttacttgcac---tgtacagCAACTTTTGTTCTTCATCATCCGGAGCATGGTCATGCAGTTGTACATCCAATTCTTTCACCCATCATAGATGGGACACTGTGCTATGATAGGCATGGTCC--------------------------
                       || ||  |  |||  |||||  | | |     | || | | ||     |||    ||| |      ||  || | |  ||      | ||||     |||||||||||||||| ||||| || ||||||||||| | ||||||| |||||   || || ||||| || |||  |||||||| |  | ||||                          
gtatagggtatttttgctttacttagtattagtttcaattatgatttactcaacagtaacttatgactatttcttgtccaaataactaatttattcattcacatgtacatccagcggtacttgttcttcatcatccagagCACGGGCATGCAGTTGTGCTTCCAATTATTTCATGTATTATTGATGGTACGCTGGACTATGATAAGACTAGTCCTCCATTTGCTTCTTTCATTTCTTTAG

upper sequence: GRMZM5G844173_T01 (Zea mays), 3'ss of exon 4
lower sequence: AT1G22770.1 (Arabidopsis thaliana), 3'ss of exon 3
--gtaatacaaacttcttatggataattgctaggaaattcaagaaagaatctgacaagtttcttttacttgcactgtacagCAACTTTTGTTCTTCATCATCCGGAGCATGGTCATGCAGTTGTACATCCAATTCTTTCACCCATCATAGATGGGACACTGTGCTATGATAGGCATGGTCC
   | ||  | | || | ||  | | ||         |    ||| |  |||  |   |||   ||   || |    ||||| |  ||||| |||||||||||||||||||||||||||||  | | ||||||  |||||    | || |||||  |  ||   ||    | | | | || 
gtatgatcaacatttatgatccacacttctctttttgtgtgtgaatg--tctatctgattttcgttttctg-atgaaacagCGATGTTTGTCCTTCATCATCCGGAGCATGGTCATGCAGTCATTCTTCCAATCATTTCATGTCTTATTGATGGCTCGTTGGTGTACAGCAAGGAAGCTCA

upper sequence: GRMZM5G844173_T01 (Zea mays), 3'ss of exon 4
lower sequence: Vv18s0157g00020.t01 (Vitis vinifera), 3'ss of exon 5
------------------------gtaatacaaacttcttatggataattgcta--------ggaaattcaagaaagaatctgacaagtttcttttacttg----cactgtacagCAACTTTTGTTCTTCATCATCCGGAGCATGGTCATGCAGTTGTACATCCAATTCTTTCACCCATCATAGATGGGACACTGTGCTATGATAGGCATGGTCC
                         ||    ||| ||  |||   | |||  |         | |  ||| |  ||     |    | || ||| || ||     || | | ||||||| |||||||||||||||||||| ||||| ||||| || || | ||||||| ||||    ||||| ||||| ||||||   |||||||||  |  |||
gtattcatgtttttcaatgttgatatacctaaaaattgatataagttattattccctaatatgaattttctatcaactgcatagtgacttccttataattaaaatcaattttcagCAACGTTTGTTCTTCATCATCCGGAACATGGGCATGCTGTCGTTCTTCCAATTATTTCGTGTATCATTGATGGTACACTGGTGTATGATAGGTGTACTCC

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|148956314|gb|EC902116.2|EC902116
EST:     TCAAAGTTCCTATCCATCAAAAGAAAGTCGCTTGATAGATGAAGTATTGG                         CAACTTTTGTTCTTCATCATCCGGAGCATGGTCATGCAGTTGTACATCCAA
genomic: TCAAAGTTCCTATCCATCAAAAGAAAGTCGCTTGATAGATGAAGTATTGGgtaatacaaa ... cactgtacagCAACTTTTGTTCTTCATCATCCGGAGCATGGTCATGCAGTTGTACATCCAA




















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: 116

CTCATTCAAAGTTCCTATCCATCAAAAGAAAGTCGCTTGATAGATGAAGTATTGGgtaatacaaa ... cactgtacagCAACTTTTGTTCTTCATCATCCGGAGCATGGTCATGCAGTTGTACATCCAATTCTTTCACCCATCATAGATGGGACACTGTGCTATGATAGGCATGGTCC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 90

CTCATTCAAAGTTCCTATCCATCAAAAGAAAGTCGCTTGATAGATGAAGTATTGGgtaatacaaa ... cactgtacagCAACTTTTGTTCTTCATCATCCGGAGCATGGTCATGCAGTTGTACATCCAATTCTTTCACCCATCATAGATGGGACACTGTGCTATGATAGGCATGGTCC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 67

CTCATTCAAAGTTCCTATCCATCAAAAGAAAGTCGCTTGATAGATGAAGTATTGGgtaatacaaa ... cactgtacagCAACTTTTGTTCTTCATCATCCGGAGCATGGTCATGCAGTTGTACATCCAATTCTTTCACCCATCATAGATGGGACACTGTGCTATGATAGGCATGGTCC


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 69

CTCATTCAAAGTTCCTATCCATCAAAAGAAAGTCGCTTGATAGATGAAGTATTGGgtaatacaaa ... cactgtacagCAACTTTTGTTCTTCATCATCCGGAGCATGGTCATGCAGTTGTACATCCAATTCTTTCACCCATCATAGATGGGACACTGTGCTATGATAGGCATGGTCC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgctaggaaattcaagaaagaatctgacaagtttcttttacttgcactgtacagCAACTTTTGTTCTTCATCATCCGGAGCATGGTCATGCAGTTGTACATCCAATTCTTTCACCCATCATAGATGGGACACTGTGCTATGATAGGCATGGTCC
                      atctgac  putative branch site (score: 69)
                                tttcttttacttgc  putative PPT
                                tttctttta  TA-rich tract