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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaggactatcatcggtgtgattctgtcttgtagagttgctagctcttgatttgtaggaagtggaatatcatgactaatgagatatcttggtattttcccttgcagCTTTCTTGTTATATGTTGCGTCAGTTATTGTGATTGTTTTTGTCCTGGTGTTCTATTTCTCCCCTCTCTATGGGCAGTCCAATGTGTTGATCTACACTGC

Basic information

species Zea mays
transcript GRMZM2G120175_T04
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G120175_T03 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os05g43790.3 (Oryza sativa), 3'ss of exon 4
--------------------------------------gtaaggactatcatcggtgtgattctgtcttgtagagttgctagctcttgatttgtaggaagtggaatatcatgactaatgagatatcttggtattttcccttgcagCTTTCTTGTTATATGTTGCGTCAGTTATTGTGATTGTTTTTGTCCTGGTGTTCTATTTCTCCCCTCTCTATGGGCAGTCCAATGTGTTGATCTACACTGC
                                      ||||| |   | ||   |          |||  | |     | | ||||||| |  ||||||||  ||||| ||   | |||||| | |    ||  ||| |||||||||||||| |||||||||| |||||||| ||| | || || || || |||||| ||||||||||||| ||||||||||| ||||||||||||||||||||
gtgagaattatcgttttatcatgggtgtgattctgtttgtaagcaaagt-attaattcccggtacccttaaaaaacgatttgttcttgatata-aggaagtg--atatc-tgttaattgagatgtttc--catcatcctttgcagCTTTCTTGCTATATGTTGCTTCAGTTATAGTGGTGGTCTTCGTGCTAGTGTTCCATTTCTCCCCTCTATATGGGCAGTCAAATGTGTTGATCTACACTGC
















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|5895870|gb|AW037116.1|AW037116
EST:     GCAGGAGATTACTTCAGTTAAGGAAATATGGAACATGGCGACACAACCTG                         CTTTCTTGTTATATGTTGCGTCAGTTATTGTGATTGTTTTTGTCCTGGTGT
genomic: GCAGGAGATTACTTCAGTTAAGGAAATATGGAACATGGCGACACAACCTGgtaaggacta ... tcccttgcagCTTTCTTGTTATATGTTGCGTCAGTTATTGTGATTGTTTTTGTCCTGGTGT
EST: gi|148934736|gb|EC878785.2|EC878785
EST:     GCAGGAGATTACTTCAGTTAAGGAAATATGGAACATGGCGACACAACCTG                         CTTTCTTGTTATATGTTGCGTCAGTTATT
genomic: GCAGGAGATTACTTCAGTTAAGGAAATATGGAACATGGCGACACAACCTGgtaaggacta ... tcccttgcagCTTTCTTGTTATATGTTGCGTCAGTTATT
EST: gi|148943741|gb|EC888811.2|EC888811
EST:     GCAGGAGAATACTTCAGTTAAGGAAATATGGAACATGGCGACACAACCTG                         CTTTCTTGTTATATGTTGCGTC
genomic: GCAGGAGATTACTTCAGTTAAGGAAATATGGAACATGGCGACACAACCTGgtaaggacta ... tcccttgcagCTTTCTTGTTATATGTTGCGTC
EST: gi|71423545|gb|DR806069.1|DR806069
EST:     GCAGGAGATTACTTCAGTTAAGGAAATATGGAACATGGCGACACAACCTG                         CTTTCTTGTTATATGTTGCGTCAGTTATTGTGATTGTTTTTGTCCTGTTGT
genomic: GCAGGAGATTACTTCAGTTAAGGAAATATGGAACATGGCGACACAACCTGgtaaggacta ... tcccttgcagCTTTCTTGTTATATGTTGCGTCAGTTATTGTGATTGTTTTTGTCCTGGTGT
EST: gi|76287458|gb|DV027026.1|DV027026
EST:     GCAGGAGATTACTTCAGTTAAGGAAATATGGAACATGGCGACACAACCTG                         CTTTCTTGTTATATGTTGCGTCAGTTATTGTGATTGTTTTTGTCCTGGTGT
genomic: GCAGGAGATTACTTCAGTTAAGGAAATATGGAACATGGCGACACAACCTGgtaaggacta ... tcccttgcagCTTTCTTGTTATATGTTGCGTCAGTTATTGTGATTGTTTTTGTCCTGGTGT
EST: gi|76281094|gb|DV020662.1|DV020662
EST:     GCAGGAGATTACTTCAGTTAAGGAAATATGGAACATGGCGACACAACCTG                         CTTTCTTGTTATATGTTGCGTCAGTTATTGTGATTGTTTTTGTCCTGGTGT
genomic: GCAGGAGATTACTTCAGTTAAGGAAATATGGAACATGGCGACACAACCTGgtaaggacta ... tcccttgcagCTTTCTTGTTATATGTTGCGTCAGTTATTGTGATTGTTTTTGTCCTGGTGT

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: 51

GTGATGTGCATTGCAGGGTCTGTGGTCATTGTTATCCACGCTCCACAGGAGCAGGAGATTACTTCAGTTAAGGAAATATGGAACATGGCGACACAACCTGgtaaggacta ... tcccttgcagCTTTCTTGTTATATGTTGCGTCAGTTATTGTGATTGTTTTTGTCCTGGTGTTCTATTTCTCCCCTCTCTATGGGCAGTCCAATGTGTTGATCTACACTGC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 176

GTGATGTGCATTGCAGGGTCTGTGGTCATTGTTATCCACGCTCCACAGGAGCAGGAGATTACTTCAGTTAAGGAAATATGGAACATGGCGACACAACCTGgtaaggacta ... tcccttgcagCTTTCTTGTTATATGTTGCGTCAGTTATTGTGATTGTTTTTGTCCTGGTGTTCTATTTCTCCCCTCTCTATGGGCAGTCCAATGTGTTGATCTACACTGC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 147

GTGATGTGCATTGCAGGGTCTGTGGTCATTGTTATCCACGCTCCACAGGAGCAGGAGATTACTTCAGTTAAGGAAATATGGAACATGGCGACACAACCTGgtaaggacta ... tcccttgcagCTTTCTTGTTATATGTTGCGTCAGTTATTGTGATTGTTTTTGTCCTGGTGTTCTATTTCTCCCCTCTCTATGGGCAGTCCAATGTGTTGATCTACACTGC


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 114

GTGATGTGCATTGCAGGGTCTGTGGTCATTGTTATCCACGCTCCACAGGAGCAGGAGATTACTTCAGTTAAGGAAATATGGAACATGGCGACACAACCTGgtaaggacta ... tcccttgcagCTTTCTTGTTATATGTTGCGTCAGTTATTGTGATTGTTTTTGTCCTGGTGTTCTATTTCTCCCCTCTCTATGGGCAGTCCAATGTGTTGATCTACACTGC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgtaggaagtggaatatcatgactaatgagatatcttggtattttcccttgcagCTTTCTTGTTATATGTTGCGTCAGTTATTGTGATTGTTTTTGTCCTGGTGTTCTATTTCTCCCCTCTCTATGGGCAGTCCAATGTGTTGATCTACACTGC
                     gactaat  putative branch site (score: 114)
                                        tattttccctt  putative PPT
             aatatcat  TA-rich tract