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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacgacatgcgccctgctgccgtttctcgctccgtgaactcgatccccaactaatctcctcccctcgattggctttcccctgcagGCGACGATGATCTGCATAGACAACTCGGAGTGGATGCGGAACGGCGACTACGCCCCGTCGCGGTTCCAGGCGCAGGCCGATGCCGTCAACCTCATATGCG

Basic information

species Zea mays
transcript GRMZM2G147671_T01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G147671_T02 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os03g13970.1 (Oryza sativa), 3'ss of exon 1
gtacgacatgcgccctgctgccgtttctcgctccg--tgaact---cgatccccaactaatctc-------ctcccctcgattggctttcccct--gcagGCGACGATGATCTGCATAGACAACTCGGAGTGGATGCGGAACGGCGACTACGCCCCGTCGCGGTTCCAGGCGCAGGCCGATGCCGTCAACCTCATATGCG
|| || |  ||  |  || ||| |  ||| | | |   ||  |   ||| | |  | | |  |        ||    | |  |||||  || ||  ||||||||||||||||||||||||||||||||||||||||||||||||||||||| | |||||||| |||||||| |||||||| |||||||||||||| || |
gttcgccgcgcagctcgccgccctccctcccacagatcgatttcgccgagctctgattcacttatttatcgctttttttgcgtggctcccctctccgcagGCGACGATGATCTGCATAGACAACTCGGAGTGGATGCGGAACGGCGACTACTCGCCGTCGCGATTCCAGGCTCAGGCCGACGCCGTCAACCTCATCTGTG

upper sequence: GRMZM2G147671_T02 (Zea mays), 3'ss of exon 1
lower sequence: PP1S14_318V6.2 (Physcomitrella patens), 3'ss of exon 1
--------------------------------------------------------------------------------------------------------gtacgacatgcgccctgctgccgtttctcgctccgtgaactcgatccccaactaatctcctcccctcgattggctt-----tcccctgcagGCGACGATGATCTGCATAGACAACTCGGAGTGGATGCGGAACGGCGACTACGCCCCGTCGCGGTTCCAGGCGCAGGCCGATGCCGTCAACCTCATATGCG
                                                                                                         | ||  |          ||  |   | |  | |||| | |            | |      |  | ||  |   |     |    | |||||||| ||| ||||||| |||||||| |||||||||||||||||||| ||  | ||  |  |||| || || || || |||||  | ||||| || ||||
gtaagtggaacatgggacgtagtgtattagggttatttgtaggtgcgaattggtttcttaggattcagtgatagtctgccgatcttgaatttctggtttgtttttttcgttactgagttgattgagggagcactgtgcgtgcatttttggtgggtagagttggaagctgttgaacgttatatgggtgttttacagGCGACCATGGTCTGCATGGACAACTCAGAGTGGATGCGGAACGGCGATTATTCACCTACTAGGTTTCAAGCTCAAGCTGATGCTATAAACCTGATTTGCG

upper sequence: GRMZM2G147671_T02 (Zea mays), 3'ss of exon 1
lower sequence: PP1S14_318V6.1 (Physcomitrella patens), 3'ss of exon 1
---------gtacgacatgcgccctgctgccgtttctcgctccgtgaactcgatccccaactaatctcctcccctcgattggctt-----tcccctgcagGCGACGATGATCTGCATAGACAACTCGGAGTGGATGCGGAACGGCGACTACGCCCCGTCGCGGTTCCAGGCGCAGGCCGATGCCGTCAACCTCATATGCG
          | ||  |          ||  |   | |  | |||| | |            | |      |  | ||  |   |     |    | |||||||| ||| ||||||| |||||||| |||||||||||||||||||| ||  | ||  |  |||| || || || || |||||  | ||||| || ||||
gtttgtttttttcgttactgagttgattgagggagcactgtgcgtgcatttttggtgggtagagttggaagctgttgaacgttatatgggtgttttacagGCGACCATGGTCTGCATGGACAACTCAGAGTGGATGCGGAACGGCGATTATTCACCTACTAGGTTTCAAGCTCAAGCTGATGCTATAAACCTGATTTGCG

upper sequence: GRMZM2G147671_T02 (Zea mays), 3'ss of exon 1
lower sequence: EFJ17485 (Selaginella moellendorffii), 3'ss of exon 1
gtacgacatgcgccctgctgccgtttctcgctccgtgaactcgatccccaactaatctcctcccctcgattggctttcccctg---cagGCGACGATGATCTGCATAGACAACTCGGAGTGGATGCGGAACGGCGACTACGCCCCGTCGCG---GTTCCAGGCGCAGGCCGATGCCGTCAACCTCATATGCG
                                           | | ||     ||||    | |  |       ||| | ||   |||||||||||||||||||||||||| || ||||||||||| || || ||||||   ||| || |    |||||| | || || ||||| ||||| || || |   
----------------------------------------gtaagctcctcgcgatctttcacgccaggcctatcttctcttgtgccagGCGACGATGATCTGCATAGACAATTCCGAGTGGATGCGAAATGGGGACTACTATCCGACGAGTAGATTCCAGTCCCAAGCTGATGCTGTCAATCTTATCT---

upper sequence: GRMZM2G147671_T02 (Zea mays), 3'ss of exon 1
lower sequence: EFJ28815 (Selaginella moellendorffii), 3'ss of exon 1
gtacgacatgcgccctgctgccgtttctcgctccgtgaactcgatccccaactaatctcctcccctcgattggctttcccctg---cagGCGACGATGATCTGCATAGACAACTCGGAGTGGATGCGGAACGGCGACTACGCCCCGTCGCG---GTTCCAGGCGCAGGCCGATGCCGTCAACCTCATATGCG
                                           | | ||     ||||    | |  |       ||| | ||   |||||||||||||||||||||||||| || ||||||||||| || || ||||||   ||| || |    |||||| | || |||||||| ||||| || || |   
----------------------------------------gtaagctcctcgcgatctttcacgccaggcctatcttctcttgtgccagGCGACGATGATCTGCATAGACAATTCCGAGTGGATGCGAAATGGGGACTACTATCCGACGAGTAGATTCCAGTCCCAAGCCGATGCTGTCAATCTTATCT---

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|211069192|gb|FL190617.1|FL190617
EST:     CAAACCAGCGCAA-SYCTTCCCTGACAGCGGCGGCGACATGGTGCTCGAG                         GCGACGATGATCTGCATAGACAACTCGGAGTGGATGCGGAACGGCGACTAC
genomic: CAAACCAGCGCAAGCCCTTCCCTGACAGCGGCGGCGACATGGTGCTCGAGgtacgacatg ... tcccctgcagGCGACGATGATCTGCATAGACAACTCGGAGTGGATGCGGAACGGCGACTAC
EST: gi|211071930|gb|FL190632.1|FL190632
EST:     CAAACCAGCGCAAGCCCTTCCCTGACAGCGGCGGCGACATGGTGCTCGAG                         GCGACGATGATCTGCATAGACAACTCGGAGTGGATGCGGAACGGCGACTAC
genomic: CAAACCAGCGCAAGCCCTTCCCTGACAGCGGCGGCGACATGGTGCTCGAGgtacgacatg ... tcccctgcagGCGACGATGATCTGCATAGACAACTCGGAGTGGATGCGGAACGGCGACTAC
EST: gi|31353854|gb|CD438211.1|CD438211
EST:     AAACCAGCGCAA-CCCTATAAGTGACAGCGGCGGCGACATGGGGCTCGAG                         GCGACGATGATCTGCATAGACAACTCGGAGTGGATGTC-GAACGGCGACTA
genomic: AAACCAGCGCAAGCCCT-TCCCTGACAGCGGCGGCGACATGGTGCTCGAGgtacgacatg ... tcccctgcagGCGACGATGATCTGCATAGACAACTCGGAGTGGATG-CGGAACGGCGACTA
EST: gi|211069191|gb|FL190616.1|FL190616
EST:     CAAACCAGCGCAAGCCCTTCCCTGACAGCGGCGGCGACATGGTGCTCGAG                         GCGACGATGATCTGCATAGACAACTCGGAGTGGATGCGGAACGGCGACTAC
genomic: CAAACCAGCGCAAGCCCTTCCCTGACAGCGGCGGCGACATGGTGCTCGAGgtacgacatg ... tcccctgcagGCGACGATGATCTGCATAGACAACTCGGAGTGGATGCGGAACGGCGACTAC
EST: gi|211071927|gb|FL190629.1|FL190629
EST:     CAAACCAGCGCAAGCCCTTCCCTGACAGCGGCGGCGACATGGTGCTCGAG                         GCGACGATGATCTGCATAGACAACTCGGAGTGGATGCGGAACGGCGACTAC
genomic: CAAACCAGCGCAAGCCCTTCCCTGACAGCGGCGGCGACATGGTGCTCGAGgtacgacatg ... tcccctgcagGCGACGATGATCTGCATAGACAACTCGGAGTGGATGCGGAACGGCGACTAC
EST: gi|29947654|gb|CB816768.1|CB816768
EST:     CAGCGG-GGCGACATGG-GCTCGAG                         GCGACGATGATCTGCATAGACAACTCGGAG-GGATGCGGAACGGCGACTAC
genomic: CAGCGGCGGCGACATGGTGCTCGAGgtacgacatg ... tcccctgcagGCGACGATGATCTGCATAGACAACTCGGAGTGGATGCGGAACGGCGACTAC
EST: gi|211069188|gb|FL190613.1|FL190613
EST:     CAAACCAGCGCAAGCCCTTCCCTGACAGCGGCGGCGACATGGTGCTCGAG                         GCGACGATGATCTGCATAGACNACTCGGAGTGGATGCGGAACGGCGACTAC
genomic: CAAACCAGCGCAAGCCCTTCCCTGACAGCGGCGGCGACATGGTGCTCGAGgtacgacatg ... tcccctgcagGCGACGATGATCTGCATAGACAACTCGGAGTGGATGCGGAACGGCGACTAC
EST: gi|5343122|gb|AI795532.1|AI795532
EST:     CAAACCAGCGCAAGCCCTTCCCTGACAGCGGCGGCGACATGGCGCTCGAG                         GCGACGATGATCTGCATAGACAACTCTGAGTGGATGCGGAACGGCGACTAC
genomic: CAAACCAGCGCAAGCCCTTCCCTGACAGCGGCGGCGACATGGTGCTCGAGgtacgacatg ... tcccctgcagGCGACGATGATCTGCATAGACAACTCGGAGTGGATGCGGAACGGCGACTAC
EST: gi|211066454|gb|FL190609.1|FL190609
EST:     CAAACCAGCGCAAGCCCTTCCCTGACAGCGGCGGCGACATGGTGCTCGAG                         GCGACGATGATCTGCATAGACAACTCGGAGTGGATGCGGAACGGCGACTAC
genomic: CAAACCAGCGCAAGCCCTTCCCTGACAGCGGCGGCGACATGGTGCTCGAGgtacgacatg ... tcccctgcagGCGACGATGATCTGCATAGACAACTCGGAGTGGATGCGGAACGGCGACTAC
EST: gi|67041049|gb|CO467304.1|CO467304
EST:     CCCTTCCTTGACAGCGGCGGCGACATGGTGCTCGAG                         GCGACGATGATCTGCATAGACAACTCGGAGTGGATGCGGAACGGCGACTAC
genomic: CCCTTCCCTGACAGCGGCGGCGACATGGTGCTCGAGgtacgacatg ... tcccctgcagGCGACGATGATCTGCATAGACAACTCGGAGTGGATGCGGAACGGCGACTAC
EST: gi|211047092|gb|FL234544.1|FL234544
EST:     CAAACCAGCGCAA-SCCTTCCCTGACAGCGGCGGCGACATGGTGCTCGAG                         GCGACGATGATCTGCATAGACAACTCGGAGTGGATGCGGAACGGCGACTAC
genomic: CAAACCAGCGCAAGCCCTTCCCTGACAGCGGCGGCGACATGGTGCTCGAGgtacgacatg ... tcccctgcagGCGACGATGATCTGCATAGACAACTCGGAGTGGATGCGGAACGGCGACTAC
EST: gi|47961624|gb|CN844333.1|CN844333
EST:     CAAACCAGCGTAAGCCCTTCCCTGACAGCGGCGGCGACATGGTGCTCGAG                         GCGACGATGATCTGCATAGACAACTCGGAGTGGATGCGGAACGGCGACTAC
genomic: CAAACCAGCGCAAGCCCTTCCCTGACAGCGGCGGCGACATGGTGCTCGAGgtacgacatg ... tcccctgcagGCGACGATGATCTGCATAGACAACTCGGAGTGGATGCGGAACGGCGACTAC
EST: gi|9824997|gb|BE575199.1|BE575199
EST:     CAAACCAGCGC-AGCCCTTCCCTGACAGCGGCGGCGACATGGTGCTCGAG                         GCGACGATGATCTGCATAGACAACTCGGAGTGGATGCGGAACGGCGACTAC
genomic: CAAACCAGCGCAAGCCCTTCCCTGACAGCGGCGGCGACATGGTGCTCGAGgtacgacatg ... tcccctgcagGCGACGATGATCTGCATAGACAACTCGGAGTGGATGCGGAACGGCGACTAC
EST: gi|211069187|gb|FL190612.1|FL190612
EST:     CTTCCCTGACAGCGGCGGCGACATGGTGCTCGAG                         GCGACGATGATCTGCATAGACAACTCGGAGTGGATGCGGAACGGCGACTAC
genomic: CTTCCCTGACAGCGGCGGCGACATGGTGCTCGAGgtacgacatg ... tcccctgcagGCGACGATGATCTGCATAGACAACTCGGAGTGGATGCGGAACGGCGACTAC
EST: gi|211069189|gb|FL190614.1|FL190614
EST:     CAAACCAGCGCAAGCCCTTCCCTGACAGCGGCGGCGACATGGTGCTCGAG                         GCGACGATGATCTGCATAGACAACTCGGAGTGGATGCGGAACGGCGACTAC
genomic: CAAACCAGCGCAAGCCCTTCCCTGACAGCGGCGGCGACATGGTGCTCGAGgtacgacatg ... tcccctgcagGCGACGATGATCTGCATAGACAACTCGGAGTGGATGCGGAACGGCGACTAC
EST: gi|211069197|gb|FL190622.1|FL190622
EST:     CAAACCAGCGCAAGCCCTTCCCTGACAGCGGCGGCGACATGGTGCTCGAG                         GCGACGATGATCTGCATAGACAACTCGGAGTGGATGCGGAACGGCGACTAC
genomic: CAAACCAGCGCAAGCCCTTCCCTGACAGCGGCGGCGACATGGTGCTCGAGgtacgacatg ... tcccctgcagGCGACGATGATCTGCATAGACAACTCGGAGTGGATGCGGAACGGCGACTAC
EST: gi|211069199|gb|FL190624.1|FL190624
EST:     CTTCCCTGACAGCGGCGGCGACATGGTGCTCGAG                         GCGACGATGATCTGCATAGACAACTCGGAGTGGATGCGGAACGGCGACTAC
genomic: CTTCCCTGACAGCGGCGGCGACATGGTGCTCGAGgtacgacatg ... tcccctgcagGCGACGATGATCTGCATAGACAACTCGGAGTGGATGCGGAACGGCGACTAC
EST: gi|211069196|gb|FL190621.1|FL190621
EST:     CAAACCAGCGCAA-SYCTTCCCTGACAGCGGCGGCGACATGGTGCTCGAG                         GCGACGATGATCTGCATAGACAACTCGGAGTGGATGCGGAACGGCGACTAC
genomic: CAAACCAGCGCAAGCCCTTCCCTGACAGCGGCGGCGACATGGTGCTCGAGgtacgacatg ... tcccctgcagGCGACGATGATCTGCATAGACAACTCGGAGTGGATGCGGAACGGCGACTAC
EST: gi|32915709|gb|CF020521.1|CF020521
EST:     CAAACCAGCGCAAGCCCTTCCCTGACAGCGGCGGCGACATGGTGCTCGAG                         GCGACGATGATCTGCATAGACAGCTCGGAGTGGATGCGGAACGGCGACTAC
genomic: CAAACCAGCGCAAGCCCTTCCCTGACAGCGGCGGCGACATGGTGCTCGAGgtacgacatg ... tcccctgcagGCGACGATGATCTGCATAGACAACTCGGAGTGGATGCGGAACGGCGACTAC
EST: gi|211069190|gb|FL190615.1|FL190615
EST:     CAAACCAGCGCAAGCCCTTCCCTGACAGCGGCGGCGACATGGTGCTCGAG                         GCGACGATGATCTGCATAGACAACTCGGAGTGGATGCGGAACGGCGACTAC
genomic: CAAACCAGCGCAAGCCCTTCCCTGACAGCGGCGGCGACATGGTGCTCGAGgtacgacatg ... tcccctgcagGCGACGATGATCTGCATAGACAACTCGGAGTGGATGCGGAACGGCGACTAC
EST: gi|31360558|gb|CD444915.1|CD444915
EST:     CAAACCAGCGCAAGCCCTTCCCTGACAGCGGCGGCGACATGGTGCTCGAG                         GCGACGATGATCTGCATAGACAACTCGGAGTGGATGCGGAACGGCGACTAC
genomic: CAAACCAGCGCAAGCCCTTCCCTGACAGCGGCGGCGACATGGTGCTCGAGgtacgacatg ... tcccctgcagGCGACGATGATCTGCATAGACAACTCGGAGTGGATGCGGAACGGCGACTAC
EST: gi|211069198|gb|FL190623.1|FL190623
EST:     CAAACCAGCGCAAGCCCTTCCCTGACAGCGGCGGCGACATGGTGCTCGAG                         GCGACGATGATCTGCATAGACAACTCGGAGTGGATGCGGAACGGCGACTAC
genomic: CAAACCAGCGCAAGCCCTTCCCTGACAGCGGCGGCGACATGGTGCTCGAGgtacgacatg ... tcccctgcagGCGACGATGATCTGCATAGACAACTCGGAGTGGATGCGGAACGGCGACTAC
EST: gi|211069194|gb|FL190619.1|FL190619
EST:     CTTCCCTGACAGCGGCGGCGACATGGTGCTCGAG                         GCGACGATGATCTGCATAGACAACTCGGAGTGGATGCGGAA-VGCGACTAC
genomic: CTTCCCTGACAGCGGCGGCGACATGGTGCTCGAGgtacgacatg ... tcccctgcagGCGACGATGATCTGCATAGACAACTCGGAGTGGATGCGGAACGGCGACTAC
EST: gi|211069200|gb|FL190625.1|FL190625
EST:     CAAACCAGCGCAAGCCCTTCCCTGACAGCGGCGGCGACATGGTGCTCGAG                         GCGACGATGATCTGCATAGACAACTCGGAGTGGATGCGGAACGGCGACTAC
genomic: CAAACCAGCGCAAGCCCTTCCCTGACAGCGGCGGCGACATGGTGCTCGAGgtacgacatg ... tcccctgcagGCGACGATGATCTGCATAGACAACTCGGAGTGGATGCGGAACGGCGACTAC

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: 699

GAGAGAGCTCACCTGAGCCTTTCCCAAGTTGTTTCTCTTCTCTTGCTCCGCAAACCAGCGCAAGCCCTTCCCTGACAGCGGCGGCGACATGGTGCTCGAGgtacgacatg ... tcccctgcagGCGACGATGATCTGCATAGACAACTCGGAGTGGATGCGGAACGGCGACTACGCCCCGTCGCGGTTCCAGGCGCAGGCCGATGCCGTCAACCTCATATGCG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 392

GAGAGAGCTCACCTGAGCCTTTCCCAAGTTGTTTCTCTTCTCTTGCTCCGCAAACCAGCGCAAGCCCTTCCCTGACAGCGGCGGCGACATGGTGCTCGAGgtacgacatg ... tcccctgcagGCGACGATGATCTGCATAGACAACTCGGAGTGGATGCGGAACGGCGACTACGCCCCGTCGCGGTTCCAGGCGCAGGCCGATGCCGTCAACCTCATATGCG


Block sizes: 48 (upstream exon), 46 (downstream exon)
Score: 205

GAGAGAGCTCACCTGAGCCTTTCCCAAGTTGTTTCTCTTCTCTTGCTCCGCAAACCAGCGCAAGCCCTTCCCTGACAGCGGCGGCGACATGGTGCTCGAGgtacgacatg ... tcccctgcagGCGACGATGATCTGCATAGACAACTCGGAGTGGATGCGGAACGGCGACTACGCCCCGTCGCGGTTCCAGGCGCAGGCCGATGCCGTCAACCTCATATGCG


Block sizes: 47 (upstream exon), 46 (downstream exon)
Score: 454

GAGAGAGCTCACCTGAGCCTTTCCCAAGTTGTTTCTCTTCTCTTGCTCCGCAAACCAGCGCAAGCCCTTCCCTGACAGCGGCGGCGACATGGTGCTCGAGgtacgacatg ... tcccctgcagGCGACGATGATCTGCATAGACAACTCGGAGTGGATGCGGAACGGCGACTACGCCCCGTCGCGGTTCCAGGCGCAGGCCGATGCCGTCAACCTCATATGCG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tccgtgaactcgatccccaactaatctcctcccctcgattggctttcccctgcagGCGACGATGATCTGCATAGACAACTCGGAGTGGATGCGGAACGGCGACTACGCCCCGTCGCGGTTCCAGGCGCAGGCCGATGCCGTCAACCTCATATGCG
                  aactaat  putative branch site (score: 454)
                        tctcctcccctcgatt  CT-rich tract
                  aactaat  TA-rich tract