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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTCTAAGCTTTTGGATGGTGTCACAAAGAAAAAGAAGATATATGTTAGGCTCCTTCTTAGTATTGATCGCCGCGAGACAACTTCGGCTGCATTGGATACCgtatgttaatatcttccagaccaaccaatattctgaactaatacaggtgggcacctattgagaatctgcacaaaatcatttgtttcccctggccag

Basic information

species Zea mays
transcript GRMZM2G137724_T01
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G137724_T01 (Zea mays), 5'ss of exon 5
lower sequence: LOC_Os07g46630.1 (Oryza sativa), 5'ss of exon 5
TTCTAAGCTT-TTGGATGGTGTCACAAAGAAAAAGAAGATATATGTTAGGCTCCTTCTTAGTATTGATCGCCGCGAGACAACTTCGGCTGCATTGGATACCgtatgttaatatcttccagaccaaccaatattctgaactaat---acaggtgggcacctattgagaatctgcacaaaatcatttgtttcccctggccag
 | | ||     ||| ||| | ||||| |||||||||||||||||||||||| ||||| || ||||| ||||| || || |||| ||||||||||||||| ||||||||| || || || ||   | || ||||| | | |||    ||    | || ||| ||| ||| |  | ||| || ||    |    | | |||
-TATGAGTGAGCTGGGTGGCGACACAAGGAAAAAGAAGATATATGTTAGGCTTCTTCTGAGCATTGACCGCCGTGAAACTACTTTGGCTGCATTGGATACTgtatgttaagattttacaaactgtctaacattctaagcaaatttagcaatatgacagctaatgacaatatctataaa-tcgttcacctttgtttgtcag

upper sequence: GRMZM2G137724_T01 (Zea mays), 5'ss of exon 5
lower sequence: AT4G04880.1 (Arabidopsis thaliana), 5'ss of exon 5
-TTCTAAGCTTTTGGATGGTGTCACAAAGAAAAAGAAGATATATGTTAGGCTCCTTCTTAGTATTGATCGCCGCGAGACAACTTCGGCTGCATTGGATACCgtatgttaatatcttccagaccaaccaatattctgaactaatacaggtgggcacctattgagaatctgcacaaaatcatttgtttcccctggccag
  |  |   |  ||| || ||  |     | ||||||||| |||||||| || |||||||||||||||||  | || |||||   | | ||| |||| ||    ||||| | | ||| | || | | ||  | || |   |||||      | ||  ||  ||||        | |   |   |||  | |      
ACTGCACAATGCTGG-TGATGGGATTGGAAGAAAGAAGATTTATGTTAGACTTCTTCTTAGTATTGATCGTAGGGAAACAACAGAGTCCGCAATGGAAAC----Tgttagtgt-ttcaaaacaagctaagctactcag--aatacttaaaag-actaatgcagaaaacatttgatactctccttttttctttaaag-

upper sequence: GRMZM2G137724_T01 (Zea mays), 5'ss of exon 5
lower sequence: Vv10s0116g00820.t01 (Vitis vinifera), 5'ss of exon 5
TTCTAAGCTTTTGGATGGTGTCACAAAGAAAAAGAAGATATATGTTAGGCTCCTTCTTAGTATTGATCGCCGCGAGACAACTTCGGCTGCATTGGATACCgtatgttaatatcttccagacca-accaatattctgaactaatacaggtgggcacctattgagaatctgcacaaaatcatttgtttcccctggccag
    ||   | |   |  ||  || |  |||||||| |||| |||||| || ||||| || ||||||||||| ||||||||| | | |||  |||| |||||||||||||  | |     |       || || || | | ||  | ||      ||||| |   |||      ||   ||| || |          
AGGCAATGATATATGTAATGGGACCACAAAAAAGAAAATATTTGTTAGACTTCTTCTCAGCATTGATCGCCGTGAGACAACTGCAGATGCGATGGAAACCgtatgttaattgcatgtgttctttgaggatgttttgcattcatgtatgta-----ctattcaatgtctaattggaacttttttttacag--------

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|76289006|gb|DV028574.1|DV028574
EST:     TCCTTCTTAGTATTGATCGCCGCGAGACAACTTCGGCTGCATTGGATACC                         GTTAATCTAGCCGTGGAAATGATGGACCAAGGTGTCATAGGCATTGACCTT
genomic: TCCTTCTTAGTATTGATCGCCGCGAGACAACTTCGGCTGCATTGGATACCgtatgttaat ... ccctggccagGTTAATCTAGCCGTGGAAATGATGGACCAAGGTGTCATAGGCATTGACCTT
EST: gi|76927229|gb|DV171186.1|DV171186
EST:     ACAACTTCGGCTGCATTGGATACC                         GTTAATCTAGCCGTGGAAATGATGGACCAAGGTGTCATAGGCATTGACCTT
genomic: ACAACTTCGGCTGCATTGGATACCgtatgttaat ... ccctggccagGTTAATCTAGCCGTGGAAATGATGGACCAAGGTGTCATAGGCATTGACCTT
EST: gi|78121520|gb|DV539904.1|DV539904
EST:     TCCTTCTTAGTATTGATCGCCGCGAGACAACTTCGGCTGCATTGGATACC                         GTTAATCTAGCCGTGGAAATGATGGACCAAGGTGTCATAGGCATTGACCTT
genomic: TCCTTCTTAGTATTGATCGCCGCGAGACAACTTCGGCTGCATTGGATACCgtatgttaat ... ccctggccagGTTAATCTAGCCGTGGAAATGATGGACCAAGGTGTCATAGGCATTGACCTT
EST: gi|76015607|gb|DT942777.1|DT942777
EST:     TCCTTCTTAGTATTGATCGCCGCGAGACAACTTCGGCTGCATTGGATACC                         GTTAATCTAGCCGTGGAAATGATGGACCAAGGTGTCATAGGCATTGACCTT
genomic: TCCTTCTTAGTATTGATCGCCGCGAGACAACTTCGGCTGCATTGGATACCgtatgttaat ... ccctggccagGTTAATCTAGCCGTGGAAATGATGGACCAAGGTGTCATAGGCATTGACCTT
EST: gi|78085656|gb|DV514049.1|DV514049
EST:     TCCTTCTTAGTATTGATCGCCGCGAGACAACTTCGGCTGCATTGGATACC                         GTTAATCTAGCCGTGGAAATGATGGACCAAGGTGTCATAGGCATTGACCTT
genomic: TCCTTCTTAGTATTGATCGCCGCGAGACAACTTCGGCTGCATTGGATACCgtatgttaat ... ccctggccagGTTAATCTAGCCGTGGAAATGATGGACCAAGGTGTCATAGGCATTGACCTT
EST: gi|71449345|gb|DR830395.1|DR830395
EST:     TCCTTCTTAGTATTGATCGCCGCGAGACAACTTCGGCTGCATTGGATACC                         GTTAATCTAGCCGTGGAAATGATGGACCAAGGTGTCATAGGCATTGACCTT
genomic: TCCTTCTTAGTATTGATCGCCGCGAGACAACTTCGGCTGCATTGGATACCgtatgttaat ... ccctggccagGTTAATCTAGCCGTGGAAATGATGGACCAAGGTGTCATAGGCATTGACCTT
EST: gi|211189276|gb|FL030579.1|FL030579
EST:     TCCTTCTTAGTATTGATCGCCGCGAGACAACTTCGGCTGCATTGGATACC                         GTTAATCTAGCCATGGAAATGATGGACCAAGGTGTCATAGGCATTGACCTT
genomic: TCCTTCTTAGTATTGATCGCCGCGAGACAACTTCGGCTGCATTGGATACCgtatgttaat ... ccctggccagGTTAATCTAGCCGTGGAAATGATGGACCAAGGTGTCATAGGCATTGACCTT
EST: gi|76927231|gb|DV171187.1|DV171187
EST:     TCCTTCTTAGTATTGATCGCCGCGAGACAACTTCGGCTGCATTGGATACC                         GTTAATCTAGCCGTGGAAATGATGGACCAAGGTGTCATAGGCATTGACCTT
genomic: TCCTTCTTAGTATTGATCGCCGCGAGACAACTTCGGCTGCATTGGATACCgtatgttaat ... ccctggccagGTTAATCTAGCCGTGGAAATGATGGACCAAGGTGTCATAGGCATTGACCTT
EST: gi|71771045|gb|DR968982.1|DR968982
EST:     TCCTTCTTAGTATTGATCGCCGCGAGACAACTTCGGCTGCATTGGATACC                         GTTAATCTAGCCGTGGAAATGATGGACCAAGGTGTCATAGGCATTGACCTT
genomic: TCCTTCTTAGTATTGATCGCCGCGAGACAACTTCGGCTGCATTGGATACCgtatgttaat ... ccctggccagGTTAATCTAGCCGTGGAAATGATGGACCAAGGTGTCATAGGCATTGACCTT
EST: gi|32854362|gb|CD994043.1|CD994043
EST:     TCCTTCTTAGTATTGATCGCCGCGAGACAACTTCGGCTGCATTGGATACC                         GTTAATCTAGCCATGGAAATGATGGACCAAGGTGTCATAGGCATTGACCTT
genomic: TCCTTCTTAGTATTGATCGCCGCGAGACAACTTCGGCTGCATTGGATACCgtatgttaat ... ccctggccagGTTAATCTAGCCGTGGAAATGATGGACCAAGGTGTCATAGGCATTGACCTT

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: 86

TTCTAAGCTTTTGGATGGTGTCACAAAGAAAAAGAAGATATATGTTAGGCTCCTTCTTAGTATTGATCGCCGCGAGACAACTTCGGCTGCATTGGATACCgtatgttaat ... ccctggccagGTTAATCTAGCCGTGGAAATGATGGACCAAGGTGTCATAGGCATTGACCTTTCTGGCAATCCAGTCGTGGGGGAATG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 71

TTCTAAGCTTTTGGATGGTGTCACAAAGAAAAAGAAGATATATGTTAGGCTCCTTCTTAGTATTGATCGCCGCGAGACAACTTCGGCTGCATTGGATACCgtatgttaat ... ccctggccagGTTAATCTAGCCGTGGAAATGATGGACCAAGGTGTCATAGGCATTGACCTTTCTGGCAATCCAGTCGTGGGGGAATG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 64

TTCTAAGCTTTTGGATGGTGTCACAAAGAAAAAGAAGATATATGTTAGGCTCCTTCTTAGTATTGATCGCCGCGAGACAACTTCGGCTGCATTGGATACCgtatgttaat ... ccctggccagGTTAATCTAGCCGTGGAAATGATGGACCAAGGTGTCATAGGCATTGACCTTTCTGGCAATCCAGTCGTGGGGGAATG


Block sizes: 41 (upstream exon), 49 (downstream exon)
Score: 28

TTCTAAGCTTTTGGATGGTGTCACAAAGAAAAAGAAGATATATGTTAGGCTCCTTCTTAGTATTGATCGCCGCGAGACAACTTCGGCTGCATTGGATACCgtatgttaat ... ccctggccagGTTAATCTAGCCGTGGAAATGATGGACCAAGGTGTCATAGGCATTGACCTTTCTGGCAATCCAGTCGTGGGGGAATG