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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatacaaaccttgtgcttttcacattctctacgctaatagcaaagctaggagataagggggagacaatataatatcactaaccttgtaagtttctttcaaaaaccttgtaagtttctttcgttctttgtaacctctggttgtcttggttagGTATATTTTGAACCGGATGAGGTCCATGCATGCATTGTCACTTGTGGAGGATTGTGCCCGGGACTTAATACTGTGATTAGGGAAATTGTATGTGGATTAT

Basic information

species Zea mays
transcript GRMZM5G816636_T02
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G816636_T02 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os06g05860.1 (Oryza sativa), 3'ss of exon 4
gtatacaaaccttgtgcttttcacattctctacgctaatagcaaagctaggagataagggggagacaatataatatcactaaccttgtaagtttctttcaaaaaccttgtaagtttct-ttcgttctttgtaacctctggttgt-cttggttagGTATATTTTGAACCGGATGAGGTCCATGCATGCATTGTCACTTGTGGAGGATTGTGCCCGGGACTTAATACTGTGATTAGGGAAATTGTATGTGGATTAT
                                                                    |||| || || |    |  ||   |      || ||  | | ||    || ||| || ||| | || ||   || | | |||| |||| | ||||||| |||||||||||||||||||||||||||| ||||||||| ||||||| ||||| || ||||| |||||||||||||||||||| ||||
-------------------------------------------------------------------gtata-taacattgtattcatatactaacacaaataagttggaaaaaaactattctttttttctcacttcatattattcctggtcagGTGTTTTTTGAATCGGATGAGGTCCATGCATGCATTGTCACATGTGGAGGACTGTGCCCTGGACTGAACACTGTCATTAGGGAAATTGTATGTGGCTTAT

upper sequence: GRMZM5G816636_T02 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA04G09180.1 (Glycine max), 3'ss of exon 4
gtatacaaaccttgtgcttttcacattctctacgctaatagcaaagctaggagataagggggagacaatataatatcactaaccttgtaagtttctttcaaaa-accttgtaagtttctttcgttctttgtaacctctggttgtct--tggttagGTATATTTTGAACCGGATGAGGTCCATGCATGCATTGTCACTTGTGGAGGATTGTGCCCGGGACTTAATACTGTGATTAGGGAAATTGTATGTGGATTAT
                                 |  | |  |   | | |    |       | |  ||||| ||| |  |||    ||||  | ||  ||||    |  | | |||  ||    ||    |||  ||  |  | |  || | ||||||| ||| || ||||||| || ||||||||||||||||| ||||| ||| | ||||| || || || ||||| || ||||||||||| |||||  | |
---------------------------------gtcatttcccttgtttgtctgtgcatat-atattatatattattaagaac----taagaatattaaaaaatgtataattaattttgtttccactcaccaacacctaatcatatgctgttcagGTATACTTTAAATCGGATGAAGTGCATGCATGCATTGTCACGTGTGGTGGACTCTGCCCTGGCCTCAACACTGTCATAAGGGAAATTGTCTGTGGTCTTT

upper sequence: GRMZM5G816636_T02 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA06G09320.1 (Glycine max), 3'ss of exon 3
gtatacaaaccttgtgcttttcacattctctacgctaatagcaaagctaggagataagggggagacaatataatatcactaaccttgtaagtttctttcaaaaaccttgtaagtttctttcgttctttgtaacctctggttgtct--tggttagGTATATTTTGAACCGGATGAGGTCCATGCATGCATTGTCACTTGTGGAGGATTGTGCCCGGGACTTAATACTGTGATTAGGGAAATTGTATGTGGATTAT
                                 |  | |  |   | | |    |   | | | |  ||||| ||| |  ||     ||||  | ||  |||    |  | | |||  |     ||    |||  ||  |  | |  || | ||||||| ||| || ||||||| || ||||||||||||||||| ||||| ||| | ||||| || || || ||||| || ||||||||||| |||||  | |
---------------------------------gtcatttcccttgtttgtctgt---gcgtatattatatattattaagaat----taagaatattaaaaatgtataattaattttgtatcaactcaccaacacctaatcatatgctgttcagGTATACTTTAAATCGGATGAAGTGCATGCATGCATTGTCACGTGTGGTGGACTCTGCCCTGGCCTCAACACTGTCATAAGGGAAATTGTCTGTGGTCTTT

upper sequence: GRMZM5G816636_T02 (Zea mays), 3'ss of exon 4
lower sequence: Vv11s0016g02850.t01 (Vitis vinifera), 3'ss of exon 4
gtatacaaaccttgtgcttttcacattctctacgctaatagcaaagctaggagataagggggagacaatataatatcactaaccttgtaagtttctttcaaaaaccttgtaagtttctttcgttctttgtaacctctggttgtcttggttagGTATATTTTGAACCGGATGAGGTCCATGCATGCATTGTCACTTGTGGAGGATTGTGCCCGGGACTTAATACTGTGATTAGGGAAATTGTATGTGGATTAT
                                                           |  || |  | |  | | | ||  | || || ||    | | |||       || || | || |    | |    |  |||| | ||    |||| ||||||||  | ||||| || |||||||| ||||| || ||||| || || ||||| || || || || |||||||||||||| |||||||| ||  
-----------------------------------------------------------gtaagtctttgtt-tgtta-tattcatggaatttgaaatgataaaagacaataggttttctcttaacatattcttttgggttttttt--ccagGTGTATTTTGAGTCTGATGAAGTTCATGCATGTATTGTGACATGTGGTGGTTTATGCCCTGGCCTCAACACAGTGATTAGGGAAATAGTATGTGGCTTGA

upper sequence: GRMZM5G816636_T02 (Zea mays), 3'ss of exon 4
lower sequence: PP1S81_165V6.4 (Physcomitrella patens), 3'ss of exon 5
gtatacaaaccttgtgcttttcacattctctacgctaatagcaaagctaggagataagggggagacaatataatatcactaacctt--gtaagtttctttcaaaaaccttgtaagtttctttcgttctttgtaacctctggttgtcttggttagGTATATTTTGAACCGGATGAGGTCCATGCATGCATTGTCACTTGTGGAGGATTGTGCCCGGGACTTAATACTGTGATTAGGGAAATTGTATGTGGATTAT
               | | || | || |  ||| ||  |  |     |   || |||   | | |||    ||  | | | ||  |    ||||  ||||  ||     |   | |||      ||| |   |  || |  |||||      || |||| ||  |  |||| || ||  | ||||||||||| |||||||||||||| ||||| ||| | |||||||||||| | || ||||| |||||  | |
---------------gttcttaatatccattactcttct--cttgatttttaggtaatttgaatacataccaagctaatttactgtcaagaagtgcctttttaagtgacttccacttttgacatttcgtgacactctttccttgtccg---cagATATACTTCCAGTCGGAGGATGTGAAGGCATGCATTGTAACTTGTGGAGGATTATGCCCCGGAATCAATACTGTGATTCGTGAGATTGTCTGTGGTCTGT

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|61118972|gb|DN559933.1|DN559933
EST:     ATGGCCCCAGAGGGAACCACTTCCGTCGTGCCGGACCTCGCCAAAGG                         GTATATTTTGAACCGGATGAGGTCCATGCATGCATTGTCACTTGTGGAGGA
genomic: ATGGCCCCAGAGGGAACCACTTCCGTCGTGCCGGACCTCGCCAAAGGgtatacaaac ... tcttggttagGTATATTTTGAACCGGATGAGGTCCATGCATGCATTGTCACTTGTGGAGGA




















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: 42 (upstream exon), 22 (downstream exon)
Score: 5

ATTGTTGTTCACAAGGATGGCCCCAGAGGGAACCACTTCCGTCGTGCCGGACCTCGCCAAAGGgtatacaaac ... tcttggttagGTATATTTTGAACCGGATGAGGTCCATGCATGCATTGTCACTTGTGGAGGATTGTGCCCGGGACTTAATACTGTGATTAGGGAAATTGTATGTGGATTAT


Block sizes: 17 (upstream exon), 49 (downstream exon)
Score: 14

ATTGTTGTTCACAAGGATGGCCCCAGAGGGAACCACTTCCGTCGTGCCGGACCTCGCCAAAGGgtatacaaac ... tcttggttagGTATATTTTGAACCGGATGAGGTCCATGCATGCATTGTCACTTGTGGAGGATTGTGCCCGGGACTTAATACTGTGATTAGGGAAATTGTATGTGGATTAT


Block sizes: 41 (upstream exon), 49 (downstream exon)
Score: 19

ATTGTTGTTCACAAGGATGGCCCCAGAGGGAACCACTTCCGTCGTGCCGGACCTCGCCAAAGGgtatacaaac ... tcttggttagGTATATTTTGAACCGGATGAGGTCCATGCATGCATTGTCACTTGTGGAGGATTGTGCCCGGGACTTAATACTGTGATTAGGGAAATTGTATGTGGATTAT


Block sizes: 39 (upstream exon), 32 (downstream exon)
Score: 19

ATTGTTGTTCACAAGGATGGCCCCAGAGGGAACCACTTCCGTCGTGCCGGACCTCGCCAAAGGgtatacaaac ... tcttggttagGTATATTTTGAACCGGATGAGGTCCATGCATGCATTGTCACTTGTGGAGGATTGTGCCCGGGACTTAATACTGTGATTAGGGAAATTGTATGTGGATTAT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcaaaaaccttgtaagtttctttcgttctttgtaacctctggttgtcttggttagGTATATTTTGAACCGGATGAGGTCCATGCATGCATTGTCACTTGTGGAGGATTGTGCCCGGGACTTAATACTGTGATTAGGGAAATTGTATGTGGATTAT
                             ttgtaac  putative branch site (score: 19)
                                          ttgtctt  putative PPT
            taagttt  TA-rich tract