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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctctccaattggatagtgcattgtgttctgtcttttgggtgcctgtttctaacctacgaaacatgctttttgacctggttatttatacctgactttgcagTTCTTGGGAAATCTGAGGAGCCTCCGAGATTCATACACTGCAATGGCTGCTGGTTCACTGTCGGCTTCTAATGAGCCTTCATCTGTGACCAAGATTATTT

Basic information

species Zea mays
transcript GRMZM2G075101_T03
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G075101_T03 (Zea mays), 3'ss of exon 7
lower sequence: LOC_Os01g64920.1 (Oryza sativa), 3'ss of exon 8
ctctccaattggatagtgcattgtgttctgtcttttgggtgcctgtttctaacctacg---aaacatgctttttgacctggttatttatacctgactttgcagTTCTTGGGAAATCTGAGGAGCCTCCGAGATTCATACACTGCAATGGCTGCTGGTTCACTGTCGGCTTCTAATGAGCCTTCATCTGTGACCAAGATTATTT
   |     ||    ||    |   || |||||  ||  | |    |  ||| ||  |   | | |   |  ||||| ||  |   |||   ||| | |||||||| |  | ||| |||||||||| || ||||| ||  | ||||||||||| || || || || || |||||||||||||||||||| ||||| ||||| |
--ttagctctgtgcggtcttcttgcttgtgtctactgtcttctgtctggtaaactgagcatataaacattgcttgacttgagtgcctatttgtga-tgtgcagTTCCTTAGTAATTTGAGGAGCCTACGGGATTCGTATGCAGCAATGGCTGCAGGATCGCTTTCAGCATCTAATGAGCCTTCATCTGTCACCAAAATTATCT
















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|93012884|gb|EB638404.1|EB638404
EST:     TCGGTCCAGCTGCTAATCGCCTCTTGGAGGCATATAATACCCTTTTAAAG                         TTCTTGGGAAATCTGAGGAGCCTCCGAGATTCATACACTGCAATGGCTGCT
genomic: TCGGTCCAGCTGCTAATCGCCTCTTGGAGGCATATAATACCCTTTTAAAGgtaattttgg ... gactttgcagTTCTTGGGAAATCTGAGGAGCCTCCGAGATTCATACACTGCAATGGCTGCT
EST: gi|37398489|gb|CF636559.1|CF636559
EST:     TCGGTCCAGCTGCTAATCGCCTCTTGGAGGCATATAATACCCTTTTAAAG                         TTCTTGGGAAATCTGAGGAGCCTCCGAGATTCATACACTGCAATGGCTGCT
genomic: TCGGTCCAGCTGCTAATCGCCTCTTGGAGGCATATAATACCCTTTTAAAGgtaattttgg ... gactttgcagTTCTTGGGAAATCTGAGGAGCCTCCGAGATTCATACACTGCAATGGCTGCT
EST: gi|74246322|gb|DT654236.1|DT654236
EST:     TCGGTCCAGCTGCTAATCGCCTCTTGGAGGCATATAATACCCTTTTAAAG                         TTCTTGGGAAATCTGAGGAGCCTCCGAGATTCATACACTGCAATGGCTGCT
genomic: TCGGTCCAGCTGCTAATCGCCTCTTGGAGGCATATAATACCCTTTTAAAGgtaattttgg ... gactttgcagTTCTTGGGAAATCTGAGGAGCCTCCGAGATTCATACACTGCAATGGCTGCT
EST: gi|71761514|gb|DR959451.1|DR959451
EST:     TCGGTCCAGCTGCTAATCGCCTCTTGGAGGCATATAATACCCTTTTAAAG                         TTCTTGGGAAATCTGAGGAGCCTCCGAGATTCATACACTGCAATGGCTGCT
genomic: TCGGTCCAGCTGCTAATCGCCTCTTGGAGGCATATAATACCCTTTTAAAGgtaattttgg ... gactttgcagTTCTTGGGAAATCTGAGGAGCCTCCGAGATTCATACACTGCAATGGCTGCT
EST: gi|32942644|gb|CF047463.1|CF047463
EST:     TCGGTCCAGCTGCTAATCGCCTCTTGGAGGCATATAATACCCTTTTAAAG                         TTCTTGGGAAATCTGAGGAGCCTCCGAGATTCATACACTGCAATGGCTGCT
genomic: TCGGTCCAGCTGCTAATCGCCTCTTGGAGGCATATAATACCCTTTTAAAGgtaattttgg ... gactttgcagTTCTTGGGAAATCTGAGGAGCCTCCGAGATTCATACACTGCAATGGCTGCT
EST: gi|6601609|gb|AW256155.1|AW256155
EST:     TCGGTCCAGCTGCTAATCGCCTCTTGGAGGCATATAATACCCTTTTAAAG                         TTCTTGGGAAATCTGAGGAGCCTCCGAGATTCATACCCTGCAATGGCTGCT
genomic: TCGGTCCAGCTGCTAATCGCCTCTTGGAGGCATATAATACCCTTTTAAAGgtaattttgg ... gactttgcagTTCTTGGGAAATCTGAGGAGCCTCCGAGATTCATACACTGCAATGGCTGCT
EST: gi|71773508|gb|DR971408.1|DR971408
EST:     TCGGTCCAGCTGCTAATCGCCTCTTGGAGGCATATAATACCCTTTTAAAG                         TTCTTGGGAAATCTGAGGAGCCTCCGAGATTCATACACTGCAATGGCTGCT
genomic: TCGGTCCAGCTGCTAATCGCCTCTTGGAGGCATATAATACCCTTTTAAAGgtaattttgg ... gactttgcagTTCTTGGGAAATCTGAGGAGCCTCCGAGATTCATACACTGCAATGGCTGCT
EST: gi|76020456|gb|DT947626.1|DT947626
EST:     TCGGTCCAGCTGCTAATCGCCTCTTGGAGGCATATAATACCCTTTTAAAG                         TTCTTGGGAAATCTGAGGAGCCTCCGAGATTCATACACTGCAATGGCTGCT
genomic: TCGGTCCAGCTGCTAATCGCCTCTTGGAGGCATATAATACCCTTTTAAAGgtaattttgg ... gactttgcagTTCTTGGGAAATCTGAGGAGCCTCCGAGATTCATACACTGCAATGGCTGCT
EST: gi|37388177|gb|CF631295.1|CF631295
EST:     TCGGTCCAGCTGCTAATCGCCTCTTGGAGGCATATAATACCCTTTTAAAG                         TTCTTGGGAAATCTGAGGAGCCTCCGAGATTCATACACTGCAATGGCTGCT
genomic: TCGGTCCAGCTGCTAATCGCCTCTTGGAGGCATATAATACCCTTTTAAAGgtaattttgg ... gactttgcagTTCTTGGGAAATCTGAGGAGCCTCCGAGATTCATACACTGCAATGGCTGCT
EST: gi|31364678|gb|CD449033.1|CD449033
EST:     TCGGTCCAGCTGCTAATCGCCTCTTGGAGGCATATAATACCCTTTTAAAG                         TTCTTGGGAAATCTGAGGAGCCTCCGAGATTCATACACTGCAATGGCTGCT
genomic: TCGGTCCAGCTGCTAATCGCCTCTTGGAGGCATATAATACCCTTTTAAAGgtaattttgg ... gactttgcagTTCTTGGGAAATCTGAGGAGCCTCCGAGATTCATACACTGCAATGGCTGCT
EST: gi|89250411|gb|DY622197.1|DY622197
EST:     TCGGTCCAGCTGCTAATCGCCTCTTGGAGGCATATAATACCCTTTTAAAG                         TTCTTGGGAAATCTGAGGAGCCTCCGAGATTCATACACTGCAATGGCTGCT
genomic: TCGGTCCAGCTGCTAATCGCCTCTTGGAGGCATATAATACCCTTTTAAAGgtaattttgg ... gactttgcagTTCTTGGGAAATCTGAGGAGCCTCCGAGATTCATACACTGCAATGGCTGCT
EST: gi|32942426|gb|CF047245.1|CF047245
EST:     TCGGTCCAGCTGCTAATCGCCTCTTGGAGGCATATAATACCCTTTTAAAG                         TTCTTGGGAAATCTGAGGAGCCTCCGAGATTCATACACTGCAATGGCTGCT
genomic: TCGGTCCAGCTGCTAATCGCCTCTTGGAGGCATATAATACCCTTTTAAAGgtaattttgg ... gactttgcagTTCTTGGGAAATCTGAGGAGCCTCCGAGATTCATACACTGCAATGGCTGCT

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), 49 (downstream exon)
Score: 103

GAAATCCATCCTTGGACCCACATGATGGAAGTGCCACAATTGCATGGCTTCGGTCCAGCTGCTAATCGCCTCTTGGAGGCATATAATACCCTTTTAAAGgtaattttgg ... gactttgcagTTCTTGGGAAATCTGAGGAGCCTCCGAGATTCATACACTGCAATGGCTGCTGGTTCACTGTCGGCTTCTAATGAGCCTTCATCTGTGACCAAGATTATTT


Block sizes: 47 (upstream exon), 43 (downstream exon)
Score: 25

GAAATCCATCCTTGGACCCACATGATGGAAGTGCCACAATTGCATGGCTTCGGTCCAGCTGCTAATCGCCTCTTGGAGGCATATAATACCCTTTTAAAGgtaattttgg ... gactttgcagTTCTTGGGAAATCTGAGGAGCCTCCGAGATTCATACACTGCAATGGCTGCTGGTTCACTGTCGGCTTCTAATGAGCCTTCATCTGTGACCAAGATTATTT


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 22

GAAATCCATCCTTGGACCCACATGATGGAAGTGCCACAATTGCATGGCTTCGGTCCAGCTGCTAATCGCCTCTTGGAGGCATATAATACCCTTTTAAAGgtaattttgg ... gactttgcagTTCTTGGGAAATCTGAGGAGCCTCCGAGATTCATACACTGCAATGGCTGCTGGTTCACTGTCGGCTTCTAATGAGCCTTCATCTGTGACCAAGATTATTT


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 70

GAAATCCATCCTTGGACCCACATGATGGAAGTGCCACAATTGCATGGCTTCGGTCCAGCTGCTAATCGCCTCTTGGAGGCATATAATACCCTTTTAAAGgtaattttgg ... gactttgcagTTCTTGGGAAATCTGAGGAGCCTCCGAGATTCATACACTGCAATGGCTGCTGGTTCACTGTCGGCTTCTAATGAGCCTTCATCTGTGACCAAGATTATTT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttctaacctacgaaacatgctttttgacctggttatttatacctgactttgcagTTCTTGGGAAATCTGAGGAGCCTCCGAGATTCATACACTGCAATGGCTGCTGGTTCACTGTCGGCTTCTAATGAGCCTTCATCTGTGACCAAGATTATTT
                                 ttatttata  TA-rich tract