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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacgtactaaactactacgagccctgttctgttgcattgcattcgcatgcacgcatttggttgtttcgcattttttgtttgttttatggagaaaccgtcggcggcggcggcgtcggcagGTTGAGCTGCTGAACAACATCCGTCACCCGAACATGGTGCGCCTGGTGGGGGCGTGCCCGGTGTACGGCTGCCTGGTGTACGAGTACATGCCGAACGGGA

Basic information

species Zea mays
transcript GRMZM2G467703_T03
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G467703_T03 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os02g05820.1 (Oryza sativa), 3'ss of exon 8
gtacgtactaaactactacgagccctgttctgttgcattgcattcgcatgcacgcatttggttgtttcgcattttttgtttgttttatggagaaaccgtcggcggcggcggcgtcggcagGTTGAGCTGCTGAACAACATCCGTCACCCGAACATGGTGCGCCTGGTGGGGGCGTGCCCGGTGTACGGCTGCCTGGTGTACGAGTACATGCCGAACGGGA
             | |||  |         |  |||||    |||   |  |   |  || |   |  | |     || | ||       ||||             | |   ||  ||||||||| || |||||||||| || |||||||| |||||||  ||| |||| || ||||| | ||| ||||| |||||||| || ||||||||||| || |
---------cctttgctaaaaagaaaaacatcatgcatcagtttcagctatatataaatgatatatctgtaaaccatgatggt------aagaattta-----aattgtgttatcaacagGTTGAGTTGTTGAACAACATTCGCCACCCGAATATGGTGCATCTGTTGGGTGCTTGCCCTGAGTATGGCTGTCTGGTGTATGAATACATGCCGAATGGCA
















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|50334248|gb|CO529374.1|CO529374
EST:     AGATCCTCTACTCTAATGTGACGCAGGGACTGAAGCAGTTTCGACAGGAG                         GTTGAGCTGCTGAACAACATCCGTCACCCGAACATGGTGCGCCTGGTGGGG
genomic: AGATCCTCTACTCTAATGTGACGCAGGGACTGAAGCAGTTTCGACAGGAGgtacgtacta ... gcgtcggcagGTTGAGCTGCTGAACAACATCCGTCACCCGAACATGGTGCGCCTGGTGGGG
EST: gi|94478727|gb|EB707685.1|EB707685
EST:     AGATCCTCTACTCTAATGTGACGCAGGGACTGAAGCAGTTTCGACAGGAG                         GTTGAGCTGCTGAACAACATCCGTCACCCGAACATGGTGCGCCTGGTGGGG
genomic: AGATCCTCTACTCTAATGTGACGCAGGGACTGAAGCAGTTTCGACAGGAGgtacgtacta ... gcgtcggcagGTTGAGCTGCTGAACAACATCCGTCACCCGAACATGGTGCGCCTGGTGGGG
EST: gi|94480228|gb|EB709186.1|EB709186
EST:     AGATCCTCTACTCTAATGTGACGCAGGGACTGAAGCAGTTTCGACAGGAG                         GTTGAGCTGCTGAACAACATCCGTCACCCGAACATGGTGCGCCTGGTGGGG
genomic: AGATCCTCTACTCTAATGTGACGCAGGGACTGAAGCAGTTTCGACAGGAGgtacgtacta ... gcgtcggcagGTTGAGCTGCTGAACAACATCCGTCACCCGAACATGGTGCGCCTGGTGGGG
EST: gi|71310305|gb|DR791446.1|DR791446
EST:     AGATCCTCTACTCTAATGTGACGCAGGGACTGAAGCAGTTTCGACAGGAG                         GTTGAGCTGCTGAACAACATCCGTCACCCGAACATGGTGCGCCTGGTGGGG
genomic: AGATCCTCTACTCTAATGTGACGCAGGGACTGAAGCAGTTTCGACAGGAGgtacgtacta ... gcgtcggcagGTTGAGCTGCTGAACAACATCCGTCACCCGAACATGGTGCGCCTGGTGGGG
EST: gi|84969860|gb|DW468272.1|DW468272
EST:     AGATCCTCTACTCTAATGTGACGCAGGGACTGAAGCAGTTTCGACAGGAG                         GTTGAGCTGCTGAACAACATCCGTCACCCGAACATGGTGCGCCTGGTGGGG
genomic: AGATCCTCTACTCTAATGTGACGCAGGGACTGAAGCAGTTTCGACAGGAGgtacgtacta ... gcgtcggcagGTTGAGCTGCTGAACAACATCCGTCACCCGAACATGGTGCGCCTGGTGGGG
EST: gi|74245183|gb|DT653097.1|DT653097
EST:     AGATCCTCTACTCTAATGTGACGCAGGGACTGAAGCAGTTTCGACAGGAG                         GTTGAGCTGCTGAACAACATCCGTCACCCGAACATGGTGCGCCTGGTGGGG
genomic: AGATCCTCTACTCTAATGTGACGCAGGGACTGAAGCAGTTTCGACAGGAGgtacgtacta ... gcgtcggcagGTTGAGCTGCTGAACAACATCCGTCACCCGAACATGGTGCGCCTGGTGGGG
EST: gi|148959318|gb|EC905384.2|EC905384
EST:     AGATCCTCTACTCTAATGTGACGCAGGGACTGAAGCAGTTTCGACAGGAG                         GTTGAGCTGCTGAACAACATCCGTCACCCGAACATGGTGCGCCTGGTGGGG
genomic: AGATCCTCTACTCTAATGTGACGCAGGGACTGAAGCAGTTTCGACAGGAGgtacgtacta ... gcgtcggcagGTTGAGCTGCTGAACAACATCCGTCACCCGAACATGGTGCGCCTGGTGGGG
EST: gi|76919470|gb|DV167726.1|DV167726
EST:     AGATCCTCTACTCTAATGTGACGCAGGGACTGAAGCAGTTTCGACAGGAG                         GTTGAGCTGCTGAACAACATCCGTCACCCGAACATGGTGCGCCTGGTGGGG
genomic: AGATCCTCTACTCTAATGTGACGCAGGGACTGAAGCAGTTTCGACAGGAGgtacgtacta ... gcgtcggcagGTTGAGCTGCTGAACAACATCCGTCACCCGAACATGGTGCGCCTGGTGGGG

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 1 RNA-Seqlibrary.


Block sizes: 26 (upstream exon), 24 (downstream exon)
Score: 1

GTATGGGCCGGTCTACAAGGCCACGCTTGACGACACTCTCGTGGCCGTCAAGATCCTCTACTCTAATGTGACGCAGGGACTGAAGCAGTTTCGACAGGAGgtacgtacta ... gcgtcggcagGTTGAGCTGCTGAACAACATCCGTCACCCGAACATGGTGCGCCTGGTGGGGGCGTGCCCGGTGTACGGCTGCCTGGTGTACGAGTACATGCCGAACGGGA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcgcattttttgtttgttttatggagaaaccgtcggcggcggcggcgtcggcagGTTGAGCTGCTGAACAACATCCGTCACCCGAACATGGTGCGCCTGGTGGGGGCGTGCCCGGTGTACGGCTGCCTGGTGTACGAGTACATGCCGAACGGGA
     attttttgtttgtttt  TA-rich tract