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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtatatttgcaattaatacttaccagagttgcattgtttcgttaacaaataagcagagatgtcagtatcctacctaagatgctgatttgctttgaaacatggtagaactaatgctctgtccctcactttgcgtcatgctaatgctattaatgggacttctttcgatcggcagGTAGCAGTATGCTCGTTCATCATCGTGGTTGGGGTTTGCTGCGCTTGTGTGGGAACATACTCGTCTCTGTCAAAGATAATCCAGAACTACACATGATACA

Basic information

species Zea mays
transcript GRMZM2G105192_T01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G105192_T03 (Zea mays), 3'ss of exon 10
lower sequence: LOC_Os02g01100.1 (Oryza sativa), 3'ss of exon 11
gtatgtatatttgcaattaatacttaccagagttgcattgtttcgttaacaaataagcagagatgtcagtatcctacctaagatgctgatttgctttgaaacatggtagaactaatgctctgtccctcactttgcgtcatgctaatgctattaatgggacttctttcgatcggcagGTAGCAGTATGCTCGTTCATCATCGTGGTTGGGGTTTGCTGCGCTTGTGTGGGAACATACTCGTCTCTGTCAAAGATAATCCAGAACTACACATGATACA
                                                                    |||    |     ||     |  ||  |   || | ||    |  ||||  |  |   | | ||  |   |   |        || || | |||     |||   ||| | ||||  ||||| |||||||||||||| ||||||||||||||||| ||||| |||||||| || || || ||||| |||||||||||||| |||    
--------------------------------------------------------------------gtacaaaaatatggaaatgaaaatgtgtaataatagggagaga--aatgagcgatgtattaattcactgtacattg-------tattgtggcttt----gatttacagATTGCAGCTTGCTCATTCATCATCGTGGTAGGGGTTTGCTGCGCTTGCGTGGGGACATACTCATCCCTCTCCAAGATTATCCAGAACTACACCTGACCTG
















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|78023016|gb|DV491403.1|DV491403
EST:     CTTGCGCGTGCTTTTTAGCAATTCTTAGGAGAAAAGTGAGCTGGCACCAG                         GTAGCAGTATGCTCGTTCATCATCGTGGTTGGGGTTTGCTGCGCTTGTGTG
genomic: CTTGCGCGTGCTTTTTAGCAATTCTTAGGAGAAAAGTGAGCTGGCACCAGgtatgtatat ... cgatcggcagGTAGCAGTATGCTCGTTCATCATCGTGGTTGGGGTTTGCTGCGCTTGTGTG
EST: gi|6056725|gb|AW091130.1|AW091130
EST:     CTTGCGCGTGCTTTTTAGCAATTCTTAGGAGAAAAGTGAGCTGGCACCAG                         GTAGCAGTATGCTCGTTCATCATCGTGGTTGGGGTTTGCTGCGCTTGTGTG
genomic: CTTGCGCGTGCTTTTTAGCAATTCTTAGGAGAAAAGTGAGCTGGCACCAGgtatgtatat ... cgatcggcagGTAGCAGTATGCTCGTTCATCATCGTGGTTGGGGTTTGCTGCGCTTGTGTG
EST: gi|4967071|gb|AI691821.1|AI691821
EST:     GGAGAAAAGTGACCTGGCACCAG                         GTAGCAGTATGCTCGTTCATCATCGTGGTTGGGGTTTGCTGCGCTTGTGTG
genomic: GGAGAAAAGTGAGCTGGCACCAGgtatgtatat ... cgatcggcagGTAGCAGTATGCTCGTTCATCATCGTGGTTGGGGTTTGCTGCGCTTGTGTG

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: 49 (upstream exon), 49 (downstream exon)
Score: 82

ACCTATATTCTACCTTGCGCGTGCTTTTTAGCAATTCTTAGGAGAAAAGTGAGCTGGCACCAGgtatgtatat ... cgatcggcagGTAGCAGTATGCTCGTTCATCATCGTGGTTGGGGTTTGCTGCGCTTGTGTGGGAACATACTCGTCTCTGTCAAAGATAATCCAGAACTACACATGATACA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 160

ACCTATATTCTACCTTGCGCGTGCTTTTTAGCAATTCTTAGGAGAAAAGTGAGCTGGCACCAGgtatgtatat ... cgatcggcagGTAGCAGTATGCTCGTTCATCATCGTGGTTGGGGTTTGCTGCGCTTGTGTGGGAACATACTCGTCTCTGTCAAAGATAATCCAGAACTACACATGATACA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 275

ACCTATATTCTACCTTGCGCGTGCTTTTTAGCAATTCTTAGGAGAAAAGTGAGCTGGCACCAGgtatgtatat ... cgatcggcagGTAGCAGTATGCTCGTTCATCATCGTGGTTGGGGTTTGCTGCGCTTGTGTGGGAACATACTCGTCTCTGTCAAAGATAATCCAGAACTACACATGATACA


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

ACCTATATTCTACCTTGCGCGTGCTTTTTAGCAATTCTTAGGAGAAAAGTGAGCTGGCACCAGgtatgtatat ... cgatcggcagGTAGCAGTATGCTCGTTCATCATCGTGGTTGGGGTTTGCTGCGCTTGTGTGGGAACATACTCGTCTCTGTCAAAGATAATCCAGAACTACACATGATACA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtccctcactttgcgtcatgctaatgctattaatgggacttctttcgatcggcagGTAGCAGTATGCTCGTTCATCATCGTGGTTGGGGTTTGCTGCGCTTGTGTGGGAACATACTCGTCTCTGTCAAAGATAATCCAGAACTACACATGATACA
                           tattaat  putative branch site (score: 62)
                                      cttctttc  putative PPT
                           tattaat  TA-rich tract