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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gcaagtctctttacaattacctttgtatcgctatgcaatcacatttaattatctgtacctactcatcaactaactgccatcatgtttgaaattcctttccacagGTCATGACTCAGAGTCCTGAATGTGCCACAGTGGACACCCCAATTCTTGATGCTCTTCACACAATGCATGATGGGAAATTTTTACATTTGCCTGTCCTGG

Basic information

species Zea mays
transcript GRMZM2G171622_T01
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G171622_T01 (Zea mays), 3'ss of exon 7
lower sequence: LOC_Os01g69900.1 (Oryza sativa), 3'ss of exon 7
gcaagtctctttacaattacctttgtatcgctatgcaatcacatttaattatctgtacctactcatcaactaac-tgccatcatgtttgaaattcctttccacagGTCATGACTCAGAGTCCTGAATGTGCCACAGTGGACACCCCAATTCTTGATGCTCTTCACACAATGCATGATGGGAAATTTTTACATTTGCCTGTCCTGG
                 ||     || |    ||| |||  |   ||  | | | |   | ||| | ||||| | || ||||||| |||||| ||||||| |||||||||||| |||| ||||||||||||||| || ||||| ||||| |||||||| || || |||||||| || || || |||||||||||||||||| | |
----------------gtaaggaagtcttaacatggaatgtctgctatgtttttcttaat-ctctttaactatcatggcatcatgcttgaaactcctttctacagGTCATGACCCAGACTCCTGAATGTGCCACGGTTGACACTCCAATCCTTGATGCCCTCCATACAATGCACGACGGAAAGTTTTTACATTTGCCTGTCTTAG

upper sequence: GRMZM2G171622_T01 (Zea mays), 3'ss of exon 7
lower sequence: GLYMA06G17720.1 (Glycine max), 3'ss of exon 6
----------------------------------------gcaagtctctttacaattacctttgtatcgctatgcaatcacatttaattatctgtacctactcatcaactaactgccatcatgtttgaaattcctt---tccacagGTCATGACTCAGAGTCCTGAATGTGCCACAGTGGACACCCCAATTCTTGATGCTCTTCACACAATGCATGATGGGAAATTTTTACATTTGCCTGTCCTGG
                                          |  | | |||  | |||   ||||||   | |    |   |  | |  |  ||    | || |    ||  ||    |  |   |   |||   |   |   |||||||||||||  | | | | ||| |    | | || || || ||| ||||||| |||||||| ||||||||||| |||||||| ||| | ||||   | |
gtgctttgtttttatttttacattgttgagaagaaactgtttacttatgtttttatttaaggttgtatgtatctatcgtgttacctgaaaaattggcaattctgagtttcttccttttcttgttgctcttatttgataaatatgcagGTCATGACTCCCAATTCAGTATGCGTAGTAATTGATACACCCATTGTTGATGCACTTCACACTATGCATGATGGAAAATTTTTGCATCTTCCTGCGGTTG

upper sequence: GRMZM2G171622_T01 (Zea mays), 3'ss of exon 7
lower sequence: GLYMA04G37370.3 (Glycine max), 3'ss of exon 8
--------------------------------------------------------------------------------------gcaagtc-tctttacaattacctttgtatcgctatgcaatcacatttaattatctgtacctactcatcaactaactgccatcatgtttgaaattcctttccacagGTCATGACTCAGAGTCCTGAATGTGCCACAGTGGACACCCCAATTCTTGATGCTCTTCACACAATGCATGATGGGAAATTTTTACATTTGCCTGTCCTGG
                                                                                       | |||  | ||||   ||   | | |      |||  | ||     ||||  |  | |  |    ||  |    |    |     ||          |   |||||||||||||  | ||| ||||||| || | | || || || ||| ||||||| |||||||| |||||||||||||||||||| ||| | |||||  | |
gtactttgtttttatttttacattgttgagacggaactgtttgcttttgttttccttttccattctttgattctgtaacatctatatctagtaatttttaaggttgtatattttctatcatgtta-catgagaaattggcaattctgagggttcttccttttcttgttgctcttatttgataaatatgcagGTCATGACTCCAAATCCAGAATGTGTCATAATTGATACACCCATTGTTGATGCACTTCACACTATGCATGATGGGAAATTTTTGCATCTTCCTGTGGTTG

upper sequence: GRMZM2G171622_T01 (Zea mays), 3'ss of exon 7
lower sequence: Vv17s0000g01200.t01 (Vitis vinifera), 3'ss of exon 8
------------------------------------------------------------------------gcaagtctctttacaattacctttgtatcgct-atgcaatcacatttaattatctgtacctact-catcaactaactgccatcatgtttgaaattcctttcca--cagGTCATGACTCAGAGTCCTGAATGTGCCACAGTGGACACCCCAATTCTTGATGCTCTTCACACAATGCATGATGGGAAATTTTTACATTTGCCTGTCCTGG
                                                                          || | | |   | |||  || || ||   | |||  |     | | || | |   |   |      ||  |||||   |  ||   |    ||  ||      |||||||||||||  | ||| |||||||| ||| | || || || ||| ||||||| || || || |||||||||||||||||||||||  | |||||| | |
gtatttgtctccagcctttctgtcaaaataaaatccaattcgttgtgtccttaaactttgctagaaatgattataaatgtgtcgcctattgtctgtgaattcttcatgataaactctcttatgaacaaaaaggataatgacatttaactctgaatataactttttttatttcatgttcagGTCATGACTCCAAATCCAGAATGTGCAACAATTGATACACCCATTGTTGATGCCCTACATACCATGCATGATGGGAAATTTTTACACCTTCCTGTCATTG

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|50329530|gb|CO524656.1|CO524656
EST:     TGCGTGTTATCGCCCAAAATCTTCCTCCTGAGTCCACCACGGTCGAGAAG                         GTCATGACTCAGAGTCCTGAATGTGCCACAGTGGACACCCCAATTCTTGAT
genomic: TGCGTGTTATCGCCCAAAATCTTCCTCCTGAGTCCACCACGGTCGAGAAGgcaagtctct ... ctttccacagGTCATGACTCAGAGTCCTGAATGTGCCACAGTGGACACCCCAATTCTTGAT
EST: gi|78091968|gb|DV520342.1|DV520342
EST:     TGCGTGTTATCGCCCAAAATCTTCCTCCTGAGTCCACCACGGTCGAGAAG                         GTCATGACTCAGAGTCCTGAATGTGCCACAGTGGACACCCCAATTCTTGAT
genomic: TGCGTGTTATCGCCCAAAATCTTCCTCCTGAGTCCACCACGGTCGAGAAGgcaagtctct ... ctttccacagGTCATGACTCAGAGTCCTGAATGTGCCACAGTGGACACCCCAATTCTTGAT

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: 79

ATCTAGAGATATATTGATGCGTGTTATCGCCCAAAATCTTCCTCCTGAGTCCACCACGGTCGAGAAGgcaagtctct ... ctttccacagGTCATGACTCAGAGTCCTGAATGTGCCACAGTGGACACCCCAATTCTTGATGCTCTTCACACAATGCATGATGGGAAATTTTTACATTTGCCTGTCCTGG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 100

ATCTAGAGATATATTGATGCGTGTTATCGCCCAAAATCTTCCTCCTGAGTCCACCACGGTCGAGAAGgcaagtctct ... ctttccacagGTCATGACTCAGAGTCCTGAATGTGCCACAGTGGACACCCCAATTCTTGATGCTCTTCACACAATGCATGATGGGAAATTTTTACATTTGCCTGTCCTGG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 162

ATCTAGAGATATATTGATGCGTGTTATCGCCCAAAATCTTCCTCCTGAGTCCACCACGGTCGAGAAGgcaagtctct ... ctttccacagGTCATGACTCAGAGTCCTGAATGTGCCACAGTGGACACCCCAATTCTTGATGCTCTTCACACAATGCATGATGGGAAATTTTTACATTTGCCTGTCCTGG


Block sizes: 49 (upstream exon), 45 (downstream exon)
Score: 119

ATCTAGAGATATATTGATGCGTGTTATCGCCCAAAATCTTCCTCCTGAGTCCACCACGGTCGAGAAGgcaagtctct ... ctttccacagGTCATGACTCAGAGTCCTGAATGTGCCACAGTGGACACCCCAATTCTTGATGCTCTTCACACAATGCATGATGGGAAATTTTTACATTTGCCTGTCCTGG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatctgtacctactcatcaactaactgccatcatgtttgaaattcctttccacagGTCATGACTCAGAGTCCTGAATGTGCCACAGTGGACACCCCAATTCTTGATGCTCTTCACACAATGCATGATGGGAAATTTTTACATTTGCCTGTCCTGG
                  aactaac  putative branch site (score: 119)
                                          ttcctttccac  putative PPT
                                   tttgaaatt  TA-rich tract