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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatttttcttttgatttcctttatatctctctcacagttttattcccaactggatcaatgtttcttttagtctgttttaggtgccgtgacaaataaacttttcgccactctaaactaagaattttccaacacggtttgttacagAATGCATTGCGGCAACAAAGATTTGTCCGTGAAGTGACTATACAGTACAATCTGTGCAATGAGCCATG

Basic information

species Zea mays
transcript GRMZM2G146118_T01
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G146118_T02 (Zea mays), 3'ss of exon 8
lower sequence: LOC_Os07g29450.1 (Oryza sativa), 3'ss of exon 8
gtatttttcttttgatttcctttatatctctctcacagttttattcccaactggatcaatgtttcttt-tagtctgttttaggtgccgtgacaaataaacttt-tcgccactctaaactaagaattttc-caacacggtttgttacagAATGCATTGCGGCAACAAAGATTTGTCCGTGAAGTGACTATACAGTACAATCTGTGCAATGAGCCATG
||| ||||||    |  |||| | | | |     |   ||| ||| | ||     |  |  |  ||||  |   | |  |   ||   | |  |  || |||| ||   | |||  ||||||  ||||  ||| |   | | |  |||||||| || || |||||||||||||| || ||||| || |||||||||||||| ||||| ||||||||
gtaattttct----acctcctctttctgttatcaatgttttcatttcaaagacattttacttcactttgcaacatttagtttttgttatcatgagcaatctttgtctatattctgtactaaggtttttttcaatataatctat-gcagAATGCGTTACGTCAACAAAGATTTGTTCGGGAAGTCACAATACAGTACAATCTCTGCAACGAGCCATG

upper sequence: GRMZM2G146118_T02 (Zea mays), 3'ss of exon 8
lower sequence: GLYMA20G35720.1 (Glycine max), 3'ss of exon 7
gtatttttcttttgatttcctttatatctctctcacagttttattcccaactggatcaatgtttcttttagtctgttttaggtgccgtgacaaa---taaacttttcgccactctaaactaagaattttccaacacggtttgttacagAATGCATTGCGGCAACAAAGATTTGTCCGTGAAGTGACTATACAGTACAATCTGTGCAATGAGCCATG
                                                ||    |  | ||| |     | | |  |||      | ||   ||   |    |||  |   || ||  |||  ||||  |   |   |||  || ||||||||||||||||||||||||||||| || ||||| || |||||||||||||| ||||||||||| ||
-----------------------------------------------aaaaaaaactattgtattcgagaattttatttttcacacatgctgaactctgggatttgtgttgctatat-ctataaattaccatgctgtgttattttcagAATGCATTGCGGCAACAAAGATTTGTTCGAGAAGTCACAATACAGTACAATCTCTGCAATGAGCCTTG

upper sequence: GRMZM2G146118_T02 (Zea mays), 3'ss of exon 8
lower sequence: GLYMA09G28530.1 (Glycine max), 3'ss of exon 6
gtatttttcttttgatttcctttatatctctctcacagttttattcccaactggatcaatgtttcttttagtctgttttaggtgccgtgacaaataaacttttcgccactctaaactaagaattttccaacacgg--tttgtta--cagAATGCATTGCGGCAACAAAGATTTGTCCGTGAAGTGACTATACAGTACAATCTGTGCAATGAGCCATG
                          | | ||  | | ||||||     | | ||  ||  |   ||| |  |||         || |  ||||| ||   ||   || ||||  || |   || |    || ||  ||||||   ||||||||||||||||| ||||||||||| || ||||| || ||||||||||| || |||||||| |||||
-------------------------gtttgtccaatatttttatcttataattgacaaacct---tttcatactg--------accat--caaattaataatttcacattctatgctcatc-ttatttggcatggcctttgttcttcagAATGCATTGCGGCAGCAAAGATTTGTACGCGAAGTTACAATACAGTACAACCTCTGCAATGAACCATG

upper sequence: GRMZM2G146118_T02 (Zea mays), 3'ss of exon 8
lower sequence: GLYMA16G33300.1 (Glycine max), 3'ss of exon 7
gtatttttcttttgatttcctttatatctctctcacagttttattcccaactggatcaatgtttcttttagtctgttttaggtgccgtgacaaataaacttttcgccactctaaactaagaattttccaacacgg--tttgtta--cagAATGCATTGCGGCAACAAAGATTTGTCCGTGAAGTGACTATACAGTACAATCTGTGCAATGAGCCATG
                          | | ||  | |  ||||   |  |  | |||||     |||||      | ||      || ||  |||||   |||| | | ||||  || |   || |       ||  || |||   ||||||||||||||||| ||||||||||| |||||||| || ||||||||||| || |||||||| || ||
-------------------------gtttgtccaatatctttaa--ctga--gaatcaacaaacctttt----catattgaccatcg-gattaataa---tttcac-attctatgctcatc-ttatttggtgtggccttcgttcttcagAATGCATTGCGGCAGCAAAGATTTGTACGTGAAGTTACAATACAGTACAACCTCTGCAATGAACCTTG

upper sequence: GRMZM2G146118_T02 (Zea mays), 3'ss of exon 8
lower sequence: GLYMA10G31960.1 (Glycine max), 3'ss of exon 8
gtatttttcttttgatttcctttatatctctctcacagttttattcccaactggatcaatgtttcttttagtctgttttaggtgccgtgacaaataaacttttcgccactctaaactaagaattttccaacacg---gtttgttacagAATGCATTGCGGCAACAAAGATTTGTCCGTGAAGTGACTATACAGTACAATCTGTGCAATGAGCCATG
                                                |     |  | ||| |     | | | ||||     |      || |      || |     ||| |   |||| || |||  | |   |||  ||  |||||||||||||||||||||||||||| || ||||| || |||||||||||||| ||||||||||||||
------------------------------------------------agaaaaactattgtattcaagaatttattttccacacatgttgaactctgggatttgtgttgctatatctagaaattaccatgatgtctgttatttttagAATGCATTGCGGCAACAAAGATTTGTTCGAGAAGTCACAATACAGTACAATCTCTGCAATGAGCCATG

upper sequence: GRMZM2G146118_T02 (Zea mays), 3'ss of exon 8
lower sequence: AT5G08450.3 (Arabidopsis thaliana), 3'ss of exon 8
gtatttttcttttgatttcctttatatct-ctctcacagttttattcccaactggatcaatgtttcttttagtctgttttaggtgccgtgacaaataaacttttcgccactctaa-actaagaattttccaacacggtttgttacagAATGCATTGCGGCAACAAAGATTTGTCCGTGAAGTGACTATACAGTACAATCTGTGCAATGAGCCATG
||||||| |||   | ||     |||||| |||||  | | || || | ||||     | | || |   | | | | ||     |   |  || ||    ||     |  || || ||| |  | ||    ||    | |  |  |||||||  ||||||||||||| ||||| || ||||| || ||||| |||||||| |||||||| || ||
gtattttccttcc-actttggaaatatctgctctcttaatcttcttac-aactcttggattattacacatgg-cggcttgcatagttttctcatat----ttcatatctttcgaacactgacgacttatttac----tgttctgtagAATGCTCTGCGGCAACAAAGGTTTGTACGAGAAGTCACAATACAATACAATCTCTGCAATGAACCTTG

upper sequence: GRMZM2G146118_T02 (Zea mays), 3'ss of exon 8
lower sequence: Vv07s0130g00270.t01 (Vitis vinifera), 3'ss of exon 7
gtatttttcttttgatttcctttatatctctctcacagttttattcccaactggatcaatgtttcttttagtctgttttaggtgccgtgacaaataaacttttcgccactctaaactaagaattttccaacacggtttgttacagAATGCATTGCGGCAACAAAGATTTGTCCGTGAAGTGACTATACAGTACAATCTGTGCAATGAGCCATG
                                |||||    | ||   ||     | | | ||  |||   ||| ||| |  ||   | | |||| |  |  ||  |    |  |    |  ||||        |||   | |||||||| |||||||||||||||||||| || ||||| || |||||||||||  | || ||||| || ||
----------------------------gtaatcacatggattttattaatcatgttagtattgtttt--atctattt-atttgttattataaatga--taatcatcttctttgat--ggtgtttt--------gtt--cttcagAATGCGTTGCGGCAACAAAGATTTGTACGAGAAGTCACAATACAGTACAACTTATGTAATGAACCTTG

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|60397960|gb|DN230776.1|DN230776
EST:     TCGCCCCAGTTGCAGTTGAGCGTACAATGACGACAAGAGCTGCAGCTTCT                         AATGCATTGCGGCAACAAAGATTTGTCCGTGAAGTGACTATACAGTACAAT
genomic: TCGCCCCAGTTGCAGTTGAGCGTACAATGACGACAAGAGCTGCAGCTTCTgtatttttct ... tttgttacagAATGCATTGCGGCAACAAAGATTTGTCCGTGAAGTGACTATACAGTACAAT




















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), 48 (downstream exon)
Score: 73

CATTGGTCTTGAGCCACGCCTTAGCCACGTGTCAGCTGTGGAGCCTACTCTCGCCCCAGTTGCAGTTGAGCGTACAATGACGACAAGAGCTGCAGCTTCTgtatttttct ... tttgttacagAATGCATTGCGGCAACAAAGATTTGTCCGTGAAGTGACTATACAGTACAATCTGTGCAATGAGCCATG


Block sizes: 49 (upstream exon), 43 (downstream exon)
Score: 30

CATTGGTCTTGAGCCACGCCTTAGCCACGTGTCAGCTGTGGAGCCTACTCTCGCCCCAGTTGCAGTTGAGCGTACAATGACGACAAGAGCTGCAGCTTCTgtatttttct ... tttgttacagAATGCATTGCGGCAACAAAGATTTGTCCGTGAAGTGACTATACAGTACAATCTGTGCAATGAGCCATG


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 41

CATTGGTCTTGAGCCACGCCTTAGCCACGTGTCAGCTGTGGAGCCTACTCTCGCCCCAGTTGCAGTTGAGCGTACAATGACGACAAGAGCTGCAGCTTCTgtatttttct ... tttgttacagAATGCATTGCGGCAACAAAGATTTGTCCGTGAAGTGACTATACAGTACAATCTGTGCAATGAGCCATG


Block sizes: 46 (upstream exon), 48 (downstream exon)
Score: 30

CATTGGTCTTGAGCCACGCCTTAGCCACGTGTCAGCTGTGGAGCCTACTCTCGCCCCAGTTGCAGTTGAGCGTACAATGACGACAAGAGCTGCAGCTTCTgtatttttct ... tttgttacagAATGCATTGCGGCAACAAAGATTTGTCCGTGAAGTGACTATACAGTACAATCTGTGCAATGAGCCATG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

caaataaacttttcgccactctaaactaagaattttccaacacggtttgttacagAATGCATTGCGGCAACAAAGATTTGTCCGTGAAGTGACTATACAGTACAATCTGTGCAATGAGCCATG
                  ctctaaa  putative branch site (score: 30)
                     taaactaagaatttt  TA-rich tract