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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaaacaaattcgttgattccatcaatctcttgtgcaagtgttgtggttgtgactggattagatctttctgcagAAATCTGGAGAGTTAGTTACCAATGTTGGGCTGAATGCTGAGAATGAGATAATACACACCCTTGCATTCTTAGCTGGTGCCATGGTTTGGTCAAAG

Basic information

species Zea mays
transcript GRMZM2G702159_T01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G702159_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os02g45650.1 (Oryza sativa), 3'ss of exon 3
gtaaaacaaattcg------ttgattccatcaatctcttgtgcaagtgttgtggttgtgactggattagatctttctgcagAAATCTGGAGAGTTAGTTACCAATGTTGGGCTGAATGCTGAGAATGAGATAATACACACCCTTGCATTCTTAGCTGGTGCCATGGTTTGGTCAAAG
|||||||||| ||       |||  ||  | ||    || ||||||| || || |||||| | |  |      || || |||||||||||||| |||  ||||||| ||| || |||||||| ||||||||| ||||||| |||||||||||||| |||| |||| |||||||| ||
gtaaaacaaaatcaatcagcttgcctctgtaaactctttatgcaagtattttg-ttgtgattagcct----tcttttgtagAAATCTGGAGAGCTAGCAACCAATGCTGGCCTAAATGCTGAAAATGAGATACTACACACTCTTGCATTCTTAGCAGGTGTCATGATTTGGTCACAG

upper sequence: GRMZM2G702159_T01 (Zea mays), 3'ss of exon 3
lower sequence: Vv15s0046g02040.t01 (Vitis vinifera), 3'ss of exon 3
---------------------gtaaaacaaattcgttgattccatcaatctcttg-tgcaagtgttgtggttgtgactggattagatctttctgcagAAATCTGGAGAGTTAGTTACCAATGTTGGGCTGAATGCTGAGAATGAGATAATACACACCCTTGCATTCTTAGCTGGTGCCATGGTTTGGTCAAAG
                      ||  | |    |       ||  |||  |   | ||||       |  ||||| |    |    | |  ||||||||||| ||||| ||  |       |||||  | ||||| |||||||||||| | || |||||||| |||||||||||||  ||| |||||||| ||
gtaagtgaatgcatttgtggattatgataggcaccccctaccccccaacatacagatgcatacaaaataattgtgcccatttgctttgtgactgcagAAATCAGGAGACTTTCTAGTGGTAGTTGGCTTAAATGCAGAGAATGAGATACTGCATACCCTTGCGTTCTTAGCTGGTGTTATGATTTGGTCACAG
















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|37361364|gb|CF602653.1|CF602653
EST:     TAATGGATACCACAATACTGTACTACAGATCCGTTCCCTGGTTTTGGAAG                         AAATCTGGAGAGTTAGTTACCAATGTTGGGCTGAATGCTGAGAATGAGATA
genomic: TAATGGATACCACAATACTGTACTACAGATCCGTTCCCTGGTTTTGGAAGgtaaaacaaa ... ctttctgcagAAATCTGGAGAGTTAGTTACCAATGTTGGGCTGAATGCTGAGAATGAGATA
EST: gi|40286942|gb|CK327334.1|CK327334
EST:     TAATGGATACCACAATACTGTACTACAGATCCGTTCCCTGGTTTTGGAAG                         AAATCTGGAGAGTTAGTTACCAATGTTGGGCTGAATGCTGAGAATGAGATA
genomic: TAATGGATACCACAATACTGTACTACAGATCCGTTCCCTGGTTTTGGAAGgtaaaacaaa ... ctttctgcagAAATCTGGAGAGTTAGTTACCAATGTTGGGCTGAATGCTGAGAATGAGATA
EST: gi|40286924|gb|CK327316.1|CK327316
EST:     TAATGGATACCACAATACTGTACTACAGATCCGTTCCCTGGTTTTGGAAG                         AAATCTGGAGAGTTAGTTACCAATGTTGGGCTGAATGCTGAGAATGAGATA
genomic: TAATGGATACCACAATACTGTACTACAGATCCGTTCCCTGGTTTTGGAAGgtaaaacaaa ... ctttctgcagAAATCTGGAGAGTTAGTTACCAATGTTGGGCTGAATGCTGAGAATGAGATA
EST: gi|91875692|gb|EB405649.1|EB405649
EST:     TAATGGATACCACAATACTGTACTACAGATCCGTTCCCTGGTTTTGGAAG                         AAATCTGGAGAGTTAGTTACCAATGTTGGGCTGAATGCTGAGAATGAGATA
genomic: TAATGGATACCACAATACTGTACTACAGATCCGTTCCCTGGTTTTGGAAGgtaaaacaaa ... ctttctgcagAAATCTGGAGAGTTAGTTACCAATGTTGGGCTGAATGCTGAGAATGAGATA
EST: gi|211231533|gb|FL255917.1|FL255917
EST:     TAATGGATACCACAATACTGTACTACAGATCCGTTCCCTGGTTTTGGAAG                         AAATCTGGAGAGTTAGTTACCAATGTTGGGCTGAATGCTGAGAATGAGATA
genomic: TAATGGATACCACAATACTGTACTACAGATCCGTTCCCTGGTTTTGGAAGgtaaaacaaa ... ctttctgcagAAATCTGGAGAGTTAGTTACCAATGTTGGGCTGAATGCTGAGAATGAGATA
EST: gi|34391316|gb|CF384544.1|CF384544
EST:     TAATGGATACCACAATACTGTACTACAGATCCGTTCCCTGGTTTTGGAAG                         AAATCTGGAGAGTTAGTTACCAATGTTGGGCTGAATGCTGAGAATGAGATA
genomic: TAATGGATACCACAATACTGTACTACAGATCCGTTCCCTGGTTTTGGAAGgtaaaacaaa ... ctttctgcagAAATCTGGAGAGTTAGTTACCAATGTTGGGCTGAATGCTGAGAATGAGATA
EST: gi|211077181|gb|FL069427.1|FL069427
EST:     TAATGGATACCACAATACTGTACTACAGATCCGTTCCCTGGTTTTGGAAG                         AAATCTGGAGAGTTAGTTACCAATGTTGGGCTGAATGCTGAGAATGACATA
genomic: TAATGGATACCACAATACTGTACTACAGATCCGTTCCCTGGTTTTGGAAGgtaaaacaaa ... ctttctgcagAAATCTGGAGAGTTAGTTACCAATGTTGGGCTGAATGCTGAGAATGAGATA
EST: gi|211074451|gb|FL069426.1|FL069426
EST:     TAATGGATACCACAATACTGTACTACAGATCCGTTCCCTGGTTTTGGAAG                         AAATCTGGAGAGTTAGTTACCAATGTTGGGCTGAATGCTGAGAATGAGATA
genomic: TAATGGATACCACAATACTGTACTACAGATCCGTTCCCTGGTTTTGGAAGgtaaaacaaa ... ctttctgcagAAATCTGGAGAGTTAGTTACCAATGTTGGGCTGAATGCTGAGAATGAGATA
EST: gi|101394395|gb|EB819132.1|EB819132
EST:     TAATGGATACCACAATACTGTACTACAGATCCGTTCCCTGGTTTTGGAAG                         AAATCTGGAGAGTTAGTTACCAATGTTGGGCTGAATGCTGAGAATGAGATA
genomic: TAATGGATACCACAATACTGTACTACAGATCCGTTCCCTGGTTTTGGAAGgtaaaacaaa ... ctttctgcagAAATCTGGAGAGTTAGTTACCAATGTTGGGCTGAATGCTGAGAATGAGATA

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 3 RNA-Seq libraries.


Block sizes: 43 (upstream exon), 49 (downstream exon)
Score: 22

CTACTTCCATTTTGTCCATGAGTTTGTGACTATTTTAATGGATACCACAATACTGTACTACAGATCCGTTCCCTGGTTTTGGAAGgtaaaacaaa ... ctttctgcagAAATCTGGAGAGTTAGTTACCAATGTTGGGCTGAATGCTGAGAATGAGATAATACACACCCTTGCATTCTTAGCTGGTGCCATGGTTTGGTCAAAG


Block sizes: 43 (upstream exon), 49 (downstream exon)
Score: 3

CTACTTCCATTTTGTCCATGAGTTTGTGACTATTTTAATGGATACCACAATACTGTACTACAGATCCGTTCCCTGGTTTTGGAAGgtaaaacaaa ... ctttctgcagAAATCTGGAGAGTTAGTTACCAATGTTGGGCTGAATGCTGAGAATGAGATAATACACACCCTTGCATTCTTAGCTGGTGCCATGGTTTGGTCAAAG


Block sizes: 25 (upstream exon), 49 (downstream exon)
Score: 18

CTACTTCCATTTTGTCCATGAGTTTGTGACTATTTTAATGGATACCACAATACTGTACTACAGATCCGTTCCCTGGTTTTGGAAGgtaaaacaaa ... ctttctgcagAAATCTGGAGAGTTAGTTACCAATGTTGGGCTGAATGCTGAGAATGAGATAATACACACCCTTGCATTCTTAGCTGGTGCCATGGTTTGGTCAAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccatcaatctcttgtgcaagtgttgtggttgtgactggattagatctttctgcagAAATCTGGAGAGTTAGTTACCAATGTTGGGCTGAATGCTGAGAATGAGATAATACACACCCTTGCATTCTTAGCTGGTGCCATGGTTTGGTCAAAG
                                            tctttctgc  CT-rich tract
                                      attagat  TA-rich tract