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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tcaaaatcttaagcaggatattgtctgacctgacctatagcaattagcaatagtcatgttaaaggccattcttgtttgtctaaacattgtttttttgcagGCCTGAAGCACTAGGTCTTGTTGTGGGGATTATCTACTTGGTCATTGCTATTATATTTCAGCAGTTTCACTATGCCCCAGACTCCATT

Basic information

species Zea mays
transcript GRMZM2G137707_T01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G137707_T01 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os07g46640.1 (Oryza sativa), 3'ss of exon 1
-tcaaaatcttaagcaggatattgtctgacctgacctatagcaattagcaatagtcatgttaaaggccattcttgtttgtctaaacatt---gtttttttgcagGCCTGAAGCACTAGGTCTTGTTGTGGGGATTATCTACTTGGTCATTGCTATTATATTTCAGCAGTTTCACTATGCCCCAGACTCCATT
 |     |   ||  |    |  || |  |  |||  |  | |  ||  |||      |||      |||||||| |||||||| ||||    ||  ||||||||||||| ||||| ||  ||||||| |||||| |||||||||||||||||||| ||||||| || ||  |||   |  ||||||| || 
ctatttgttcgaaatatttaagagtttagcaggactcactggaggtacaaatcaaatagttt----tcattcttgcttgtctaagcattttacttgctttgcagGCCTGAGGCACTTGGCATTGTTGTTGGGATTGTCTACTTGGTCATTGCTATTCTATTTCAACATTTCAACTTCACAGCAGACTCTATG

upper sequence: GRMZM2G137707_T01 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os07g46640.2 (Oryza sativa), 3'ss of exon 1
-tcaaaatcttaagcaggatattgtctgacctgacctatagcaattagcaatagtcatgttaaaggccattcttgtttgtctaaacattgtttt---tttgcagGCCTGAAGCACTAGGTCTTGTTGTGGGGATTATCTACTTGGTCATTGCTATTATATTTCAGCAGTTTCACTATGCCCCAGACTCCATT------------
 |     |   ||  |    |  || |  |  |||  |  | |  ||  |||      |||      |||||||| |||||||| |||| |  |   ||||||||||||| ||||| ||  ||||||| |||||| |||||||||||||||||||| ||||||| || ||  |||   |  ||||||| ||             
ctatttgttcgaaatatttaagagtttagcaggactcactggaggtacaaatcaaatagttt----tcattcttgcttgtctaagcattttacttgctttgcagGCCTGAGGCACTTGGCATTGTTGTTGGGATTGTCTACTTGGTCATTGCTATTCTATTTCAACATTTCAACTTCACAGCAGACTCTATGGTATGTTGACTA

upper sequence: GRMZM2G137707_T01 (Zea mays), 3'ss of exon 1
lower sequence: Vv08s0007g05920.t01 (Vitis vinifera), 3'ss of exon 1
tcaaaatcttaagcaggatattg-tctg-acctgacctatagcaattagcaatagtcatgttaaaggccattcttgtttgtcta--aacattgtttttttgcagGCCTGAAGCACTAGGTCTTGTTGTGGGGATTATCTACTTGGTCATTGCTATTATATTTCAGCAGTTTCACTATGCCCCAGACTCCATT
   ||||   |   | ||  ||| | || | || |  | |  |   |  |  |  | || | || |     |||||  |  ||   |  |||  | | ||||||||||||| |||| ||| ||||||| |||||| ||| ||||||| | || ||  |||||||| | ||| | |   |  |||| || | |
---aaatagaagctaagagcttgatatgtatctaatatttgcctcctttctttt-ttatatcaatgctttatcttgaattactggtattatttctgtcttgcagGCCTGAATCACTGGGTATTGTTGTTGGGATTGTCTTCTTGGTCTTGGCAATCTTATTTCAGTATTTTAATTTCACATCAGATTCAAAT

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|50339588|gb|CO534714.1|CO534714
EST:     TTCGGCTACGACATCAACAAGAAAGGCTTGCCCACGGGCCAAATTAAAGT                         GCCTGAAGCACTAGGTCTTGTTGTGGGGATTATCTACT
genomic: TTCGGCTACGACATCAACAAGAAAGGCTTGCCCACGGGCCAAATTAAAGTgtgagtgcgc ... ttttttgcagGCCTGAAGCACTAGGTCTTGTTGTGGGGATTATCTACT
EST: gi|71438733|gb|DR819783.1|DR819783
EST:     TTCGGCTACGACATCAACAAGAAAGGCTTGCCCACGGGCCAAATTAAAGT                         GCCTGAAGCACTAGGTCTTGTTGTGGGGATTATCTACTTGGTCATTGCTAT
genomic: TTCGGCTACGACATCAACAAGAAAGGCTTGCCCACGGGCCAAATTAAAGTgtgagtgcgc ... ttttttgcagGCCTGAAGCACTAGGTCTTGTTGTGGGGATTATCTACTTGGTCATTGCTAT
EST: gi|74232443|gb|DT640357.1|DT640357
EST:     TTCGGCTACGACATCAACAAGAAAGGCTTGCCCACGGGCCAAATTAAAGT                         GCCTGAAGCACTAGGTCTTGTTGTGGGGATTATCTACTTGGTCATTGCTAT
genomic: TTCGGCTACGACATCAACAAGAAAGGCTTGCCCACGGGCCAAATTAAAGTgtgagtgcgc ... ttttttgcagGCCTGAAGCACTAGGTCTTGTTGTGGGGATTATCTACTTGGTCATTGCTAT
EST: gi|50331152|gb|CO526278.1|CO526278
EST:     TTCGGCTACGACATCAACAAGAAAGGCTTGCCCACGGGCCAAATTAAAGT                         GCCTGAAGCACTAGGTCTTGTTGTGGGGATTATCTACTTGGTCATTGCTAT
genomic: TTCGGCTACGACATCAACAAGAAAGGCTTGCCCACGGGCCAAATTAAAGTgtgagtgcgc ... ttttttgcagGCCTGAAGCACTAGGTCTTGTTGTGGGGATTATCTACTTGGTCATTGCTAT
EST: gi|50337237|gb|CO532363.1|CO532363
EST:     TTCGGCTACGACATCAACAAGAAAGGCTTGCCCACGGGCCAAATTAAAGT                         GCCTGAAGCACTAGGTCTTGTTGTGGGGATTATCTACTTGGTCATTGCTAT
genomic: TTCGGCTACGACATCAACAAGAAAGGCTTGCCCACGGGCCAAATTAAAGTgtgagtgcgc ... ttttttgcagGCCTGAAGCACTAGGTCTTGTTGTGGGGATTATCTACTTGGTCATTGCTAT
EST: gi|91874805|gb|EB404762.1|EB404762
EST:     TTCGGCTACGACATCAACAAGAAAGGCTTGCCCACGGGCCAAATTAAAGT                         GCCTGAAGCACTAGGTCTTGTTGTGGGGATTATCTACTTGGTCATTGCTAT
genomic: TTCGGCTACGACATCAACAAGAAAGGCTTGCCCACGGGCCAAATTAAAGTgtgagtgcgc ... ttttttgcagGCCTGAAGCACTAGGTCTTGTTGTGGGGATTATCTACTTGGTCATTGCTAT
EST: gi|149084051|gb|EE173446.2|EE173446
EST:     TTCGGCTACGACATCAACAAGAAAGGCTTGCCCACGGGCCAAATTAAAGT                         GCCTGAAGCACTAGGTCTTGTTGTGGGGATTATCTACTTGGTCATTGCTAT
genomic: TTCGGCTACGACATCAACAAGAAAGGCTTGCCCACGGGCCAAATTAAAGTgtgagtgcgc ... ttttttgcagGCCTGAAGCACTAGGTCTTGTTGTGGGGATTATCTACTTGGTCATTGCTAT
EST: gi|101388899|gb|EB816431.1|EB816431
EST:     TTCGGCTACGACATCAACAAGAAAGGCTTGCCCACGGGCCAAATTAAAGT                         GCCTGAAGCACTAGGTCTTGTTGTGGGGATTATCTACTTGGTCATTGCTAT
genomic: TTCGGCTACGACATCAACAAGAAAGGCTTGCCCACGGGCCAAATTAAAGTgtgagtgcgc ... ttttttgcagGCCTGAAGCACTAGGTCTTGTTGTGGGGATTATCTACTTGGTCATTGCTAT
EST: gi|149041344|gb|EE046982.2|EE046982
EST:     TTCGGCTACGACATCAACAAGAAAGGCTTGCCCACGGGCCAAATTAAAGT                         GCCTGAAGCACTAGGTCTTGTTGTGGGGATTATCTACTTGGTCATTGCTAT
genomic: TTCGGCTACGACATCAACAAGAAAGGCTTGCCCACGGGCCAAATTAAAGTgtgagtgcgc ... ttttttgcagGCCTGAAGCACTAGGTCTTGTTGTGGGGATTATCTACTTGGTCATTGCTAT
EST: gi|149078632|gb|EE167420.2|EE167420
EST:     TTCGGCTACGACATCAACAAGAAAGGCTTGCCCACGGGCCAAATTAAAGT                         GCCTGAAGCACTAGGTCTTGTTGTGGGGATTATCTACTTGGTCATTGCTAT
genomic: TTCGGCTACGACATCAACAAGAAAGGCTTGCCCACGGGCCAAATTAAAGTgtgagtgcgc ... ttttttgcagGCCTGAAGCACTAGGTCTTGTTGTGGGGATTATCTACTTGGTCATTGCTAT
EST: gi|149107025|gb|EE188920.2|EE188920
EST:     TTCGGCTACGACATCAACAAGAAAGGCTTGCCCACGGGCCAAATTAAAGT                         GCCTGAAGCACTAGGTCTTGTTGTGGGGATTATCTACTTGGTCATTGCTAT
genomic: TTCGGCTACGACATCAACAAGAAAGGCTTGCCCACGGGCCAAATTAAAGTgtgagtgcgc ... ttttttgcagGCCTGAAGCACTAGGTCTTGTTGTGGGGATTATCTACTTGGTCATTGCTAT
EST: gi|78122710|gb|DV541094.1|DV541094
EST:     TTCGGCTACGACATCAACAAGAAAGGCTTGCCCACGGGCCAAATTAAAGT                         GCCTGAAGCACTAGGTCTTGTTGTGGGGATTATCTACTTGGTCATTGCTAT
genomic: TTCGGCTACGACATCAACAAGAAAGGCTTGCCCACGGGCCAAATTAAAGTgtgagtgcgc ... ttttttgcagGCCTGAAGCACTAGGTCTTGTTGTGGGGATTATCTACTTGGTCATTGCTAT
EST: gi|78108109|gb|DV526527.1|DV526527
EST:     TTCGGCTACGACATCAACAAGAAAGGCTTGCCCACGGGCCAAATTAAAGT                         GCCTGAAGCACTAGGTCTTGTTGTGGGGATTATCTACTTGGTCATTGCTAT
genomic: TTCGGCTACGACATCAACAAGAAAGGCTTGCCCACGGGCCAAATTAAAGTgtgagtgcgc ... ttttttgcagGCCTGAAGCACTAGGTCTTGTTGTGGGGATTATCTACTTGGTCATTGCTAT
EST: gi|71442204|gb|DR823254.1|DR823254
EST:     TTCGGCTACGACATCAACAAGAAAGGCTTGCCCACGGGCCAAATTAAAGT                         GCCTGAAGCACTAGGTCTTGTTGTGGGGATTATCTACTTGGTCATTGCTAT
genomic: TTCGGCTACGACATCAACAAGAAAGGCTTGCCCACGGGCCAAATTAAAGTgtgagtgcgc ... ttttttgcagGCCTGAAGCACTAGGTCTTGTTGTGGGGATTATCTACTTGGTCATTGCTAT

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), 47 (downstream exon)
Score: 65

CGCTCAAGCTCATCCCTGTCGCGGCCAGCTACCACCTCCGCCGCCGGATGTTCGGCTACGACATCAACAAGAAAGGCTTGCCCACGGGCCAAATTAAAGTgtgagtgcgc ... ttttttgcagGCCTGAAGCACTAGGTCTTGTTGTGGGGATTATCTACTTGGTCATTGCTATTATATTTCAGCAGTTTCACTATGCCCCAGACTCCATT


Block sizes: 46 (upstream exon), 40 (downstream exon)
Score: 52

CGCTCAAGCTCATCCCTGTCGCGGCCAGCTACCACCTCCGCCGCCGGATGTTCGGCTACGACATCAACAAGAAAGGCTTGCCCACGGGCCAAATTAAAGTgtgagtgcgc ... ttttttgcagGCCTGAAGCACTAGGTCTTGTTGTGGGGATTATCTACTTGGTCATTGCTATTATATTTCAGCAGTTTCACTATGCCCCAGACTCCATT


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 53

CGCTCAAGCTCATCCCTGTCGCGGCCAGCTACCACCTCCGCCGCCGGATGTTCGGCTACGACATCAACAAGAAAGGCTTGCCCACGGGCCAAATTAAAGTgtgagtgcgc ... ttttttgcagGCCTGAAGCACTAGGTCTTGTTGTGGGGATTATCTACTTGGTCATTGCTATTATATTTCAGCAGTTTCACTATGCCCCAGACTCCATT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 43

CGCTCAAGCTCATCCCTGTCGCGGCCAGCTACCACCTCCGCCGCCGGATGTTCGGCTACGACATCAACAAGAAAGGCTTGCCCACGGGCCAAATTAAAGTgtgagtgcgc ... ttttttgcagGCCTGAAGCACTAGGTCTTGTTGTGGGGATTATCTACTTGGTCATTGCTATTATATTTCAGCAGTTTCACTATGCCCCAGACTCCATT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agcaatagtcatgttaaaggccattcttgtttgtctaaacattgtttttttgcagGCCTGAAGCACTAGGTCTTGTTGTGGGGATTATCTACTTGGTCATTGCTATTATATTTCAGCAGTTTCACTATGCCCCAGACTCCATT
                                gtctaaa  putative branch site (score: 43)
                                         ttgttttttt  putative PPT
                                   taaacattgttttttt  TA-rich tract