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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTGGATCATGCACGAGTACCGCCTCGCGGATGCGGCGAGCTCAACCACCAGCCGGCCGCCGCCGCCTTGCAACGCCGGAGGCAAGGCCACGTCTCTCAGGgtatgtgtgctactttgtaaaaaaacctgcatatacaagccgatctatagctagcctgagattgcatcgaccaatatatatgcatgcatatcaataacctcccataatgttttcgctaaatataatagctggtgtggttagttgatcaagctctacctagtgtctcag

Basic information

species Zea mays
transcript GRMZM2G179885_T04
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G179885_T02 (Zea mays), 5'ss of exon 2
lower sequence: PP1S15_200V6.1 (Physcomitrella patens), 5'ss of exon 2
------------------------CTGGATCATGCACGAGTACCGCCTCGCGGATGCGGCGAGCTCAACCACCAGCCGGCCGCCGCCGCCTTGCAACGCCGGAGGCAAGGCCACGTCTCTCAGGgtatgtgtgctactttgtaaaaaaacctgcatatacaagccgatctatagctagcctgagattgcatcgaccaatatatatgcatgcatatcaataacctcccataatgttttcgctaaatataatagctggtgtggttagttgatcaagctctacctagtgtctcag
                        |||||||||||||||||||||||||||||| |  |    ||||||| |||     ||  | |||    |   | | |   | | | ||     ||||            |     |||     |   | | |||    |  | | | |      | |  ||||    | ||     ||  | |    || ||  |    ||    ||  |   |   || |||  |||   |    | |        || ||  |  | |||   |||
GGCACCCAAGGGCGAGAAGACGAACTGGATCATGCACGAGTACCGCCTCGCGGAAGGCGT---CTCAACCTCCAAT-AACCATCACCGAAGGGGCTCTCTGCGTgtatgtcctgcattctcctacctcacaaacattcatgtccgcta--ttacgtattttggt-gttttctgaaggactttcgattaacccaactcccctacgttcg---atttctcttgtttcgtggaacatccac---aactatgttaggacgctccgatctgaacgtaacctacatttggtgatgcag

upper sequence: GRMZM2G179885_T02 (Zea mays), 5'ss of exon 2
lower sequence: EFJ20531 (Selaginella moellendorffii), 5'ss of exon 1
------------CTGGATCATGCACGAGTACCGCCTCGCGGATGCGGCGAGCTCAACCACCAGCCGGCCGCCGCCGCCTTGCAACGCCGGAGGCAAGGCCACGTCTCTCAGGgtatgtgtgctactttgtaaaaaaacctgcatatacaagccgatctatagctagcctgagattgcatcgaccaatatatatgcatgcatatcaataacctcccataatgttttcgctaaatataatagctggtgtggttagttgatcaagctctacctagtgtctcag
             |||||||||||||||||||||||||| |||      |||   | | |||   ||||||||| ||  | |   |||    |||||      || ||||||||| |     | ||  || |      |  ||   |        |   |   |    || | |   |||  | | |   |     || |  ||      ||  | | |                                                             
ATCCAAGACGAATTGGATCATGCACGAGTACCGCCTCGCCGAT------AGC---AGCGCCAA--GGCCGCCGCAGCGATTCCG-GCCATGCGCAAGAAAGGATCGCTCAGGgtaagaagaat-ctccgtcatcg---cctcagtcatggcttctttcttgcattctttgtggtgaaatcctcgatttcctg---gtgaaattcgcgtttcttgcttga-------------------------------------------------------------

upper sequence: GRMZM2G179885_T02 (Zea mays), 5'ss of exon 2
lower sequence: EFJ28600 (Selaginella moellendorffii), 5'ss of exon 1
------------CTGGATCATGCACGAGTACCGCCTCGCGGATGCGGCGAGCTCAACCACCAGCCGGCCGCCGCCGCCTTGCAACGCCGGAGGCAAGGCCACGTCTCTCAGGgtatgtgtgctactttgtaaaaaaacctgcatatacaagccgatctatagctagcctgagattgcatcgaccaatatatatgcatgcatatcaataacctcccataatgttttcgctaaatataatagctggtgtggttagttgatcaagctctacctagtgtctcag
             |||||||||||||||||||||||||| |||      |||   | | |||   ||||||||| ||  | |   |||    |||||      || |||||||||               | || || || |     |    || || || |||    |    ||||||         |  |  | |  || ||  |              || | |||  |                                                
ATCCAAGACGAATTGGATCATGCACGAGTACCGCCTCGCCGAT------AGC---AGCGCCAA--GGCCGCCGCAGCGATTCCG-GCCATGCGCAAGAAAGGATCGCTCAGGgta---------------agaagaatctccgccatcgcctcggtc-atggcttctttc---ttgcattctttgtggtgaaatcctcgatttcc-tggtgaaattcgcgtttcttgcttga------------------------------------------------

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|148965670|gb|EE016522.2|EE016522
EST:     GCCGGCCGCCGCCGCCTTGCAACGCCGGAGGCAAGGCCACGTCTCTCAGG                         CTCGACGACTGGGTGTTATGCCGCATCTACAAGAAGATCGACAAACTTGGA
genomic: GCCGGCCGCCGCCGCCTTGCAACGCCGGAGGCAAGGCCACGTCTCTCAGGgtatgtgtgc ... agtgtctcagCTCGACGACTGGGTGTTATGCCGCATCTACAAGAAGATCGACAAACTTGGA
EST: gi|148928954|gb|EC874063.2|EC874063
EST:     AGGCAAGGCCACGTCTCTCAGG                         CTCGACGAATGGGTGTTATGCCGCATCTACAAGAAGATCGACAAACTTGGA
genomic: AGGCAAGGCCACGTCTCTCAGGgtatgtgtgc ... agtgtctcagCTCGACGACTGGGTGTTATGCCGCATCTACAAGAAGATCGACAAACTTGGA
EST: gi|148994538|gb|EE034127.2|EE034127
EST:     GCCGGCCGCCGCCGCCTTGCAACGCCGGAGGCAAGGCCACGTCTCTCAGG                         CTCGACGACTGGGTGTTATGCCGCATCTACAAGAAGATCGACAAACTTGGA
genomic: GCCGGCCGCCGCCGCCTTGCAACGCCGGAGGCAAGGCCACGTCTCTCAGGgtatgtgtgc ... agtgtctcagCTCGACGACTGGGTGTTATGCCGCATCTACAAGAAGATCGACAAACTTGGA
EST: gi|148991087|gb|EE032535.2|EE032535
EST:     GCCGGCCGCCGCCGCCTTGCAACGCCGGAGGCAAGGCCACGTCTCTCAGG                         CTCGACGACTGGGTGTTATGCCGCATCTACAAGAAGATCGACAAACTTGGA
genomic: GCCGGCCGCCGCCGCCTTGCAACGCCGGAGGCAAGGCCACGTCTCTCAGGgtatgtgtgc ... agtgtctcagCTCGACGACTGGGTGTTATGCCGCATCTACAAGAAGATCGACAAACTTGGA
EST: gi|149076917|gb|EE165573.2|EE165573
EST:     GCCGGCCGCCGCCGCCTTGCAACGCCGGAGGCAAGGCCACGTCTCTCAGG                         CTCGACGACTGGGTGTTATGCCGCATCTACAAGAAGATCGACAAACTTGGA
genomic: GCCGGCCGCCGCCGCCTTGCAACGCCGGAGGCAAGGCCACGTCTCTCAGGgtatgtgtgc ... agtgtctcagCTCGACGACTGGGTGTTATGCCGCATCTACAAGAAGATCGACAAACTTGGA
EST: gi|149099135|gb|EE185158.2|EE185158
EST:     GCCGGCCGCCGCCGCCTAGCAACGCCGGAGGCAAGGCCACGTCTCTCAGG                         CTCGACGACTGGGTGTTATGCCGCATCTACAAGAAGATCGACAAACTTGGA
genomic: GCCGGCCGCCGCCGCCTTGCAACGCCGGAGGCAAGGCCACGTCTCTCAGGgtatgtgtgc ... agtgtctcagCTCGACGACTGGGTGTTATGCCGCATCTACAAGAAGATCGACAAACTTGGA
EST: gi|148969854|gb|EE020750.2|EE020750
EST:     CCCGGCCGCCGCCGCCTGGCAACGCCGGAGGCAAGGCCACGTCTCTCAGG                         CTCGAGGACTGGGTGTTATGCCGCATCTACAAGAAGATCGACAAACTTGGA
genomic: GCCGGCCGCCGCCGCCTTGCAACGCCGGAGGCAAGGCCACGTCTCTCAGGgtatgtgtgc ... agtgtctcagCTCGACGACTGGGTGTTATGCCGCATCTACAAGAAGATCGACAAACTTGGA
EST: gi|71756878|gb|DR954815.1|DR954815
EST:     GCCGGCCGCCGCCGCCTTGCAACGCCGGAGGCAAGGCCACGTCTCTCAGG                         CTCGACGACTGGGTGTTATGCCGCATCTACAAGAAGATCGACAAACTTGGA
genomic: GCCGGCCGCCGCCGCCTTGCAACGCCGGAGGCAAGGCCACGTCTCTCAGGgtatgtgtgc ... agtgtctcagCTCGACGACTGGGTGTTATGCCGCATCTACAAGAAGATCGACAAACTTGGA
EST: gi|71760843|gb|DR958780.1|DR958780
EST:     CCGGCCGCCGCCGCC-TGACAACGCCAGAGGCAAGGCCACGTCTCTCAGG                         CTCGACGACTGGGTGTTATGCCGCATCTACAAGAAGATCGACAAACTTGGA
genomic: CCGGCCGCCGCCGCCTTG-CAACGCCGGAGGCAAGGCCACGTCTCTCAGGgtatgtgtgc ... agtgtctcagCTCGACGACTGGGTGTTATGCCGCATCTACAAGAAGATCGACAAACTTGGA
EST: gi|149076918|gb|EE165574.2|EE165574
EST:     GCCGGCCGCCGCCGCCTTGCAACGCCGGAGGCAAGGCCACGTCTCTCAGG                         CTCGACGACTGGGTGTTATGCCGCATCTACAAGAAGATCGACAAACTTGGA
genomic: GCCGGCCGCCGCCGCCTTGCAACGCCGGAGGCAAGGCCACGTCTCTCAGGgtatgtgtgc ... agtgtctcagCTCGACGACTGGGTGTTATGCCGCATCTACAAGAAGATCGACAAACTTGGA
EST: gi|71449659|gb|DR830709.1|DR830709
EST:     GCCGGCCGCCGCCGCCTTGCAACGCCGGAGGCAAGGCCACGTCTCTCAGG                         CTCGACGACTGGGTGTTATGCCGCATCTACAAGAAGATCGACAAACTTGGA
genomic: GCCGGCCGCCGCCGCCTTGCAACGCCGGAGGCAAGGCCACGTCTCTCAGGgtatgtgtgc ... agtgtctcagCTCGACGACTGGGTGTTATGCCGCATCTACAAGAAGATCGACAAACTTGGA
EST: gi|148958368|gb|EC904597.2|EC904597
EST:     GCCGGCCGCCGCCGCCTTGCAACGCCGGAGGCAAGGCCACGTCTCTCAGG                         CTCGACGACTGGGTGTTATGCCGCATCTACAAGAAGATCGACAAACTTGGA
genomic: GCCGGCCGCCGCCGCCTTGCAACGCCGGAGGCAAGGCCACGTCTCTCAGGgtatgtgtgc ... agtgtctcagCTCGACGACTGGGTGTTATGCCGCATCTACAAGAAGATCGACAAACTTGGA
EST: gi|149077513|gb|EE166211.2|EE166211
EST:     GCCGGCCGCCGCCGCCTGGCAACGCCGGAGGCAAGGCCACGTCTCTCAGG                         CTCGACGACTGGGTGTTATGCCGCATCTACAAGAAGATCGACAAACTTGGA
genomic: GCCGGCCGCCGCCGCCTTGCAACGCCGGAGGCAAGGCCACGTCTCTCAGGgtatgtgtgc ... agtgtctcagCTCGACGACTGGGTGTTATGCCGCATCTACAAGAAGATCGACAAACTTGGA
EST: gi|149086510|gb|EE176054.2|EE176054
EST:     GCCGGCCGCCGCCGCCTTGCAACGCCGGAGGCAAGGCCACGTCTCTCAGG                         CTCGACGACTGGGTGTTATGCCGCATCTACAAGAAGATCGACAAACTTGGA
genomic: GCCGGCCGCCGCCGCCTTGCAACGCCGGAGGCAAGGCCACGTCTCTCAGGgtatgtgtgc ... agtgtctcagCTCGACGACTGGGTGTTATGCCGCATCTACAAGAAGATCGACAAACTTGGA
EST: gi|149075036|gb|EE163511.2|EE163511
EST:     GCCGGCCGCCGCCGCCTTGCAACGCCGGAGGCAAGGCCACGTCTCTCAGG                         CTCGACGACTGGGTGTTATGCCGCATCTACAAGAAGATCGACAAACTTGGA
genomic: GCCGGCCGCCGCCGCCTTGCAACGCCGGAGGCAAGGCCACGTCTCTCAGGgtatgtgtgc ... agtgtctcagCTCGACGACTGGGTGTTATGCCGCATCTACAAGAAGATCGACAAACTTGGA
EST: gi|71441634|gb|DR822684.1|DR822684
EST:     CCGGCCGCCGCCGCCTTGCAACGCCGGAGGGCA-GGCCACGTCTCTCAGG                         CTCGACGACTGGGTGTTATGCCGCATCTACAAGAAGATCGACAAACTTGGA
genomic: CCGGCCGCCGCCGCCTTGCAACGCCGGAGG-CAAGGCCACGTCTCTCAGGgtatgtgtgc ... agtgtctcagCTCGACGACTGGGTGTTATGCCGCATCTACAAGAAGATCGACAAACTTGGA
EST: gi|148991089|gb|EE032537.2|EE032537
EST:     GCCGGCCGCCGCCGCCTTGCAACGCCGGAGGCAAGGCCACGTCTCTCAGG                         CTCGACGACTGGGTGTTATGCCGCATCTACAAGAAGATCGACAAACTTGGA
genomic: GCCGGCCGCCGCCGCCTTGCAACGCCGGAGGCAAGGCCACGTCTCTCAGGgtatgtgtgc ... agtgtctcagCTCGACGACTGGGTGTTATGCCGCATCTACAAGAAGATCGACAAACTTGGA
EST: gi|149099136|gb|EE185159.2|EE185159
EST:     GCCGGCCGCCGCCGCCTTGCAACGCCGGAGGCAAGGCCACGTCTCTCAGG                         CTCGACGACTGGGTGTTATGCCGCATCTACAAGAAGATCGACAAACTTGGA
genomic: GCCGGCCGCCGCCGCCTTGCAACGCCGGAGGCAAGGCCACGTCTCTCAGGgtatgtgtgc ... agtgtctcagCTCGACGACTGGGTGTTATGCCGCATCTACAAGAAGATCGACAAACTTGGA
EST: gi|148991088|gb|EE032536.2|EE032536
EST:     GCCGGCCGCCGCCGCCTTGCAACGCCGGAGGCAAGGCCACGTCTCTCAGG                         CTCGACGACTGGGTGTTATGCCGCATCTACAAGAAGATCGACAAACTTGGA
genomic: GCCGGCCGCCGCCGCCTTGCAACGCCGGAGGCAAGGCCACGTCTCTCAGGgtatgtgtgc ... agtgtctcagCTCGACGACTGGGTGTTATGCCGCATCTACAAGAAGATCGACAAACTTGGA
EST: gi|78116101|gb|DV534489.1|DV534489
EST:     CGGCCGCCGCCGCCCTGCAACGCCGGGA-GCAAAGGCCACGTCTCTCAGG                         CTCGACGACTGGGTGTTATGCCGCATCTACAAGAAGATCGACAAACTTGGA
genomic: CGGCCGCCGCCGCCTTGCAACGCC-GGAGGC-AAGGCCACGTCTCTCAGGgtatgtgtgc ... agtgtctcagCTCGACGACTGGGTGTTATGCCGCATCTACAAGAAGATCGACAAACTTGGA
EST: gi|148941728|gb|EC886680.2|EC886680
EST:     GCCGGCCGCCGCCGCCTTGCAACGCCGGAGGCAAGGCCACGTCTCTCAGG                         CTCGACGACTGGGTGTTATGCCGCATCTACAAGAAGATCGACAAACTTGGA
genomic: GCCGGCCGCCGCCGCCTTGCAACGCCGGAGGCAAGGCCACGTCTCTCAGGgtatgtgtgc ... agtgtctcagCTCGACGACTGGGTGTTATGCCGCATCTACAAGAAGATCGACAAACTTGGA
EST: gi|148931258|gb|EC874064.2|EC874064
EST:     GCCGGCCGCCGCCGCCTTGCAACGCCGGAGGCAAGGCCACGTCTCTCAGG                         CTCGACGACTGGGTGTTATGCCGCATCTACAAGAAGATCGACAAACTTGGA
genomic: GCCGGCCGCCGCCGCCTTGCAACGCCGGAGGCAAGGCCACGTCTCTCAGGgtatgtgtgc ... agtgtctcagCTCGACGACTGGGTGTTATGCCGCATCTACAAGAAGATCGACAAACTTGGA
EST: gi|78089362|gb|DV517736.1|DV517736
EST:     GCCGGCCGCCGCCGCCTTGCAACGCCGGAGGCAAGGCCACGTCTCTCAGG                         CTCGACGACTGGGTGTTATGCCGCATCTACAAGAAGATCGACAAACTTGGA
genomic: GCCGGCCGCCGCCGCCTTGCAACGCCGGAGGCAAGGCCACGTCTCTCAGGgtatgtgtgc ... agtgtctcagCTCGACGACTGGGTGTTATGCCGCATCTACAAGAAGATCGACAAACTTGGA
EST: gi|71435611|gb|DR816661.1|DR816661
EST:     GCCGGCCGCCGCCGCCTTGCAACGCCGGAGGCAAGGCCACGTCTCTCAGG                         CTCGACGACTGGGTGTTATGCCGCATCTACAAGAAGATCGACAAACTTGGA
genomic: GCCGGCCGCCGCCGCCTTGCAACGCCGGAGGCAAGGCCACGTCTCTCAGGgtatgtgtgc ... agtgtctcagCTCGACGACTGGGTGTTATGCCGCATCTACAAGAAGATCGACAAACTTGGA
EST: gi|78074655|gb|DV503089.1|DV503089
EST:     GCCGGCCGCCGCCGCCTTGCAACGCCGGAGGCAAGGCCACGTCTCTCAGG                         CTCGACGACTGGGTGTTATGCCGCATCTACAAGAAGATCGACAAACTTGGA
genomic: GCCGGCCGCCGCCGCCTTGCAACGCCGGAGGCAAGGCCACGTCTCTCAGGgtatgtgtgc ... agtgtctcagCTCGACGACTGGGTGTTATGCCGCATCTACAAGAAGATCGACAAACTTGGA
EST: gi|148969855|gb|EE020751.2|EE020751
EST:     GCCGGCCGCCGCCGCCTTGCAACGCCGGAGGCAAGGCCACGTCTCTCAGG                         CTCGACGACTGGGTGTTATGCCGCATCTACAAGAAGATCGACAAACTTGGA
genomic: GCCGGCCGCCGCCGCCTTGCAACGCCGGAGGCAAGGCCACGTCTCTCAGGgtatgtgtgc ... agtgtctcagCTCGACGACTGGGTGTTATGCCGCATCTACAAGAAGATCGACAAACTTGGA
EST: gi|148943109|gb|EC888166.2|EC888166
EST:     CTTGCAACGCCGGAGGCAAGGCCACGTCTCTCAGG                         CTCGACGACTGGGTGTTATGCCGCATCTACAAGAAGATCGACAAACTTGGA
genomic: CTTGCAACGCCGGAGGCAAGGCCACGTCTCTCAGGgtatgtgtgc ... agtgtctcagCTCGACGACTGGGTGTTATGCCGCATCTACAAGAAGATCGACAAACTTGGA
EST: gi|148958367|gb|EC904596.2|EC904596
EST:     GCCGGCCGCCGCCGCCTTGCAACGCCGGAGGCAAGGCCACGTCTCTCAGG                         CTCGACGACTGGGTGTTATGCCGCATCTACAAGAAGATCGACAAACTTGGA
genomic: GCCGGCCGCCGCCGCCTTGCAACGCCGGAGGCAAGGCCACGTCTCTCAGGgtatgtgtgc ... agtgtctcagCTCGACGACTGGGTGTTATGCCGCATCTACAAGAAGATCGACAAACTTGGA
EST: gi|91877992|gb|EB407949.1|EB407949
EST:     GGAGGCAAGGCCACGTCTCTCAGG                         CTGGACGACTGGGTGGTATGCCGCATCTACAAGAAGATCGACAAACTTGGA
genomic: GGAGGCAAGGCCACGTCTCTCAGGgtatgtgtgc ... agtgtctcagCTCGACGACTGGGTGTTATGCCGCATCTACAAGAAGATCGACAAACTTGGA

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 1 RNA-Seqlibrary.


Block sizes: 30 (upstream exon), 38 (downstream exon)
Score: 9

CTGGATCATGCACGAGTACCGCCTCGCGGATGCGGCGAGCTCAACCACCAGCCGGCCGCCGCCGCCTTGCAACGCCGGAGGCAAGGCCACGTCTCTCAGGgtatgtgtgc ... agtgtctcagCTCGACGACTGGGTGTTATGCCGCATCTACAAGAAGATCGACAAACTTGGAGTCGGCGATCCGCCGCGGATCATGGAGTGCGGCGAGGACTCCGTGGAGA




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