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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatttatcagttggatataagctgtaaataaattatttctctgttattgatatctaatccacctggtcatcttttctagTATTGGCTTGGCACACAGGGAGGAAGGTGATCTAGGTCCAGTTTATGGATTTCAATGGCGACACTTTGGTGCCGA

Basic information

species Zea mays
transcript GRMZM2G139880_T01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G139880_T01 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os11g29390.1 (Oryza sativa), 3'ss of exon 6
gtatttatc--agttggatataagctgtaaataaat---tatt-----tctctgttattgatatctaatccacctggtcatctttt--------ctagTATTGGCTTGGCACACAGGGAGGAAGGTGATCTAGGTCCAGTTTATGGATTTCAATGGCGACACTTTGGTGCCGA
||||||||| | | | | || | || ||| |||| ||| ||| | | ||| ||||| ||| | |||| ||||| ||||||| ||||| ||||| |||||||||||||||||||||||||||||||||||||||||||||||||| ||
gtatttatcttggatccacactagtcgagaaacaatggatattgctgttcttggttctcgtgctctgatccatttggcaaaattttactgtgttctagTGTTGGCTTAGCACATAGGGAAGAAGGTGATCTAGGTCCAGTTTATGGATTTCAATGGCGACACTTTGGTGCTGA

upper sequence: GRMZM2G139880_T01 (Zea mays), 3'ss of exon 5
lower sequence: AT2G16370.1 (Arabidopsis thaliana), 3'ss of exon 6
---gtatttatcagttggat-ataagct--gtaaataaattatt--tctctgttattgatat-ctaatccacctggtcatcttttctagTATTGGCTTGGCACACAGGGAGGAAGGTGATCTAGGTCCAGTTTATGGATTTCAATGGCGACACTTTGGTGCCGA
||||| | | || || || | || || || |||| ||| | || | || || | | | | ||||| ||||| ||| || || | || |||||||| || || || || || || |||||||||||||||||||||||||| |
gtaatatttgtaacctgcattatctttttggttaaagaaatattgatcttgacgacctatttgctgatttatcca-ccgtattttc-agTATCGGCCTGACAGAGAGAGAGGAAGGCGACCTTGGACCTGTATACGGATTTCAATGGCGACACTTTGGTGCTAA

upper sequence: GRMZM2G139880_T01 (Zea mays), 3'ss of exon 5
lower sequence: AT4G34570.1 (Arabidopsis thaliana), 3'ss of exon 8
gtatttatcagttggatataagctgtaaataaattatttctctgttattgatatctaatccacctggtcatcttt---tctagTATTGGCTTGGCACACAGGGAGGAAGGTGATCTAGGTCCAGTTTATGGATTTCAATGGCGACACTTTGGTGCCGA
||| | | || || | | || || || ||| || | || | ||| | |||||||| || | | || ||||||||||| || || || |||||||||||||| ||| ||||||||||||| |
gtaaactttaattcagcatttttctttcacaacttgaagctttgtggccattacactgataaattgaaagtttttaatttcagTATTGGACTGACTGAGAGAGAGGAAGGTGACCTTGGACCCGTTTATGGATTTCAGTGGAGACACTTTGGTGCTAA

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|84980638|gb|DW530987.1|DW530987
EST:     AAGGGTATTCATATCTGGGATGGCAATGCTTCAAGAGAGTATCTTGATCG                         TATTGGCTTGGCACACAGGGAGGAAGGTGATCTAGGTCCAGTTTATGGATT
genomic: AAGGGTATTCATATCTGGGATGGCAATGCTTCAAGAGAGTATCTTGACCGgtatttatca ... tcttttctagTATTGGCTTGGCACACAGGGAGGAAGGTGATCTAGGTCCAGTTTATGGATT
EST: gi|32838087|gb|CD977765.1|CD977765
EST:     AAGGGTATTCATATCTGGGATGGCAATGCTTCAAGAGAGTATCTTGACCG                         TATTGACTTGGCACACAGGGAGGAAGGTGATCTAGGTCCAGTTTATGGATT
genomic: AAGGGTATTCATATCTGGGATGGCAATGCTTCAAGAGAGTATCTTGACCGgtatttatca ... tcttttctagTATTGGCTTGGCACACAGGGAGGAAGGTGATCTAGGTCCAGTTTATGGATT
EST: gi|67012996|gb|CO441745.1|CO441745
EST:     AAGGGTATTCATATCTGGGATGGCAATGCTTCAAGAGAGTATCTTGACCG                         TATTGGCTTGGCACACAGGGAGGAAGGTGATCTAGGTCCAGTTTATGGATT
genomic: AAGGGTATTCATATCTGGGATGGCAATGCTTCAAGAGAGTATCTTGACCGgtatttatca ... tcttttctagTATTGGCTTGGCACACAGGGAGGAAGGTGATCTAGGTCCAGTTTATGGATT
EST: gi|32930437|gb|CF035249.1|CF035249
EST:     AAGGGTATTCATATCTGGGATGGCAATGCTTCAAGAGAGTATCTTGACCG                         TATTGGCTTGGCACACAGGGAGGAAGGTGATCTAGGTCCAGTTTATGGATT
genomic: AAGGGTATTCATATCTGGGATGGCAATGCTTCAAGAGAGTATCTTGACCGgtatttatca ... tcttttctagTATTGGCTTGGCACACAGGGAGGAAGGTGATCTAGGTCCAGTTTATGGATT

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), 49 (downstream exon)
Score: 114

GTTTTGCAAGAAAAGGGTATTCATATCTGGGATGGCAATGCTTCAAGAGAGTATCTTGACCGgtatttatca ... tcttttctagTATTGGCTTGGCACACAGGGAGGAAGGTGATCTAGGTCCAGTTTATGGATTTCAATGGCGACACTTTGGTGCCGA


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 62

GTTTTGCAAGAAAAGGGTATTCATATCTGGGATGGCAATGCTTCAAGAGAGTATCTTGACCGgtatttatca ... tcttttctagTATTGGCTTGGCACACAGGGAGGAAGGTGATCTAGGTCCAGTTTATGGATTTCAATGGCGACACTTTGGTGCCGA


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 45

GTTTTGCAAGAAAAGGGTATTCATATCTGGGATGGCAATGCTTCAAGAGAGTATCTTGACCGgtatttatca ... tcttttctagTATTGGCTTGGCACACAGGGAGGAAGGTGATCTAGGTCCAGTTTATGGATTTCAATGGCGACACTTTGGTGCCGA


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 37

GTTTTGCAAGAAAAGGGTATTCATATCTGGGATGGCAATGCTTCAAGAGAGTATCTTGACCGgtatttatca ... tcttttctagTATTGGCTTGGCACACAGGGAGGAAGGTGATCTAGGTCCAGTTTATGGATTTCAATGGCGACACTTTGGTGCCGA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taaataaattatttctctgttattgatatctaatccacctggtcatcttttctagTATTGGCTTGGCACACAGGGAGGAAGGTGATCTAGGTCCAGTTTATGGATTTCAATGGCGACACTTTGGTGCCGA
                           atctaat  putative branch site (score: 37)
 tcatcttttct  putative PPT
 ttattgatatctaat  TA-rich tract