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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGCATCTGGAGGACCAAGGTGGACCTGCCGGAGGAGCTCATCTTCCACATCAACTACCTCGGCGCCGACCAGCCCACCTTCACCCTCAACTTCTCCAAAGgtgccattttcggctcctttttccgtgttctttgatgcagtgtgtgtcgtcagtcacaagcaggcaggctaatctggtcatggcgcacaaaacaatttcag

Basic information

species Zea mays
transcript GRMZM5G826838_T01
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G826838_T01 (Zea mays), 5'ss of exon 5
lower sequence: LOC_Os03g51080.1 (Oryza sativa), 5'ss of exon 5
TGCATCTGGAGGACCAAGGTGGACCTGCCGGAGGAGCTCATCTTCCACATCAACTACCTCGGCGCCGACCAGCCCACCTTCACCCTCAACTTCTCCAAAGgtgccattttcggctcctttttccg--tgttctttgatgcagtgtgtgtcgtcagtcacaagcaggcaggctaatctggt------catggcgcacaaa-acaatttcag----------------------
||||||||||||| ||||| ||| ||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||   | | ||  ||| || ||  |   ||| |  | |    ||  | | |   |  |    |||   || | |||||||      ||||  ||||  | |||||  |||                      
TGCATCTGGAGGAGCAAGGAGGATCTGCCTGAGGAGCTCATCTTCCACATCAACTACCTCGGCGCCGACCAGCCCACCTTCACCCTCAACTTCTCCAAGGgtaaaaatctcctctctttgttttgacagttttacggtttcttgaatcttgatggctatgt-cagttcggttcatctggttacatgcatgatgcacgcacacaataacagaatggcacaatcttttttccag

upper sequence: GRMZM5G826838_T01 (Zea mays), 5'ss of exon 5
lower sequence: PP1S8_163V6.1 (Physcomitrella patens), 5'ss of exon 4
TGCATCTGGAGGACCAAGGTGGACCTGCCGGAGGAGCTCATCTTCCACATCAACTACCTCGGCGCCGACCAGCCCACCTTCACCCTCAACTTCTCCAAAGgt----gccattttcg----gctcctttttccgtgttctttgatgcagtgtg---tgtcgtcagtcacaagcaggcaggctaatctggtcatggcgcacaaaacaatttcag---------------------------------------------------------------------------------------
    | ||| | | ||||| |||||| || |||||| | || || ||| |||||||| | || ||||| |||||||||||||||||||||||||| ||||||     |   | | |     |  |||   | | ||    ||||    | |    |   || | ||     | |      |  ||| |  |  | |||   | ||   ||                                                                                         
GTTGTGTGGCGCAGCAAGGAGGACCTTCCCGAGGAGTTGATTTTTCACGTCAACTACTTGGGAGCCGATCAGCCCACCTTCACCCTCAACTTCTCTAAAGgtttgcactgctcttgttaaacgacttcaccagagtaaactgatctcttctaacctacggttactcttttcctgcagccatcgtctaga-acagagcattcagcagcctcgagaacctcctgcgtgagggaaatgttgacagattggcgaggtcatcactacatctcactgtactaacgaccgttgtcttgtgagtcag

upper sequence: GRMZM5G826838_T01 (Zea mays), 5'ss of exon 5
lower sequence: EFJ36644 (Selaginella moellendorffii), 5'ss of exon 5
TGCATCTGGAGGACCAAGGTGGACCTGCCGGAGGAGCTCATCTTCCACATCAACTACCTCGGCGCCGACCAGCCCACCTTCACCCTCAACTTCTCCAAAGgtgccattttcggctcctttttccgtgttctttgatgcagtgtgtgtcgtcagtcacaagcaggcaggctaatctggtcatggcgcacaaaacaatttcag
   ||||||||   |||||  || || ||||| |||||| ||||||||||||| || || || ||||||||||| || ||||| ||||| || |||||||||  | ||    | || ||| | |     || |  | |  | | | || |    ||||                                           
GTTATCTGGAGAGGCAAGGAAGATCTTCCGGAAGAGCTCGTCTTCCACATCAATTATCTTGGGGCCGACCAGCCAACTTTCACTCTCAATTTTTCCAAAGgt-tctttgagtgttcttttgttctatcactctcttaccat-tctctcttttaccacag------------------------------------------

upper sequence: GRMZM5G826838_T01 (Zea mays), 5'ss of exon 5
lower sequence: EFJ18071 (Selaginella moellendorffii), 5'ss of exon 5
TGCATCTGGAGGACCAAGGTGGACCTGCCGGAGGAGCTCATCTTCCACATCAACTACCTCGGCGCCGACCAGCCCACCTTCACCCTCAACTTCTCCAAAGgtgccattttcggctcctttttccgtgttctttgatgcagtgtgtgtcgtcagtcacaagcaggcaggctaatctggtcatggcgcacaaaacaatttcag
   ||||||||   |||||  || || ||||| |||||| ||||||||||||| || || || ||||||||||| || ||||| ||||| || |||||||||  | ||    | || ||| | |     || |  |    | | |||| |    ||||                                           
GTTATCTGGAGAGGCAAGGAAGATCTTCCGGAAGAGCTCGTCTTCCACATCAATTATCTTGGAGCCGACCAGCCAACTTTCACTCTCAATTTTTCCAAAGgt-tctttgagtgttcttttgttctatcactctcttatcat-tctgtcttttaccacag------------------------------------------

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|149078676|gb|EE167467.2|EE167467
EST:     CAACTACCTCGGCGCCGACCAGCCCACCTTCACCCTCAACTTCTCCAAAG                         GTTCCAGCCAGGTTATTGCACAGTACTACCAGCTGATCCGCCTTGGCTTTG
genomic: CAACTACCTCGGCGCCGACCAGCCCACCTTCACCCTCAACTTCTCCAAAGgtgccatttt ... acaatttcagGTTCCAGCCAGGTTATTGCACAGTACTACCAGCTGATCCGCCTTGGCTTTG
EST: gi|67023766|gb|CO452515.1|CO452515
EST:     CAACTACCTCGGNGCCGACCAGCCCAACTTTACCCTCAACTTTTCCAAAG                         GTTC-AGCCANGTTATTGCACAGTACTACCAGCTGA
genomic: CAACTACCTCGGCGCCGACCAGCCCACCTTCACCCTCAACTTCTCCAAAGgtgccatttt ... acaatttcagGTTCCAGCCAGGTTATTGCACAGTACTACCAGCTGA
EST: gi|40335582|gb|CK369652.1|CK369652
EST:     CAACTACCTCGGCGCCGACCAGCCCACCTTCACCCTCAACTTCTCCAAAG                         GTTCCAGCCAGGTTATTGCACAGTACTACCAGCTGATCCGCCTTGGCTTTG
genomic: CAACTACCTCGGCGCCGACCAGCCCACCTTCACCCTCAACTTCTCCAAAGgtgccatttt ... acaatttcagGTTCCAGCCAGGTTATTGCACAGTACTACCAGCTGATCCGCCTTGGCTTTG

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: 43 (upstream exon), 49 (downstream exon)
Score: 64

TGCATCTGGAGGACCAAGGTGGACCTGCCGGAGGAGCTCATCTTCCACATCAACTACCTCGGCGCCGACCAGCCCACCTTCACCCTCAACTTCTCCAAAGgtgccatttt ... acaatttcagGTTCCAGCCAGGTTATTGCACAGTACTACCAGCTGATCCGCCTTGGCTTTGAA


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 154

TGCATCTGGAGGACCAAGGTGGACCTGCCGGAGGAGCTCATCTTCCACATCAACTACCTCGGCGCCGACCAGCCCACCTTCACCCTCAACTTCTCCAAAGgtgccatttt ... acaatttcagGTTCCAGCCAGGTTATTGCACAGTACTACCAGCTGATCCGCCTTGGCTTTGAA


Block sizes: 43 (upstream exon), 47 (downstream exon)
Score: 95

TGCATCTGGAGGACCAAGGTGGACCTGCCGGAGGAGCTCATCTTCCACATCAACTACCTCGGCGCCGACCAGCCCACCTTCACCCTCAACTTCTCCAAAGgtgccatttt ... acaatttcagGTTCCAGCCAGGTTATTGCACAGTACTACCAGCTGATCCGCCTTGGCTTTGAA


Block sizes: 43 (upstream exon), 46 (downstream exon)
Score: 120

TGCATCTGGAGGACCAAGGTGGACCTGCCGGAGGAGCTCATCTTCCACATCAACTACCTCGGCGCCGACCAGCCCACCTTCACCCTCAACTTCTCCAAAGgtgccatttt ... acaatttcagGTTCCAGCCAGGTTATTGCACAGTACTACCAGCTGATCCGCCTTGGCTTTGAA