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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgacgcctgcgcgacacacacacatagccatcagctttgtctgtcaatcggataatccgcaattcggttgctgaccacgctcccttctctctcagGTGTTCTGCTGCTTCGGCAACTCGGTAGCTTCAACCCGGTTCCTGCTGCAGGACGAGTTCAACATCCAGACAACGCAGTGCGACAACTGCATCATC

Basic information

species Zea mays
transcript GRMZM2G065696_T01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G065696_T01 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os10g39100.1 (Oryza sativa), 3'ss of exon 4
-----------------gtgac-gcctgcgc-gacacacacacatagcc---atcagctttgtctgtcaatcggataatccgcaattcggttgctgaccacgctcccttctctctcagGTGTTCTGCTGCTTCGGCAACTCGGTAGCTTCAACCCGGTTCCTGCTGCAGGACGAGTTCAACATCCAGACAACGCAGTGCGACAACTGCATCATC
                 ||  |  || | || ||  ||     ||   |   || | |||    ||| |       || | | |        |||||  |  ||   || | | |||||||||||||||||| || |||||||| ||||||||| ||||||||||||| || ||||||||||| |||||||| |||||||||||||||||||| 
gtagccatctgcgtactgtagccacccgagctgaatcagttcgatgatctacatgatcttgacatgtaatgtattcaagctgaaccgattcagctgatgaaactgtatt-tgtttcagGTGTTCTGCTGCTTTGGTAACTCGGTGGCTTCAACCAGGTTCCTGCTGCAAGATGAGTTCAACATTCAGACAACCCAGTGCGACAACTGCATCATT

upper sequence: GRMZM2G065696_T01 (Zea mays), 3'ss of exon 5
lower sequence: AT1G63830.1 (Arabidopsis thaliana), 3'ss of exon 5
gtgacgcctgcgcgacacacacacatagccatcagctttgtctg--tcaatcggataatccgcaattcggttgc-tgaccacgctcccttct--ctctcagGTGTTCTGCTGCTTCGGCAACTCGGTAGCTTCAACCCGGTTCCTGCTGCAGGACGAGTTCAACATCCAGACAACGCAGTGCGACAACTGCATCATC
|||| |     |  |      ||  ||   | | ||||    |   ||||| |     | |   ||||   ||  | | ||    |  ||     | |||||| |||   |||||||| ||||| || || || ||||| || || |||||||| || ||||||||||||||||| || |||||||| ||||| || 
gtgatgttcttgatattttggcatttaaa-acctgcttgcaataattcaatagatctcttcatgattcttatgaattagcatttgcaattgaaattttcagGTCTTCCTTTGCTTCGGAAACTCTGTGGCCTCTACCCGCTTTCTTCTGCAGGATGAATTCAACATCCAGACAACACAATGCGACAATTGCATAATT

upper sequence: GRMZM2G065696_T01 (Zea mays), 3'ss of exon 5
lower sequence: Vv02s0025g00130.t01 (Vitis vinifera), 3'ss of exon 4
--gtgacgcctgcgcg-acacacacacatagccatc---agctttgtctgtcaatcggataatccgcaattcggttgctgaccacgctcccttctctctcagGTGTTCTGCTGCTTCGGCAACTCGGTAGCTTCAACCCGGTTCCTGCTGCAGGACGAGTTCAACATCCAGACAACGCAGTGCGACAACTGCATCATC
  || ||   | |  | |  |    |   ||    |    ||||||||  | |  | |||      |||||           |     | ||| |   | ||||  ||  |||||| || || |||||||| |||||||| || ||| |||| || ||||||||||| ||||||||  | || ||||| |||||||| 
gtgtaacaaattcatggattcttttagtcagttcactgaggctttgtcaattatcctgatg--tgacaattattccaagcttcttttccactttttgtttagGTTCTCCTCTGCTTTGGAAATTCGGTAGCATCAACCCGCTTTCTGTTGCAAGATGAGTTCAACATACAGACAACAAAATGTGACAATTGCATCATT

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|14242658|gb|BG840354.2|BG840354
EST:     GCGGCAAGTGCGGCGAGAGCCAGTGCCCGGAAGTATGCCTTGCAACCGAG                         GTGTTCTGCTGCTTCGGCAACTCGGTAGCTTCAACCCGGTTCCTGCTGCAG
genomic: GCGGCAAGTGCGGCGAGAGCCAGTGCCCGGAAGTATGCCTTGCAACCGAGgtgacgcctg ... tctctctcagGTGTTCTGCTGCTTCGGCAACTCGGTAGCTTCAACCCGGTTCCTGCTGCAG
EST: gi|51592820|gb|CV071966.1|CV071966
EST:     GCGGCAAGTGCGGCGAGAGCCAGTGCCCGGAAGTATGCCTTGCAACCGAG                         GTGTTCTGCTGCTTCGGCAACTCGGTAGCTTCAACCCGGTTCCTGCTGCAG
genomic: GCGGCAAGTGCGGCGAGAGCCAGTGCCCGGAAGTATGCCTTGCAACCGAGgtgacgcctg ... tctctctcagGTGTTCTGCTGCTTCGGCAACTCGGTAGCTTCAACCCGGTTCCTGCTGCAG
EST: gi|51592771|gb|CV071917.1|CV071917
EST:     GCGGCAAGTGCGGCGAGAACCAGTGCCCGGAAGTATGCCTTGCAACCGAG                         GTGTTCTGCTGCTTCGGCAACTCGGTAGCTTCAACCCGGTTCCTGCTGCAG
genomic: GCGGCAAGTGCGGCGAGAGCCAGTGCCCGGAAGTATGCCTTGCAACCGAGgtgacgcctg ... tctctctcagGTGTTCTGCTGCTTCGGCAACTCGGTAGCTTCAACCCGGTTCCTGCTGCAG
EST: gi|16918930|gb|BM073956.1|BM073956
EST:     GCGGCAAGTGCGGCGAGAGCCAGTGCCCGGAAGTATGCCTTGCAACCGAG                         GTGTTCTGCTGCTTCGGCAACTCGGTAGCTTCAACCCGGTTCCTGCTGCAG
genomic: GCGGCAAGTGCGGCGAGAGCCAGTGCCCGGAAGTATGCCTTGCAACCGAGgtgacgcctg ... tctctctcagGTGTTCTGCTGCTTCGGCAACTCGGTAGCTTCAACCCGGTTCCTGCTGCAG
EST: gi|47961905|gb|CN844614.1|CN844614
EST:     GCGGCAAGTGCGGCGAGAGCCAGTGCCCGGAAGTATGCCTTGCAACCGAG                         GTGTTCTGCTGCTTCGGCAACTCGGTAGCTTCAACCCGGTTCCTGCTGCAG
genomic: GCGGCAAGTGCGGCGAGAGCCAGTGCCCGGAAGTATGCCTTGCAACCGAGgtgacgcctg ... tctctctcagGTGTTCTGCTGCTTCGGCAACTCGGTAGCTTCAACCCGGTTCCTGCTGCAG
EST: gi|32919836|gb|CF024648.1|CF024648
EST:     GCGGCAAGTGCGGCGAGAGCCAGTGCCCGGAAGTATGCCTTGCAACCGAG                         GTGTTCTGCTGCTTCGGCAACTCGGTAGCTTCCACCCGGTTCCTGCTGCAG
genomic: GCGGCAAGTGCGGCGAGAGCCAGTGCCCGGAAGTATGCCTTGCAACCGAGgtgacgcctg ... tctctctcagGTGTTCTGCTGCTTCGGCAACTCGGTAGCTTCAACCCGGTTCCTGCTGCAG

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: 48 (upstream exon), 39 (downstream exon)
Score: 9

GTACGTGTGCTGCGCCGGGTACATGCCGTGCAGCGGCAAGTGCGGCGAGAGCCAGTGCCCGGAAGTATGCCTTGCAACCGAGgtgacgcctg ... tctctctcagGTGTTCTGCTGCTTCGGCAACTCGGTAGCTTCAACCCGGTTCCTGCTGCAGGACGAGTTCAACATCCAGACAACGCAGTGCGACAACTGCATCATC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 211

GTACGTGTGCTGCGCCGGGTACATGCCGTGCAGCGGCAAGTGCGGCGAGAGCCAGTGCCCGGAAGTATGCCTTGCAACCGAGgtgacgcctg ... tctctctcagGTGTTCTGCTGCTTCGGCAACTCGGTAGCTTCAACCCGGTTCCTGCTGCAGGACGAGTTCAACATCCAGACAACGCAGTGCGACAACTGCATCATC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 262

GTACGTGTGCTGCGCCGGGTACATGCCGTGCAGCGGCAAGTGCGGCGAGAGCCAGTGCCCGGAAGTATGCCTTGCAACCGAGgtgacgcctg ... tctctctcagGTGTTCTGCTGCTTCGGCAACTCGGTAGCTTCAACCCGGTTCCTGCTGCAGGACGAGTTCAACATCCAGACAACGCAGTGCGACAACTGCATCATC


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 6

GTACGTGTGCTGCGCCGGGTACATGCCGTGCAGCGGCAAGTGCGGCGAGAGCCAGTGCCCGGAAGTATGCCTTGCAACCGAGgtgacgcctg ... tctctctcagGTGTTCTGCTGCTTCGGCAACTCGGTAGCTTCAACCCGGTTCCTGCTGCAGGACGAGTTCAACATCCAGACAACGCAGTGCGACAACTGCATCATC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctgtcaatcggataatccgcaattcggttgctgaccacgctcccttctctctcagGTGTTCTGCTGCTTCGGCAACTCGGTAGCTTCAACCCGGTTCCTGCTGCAGGACGAGTTCAACATCCAGACAACGCAGTGCGACAACTGCATCATC
                            tgctgac  putative branch site (score: 6)
                                  ccacgctcccttctct  CT-rich tract
           ataat  TA-rich tract