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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagttgtctttagtatgaccaaaggaaataaattcaaaaaaaaattacaagtgtcgcttacatatccttgtagactggaactgaatgaaatgtttctggtgtactctgacagGAGTTGGCAATGATCCACGAGAAGATCGATACTTCAGTATCCCAAAACAA

Basic information

species Zea mays
transcript GRMZM2G103897_T02
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G103897_T02 (Zea mays), 3'ss of exon 10
lower sequence: LOC_Os06g45100.1 (Oryza sativa), 3'ss of exon 10
--------------------------------------gttagttgtctttagt--atgaccaaaggaaataaattcaaaaaaaaattacaagtgtcgcttacatatccttgtagactggaactgaatgaaatgtttctggtgtactct-gacagGAGTTGGCAATGATCCACGAGAAGATCGATACTTCAGTATCCCAAAACAA
                                      |  ||   | | || |   |   ||||| ||| ||||   | | |||| |   ||  ||  ||||||||| |   |||||   |  || |||| || | ||  |||| ||| |||||||||||||||||||||| ||||||| |||||||||||||| || || |||
gttagtgtttctttcctcatatacagttacttattcttgaaagcattgtataatcattagtcaaagcaaacaaat--gacacaaaagtgggagc-tcatttacatatcatgccagactctga--gactgaactgctactactgtaatcttgacagGAGTTGGCAATGATCCAAGAGAAGACCGATACTTCAGTATACCTAAGCAA

upper sequence: GRMZM2G103897_T02 (Zea mays), 3'ss of exon 10
lower sequence: GLYMA04G07870.1 (Glycine max), 3'ss of exon 11
gttagttgtctttagtatgaccaaaggaaataaattcaaaaaaaaattacaagtgtcgcttacatatccttgtagactggaactgaatgaaatgtttctggtgtactctgacagGAGTTGGCAATGATCCACGAGAAGATCGATACTTCAGTATCCCAAAACAA
             ||  | |  | | |  ||    |||  |  |  ||     | |   || |  | |  || | |    ||   | |    | | |||| | | |     |||||||||| ||||||||  |||||||||| || ||||| ||||||||||||
-----------ccagattcataatatgccatgccctcattactattttgttcatat--ttttctaaacaatgaaaatcacaatcca-tattctctgtctgttcttcctgttcagGAGTTGGGAATGATCCCAGAGAAGATCGTTATTTCAGCATCCCAAAACAA

upper sequence: GRMZM2G103897_T02 (Zea mays), 3'ss of exon 10
lower sequence: PP1S488_10V6.1 (Physcomitrella patens), 3'ss of exon 12
gttagttgtctttagtatgaccaaaggaaataaattcaaaaaaaaattacaagtgtcgcttacatatcct-tgtagactggaactgaatgaaatgtttctggtgtact-ctgac---agGAGTTGGCAATGATCCACGAGAAGATCGATACTTCAGTATCCCAAAACAA
                   |       | |    ||         ||| | |   ||  |||||   | | |  |   |  ||   |      || | ||| || |   ||||    ||| || ||||||||||| ||||||||||| |||||||| || ||||| || 
-------------------agattttcacacccctttgtccttgtattgctaacatcttttacacgacttgtacatcttctaagcaatctgtttgctactgatgcatcactgattgtagGCGTAGGCAATGATCCTCGAGAAGATCGCTACTTCAGCATTCCAAAGCAG

upper sequence: GRMZM2G103897_T02 (Zea mays), 3'ss of exon 10
lower sequence: EFJ18278 (Selaginella moellendorffii), 3'ss of exon 11
gttagttgtctttagtatgaccaaaggaaataaattcaaaaaaaaattacaagtgtcgct-tacatatccttgtagactggaactgaatgaaatgtttctggtgtactctgacagGAGTTGGCAATGATCCACGAGAAGATCGATACTTCAGTATCCCAAAACAA
                                                      ||  ||  |  | | | |  |   |  |   |  ||| | |   |  || |   ||| |||| ||||| |||||||||||||||||||| |||||||| || || ||||| 
------------------------------------------------------gtaactacatttttacgttcaagtttaagaagcttgacacgc--cgagtttttgctg-cagGGGTTGGGAATGATCCACGAGAAGATCGCTACTTCAGCATTCCCAAACAG

upper sequence: GRMZM2G103897_T02 (Zea mays), 3'ss of exon 10
lower sequence: EFJ22017 (Selaginella moellendorffii), 3'ss of exon 11
gttagttgtctttagtatgaccaaaggaaataaattcaaaaaaaaattacaagtgtcgct-tacatatccttgtagactggaactgaatgaaatgtttctggtgtactctgacagGAGTTGGCAATGATCCACGAGAAGATCGATACTTCAGTATCCCAAAACAA
                                                      ||  ||  |  | | | |  |   || |   |  ||| | |   |  || |   ||| |||| ||||| |||||||||||||||||||| |||||||| || || ||||| 
------------------------------------------------------gtaactacatttttacgttcaagttgaagaagcttgacacgc--cgagtttttgctg-cagGGGTTGGGAATGATCCACGAGAAGATCGCTACTTCAGCATTCCCAAACAG

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|76283830|gb|DV023398.1|DV023398
EST:     ATTGGATTATGACCCAGCTTCGAATTATGGCAATTGGACATATGGAGCAG                         GAGTTGGCAATGATCCACGAGAAGATCGATACTTCAGTATCCCAAAACAA
genomic: ATTGGATTATGACCCAGCTTCGAATTATGGCAATTGGACATATGGAGCAGgttagttgtc ... actctgacagGAGTTGGCAATGATCCACGAGAAGATCGATACTTCAGTATCCCAAAACAA
EST: gi|32909346|gb|CF014158.1|CF014158
EST:     ATTGGATTATGACCCAGCTTCGAATTATGGCAATTGGACATATGGAGCAG                         GAGTTGGCAATGATCCACGAGAAGATCGATACTTCAGGTATCCCAAAACAA
genomic: ATTGGATTATGACCCAGCTTCGAATTATGGCAATTGGACATATGGAGCAGgttagttgtc ... actctgacagGAGTTGGCAATGATCCACGAGAAGATCGATACTTCAG-TATCCCAAAACAA
EST: gi|110957435|gb|EE177487.1|EE177487
EST:     ATTGGATTATGACCCAGCTTCGAATTATGGCAATTGGACATATGGAGCAG                         GAGTTGGCAATGATCCACGAGAAGATCGATACTTCAGTATCCCAAAACAA
genomic: ATTGGATTATGACCCAGCTTCGAATTATGGCAATTGGACATATGGAGCAGgttagttgtc ... actctgacagGAGTTGGCAATGATCCACGAGAAGATCGATACTTCAGTATCCCAAAACAA
EST: gi|148999289|gb|EE036219.2|EE036219
EST:     ATTGGATTATGACCCAGCTTCGAATTATGGCAATTGGACATATGGAGCAG                         GAGTTGGCAATGATCCACGAGAAGATCGATACTTCAGTATCCCAAAACAA
genomic: ATTGGATTATGACCCAGCTTCGAATTATGGCAATTGGACATATGGAGCAGgttagttgtc ... actctgacagGAGTTGGCAATGATCCACGAGAAGATCGATACTTCAGTATCCCAAAACAA
EST: gi|13149731|gb|BG320053.1|BG320053
EST:     ATTGGATTATGACCCAGCTTCGAATTWTGGCAATTGGACATWTGGVGCRG                         GAGTTGGCAATGATCCACGAGAAGATCGATACTTCAGTATCCCAAAACAA
genomic: ATTGGATTATGACCCAGCTTCGAATTATGGCAATTGGACATATGGAGCAGgttagttgtc ... actctgacagGAGTTGGCAATGATCCACGAGAAGATCGATACTTCAGTATCCCAAAACAA

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 3 RNA-Seq libraries.


Block sizes: 42 (upstream exon), 48 (downstream exon)
Score: 3

GATATGGGTGTTGATTGGCGAATGGGAGCCGAATGGTTCGAGACATGCTTATTGGATTATGACCCAGCTTCGAATTATGGCAATTGGACATATGGAGCAGgttagttgtc ... actctgacagGAGTTGGCAATGATCCACGAGAAGATCGATACTTCAGTATCCCAAAACAA


Block sizes: 19 (upstream exon), 31 (downstream exon)
Score: 2

GATATGGGTGTTGATTGGCGAATGGGAGCCGAATGGTTCGAGACATGCTTATTGGATTATGACCCAGCTTCGAATTATGGCAATTGGACATATGGAGCAGgttagttgtc ... actctgacagGAGTTGGCAATGATCCACGAGAAGATCGATACTTCAGTATCCCAAAACAA


Block sizes: 15 (upstream exon), 35 (downstream exon)
Score: 3

GATATGGGTGTTGATTGGCGAATGGGAGCCGAATGGTTCGAGACATGCTTATTGGATTATGACCCAGCTTCGAATTATGGCAATTGGACATATGGAGCAGgttagttgtc ... actctgacagGAGTTGGCAATGATCCACGAGAAGATCGATACTTCAGTATCCCAAAACAA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttacatatccttgtagactggaactgaatgaaatgtttctggtgtactctgacagGAGTTGGCAATGATCCACGAGAAGATCGATACTTCAGTATCCCAAAACAA
 cgcttac  putative branch site (score: 3)
                          aatgaaat  TA-rich tract