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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgaaaaataaaaggcttactatttgcttagtgttttgtcttttcatgggtggaccaactcagcttgtaacctgacatttcttcaccttgccatctcatagATATGTGGGCAATGGGTGCCATAATGGCTGAGTTGTTGACACTCCATCCTCTCTTTCCTGGAACTAG

Basic information

species Zea mays
transcript GRMZM2G108829_T01
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G108829_T01 (Zea mays), 3'ss of exon 10
lower sequence: LOC_Os02g47220.3 (Oryza sativa), 3'ss of exon 5
gtatgaaaaataaaaggcttactatttgcttagtgttttgtcttttcatgggtggaccaactcagcttgtaacctgacatttcttcaccttgccatctcatagATATGTGGGCAATGGGTGCCATAATGGCTGAGTTGTTGACACTCCATCCTCTCTTTCCTGGAACTAG
          ||||     |||||| | ||| || ||||| |   |   |     || || |||     | |   ||   | |      |||||| ||   |||||||||||| ||||||||||||||||| ||| |||||||||| |||||||| |||||||| || ||
---------gtaaagtttctactatctactttgtattttggcacatatagtacatactaagtca-----tgattggatgatcccct-ttttgccaacttgcagATATGTGGGCTATGGGTGCCATAATGGCCGAGCTGTTGACACTTCATCCTCTTTTTCCTGGCACAAG

upper sequence: GRMZM2G108829_T01 (Zea mays), 3'ss of exon 10
lower sequence: GLYMA01G35190.2 (Glycine max), 3'ss of exon 7
------------------gtatgaaa--aataaaaggcttactatttgct------tagtgttttgtcttttcatgggtggaccaactcagcttgtaacctgacatttctt--caccttgccatctcatagATATGTGGGCAATGGGTGCCATAATGGCTGAGTTGTTGACACTCCATCCTCTCTTTCCTGGAACTAG
                  || ||  |  ||  || ||  |  | | || |      ||  | ||| |   || |||         | |    || || | |    ||| ||  ||  |  ||  ||  |||| ||||||||||||||||| |||||||||||| | ||  | || | |||||| || || ||  | ||
gtgagtgtctgactgggagtttgggactaactaatggtgtcatttatgttcttcactaacgctttctgcattgatgatgatgatgagtaccattctaccattttgtttattaacatttcccccccttctagACATGTGGGCAATGGGTGCTATAATGGCTGAGCTTTTCTCTCTTCGTCCTCTTTTCCCAGGTGCCAG

upper sequence: GRMZM2G108829_T01 (Zea mays), 3'ss of exon 10
lower sequence: GLYMA09G34610.1 (Glycine max), 3'ss of exon 7
---------gtatgaaaaataaaaggcttact-atttgcttagtgttttgtcttttcatgggtg--gaccaac-tcagcttgtaacctgacatttcttcaccttgccatctcatagATATGTGGGCAATGGGTGCCATAATGGCTGAGTTGTTGACACTCCATCCTCTCTTTCCTGGAACTAG
           ||    | |||  |  | | | || | |||      |  | | | ||| | ||  ||  |    ||   ||  |  ||    ||     ||   ||  ||  |||||||||||||||||||||| |||||||||||| | ||  | || | |||||| || || ||  | ||
gtgagtatctgattgggactaatggtgtcatttatgttcttcactaatgctttctgcattgatgatgatgagtaccatgctgccatttgtttattaactcccccccccccttctagATATGTGGGCAATGGGTGCTATAATGGCTGAGCTTTTCTCTCTTCGTCCTCTTTTCCCAGGTGCCAG

upper sequence: GRMZM2G108829_T01 (Zea mays), 3'ss of exon 10
lower sequence: GLYMA16G08080.1 (Glycine max), 3'ss of exon 7
---------------------------------------------gtatgaaaaataaaaggcttactatttgcttagtgttttgtcttttcatgggtggaccaactcagcttgtaacctgacatttcttcaccttgccatctcat----agATATGTGGGCAATGGGTGCCATAATGGCTGAGTTGTTGACACTCCATCCTCTCTTTCCTGGAACTAG
                                              |   ||||      ||  ||   | |    | ||  || |||| |  ||  || |  ||       |||    |   ||   || | | |    | ||||    ||||||||||||||||||||| ||||||||||||||||| || |||| |||||| || || ||  | ||
gtaagcatctgatattgaataattgccatttatggtgacttatgttttccaaaagattgtggtctagagtctagacaatgcatt-tcttgtagtga-tgaattaatgacaagtgttgagtactataagtttaacattttttttcatctgcagATATGTGGGCAATGGGTGCTATAATGGCTGAGTTGTTCACTCTCCGTCCTCTATTCCCCGGTTCCAG

upper sequence: GRMZM2G108829_T01 (Zea mays), 3'ss of exon 10
lower sequence: GLYMA16G17580.1 (Glycine max), 3'ss of exon 7
---------------------------------------------gtatgaaaaataaaaggcttactatttgcttagtgttttgtcttt--tcatgggtggaccaactcagcttgtaacctgacatttcttcaccttgccatctc-atagATATGTGGGCAATGGGTGCCATAATGGCTGAGTTGTTGACACTCCATCCTCTCTTTCCTGGAACTAG
                                              |   ||||    | ||  ||   | |    | ||  ||   | |  | |||  | ||  |     | |    ||   |||||| |     |||     ||   ||||||||||||||||||||| ||||||||||||||||| || || | |||||| || |||||  | ||
gtgagcatctgatgttgaataattttcatttatggtgacttatgttttccaaaagattatggtctagagtctagacaatgcattccttgtagtgatgaattgatgacaagtgttgaatactgtacatttatcttttttgtttcatctgcagATATGTGGGCAATGGGTGCTATAATGGCTGAGTTGTTCACTCTGCGTCCTCTATTCCCTGGTTCCAG

upper sequence: GRMZM2G108829_T01 (Zea mays), 3'ss of exon 10
lower sequence: AT5G45430.1 (Arabidopsis thaliana), 3'ss of exon 9
gtatgaaaaataaaaggcttactatttgcttagtgttttgtcttttcatgggtggaccaactcagcttgtaacctgacatttcttcaccttg-ccatctcatagATATGTGGGCAATGGGTGCCATAATGGCTGAGTTGTTGACACTCCATCCTCTCTTTCCTGGAACTAG
              || ||| | | |     | |        |||   |   |     |    ||   |   | | ||| |  || |  ||     | |   |||||||||||| |||||||| || ||||| ||| ||||| | || |  ||||||||||||||| ||||
-----------gttagtcttcccaatataccaataacagaagtttctttt--taagatagtctagtgcggtgcttaacaatggttaattttaattgtgtttcagATATGTGGGCGATGGGTGCTATTATGGCGGAGCTGTTGTCTCTTCGCCCTCTCTTTCCTGGAGCTAG

upper sequence: GRMZM2G108829_T01 (Zea mays), 3'ss of exon 10
lower sequence: Vv09s0070g00320.t01 (Vitis vinifera), 3'ss of exon 2
---------------------------------------gtatgaaaaataaaaggcttactatttgcttagtgttttgtcttttcatgggtggaccaa-ctcagcttgtaacctgacatttcttcacctt--gccatctcatagATATGTGGGCAATGGGTGCCATAATGGCTGAGTTGTTGACACTCCATCCTCTCTTTCCTGGAACTAG
                                       |   | || || ||      || |       |    | ||||| | || |   | | | | |||     ||     | || |  | ||| |   |   |    | |||||||||||||||||| | || |||||||| ||||| || |||| |||||||||||| ||      
gttacaaaagatgtaataaaaattgctgattttggtcttgctcggaagatcaattctcaaccaccatacaaagaatatgtctctacacgctggtatcgagctccagAGGTTCTGCGTCAATCATCCACATATGGTTCTGCAGTCGATATGTGGGCAATGGGTACTATCATGGCTGAATTGTTTACTCTCCTTCCTCTCTTTCCAGG------

upper sequence: GRMZM2G108829_T01 (Zea mays), 3'ss of exon 10
lower sequence: Vv02s0033g01110.t01 (Vitis vinifera), 3'ss of exon 7
gtatgaaaaataaaaggcttactatttgcttagtgttt-tgtcttttcatgggtggaccaa--ctcagcttgtaacc--tgacatttcttcaccttgccatctcat-agATATGTGGGCAATGGGTGCCATAATGGCTGAGTTGTTGACACTCCATCCTCTCTTTCCTGGAACTAG
        | || |  | |    |    || |   ||| ||   ||| |        |||    |  |  ||||  |  ||| ||||  |  || |    || |   ||||||||||||||||||||| || |||||||| ||||| || |||| |||||||||||| ||| | ||
-----gtcagtatatagttggaaagagactgaaattttatgaagtttgaaaaaatatccatatttttgtctgtagacactgaaattttatttccattttttccctccagATATGTGGGCAATGGGTGCTATCATGGCTGAATTGTTTACTCTCCGTCCTCTCTTTCCAGGATCGAG

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|60349468|gb|DN216441.1|DN216441
EST:     TCGGGCACCAGAAGTATTGCTCCAGTCATCTGCTTATGATTCTGCAGTTG                         ATATGTGGGCAATGGGTGCCATAATGGCTGAGTTGTTGACACTCCATCCTC
genomic: TCGGGCACCAGAAGTATTGCTCCAGTCATCTGCTTATGATTCTGCAGTTGgtatgaaaaa ... catctcatagATATGTGGGCAATGGGTGCCATAATGGCTGAGTTGTTGACACTCCATCCTC
EST: gi|211496286|gb|FL041698.1|FL041698
EST:     TCGGGCACCAGAAGTATTGCTCCAGTCATATGCTTATGATTCTGCAGTTG                         ATATGTGGGCAATGGGTGCCATAATGGCTGAGTTGTTGACACTCCATCCTC
genomic: TCGGGCACCAGAAGTATTGCTCCAGTCATCTGCTTATGATTCTGCAGTTGgtatgaaaaa ... catctcatagATATGTGGGCAATGGGTGCCATAATGGCTGAGTTGTTGACACTCCATCCTC
EST: gi|32871065|gb|CF010747.1|CF010747
EST:     TCGGGCACCAGAAGTATTGCTCCAGTCATCTGCTTATGATTCTGCAGTTG                         ATATGTGGGCAATGGGTGCCATAATGGCTGAGTTGTTGACACTCCATCCTC
genomic: TCGGGCACCAGAAGTATTGCTCCAGTCATCTGCTTATGATTCTGCAGTTGgtatgaaaaa ... catctcatagATATGTGGGCAATGGGTGCCATAATGGCTGAGTTGTTGACACTCCATCCTC
EST: gi|32932540|gb|CF037352.1|CF037352
EST:     TCGGGCACCAGAAGTATTGCTCCAGTCATCTGCTTATGATTCTGCAGTTG                         ATATGTGGGCAATGGGTGCCATAATGGCTGAGTTGTTGACACTCCATCCTC
genomic: TCGGGCACCAGAAGTATTGCTCCAGTCATCTGCTTATGATTCTGCAGTTGgtatgaaaaa ... catctcatagATATGTGGGCAATGGGTGCCATAATGGCTGAGTTGTTGACACTCCATCCTC
EST: gi|71304777|gb|DR788504.1|DR788504
EST:     TCGGGCACCAGAAGTATTGCTCCAGTCATCTGCTTATGATTCTGCAGTTG                         ATATGTGGGCAATGGGTGCCATAATGGCTGAGTTGTTGACACTCCATCCTC
genomic: TCGGGCACCAGAAGTATTGCTCCAGTCATCTGCTTATGATTCTGCAGTTGgtatgaaaaa ... catctcatagATATGTGGGCAATGGGTGCCATAATGGCTGAGTTGTTGACACTCCATCCTC
EST: gi|31350422|gb|CD434779.1|CD434779
EST:     TCGGGCACCAGAAGTATTGCTCCAGTCATCTGCTTATGATTCTGCAGTTG                         ATATGTGGGCAATGGGTGCCATAATGGCTGAGTTGTTGACACTCCATCCTC
genomic: TCGGGCACCAGAAGTATTGCTCCAGTCATCTGCTTATGATTCTGCAGTTGgtatgaaaaa ... catctcatagATATGTGGGCAATGGGTGCCATAATGGCTGAGTTGTTGACACTCCATCCTC
EST: gi|32869779|gb|CF009461.1|CF009461
EST:     TCGGGCACCAGAAGTATTGCTCCAGTCATCTGCTTATGATTCTGCAGTTG                         ATATGTGGGCAATGGGTGCCATAATGGCTGAGTTGTTGACACTCCATCCTC
genomic: TCGGGCACCAGAAGTATTGCTCCAGTCATCTGCTTATGATTCTGCAGTTGgtatgaaaaa ... catctcatagATATGTGGGCAATGGGTGCCATAATGGCTGAGTTGTTGACACTCCATCCTC
EST: gi|47961778|gb|CN844487.1|CN844487
EST:     CGGGCACCAGAAGTATTGCTCCAGTCATCTGCTTATGATTCTGCAGTTTG                         ATATGTGGGCAATGGGGGCCATAATGGCTGA
genomic: CGGGCACCAGAAGTATTGCTCCAGTCATCTGCTTATGATTCTGCAGTT-Ggtatgaaaaa ... catctcatagATATGTGGGCAATGGGTGCCATAATGGCTGA
EST: gi|67011156|gb|CO439905.1|CO439905
EST:     TCGGGCACCAGAAGTATTGCTCCAGTCATCTGCTTATGATTCTGCAGTTG                         ATATGTGGGCAATGGGTGCCATAATGGCTGAGTTGTTGACACTCCATCCTC
genomic: TCGGGCACCAGAAGTATTGCTCCAGTCATCTGCTTATGATTCTGCAGTTGgtatgaaaaa ... catctcatagATATGTGGGCAATGGGTGCCATAATGGCTGAGTTGTTGACACTCCATCCTC
EST: gi|211496285|gb|FL041697.1|FL041697
EST:     TCGGGCACCAGAAGTATTGCTCCAGTCATCTGCTTATGATTCTGCAGTTG                         ATATGTGGGCAATGGGTGCCATAATGGCTGAGTTGTTGACACTCCATCCTC
genomic: TCGGGCACCAGAAGTATTGCTCCAGTCATCTGCTTATGATTCTGCAGTTGgtatgaaaaa ... catctcatagATATGTGGGCAATGGGTGCCATAATGGCTGAGTTGTTGACACTCCATCCTC
EST: gi|5932684|gb|AW057045.1|AW057045
EST:     TCGGGCACCAGAAGTATTGCTCCAGTCATCTGCTTATGATTCTGCAGTTG                         ATATGTGGGCAATGGGTGCCATAATGGCTGAGTTGTTGACACTCCATCCTC
genomic: TCGGGCACCAGAAGTATTGCTCCAGTCATCTGCTTATGATTCTGCAGTTGgtatgaaaaa ... catctcatagATATGTGGGCAATGGGTGCCATAATGGCTGAGTTGTTGACACTCCATCCTC

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: 292

GTATCGGGCACCAGAAGTATTGCTCCAGTCATCTGCTTATGATTCTGCAGTTGgtatgaaaaa ... catctcatagATATGTGGGCAATGGGTGCCATAATGGCTGAGTTGTTGACACTCCATCCTCTCTTTCCTGGAACTAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 166

GTATCGGGCACCAGAAGTATTGCTCCAGTCATCTGCTTATGATTCTGCAGTTGgtatgaaaaa ... catctcatagATATGTGGGCAATGGGTGCCATAATGGCTGAGTTGTTGACACTCCATCCTCTCTTTCCTGGAACTAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 163

GTATCGGGCACCAGAAGTATTGCTCCAGTCATCTGCTTATGATTCTGCAGTTGgtatgaaaaa ... catctcatagATATGTGGGCAATGGGTGCCATAATGGCTGAGTTGTTGACACTCCATCCTCTCTTTCCTGGAACTAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 239

GTATCGGGCACCAGAAGTATTGCTCCAGTCATCTGCTTATGATTCTGCAGTTGgtatgaaaaa ... catctcatagATATGTGGGCAATGGGTGCCATAATGGCTGAGTTGTTGACACTCCATCCTCTCTTTCCTGGAACTAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgggtggaccaactcagcttgtaacctgacatttcttcaccttgccatctcatagATATGTGGGCAATGGGTGCCATAATGGCTGAGTTGTTGACACTCCATCCTCTCTTTCCTGGAACTAG
                               tttcttcaccttgcc  CT-rich tract
                              atttctt  TA-rich tract