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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttggttggttggttggttgctggaacaatctcatggacatttcatttgaaacagtatatcttgcctcttgaggggaacctggtccctgcttagtaaattatttgacctgtaatcaccattttactggaaacagGTCCTCCATCAGGATGAGACGCCCTTTCTGTACAGTCTCGTGTTCGGTGAGGGAGTCGTGAACGATGCCACGTCTGTTGTGCTCTTCAACGCACTCCAGA

Basic information

species Zea mays
transcript GRMZM2G027851_T03
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G027851_T03 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os07g47100.2 (Oryza sativa), 3'ss of exon 5
gttggttggttggttggttgctggaacaatctcatggacatttcatttgaaacagtatatcttgcctcttgaggggaacctggtccctgcttagtaaattatttgacctgtaatcaccattttactggaaacagGTCCTCCATCAGGATGAGACGCCCTTTCTGTACAGTCTCGTGTTCGGTGAGGGAGTCGTGAACGATGCCACGTCTGTTGTGCTCTTCAACGCACTCCAGA
                                         ||  ||  | | | | |  | | ||||  ||| |  ||||||   |  | |  |||           |||||| | | ||   |   |||||||||||| ||||||||||||| |||||| |||||||||| || |||||||| || || ||||||||||| || ||  ||||||| ||||||||||| ||||
----------------------------------------gttagttgaacaaattttgccatacctc--gagagagacctggattcaacgtgctaa-----------tgtaatgatc-ttaaccccaaaacagGTCCTCAATCAGGATGAGACACCCTTTTTGTACAGTCTGGTATTCGGTGAAGGTGTTGTGAACGATGCTACATCAATTGTGCTTTTCAACGCACTACAGA

upper sequence: GRMZM2G027851_T03 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA19G42900.1 (Glycine max), 3'ss of exon 5
gttggttggttggttggttgctggaacaatctcatggacatttcatttgaaacagtatatcttgcctcttgaggggaacctggtccctgcttagtaaattatttgacctgtaatcaccattttactggaaacagGTCCTCCATCAGGATGAGACGCCCTTTCTGTACAGTCTCGTGTTCGGTGAGGGAGTCGTGAACGATGCCACGTCTGTTGTGCTCTTCAACGCACTCCAGA
                                             |||| |||  ||| |      |    |  | | |   |   |      || |||  |  |  ||| | | |  | |    | |   ||||| ||  | ||||||||||| || || ||||||||||| || || || ||||| || ||||| ||||| || ||||||||||| || || ||| |  | |
--------------------------------------------gtttggaacgatatgtgcctttttcgcaatgtagc--agcaacgaaggtgtcaatgctaagtactgaatttataaatgatgttg---cagGTGCTAAACCAGGATGAGACACCTTTACTGTACAGTCTTGTATTTGGCGAGGGTGTTGTGAATGATGCTACATCTGTTGTGCTTTTTAATGCAATAAAAA

upper sequence: GRMZM2G027851_T03 (Zea mays), 3'ss of exon 3
lower sequence: AT3G05030.2 (Arabidopsis thaliana), 3'ss of exon 2
gttggttggttggttggttgctggaacaatctcatggacatttcatttgaaacagtatatcttgcctcttgagggga----acctggtccctgcttagtaaattatttgacctgtaatcaccattttactg-gaaacagGTCCTCCATCAGGATGAGACGCCCTTTCTGTACAGTCTCGTGTTCGGTGAGGGAGTCGTGAACGATGCCACGTCTGTTGTGCTCTTCAACGCACTCCAGA
                                                     | | |   | |||  ||    | |    |    | ||| |  |   |   || || ||    | ||    |  |   | || |||||| ||| |||| |||||||| || || || |||||||| || || || ||||| || ||||| |||||||| ||||||||||||||||| ||  | ||||
---------------------------------------------------gtaatgtgattcgccaattagcagaagtacatacaggcccagaatcaaagtgtaattaacaaaaactcttgttcctttggtgatacagGTTCTCAATCAAGATGAGACACCTTTGCTTTACAGTCTTGTATTTGGAGAGGGCGTTGTGAATGATGCCACATCTGTTGTGCTCTTCAATGCTATTCAGA

upper sequence: GRMZM2G027851_T03 (Zea mays), 3'ss of exon 3
lower sequence: Vv05s0020g01960.t01 (Vitis vinifera), 3'ss of exon 6
gttggttggttggttggttgctggaacaatctcatggacatttcatt-tgaaacagtatatcttgcctcttgaggggaacctggtccctgcttagtaaattatttgacctgtaatcaccattttactggaaacagGTCCTCCATCAGGATGAGACGCCCTTTCTGTACAGTCTCGTGTTCGGTGAGGGAGTCGTGAACGATGCCACGTCTGTTGTGCTCTTCAACGCACTCCAGA
                                  |  | ||  | ||   || | ||  ||| ||   ||  ||    |   |    |   |    || ||||||  ||   |||| | ||| |        ||||| ||  ||||||||||||| ||||| || |||||||| || || || || || || ||||| |||||||| ||||| ||||| ||||| ||| ||||||
---------------------------------gtacagatggccttactaagctgtg-atcctgttact--agttctaagggacaacacttccacaacttatttatcc---aatc-caattgtg-------cagGTGCTTAATCAGGATGAGACACCCTTACTCTACAGTCTGGTTTTTGGAGAAGGTGTTGTGAATGATGCCACATCTGTGGTGCTTTTCAATGCAATCCAGA

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|89755589|gb|DY685958.1|DY685958
EST:     CTATTGGAGCTATCTTTTCTGCAACGGATTCTGTGTGCACGCTGCAG                         GTCCTCCATCAGGATGAGACGCCCTTTCTGTACAGTCTCGTGTTCGGTGAG
genomic: CTATTGGAGCTATCTTTTCTGCAACGGATTCTGTGTGCACGCTGCAGgttggttggt ... ctggaaacagGTCCTCCATCAGGATGAGACGCCCTTTCTGTACAGTCTCGTGTTCGGTGAG
EST: gi|76936699|gb|DV174843.1|DV174843
EST:     CTATTGGAGCTATCTTTTCTGCAACGGATTCTGTGTGCACGCTGCAG                         GTCCTCCATCAGGATGAGACGCCCTTTCTGTACAGTCTCGTGTTCGGTGAG
genomic: CTATTGGAGCTATCTTTTCTGCAACGGATTCTGTGTGCACGCTGCAGgttggttggt ... ctggaaacagGTCCTCCATCAGGATGAGACGCCCTTTCTGTACAGTCTCGTGTTCGGTGAG

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), 49 (downstream exon)
Score: 40

CTATTGGAGCTATCTTTTCTGCAACGGATTCTGTGTGCACGCTGCAGgttggttggt ... ctggaaacagGTCCTCCATCAGGATGAGACGCCCTTTCTGTACAGTCTCGTGTTCGGTGAGGGAGTCGTGAACGATGCCACGTCTGTTGTGCTCTTCAACGCACTCCAGA


Block sizes: 47 (upstream exon), 47 (downstream exon)
Score: 18

CTATTGGAGCTATCTTTTCTGCAACGGATTCTGTGTGCACGCTGCAGgttggttggt ... ctggaaacagGTCCTCCATCAGGATGAGACGCCCTTTCTGTACAGTCTCGTGTTCGGTGAGGGAGTCGTGAACGATGCCACGTCTGTTGTGCTCTTCAACGCACTCCAGA


Block sizes: 47 (upstream exon), 47 (downstream exon)
Score: 26

CTATTGGAGCTATCTTTTCTGCAACGGATTCTGTGTGCACGCTGCAGgttggttggt ... ctggaaacagGTCCTCCATCAGGATGAGACGCCCTTTCTGTACAGTCTCGTGTTCGGTGAGGGAGTCGTGAACGATGCCACGTCTGTTGTGCTCTTCAACGCACTCCAGA


Block sizes: 47 (upstream exon), 47 (downstream exon)
Score: 33

CTATTGGAGCTATCTTTTCTGCAACGGATTCTGTGTGCACGCTGCAGgttggttggt ... ctggaaacagGTCCTCCATCAGGATGAGACGCCCTTTCTGTACAGTCTCGTGTTCGGTGAGGGAGTCGTGAACGATGCCACGTCTGTTGTGCTCTTCAACGCACTCCAGA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctggtccctgcttagtaaattatttgacctgtaatcaccattttactggaaacagGTCCTCCATCAGGATGAGACGCCCTTTCTGTACAGTCTCGTGTTCGGTGAGGGAGTCGTGAACGATGCCACGTCTGTTGTGCTCTTCAACGCACTCCAGA
                     atttgac  putative branch site (score: 33)
                                        ttttact  putative PPT
           ttagtaaattatttga  TA-rich tract