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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGACCGGCTCCTTCGACAGTGCGGGGCCGATATCCCCCACGAGCGCGCCATGGATTCAATCAGCCTTGAGCGCGAGCGCGGCATTACCATTGCCTCCAAGgtaggtaacacatctcgcaggactcgtgcttgcatgcgtggtcttcaatttcgttgagcaagttgcgtgcatcacagtactgatcttaacataatccgct...

Basic information

species Zea mays
transcript GRMZM2G128688_T01
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G128688_T02 (Zea mays), 5'ss of exon 1
lower sequence: LOC_Os01g54910.1 (Oryza sativa), 5'ss of exon 1
GGACCGGCTCCTTCGACAGTGCGGGGCCGATATCCCCCACGAGCGCGCCATGGATTCAATCAGCCTTGAGCGCGAGCGCGGCATTACCATTGCCTCCAAGgtaggtaacacatctcgcaggactcgtgcttgcatgcgtggtcttcaatttcgttgagcaagttgcgtgcatcacagtactgatctta--acataatccgct----
|||||||||||| || |||||||| ||||| ||||| ||||||||||||||||| || |||||||| ||||||||||||||||| ||||||||||||||||||    || || ||  ||  ||||| ||  ||  |||||||     |   |       | |||   ||   ||       || | ||   | |    | |     
GGACCGGCTCCTGCGGCAGTGCGGCGCCGACATCCCACACGAGCGCGCCATGGACTCCATCAGCCTCGAGCGCGAGCGCGGCATCACCATTGCCTCCAAGgta----acccaccttccaccactcgcgcgcgc-cgcgtggttagtgagggcacacgagaggttaaatgt-ccattccgtcgaacatactgcgtgcatcacgtgag

upper sequence: GRMZM2G128688_T02 (Zea mays), 5'ss of exon 1
lower sequence: GLYMA06G43820.2 (Glycine max), 5'ss of exon 1
GGACCGGCTCCTTCGACAGTGCGGGGCCGATATCCCCCACGAGCGCGCCATGGATTCAATCAGCCTTGAGCGCGAGCGCGGCATTACCATTGCCTCCAAGgtaggtaacacatctcgcaggactcgtgcttgcat-gcgtggtcttcaatttcgttgagcaagttgcgtgcatc---acagtactgatcttaacataatccgct---
|||||| ||||| || |||||||| |||||  |||||||||||||||||||||| || |||   || ||||||||||||||||| |||||  | ||||||||   |  |  |  |   |    |    |   |   || | || ||||||    | |       |  | | |||   | || ||| ||     | | |     |   
GGACCGCCTCCTCCGCCAGTGCGGCGCCGACCTCCCCCACGAGCGCGCCATGGACTCCATCTCGCTCGAGCGCGAGCGCGGCATCACCATCTCTTCCAAGgtccctgccctaatttcaattcttttcaccctctccgcttcgttttcaatcgaatcggatcttctttgagaatccggaaagcactaatgaatgcttcaatttttcag

upper sequence: GRMZM2G128688_T02 (Zea mays), 5'ss of exon 1
lower sequence: GLYMA12G14080.1 (Glycine max), 5'ss of exon 1
GGACCGGCTCCTTCGACAGTGCGGGGCCGATATCCCCCACGAGCGCGCCATGGATTCAATCAGCCTTGAGCGCGAGCGCGGCATTACCATTGCCTCCAAGgtaggtaacacatctcgcaggactcgtgcttgcatgcgtggtcttcaatttcgttgagcaagttgcgtgcatcacagtactgatcttaacataatccgct--
|||||| ||||| || |||||||| |||||  |||||||||||||||||||||| || |||   || ||||||||||||||||| |||||  | ||||||||   |  |  |  |  |||   |    | |    |  | || ||||||    | |      | | |      | ||   | |   |     |||       
GGACCGCCTCCTCCGCCAGTGCGGCGCCGACCTCCCCCACGAGCGCGCCATGGACTCCATCTCGCTCGAGCGCGAGCGCGGCATCACCATCTCTTCCAAGgtccctgccctaatttccagtttttcaccgtctccggttcgttttcaatcgaatcggatct-tcgagaatgcaaaagcgttaacggtgcttgaatttttcag

upper sequence: GRMZM2G128688_T02 (Zea mays), 5'ss of exon 1
lower sequence: Vv12s0028g02640.t01 (Vitis vinifera), 5'ss of exon 1
GGACCGGCTCCTTCGACAGTGCGGGGCCGATATCCCCCACGAGCGCGCCATGGATTCAATCAGCCTTGAGCGCGAGCGCGGCATTACCATTGCCTCCAAGgta--ggtaacacatctcgcaggactcgtgcttgcatgcgtggtcttcaatttcgttgagcaagttgcgtgcatcacagtactgatcttaacataatccgct
|||||||||||| || ||||| || ||||| |||||||||||||||||| | || || ||||| || ||||||||||||||||| |||||||| ||||||||     |  |||    |  |  | || | | |         |     | ||  |   || |||     || |  |   ||   |  || |  || |    |
GGACCGGCTCCTCCGGCAGTGTGGCGCCGACATCCCCCACGAGCGCGCCCTCGACTCCATCAGTCTCGAGCGCGAGCGCGGCATCACCATTGCTTCCAAGgtcctattctcactaaccataaaaatccttcctttggtttccgaaagaatttgggaaaagaaagagttttgga--aagttatgaaatttgatttagttttgt

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|149065568|gb|EE286688.2|EE286688
EST:     TGGATTCAATCAGCCTTGAGCGCGAGCGCGGCATTACCATTGCCTCCAAG                         GTCACTTCTGTCTCTTGGAAGGAAAATGAACTCAACATGGTTGATACACCT
genomic: TGGATTCAATCAGCCTTGAGCGCGAGCGCGGCATTACCATTGCCTCCAAGgtaggtaaca ... ctgcttttagGTCACTTCTGTCTCTTGGAAGGAAAATGAACTCAACATGGTTGATACACCT
EST: gi|30705082|gb|CD058659.1|CD058659
EST:     TGGATTCAATCAGCCTTGAGCGCGAGCGCGGCATTACCATTGCCTCCAAG                         GTCACTTCTGTCTCTTGGAAGGAAAATGAACTCAACATGGTTGATACACCT
genomic: TGGATTCAATCAGCCTTGAGCGCGAGCGCGGCATTACCATTGCCTCCAAGgtaggtaaca ... ctgcttttagGTCACTTCTGTCTCTTGGAAGGAAAATGAACTCAACATGGTTGATACACCT
EST: gi|149096163|gb|EE181859.2|EE181859
EST:     TGGATTCAATCAGCCTTGAGCGCGAGCGCGGCATTACCATTGCCTCCAAG                         GTCACTTCTGTCTCTTGGAAGGAAAATGAACTCAACATGGTTGATACACCT
genomic: TGGATTCAATCAGCCTTGAGCGCGAGCGCGGCATTACCATTGCCTCCAAGgtaggtaaca ... ctgcttttagGTCACTTCTGTCTCTTGGAAGGAAAATGAACTCAACATGGTTGATACACCT
EST: gi|94477374|gb|EB706332.1|EB706332
EST:     TGGATTCAATCAGCCTTGAGCGCGAGCGCGGCATTACCATTGCCTCCAAG                         GTCACTTCTGTCTCTTGGAAGGAAAATGAACTCAACATGGTTGATACACCT
genomic: TGGATTCAATCAGCCTTGAGCGCGAGCGCGGCATTACCATTGCCTCCAAGgtaggtaaca ... ctgcttttagGTCACTTCTGTCTCTTGGAAGGAAAATGAACTCAACATGGTTGATACACCT
EST: gi|71428852|gb|DR809902.1|DR809902
EST:     TGGATTCAATCAGCCTTGAGCGCGAGCGCGGCATTACCATTGCCTCCAAG                         GTCACTTCTGTCTCTTGGAAGGAAAATGAACTCAACATGGTTGATACACCT
genomic: TGGATTCAATCAGCCTTGAGCGCGAGCGCGGCATTACCATTGCCTCCAAGgtaggtaaca ... ctgcttttagGTCACTTCTGTCTCTTGGAAGGAAAATGAACTCAACATGGTTGATACACCT
EST: gi|149075128|gb|EE163621.2|EE163621
EST:     TGGATTCAATCAGCCTTGAGCGCGAGCGCGGCATTACCATTGCCTCCAAG                         GTCACTTCTGTCTCTTGGAAGGAAAATGAACTCAACATGGTTGATACACCT
genomic: TGGATTCAATCAGCCTTGAGCGCGAGCGCGGCATTACCATTGCCTCCAAGgtaggtaaca ... ctgcttttagGTCACTTCTGTCTCTTGGAAGGAAAATGAACTCAACATGGTTGATACACCT

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: 47 (upstream exon), 48 (downstream exon)
Score: 44

GGACCGGCTCCTTCGACAGTGCGGGGCCGATATCCCCCACGAGCGCGCCATGGATTCAATCAGCCTTGAGCGCGAGCGCGGCATTACCATTGCCTCCAAGgtaggtaaca ... ctgcttttagGTCACTTCTGTCTCTTGGAAGGAAAATGAACTCAACATGGTTGATACACCTGGCCACGCTGATTTTGGTGGTGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 34

GGACCGGCTCCTTCGACAGTGCGGGGCCGATATCCCCCACGAGCGCGCCATGGATTCAATCAGCCTTGAGCGCGAGCGCGGCATTACCATTGCCTCCAAGgtaggtaaca ... ctgcttttagGTCACTTCTGTCTCTTGGAAGGAAAATGAACTCAACATGGTTGATACACCTGGCCACGCTGATTTTGGTGGTGAG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 38

GGACCGGCTCCTTCGACAGTGCGGGGCCGATATCCCCCACGAGCGCGCCATGGATTCAATCAGCCTTGAGCGCGAGCGCGGCATTACCATTGCCTCCAAGgtaggtaaca ... ctgcttttagGTCACTTCTGTCTCTTGGAAGGAAAATGAACTCAACATGGTTGATACACCTGGCCACGCTGATTTTGGTGGTGAG


Block sizes: 47 (upstream exon), 46 (downstream exon)
Score: 25

GGACCGGCTCCTTCGACAGTGCGGGGCCGATATCCCCCACGAGCGCGCCATGGATTCAATCAGCCTTGAGCGCGAGCGCGGCATTACCATTGCCTCCAAGgtaggtaaca ... ctgcttttagGTCACTTCTGTCTCTTGGAAGGAAAATGAACTCAACATGGTTGATACACCTGGCCACGCTGATTTTGGTGGTGAG