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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacgtgctctcctcccccccaatccatcggattcgccgcccggggagcgcccaggcggttggttttccgtcccgattcggctaacaattcgatcgatcccttttcgcctgtgcagGCGCTGAGCAAGATCGCTTGCAATCGGCTGCAGAAAGAGCTCGCCGAGTGGCAGCAAAACCCCCCCGTCGGGTTCAAGCACAAGGTCTCCGATAACCTCC

Basic information

species Zea mays
transcript GRMZM2G007381_T01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G007381_T01 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os12g44000.2 (Oryza sativa), 3'ss of exon 1
gtacgtgctctcctcccccccaatccatcggattcgccgcccggggagcgcccaggcggttggttttccgtcccgattcggctaacaattcgatcgatcccttttcgcctgtgcagGCGCTGAGCAAGATCGCTTGCAATCGGCTGCAGAAAGAGCTCGCCGAGTGGCAGCAAAACCCCCCCGTCGGGTTCAAGCACAAGGTCTCCGATAACCTCC
|||  |  ||| ||||  ||     |  |  | ||  || | |     |||     | ||     ||  |  |  |||   |   |  ||       |   | | |    | ||||||||||||||||||||||||||||||||||||||| ||||||||||||||||||   | ||| |||  |||||||||| ||| |||||||||||||||||
gtat-tattctactccttcctctctctccccaatc--cgtctgattctcgct--atctgtgaacgttttggtctaatttccccccctttt-------tttttgtacctgcgcgcagGCGCTGAGCAAGATCGCTTGCAATCGGCTGCAGAAGGAGCTCGCCGAGTGGCAGGTCAGCCCTCCCTCCGGGTTCAAGTACAGGGTCTCCGATAACCTCC

upper sequence: GRMZM2G007381_T01 (Zea mays), 3'ss of exon 1
lower sequence: Vv04s0023g02620.t01 (Vitis vinifera), 3'ss of exon 1
--------------------------------------gtacgtgctc-tcctcccccccaatccatcggattcgccgcccggggagcgcccaggcggttggt-------tttccgtcccgattcggctaac--aattcgatcgatcccttttcgcctgtgcagGCGCTGAGCAAGATCGCTTGCAATCGGCTGCAGAAAGAGCTCGCCGAGTGGCAGCAAAACCCCCCCGTCGGGTTCAAGCACAAGGTCTCCGATAACCTCC
                                        | ||  |  |  |         |   | |||      || | ||       |||||  ||||         || |     ||||   || |     ||  || |     | |     | |  |||| || ||||| ||||||||||||||||| ||||||||||| |  |||||||||   || || |||| ||| ||||| ||||| ||| |||| || || |
gtctgttcctctctcctgatgtctagccctaatttttgtcatgtctttgtgatttgtggtgttttctaggaaattttgctctggtgattttcaggcacttggcaagattgcttgcaaattgatttttctcatctggttgtattgtgatttgtggtgttttcaagGCACTTAGCAAAATCGCTTGCAATCGGCTCCAGAAAGAGCTTGTTGAGTGGCAGGTCAATCCACCCGCCGGTTTCAAACACAAAGTCACCGACAATCTTC
















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|211242854|gb|FL389165.1|FL389165
EST:     CAAGAACCCAGCCCCCCACCATGACGAGCTCCTCCTCTCCTTCCAGAAAG                         GCGCTGAGCAAGATCGCTTGCAATCGGCTGCAGAAAGAGCTCGCCGAGTGG
genomic: CAAGAACCCAGCCCCCCACCATGACGAGCTCCTCCTCTCCTTCCAGAAAGgtacgtgctc ... gcctgtgcagGCGCTGAGCAAGATCGCTTGCAATCGGCTGCAGAAAGAGCTCGCCGAGTGG
EST: gi|71431746|gb|DR812796.1|DR812796
EST:     CAAGAACCCAGCCCCCCACCATGACGAGCTCCTCCTCTCCTTCCAGAAAG                         GCGCTGAGCAAGATCGCTTGCAATCGGCTGCAGAAAGAGCTCGCCGAGTGG
genomic: CAAGAACCCAGCCCCCCACCATGACGAGCTCCTCCTCTCCTTCCAGAAAGgtacgtgctc ... gcctgtgcagGCGCTGAGCAAGATCGCTTGCAATCGGCTGCAGAAAGAGCTCGCCGAGTGG
EST: gi|211172115|gb|FK994020.1|FK994020
EST:     CAAGAACCCAGCCCCCCACCATGACGAGCTCCTCCTCTCCTTCCAGAAAG                         GCGCTGAGCAAGATCGCTTGCAATCGGCTGCAGAAAGAGCTCGCCGAGTGG
genomic: CAAGAACCCAGCCCCCCACCATGACGAGCTCCTCCTCTCCTTCCAGAAAGgtacgtgctc ... gcctgtgcagGCGCTGAGCAAGATCGCTTGCAATCGGCTGCAGAAAGAGCTCGCCGAGTGG
EST: gi|211172114|gb|FK994019.1|FK994019
EST:     AAGAACCCAGCCCCCCACCATGACGAGCTCCTCCTCTCCTTCCAGAAAG                         GCGCTGAGCAAGATCGCTTGCAATCGGCTGCAGAAAGAGCTCGCCGAGTGG
genomic: AAGAACCCAGCCCCCCACCATGACGAGCTCCTCCTCTCCTTCCAGAAAGgtacgtgctc ... gcctgtgcagGCGCTGAGCAAGATCGCTTGCAATCGGCTGCAGAAAGAGCTCGCCGAGTGG
EST: gi|78081936|gb|DV510348.1|DV510348
EST:     CAAGAACCCAGCCCCCCACCATGACGAGCTCCTCCTCTCCTTCCAGAAAG                         GCGCTGAGCAAGATCGCTTGCAATCGGCTGCAGAAAGAGCTCGCCGAGTGG
genomic: CAAGAACCCAGCCCCCCACCATGACGAGCTCCTCCTCTCCTTCCAGAAAGgtacgtgctc ... gcctgtgcagGCGCTGAGCAAGATCGCTTGCAATCGGCTGCAGAAAGAGCTCGCCGAGTGG
EST: gi|6536593|gb|AW224906.1|AW224906
EST:     CAAGAACCCAGCCCCCCACCATGACGAGCTCCTCCTCTCCTTCCAGAAAG                         GCGCTGAGCAAGATCGCTTGCAATCGGCTGCAGAAAGAGCTCGCCGAGTGG
genomic: CAAGAACCCAGCCCCCCACCATGACGAGCTCCTCCTCTCCTTCCAGAAAGgtacgtgctc ... gcctgtgcagGCGCTGAGCAAGATCGCTTGCAATCGGCTGCAGAAAGAGCTCGCCGAGTGG
EST: gi|211215511|gb|FL424481.1|FL424481
EST:     CAAGAACCCAGCCCCCCACCATGACGAGCTCCTCCTCTCCTTCCAGAAAG                         GCGCTGAGCAAGATCGCTTGCAATCGGCTGCAGAAAGAGCTCGCCGAGTGG
genomic: CAAGAACCCAGCCCCCCACCATGACGAGCTCCTCCTCTCCTTCCAGAAAGgtacgtgctc ... gcctgtgcagGCGCTGAGCAAGATCGCTTGCAATCGGCTGCAGAAAGAGCTCGCCGAGTGG
EST: gi|29946817|gb|CB816340.1|CB816340
EST:     CAAGAACCCAGCCCCCCACCATGACGAGCTCCTCCTCTCCTTCCAGAAAG                         GCGCTGAGCAAGATCGCTTGCAATCGGCTGCAGAAAGAGCTCGCCGAGTGG
genomic: CAAGAACCCAGCCCCCCACCATGACGAGCTCCTCCTCTCCTTCCAGAAAGgtacgtgctc ... gcctgtgcagGCGCTGAGCAAGATCGCTTGCAATCGGCTGCAGAAAGAGCTCGCCGAGTGG
EST: gi|22819231|gb|BU499321.1|BU499321
EST:     AAGAACCCAAGCCCCCCACCATGACGAGCTCCTCCTCTCCTTCCAGAAAG                         GCGCTGAGCAAGATCGCTTGCAATCGGCTGCAGAAAGAGCTCGCCGAGTGG
genomic: AAGAACCC-AGCCCCCCACCATGACGAGCTCCTCCTCTCCTTCCAGAAAGgtacgtgctc ... gcctgtgcagGCGCTGAGCAAGATCGCTTGCAATCGGCTGCAGAAAGAGCTCGCCGAGTGG
EST: gi|211172116|gb|FK994021.1|FK994021
EST:     CAAGAACCCAGCCCCCCACCATGACGAGCTCCTCCTCTCCTTCCAGAAAG                         GCGCTGAGCAAGATCGCTTGCAATCGGCTGCAGAAAGAGCTCGCCGAGTGG
genomic: CAAGAACCCAGCCCCCCACCATGACGAGCTCCTCCTCTCCTTCCAGAAAGgtacgtgctc ... gcctgtgcagGCGCTGAGCAAGATCGCTTGCAATCGGCTGCAGAAAGAGCTCGCCGAGTGG
EST: gi|211172113|gb|FK994018.1|FK994018
EST:     CAAGAACCCAGCCCCCCACCATGACGAGCTCCTCCTCTCCTTCCAGAAAG                         GCGCTGAGCAAGATCGCTTGCAATCGGCTGCAGAAAGAGCTCGCCGAGTGG
genomic: CAAGAACCCAGCCCCCCACCATGACGAGCTCCTCCTCTCCTTCCAGAAAGgtacgtgctc ... gcctgtgcagGCGCTGAGCAAGATCGCTTGCAATCGGCTGCAGAAAGAGCTCGCCGAGTGG
EST: gi|211172112|gb|FK994017.1|FK994017
EST:     CAAGAACCCAGCCCCCCACCATGACGAGCTCCTCCTCTCCTTCCAGAAAG                         GCGCTGAGCAAGATCGCTTGCAATCGGCTGCAGAAAGAGCTCGCCGAGTGG
genomic: CAAGAACCCAGCCCCCCACCATGACGAGCTCCTCCTCTCCTTCCAGAAAGgtacgtgctc ... gcctgtgcagGCGCTGAGCAAGATCGCTTGCAATCGGCTGCAGAAAGAGCTCGCCGAGTGG

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), 47 (downstream exon)
Score: 74

GTCTCCGCCTTCCGACTTCCTCTAGAATTCGATTCCCTTTCCCAAGAAACCAAGAACCCAGCCCCCCACCATGACGAGCTCCTCCTCTCCTTCCAGAAAGgtacgtgctc ... gcctgtgcagGCGCTGAGCAAGATCGCTTGCAATCGGCTGCAGAAAGAGCTCGCCGAGTGGCAGCAAAACCCCCCCGTCGGGTTCAAGCACAAGGTCTCCGATAACCTCC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 203

GTCTCCGCCTTCCGACTTCCTCTAGAATTCGATTCCCTTTCCCAAGAAACCAAGAACCCAGCCCCCCACCATGACGAGCTCCTCCTCTCCTTCCAGAAAGgtacgtgctc ... gcctgtgcagGCGCTGAGCAAGATCGCTTGCAATCGGCTGCAGAAAGAGCTCGCCGAGTGGCAGCAAAACCCCCCCGTCGGGTTCAAGCACAAGGTCTCCGATAACCTCC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 240

GTCTCCGCCTTCCGACTTCCTCTAGAATTCGATTCCCTTTCCCAAGAAACCAAGAACCCAGCCCCCCACCATGACGAGCTCCTCCTCTCCTTCCAGAAAGgtacgtgctc ... gcctgtgcagGCGCTGAGCAAGATCGCTTGCAATCGGCTGCAGAAAGAGCTCGCCGAGTGGCAGCAAAACCCCCCCGTCGGGTTCAAGCACAAGGTCTCCGATAACCTCC


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 136

GTCTCCGCCTTCCGACTTCCTCTAGAATTCGATTCCCTTTCCCAAGAAACCAAGAACCCAGCCCCCCACCATGACGAGCTCCTCCTCTCCTTCCAGAAAGgtacgtgctc ... gcctgtgcagGCGCTGAGCAAGATCGCTTGCAATCGGCTGCAGAAAGAGCTCGCCGAGTGGCAGCAAAACCCCCCCGTCGGGTTCAAGCACAAGGTCTCCGATAACCTCC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggttttccgtcccgattcggctaacaattcgatcgatcccttttcgcctgtgcagGCGCTGAGCAAGATCGCTTGCAATCGGCTGCAGAAAGAGCTCGCCGAGTGGCAGCAAAACCCCCCCGTCGGGTTCAAGCACAAGGTCTCCGATAACCTCC
                  ggctaac  putative branch site (score: 136)
                                    tcccttttcgcctgt  putative PPT
                     taacaatt  TA-rich tract