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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagttgattgaaatatttggttctgaactgtgaattgcctgattcccttgtctggattatgcttgttcgtcgagacatttctgaagctttgctgaaaatttctgttgttttgaatacctcagGTTTGACAGAAAACTGAACAACACATATGACCACCTTCTTTTCAGCAG

Basic information

species Zea mays
transcript GRMZM2G410515_T01
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G410515_T01 (Zea mays), 3'ss of exon 10
lower sequence: LOC_Os03g08570.1 (Oryza sativa), 3'ss of exon 10
gttagttgattgaaatatttggttctgaactgtgaattgcctgattcccttgtctggattatgcttgttcgtcgagacatttctgaagctttgctgaaaatttctgttgttttgaatacctcagGTTTGACAGAAAACTGAACAACACATATGACCACCTTCTTTTCAGCAG
||| |||| ||||| ||||||||||  |   |  |||| |         |  ||  | || || || | |          || |||  ||    | |  |||||||||| |||||| |  |||||||||| ||||||||||| |||||||||||||||||||||||||||||
gttggttggttgaattatttggttccaagtcggaaattactca------tcatcgagtttgtggttctcc----------ttatga--ctcatattagtatttctgttggtttgaacatttcagGTTTGATAGAAAACTGAAGAACACATATGACCACCTTCTTTTCAGCAG

upper sequence: GRMZM2G410515_T01 (Zea mays), 3'ss of exon 10
lower sequence: GLYMA18G00720.2 (Glycine max), 3'ss of exon 5
gttagttgattgaaatatttggttctgaactgtgaattgcctgattcccttgtctggattatgcttgttcgtcgagacatttctgaagctttgctgaaaatttctgt-tgttttgaatacctcagGTTTGACAGAAAACTGAACAACACATATGACCACCTTCTTTTCAGCAG
                    || |     |    || |   |   |    | | ||||| ||| || |          || ||    | | || ||| |   | | | ||  | | ||    ||||||||||||||||||||| ||||||||||| |||||||| || |||||
--------------------ggataacgccaacaaagttaatttgtaatgtttgtggataatgattatatt----attatctccactggtgtgatgacatactatatatgcatcgcat-ttgcagGTTTGACAGAAAACTGAAGAACACATATGATCACCTTCTCTTTAGCAG

upper sequence: GRMZM2G410515_T01 (Zea mays), 3'ss of exon 10
lower sequence: GLYMA11G36810.1 (Glycine max), 3'ss of exon 9
gttagttgattgaaatatttggttctgaactgtgaattgcctgattcccttgtctggattatgcttgttcgtcgagacatttctgaagctttgctgaaaatttctgttgttttgaatacctcagGTTTGACAGAAAACTGAACAACACATATGACCACCTTCTTTTCAGCAG
               |   |    |  |      |||    ||      ||||  |||| ||| || |      |    | ||    | | || ||| |   | | |     ||  |    ||||||||||||||||||||| ||||||||||| |||||||| || |||||
---------------tgggtaacaccaa--caaaaataatttgtaatgtttgt--ggataatgattatattataa----tctccactgttgtggtgacatactatatatgcatgtgt-ttgcagGTTTGACAGAAAACTGAAGAACACATATGATCACCTTCTCTTTAGCAG

upper sequence: GRMZM2G410515_T01 (Zea mays), 3'ss of exon 10
lower sequence: Vv09s0002g00100.t01 (Vitis vinifera), 3'ss of exon 10
gttagttgattgaaatatttggttctgaactg-tgaattgcctgattcccttgtctggattatgcttgttcgtcgagacatttctgaagctttgctgaaaatttctgttgttttgaatacctcagGTTTGACAGAAAACTGAACAACACATATGACCACCTTCTTTTCAGCAG
                 || |  | ||      || ||    | ||    ||||||   |     ||| | ||  |    |||    |    | ||| ||  |    |  |||||| | |   ||||||||||| |||||||| |||||||| || || ||||||||||||||
-----------------ttagtctttgggtcaatgcatattttaata--tttgtcttagtcg---ttgatagttaatgtgtttgctcattggtcctgtaatgtaaattaattttgattgc---agGTTTGACAGGAAACTGAAGAACACATACGATCATCTTCTTTTCAGCAG

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|211323425|gb|FL039625.1|FL039625
EST:     AAGAAACTGGAGAAGTTGGTGGGAGTTCCTGTTATCAATGTTCATATATG                         GTTTGACAGAAAACTGAACAACACATATGACCACCTTCTTTTCAGCAG
genomic: AAGAAACTGGAGAAGTTGGTGGGAGTTCCTGTTATCAATGTTCATATATGgttagttgat ... aatacctcagGTTTGACAGAAAACTGAACAACACATATGACCACCTTCTTTTCAGCAG
EST: gi|13558607|gb|BG549963.1|BG549963
EST:     AAGAAACTGGAGAAGTTGGTGGGAGTTCCTGTTATCAATGTTCATATATG                         GTTTTGTCTTGAAAACTGAACAACACATATGACCACCTTCTTTTCAGCAG
genomic: AAGAAACTGGAGAAGTTGGTGGGAGTTCCTGTTATCAATGTTCATATATGgttagttgat ... aatacctcagG-TTTGAC-AGAAAACTGAACAACACATATGACCACCTTCTTTTCAGCAG
EST: gi|31350094|gb|CD434451.1|CD434451
EST:     AAGAAACTGGAGAAGTTGGTGGGAGTTCCTGTTATCAATGTTCATATATG                         GTTTGACAGAAAACTGAACAACACATATGACCACCTTCTTTTCAGCAG
genomic: AAGAAACTGGAGAAGTTGGTGGGAGTTCCTGTTATCAATGTTCATATATGgttagttgat ... aatacctcagGTTTGACAGAAAACTGAACAACACATATGACCACCTTCTTTTCAGCAG

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: 46 (upstream exon), 45 (downstream exon)
Score: 101

ATATCTTCAAGCTTCTTGTACCTCAAGAGTGGAGTGAAATTACTTATTTCAAGAAACTGGAGAAGTTGGTGGGAGTTCCTGTTATCAATGTTCATATATGgttagttgat ... aatacctcagGTTTGACAGAAAACTGAACAACACATATGACCACCTTCTTTTCAGCAG


Block sizes: 47 (upstream exon), 48 (downstream exon)
Score: 259

ATATCTTCAAGCTTCTTGTACCTCAAGAGTGGAGTGAAATTACTTATTTCAAGAAACTGGAGAAGTTGGTGGGAGTTCCTGTTATCAATGTTCATATATGgttagttgat ... aatacctcagGTTTGACAGAAAACTGAACAACACATATGACCACCTTCTTTTCAGCAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 242

ATATCTTCAAGCTTCTTGTACCTCAAGAGTGGAGTGAAATTACTTATTTCAAGAAACTGGAGAAGTTGGTGGGAGTTCCTGTTATCAATGTTCATATATGgttagttgat ... aatacctcagGTTTGACAGAAAACTGAACAACACATATGACCACCTTCTTTTCAGCAG


Block sizes: 47 (upstream exon), 45 (downstream exon)
Score: 199

ATATCTTCAAGCTTCTTGTACCTCAAGAGTGGAGTGAAATTACTTATTTCAAGAAACTGGAGAAGTTGGTGGGAGTTCCTGTTATCAATGTTCATATATGgttagttgat ... aatacctcagGTTTGACAGAAAACTGAACAACACATATGACCACCTTCTTTTCAGCAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cgtcgagacatttctgaagctttgctgaaaatttctgttgttttgaatacctcagGTTTGACAGAAAACTGAACAACACATATGACCACCTTCTTTTCAGCAG
                         tgaaaattt  TA-rich tract