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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCAAAGATGACTGAAGAAGAGGAAGATGAAGAATACCTCAAAGAGGAAGAAGATGCCCTTGCTGGTGCAGGGGGAACACGTTTAGTTTCACAGCCTTCATgtgagccctttgctggctttgttactaccttgacatatgttatttccttgctttaataacctacatcaagtcgatggaagaattacttgttaaatagata...

Basic information

species Zea mays
transcript AC235535.1_FGT001
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AC235535.1_FGT001 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os01g27040.1 (Oryza sativa), 5'ss of exon 4
TCAAAGATGACTGAAGAAGAGGAAGATGAAGAATACCTCAAAGAGGAAGAAGATGCCCTTGCTGGTGCAGGGGGAACACGTTTAGTTTCACAGCCTTCATgtgagccctttgctggctttgttactaccttgacatatgttatttc--cttgctttaataacctacatcaagtcgatggaagaattacttgttaaatagata-------------------
||||||||||| ||||| |||||||||||||||||||| ||||| || |||||||||||||||||| ||||||||||||| ||  ||||||||||||||||||||| | || |   |||    | ||  |  |  | | | ||       ||||   |  |      | |  |   | ||| ||| | ||||||||  |  |                   
TCAAAGATGACAGAAGAGGAGGAAGATGAAGAATACCTTAAAGAAGAGGAAGATGCCCTTGCTGGTTCAGGGGGAACACGCTTGCTTTCACAGCCTTCATgtgagctcctttcc--cttcacaattatttgtaactgtatcataagagtatgctgccaccattctgttaatataagttgaataataaattgttaaaatgtaatatattttttgctctgcag

upper sequence: AC235535.1_FGT001 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os05g05780.1 (Oryza sativa), 5'ss of exon 4
TCAAAGATGACTGAAGAAGAGGAAGATGAAGAATACCTCAAAGAGGAAGAAGATGCCCTTGCTGGTGCAGGGGGAACACGTTTAGTTTCACAGCCTTCATgtgagccct---ttgctggctttgttactaccttgacatatgttatttccttgctttaa---taacctacatcaagtcgatggaagaattacttgttaaatagata
||||||||||| || || || |||||||| || || ||||| ||||| ||||||||||||| ||||||||| || || ||| | |||||||| || ||||||||||  |   ||| ||  | ||| |   | ||    | | |||    |  |  ||||    |   |   | | |   |||      || | ||  |  |     
TCAAAGATGACAGAGGAGGAAGAAGATGAGGAGTATCTCAAGGAGGAGGAAGATGCCCTTGATGGTGCAGGAGGGACCCGTCTGGTTTCACAACCATCATgtgagcatttgcttgatgattctgtcaaaccttt----tgttttacaagccagtcttaaatgcagtttgtgtaacgaaaatgtttattttgcatggaaggttcg--

upper sequence: AC235535.1_FGT001 (Zea mays), 5'ss of exon 4
lower sequence: GLYMA17G02640.1 (Glycine max), 5'ss of exon 4
---------TCAAAGATGACTGAAGAAGAGGAAGATGAAGAATACCTCAAAGAGGAAGAAGATGCCCTTGCTGGTGCAGGGGGAACACGTTTAGTTTCACAGCCTTCATgtgagcc--ctttgctggctt-tgttactaccttgacatatgttatttccttgctttaataacctacatcaagtcgatggaagaattacttgttaaatagata
         |||||  | ||||||||||||||||||||||||||||| |||| ||||||||||| | | ||   |         ||||| || ||  | || || |||||| ||    |||| || | || |||   ||| | ||        ||| |  | ||||  | || |||||   || | |       |  ||  |    |   | 
CGCCATGCATCAAAAGTAACTGAAGAAGAGGAAGATGAAGAATACCTTAAAGGGGAAGAAGATGGCTTAGCAAAT---------ACACGGTTGGTGACTCAACCATCATgtaagttttctttccttgtttatgtgcatacttggatgggcac-attactctactttggttacttacattt-gtggctatgcttgtgcctcctccccttact-

upper sequence: AC235535.1_FGT001 (Zea mays), 5'ss of exon 4
lower sequence: GLYMA13G28720.1 (Glycine max), 5'ss of exon 4
---------TCAAAGATGACTGAAGAAGAGGAAGATGAAGAATACCTCAAAGAGGAAGAAGATGCCCTTGCTGGTGCAGGGGGAACACGTTTAGTTTCACAGCCTTCATgtgagccctttgctggctttgttactaccttgacatatgttatttccttgctttaataacctacatcaagtcgatggaagaattacttgttaaata-gata-------
         || ||  | ||||| ||||| ||||||||||||||||| ||||  ||||||||||  || ||             |||||| | ||  |||| || |||||| ||     || | ||||  | |     |||| |     |||||      | | |||   | ||      | | | |    |  ||| ||  ||   |||       
CGCCATGCATCCAATTTCACTGAGGAAGAAGAAGATGAAGAATACCTAAAAGGAGAAGAAGATGGTCTAGCAAAC---------ACACGTCTGGTGACACAACCATCATgtaag-----tgtttgctt--tcatggatttga-aggctctattttaagcatctcatattgtgcagttgtaccacgtactcttccctttttgtatttaatatgccaat

upper sequence: AC235535.1_FGT001 (Zea mays), 5'ss of exon 4
lower sequence: GLYMA07G38050.2 (Glycine max), 5'ss of exon 4
---------TCAAAGATGACTGAAGAAGAGGAAGATGAAGAATACCTCAAAGAGGAAGAAGATGCCCTTGCTGGTGCAGGGGGAACACGTTTAGTTTCACAGCCTTCATgtgagccct-ttgctggctttgttactaccttgacatatgt---tatttccttgctttaataacctacatcaagtcgatggaagaattacttgttaaatagata
         |||||  | ||||||||||||||||||||||||||||| |||| ||||||||||| | | ||   |         |||||  | ||  | || || |||||| ||   | || |    ||| |    |   |  ||| |||    ||   | |  | | |    || | | || |    ||||||||   || | |  |     
CGCCATGCATCAAAAGTAACTGAAGAAGAGGAAGATGAAGAATACCTTAAAGGGGAAGAAGATGGCTTAGCAAAT---------ACACGACTGGTGACTCAACCATCATgtaagtattatttccatgtttatgtgcatacttgcatttgtggccatgctcattttctcaatgtctcctttaattgtgcggaagaata--ttatgatgtcag--

upper sequence: AC235535.1_FGT001 (Zea mays), 5'ss of exon 4
lower sequence: Vv05s0020g01780.t01 (Vitis vinifera), 5'ss of exon 4
TCAAAGATGACTGAAGAAGAGGAAGATGAAGAATACCTCAAAGAGGAAGAAGATGCCCTTGCTGGTGCAGGGGGAACACGTTTAGTTTCACAGCCTTCATgtgagccctttgctggctttgttactaccttgacatatgttatttccttgctttaata-acctacatcaag-tcgatggaagaattacttgttaaatagata
|||||  |||||||||| || ||||||||||| | ||| ||||||||||||||||   |  ||||  ||||    || ||  | ||  ||||||| ||||||||||  | |       ||| |    | ||  |     || | |    |  | |||| | || ||| | | |   ||  ||| ||     |  |||  |  
TCAAAAGTGACTGAAGAGGAAGAAGATGAAGAGTGCCTGAAAGAGGAAGAAGATGGTTTATCTGGGACAGGAAACACGCGGCTGGTGACACAGCCCTCATgtgagctttctctctctcttggttgatcttttgcgaggattttcttgaagagtaaatatatctgcataatgatttttgatagacttgagcatagaatgca--

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|149075149|gb|EE163643.2|EE163643
EST:     AGATGCCCTTGCTGGTGCAGGGGGAACACGTTTAGTTTCACAGCCTTCAT                         GCATCAAGGGAAAGATGCGT
genomic: AGATGCCCTTGCTGGTGCAGGGGGAACACGTTTAGTTTCACAGCCTTCATgtgagccctt ... atctttgcagGCATCAAGGGAAAGATGCGT
EST: gi|22491353|gb|BU051276.1|BU051276
EST:     AGATGCCCTTGCTGGTGCAGGGGGAACACGTTTAGTTTCACAGCCTTCAT                         GCATCAAGGGAAAGATGCGTGATTATCAATTAGCTGGACTTAATTGGCTTA
genomic: AGATGCCCTTGCTGGTGCAGGGGGAACACGTTTAGTTTCACAGCCTTCATgtgagccctt ... atctttgcagGCATCAAGGGAAAGATGCGTGATTATCAATTAGCTGGACTTAATTGGCTTA
EST: gi|19351041|gb|BM895573.1|BM895573
EST:     AGATGCCCTTGCTGGTGCAGGGGGAACACGTTTAGTTTCACAGCCTTCAT                         GCATCAAGGGAAAGATGCGTGATTATCAATTAGCTGGACTTAATTGGCTTA
genomic: AGATGCCCTTGCTGGTGCAGGGGGAACACGTTTAGTTTCACAGCCTTCATgtgagccctt ... atctttgcagGCATCAAGGGAAAGATGCGTGATTATCAATTAGCTGGACTTAATTGGCTTA
EST: gi|20300252|gb|BQ163195.1|BQ163195
EST:     CCCTTGCTGGTGCAGGGGGAACACGTTTAGTTTCACAGCCTTCAT                         GCATCAAGGGAAAGATGCGTGATTATCAATTAGCTGGACTTAATTGGCTTA
genomic: CCCTTGCTGGTGCAGGGGGAACACGTTTAGTTTCACAGCCTTCATgtgagccctt ... atctttgcagGCATCAAGGGAAAGATGCGTGATTATCAATTAGCTGGACTTAATTGGCTTA
EST: gi|19350725|gb|BM895257.1|BM895257
EST:     AGATGCCCTTGCTGGTGCAGGGGGAACACGTTTAGTTTCACAGCCTTCAT                         GCATCAAGGGAAAGATGCGTGATTATCAATTAGCTGGACTTAATTGGCTTA
genomic: AGATGCCCTTGCTGGTGCAGGGGGAACACGTTTAGTTTCACAGCCTTCATgtgagccctt ... atctttgcagGCATCAAGGGAAAGATGCGTGATTATCAATTAGCTGGACTTAATTGGCTTA
EST: gi|20300542|gb|BQ163485.1|BQ163485
EST:     AGATGCCC-TGCTGG-GCAGGGGGAACACGTTTAGTTTCACAGCCTTCAT                         GCATCAAGGGAAAGATGCGTGATTATCAATTAGCTGGACTTAATTGGCTTA
genomic: AGATGCCCTTGCTGGTGCAGGGGGAACACGTTTAGTTTCACAGCCTTCATgtgagccctt ... atctttgcagGCATCAAGGGAAAGATGCGTGATTATCAATTAGCTGGACTTAATTGGCTTA
EST: gi|87153564|gb|DY398353.1|DY398353
EST:     AGATGCCCTTGCTGGTGCAGGGGGAACACGTTTAGTTTCACAGCCTTCAT                         GCATCAAGGGAAAGATGCGTGATTATCAATTAGCTGGACTTAATTGGCTTA
genomic: AGATGCCCTTGCTGGTGCAGGGGGAACACGTTTAGTTTCACAGCCTTCATgtgagccctt ... atctttgcagGCATCAAGGGAAAGATGCGTGATTATCAATTAGCTGGACTTAATTGGCTTA

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: 479

TCAAAGATGACTGAAGAAGAGGAAGATGAAGAATACCTCAAAGAGGAAGAAGATGCCCTTGCTGGTGCAGGGGGAACACGTTTAGTTTCACAGCCTTCATgtgagccctt ... atctttgcagGCATCAAGGGAAAGATGCGTGATTATCAATTAGCTGGACTTAATTGGCTTATACGATTGTATGAGAATGGTATCAATGGGATATTAGCTGATGAGATG


Block sizes: 47 (upstream exon), 48 (downstream exon)
Score: 214

TCAAAGATGACTGAAGAAGAGGAAGATGAAGAATACCTCAAAGAGGAAGAAGATGCCCTTGCTGGTGCAGGGGGAACACGTTTAGTTTCACAGCCTTCATgtgagccctt ... atctttgcagGCATCAAGGGAAAGATGCGTGATTATCAATTAGCTGGACTTAATTGGCTTATACGATTGTATGAGAATGGTATCAATGGGATATTAGCTGATGAGATG


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 178

TCAAAGATGACTGAAGAAGAGGAAGATGAAGAATACCTCAAAGAGGAAGAAGATGCCCTTGCTGGTGCAGGGGGAACACGTTTAGTTTCACAGCCTTCATgtgagccctt ... atctttgcagGCATCAAGGGAAAGATGCGTGATTATCAATTAGCTGGACTTAATTGGCTTATACGATTGTATGAGAATGGTATCAATGGGATATTAGCTGATGAGATG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 282

TCAAAGATGACTGAAGAAGAGGAAGATGAAGAATACCTCAAAGAGGAAGAAGATGCCCTTGCTGGTGCAGGGGGAACACGTTTAGTTTCACAGCCTTCATgtgagccctt ... atctttgcagGCATCAAGGGAAAGATGCGTGATTATCAATTAGCTGGACTTAATTGGCTTATACGATTGTATGAGAATGGTATCAATGGGATATTAGCTGATGAGATG