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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgaggaaggatttaagttttcccattcgtacagacgagatagtggcgtttacttataaagttgcgtttaaatgaatctccttttctgcttagagttttcggactgtcccttttgtagatggtgcatactgtttcggtgtgtgaactataatgaagcggttagttctttattttagGTCTGGCAACCGGGTGTAGATGCACTGGAAGATGGGGAGGAGCTTCAGTTTGATCCTGAGGCTTATAATTATCTCCGAGGTTTTGGCATTGGCTGGTCTT

Basic information

species Zea mays
transcript GRMZM2G458888_T01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G458888_T02 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os11g03990.1 (Oryza sativa), 3'ss of exon 2
gtgaggaaggatttaagttttcccattcgtacagacgagatagtggcgtttacttataaagttgcgtttaaatgaat---ctccttttctgcttagagttttc---------ggactgtcccttttgtagatggtgcatactgtttcggtgtgtgaact---------ataatgaagcggttagttctttattttagGTCTGGCAACCGGGTGTAGATGCACTGGAAGATGGGGAGGAGCTTCAGTTTGATCCTGAGGCTTATAATTATCTCCGAGGTTTTGGCATTGGCTGGTCTT
|||||   | |||||  |   || |||  ||||  | | ||     | |    || |  ||| ||  | | | | |     ||  | | || ||||  ||||          || || |   ||    || |   ||| | || | | ||   ||  ||         | | |||   | |||||  ||  | | |||| |||||||| || || ||| |||||||||| ||||||||||| ||||| |||||| ||||||| |||||||||||||| |||  |||||||||| | |
gtgagagggcatttacatg--ccaattattacaagcaa-atgcacacata-gtttttttagtcgcagtgagagggaaaggttcgatgtgtgattagttttttttctccttttggtctataatttcctaagctaaggcaaattgctcctgtcactgcccttcgaaagaaacactgacctgattagtatttcttgtcagGTATGGCAACCTGGCGTGGATACACTGGAAGAGGGGGAGGAGCTCCAGTTCGATCCTCAGGCTTACAATTATCTCCGAGGGTTTAACATTGGCTGGCCAT

upper sequence: GRMZM2G458888_T02 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os12g03822.1 (Oryza sativa), 3'ss of exon 2
gtgaggaaggatttaagttttcccattcgtacagacgagatagtggcgtttacttataaagttgcgtttaaatgaatctccttttctgcttagagttttcggactgtcc-cttttgtagatggtgcatactgtttcggtgtgtgaactataatgaagcggttagttctttattttagGTCTGGCAACCGGGTGTAGATGCACTGGAAGATGGGGAGGAGCTTCAGTTTGATCCTGAGGCTTATAATTATCTCCGAGGTTTTGGCATTGGCTGGTCTT
                                                                            | |  |||||| | || ||||||       |   ||   | | || |  | |     | |  |  |      | | |||  || || ||  ||  ||| |||| |||||||| ||||| ||| |||||||||| ||||||||||| ||||| |||||| ||||||| ||||||||| |||| |||  |||||||||| | |
----------------------------------------------------------------------------tttttttttct-cctatagttttaatttcctaagctaaggcaaattgctcctgtcactgctcttcgaatgaaacactgacccgattggtatttcttttcagGTATGGCAACCTGGTGTGGATACACTGGAAGAAGGGGAGGAGCTCCAGTTCGATCCTCAGGCTTACAATTATCTCAGAGGGTTTAACATTGGCTGGCCGT
















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|211200632|gb|FL339646.1|FL339646
EST:     CTGAAGCGTCTTCATCGTCCAATCATGCGGTTGCCTCTGGTCCGGCTAAG                         GTCTGGCAACCGGGTGTAGATGCACTGGAAGATGGGGAGGAGCTTCAGTTT
genomic: CTGAAGCGTCTTCATCGTCCAATCATGCGGTTGCCTCTGGTCCGGCTAAGgtgaggaagg ... tttattttagGTCTGGCAACCGGGTGTAGATGCACTGGAAGATGGGGAGGAGCTTCAGTTT
EST: gi|211253033|gb|FL340096.1|FL340096
EST:     CTGAAGCGTCTTCATCGTCCAATCATGCGGTTGCCTCTGGTCCGGCTAAG                         GTCTGGCAACCGGGTGTAGATGCACTGGAAGATGGGGAGGAGCTTCAGTTT
genomic: CTGAAGCGTCTTCATCGTCCAATCATGCGGTTGCCTCTGGTCCGGCTAAGgtgaggaagg ... tttattttagGTCTGGCAACCGGGTGTAGATGCACTGGAAGATGGGGAGGAGCTTCAGTTT

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: 45 (upstream exon), 45 (downstream exon)
Score: 144

GCATGTTCTTTGGCTCAATTCATTCTTCTGTATTTCTGTGCTGCAGAAAACTGAAGCGTCTTCATCGTCCAATCATGCGGTTGCCTCTGGTCCGGCTAAGgtgaggaagg ... tttattttagGTCTGGCAACCGGGTGTAGATGCACTGGAAGATGGGGAGGAGCTTCAGTTTGATCCTGAGGCTTATAATTATCTCCGAGGTTTTGGCATTGGCTGGTCTT


Block sizes: 45 (upstream exon), 45 (downstream exon)
Score: 125

GCATGTTCTTTGGCTCAATTCATTCTTCTGTATTTCTGTGCTGCAGAAAACTGAAGCGTCTTCATCGTCCAATCATGCGGTTGCCTCTGGTCCGGCTAAGgtgaggaagg ... tttattttagGTCTGGCAACCGGGTGTAGATGCACTGGAAGATGGGGAGGAGCTTCAGTTTGATCCTGAGGCTTATAATTATCTCCGAGGTTTTGGCATTGGCTGGTCTT


Block sizes: 45 (upstream exon), 45 (downstream exon)
Score: 120

GCATGTTCTTTGGCTCAATTCATTCTTCTGTATTTCTGTGCTGCAGAAAACTGAAGCGTCTTCATCGTCCAATCATGCGGTTGCCTCTGGTCCGGCTAAGgtgaggaagg ... tttattttagGTCTGGCAACCGGGTGTAGATGCACTGGAAGATGGGGAGGAGCTTCAGTTTGATCCTGAGGCTTATAATTATCTCCGAGGTTTTGGCATTGGCTGGTCTT


Block sizes: 45 (upstream exon), 47 (downstream exon)
Score: 90

GCATGTTCTTTGGCTCAATTCATTCTTCTGTATTTCTGTGCTGCAGAAAACTGAAGCGTCTTCATCGTCCAATCATGCGGTTGCCTCTGGTCCGGCTAAGgtgaggaagg ... tttattttagGTCTGGCAACCGGGTGTAGATGCACTGGAAGATGGGGAGGAGCTTCAGTTTGATCCTGAGGCTTATAATTATCTCCGAGGTTTTGGCATTGGCTGGTCTT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtgcatactgtttcggtgtgtgaactataatgaagcggttagttctttattttagGTCTGGCAACCGGGTGTAGATGCACTGGAAGATGGGGAGGAGCTTCAGTTTGATCCTGAGGCTTATAATTATCTCCGAGGTTTTGGCATTGGCTGGTCTT
                                          ttctttatttt  CT-rich tract
                                      ttagttctttatttta  TA-rich tract