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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagttggctattgcaatagagaatcacttttcagctactatcaccatcatcattttgttgcttttcgggtgcttatagccagctgtactgcctgtatattcttctttgtacattagacatctctctcatttagtcagtcaaataatgaaagtatctatttatgatctattttagAGATCCTGGTGCTGAACAAAAGTTCAAGGATATCAGTAATGCTTATGAG

Basic information

species Zea mays
transcript GRMZM5G856084_T01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G856084_T01 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os05g26914.1 (Oryza sativa), 3'ss of exon 5
gtgagt--tggctattgcaatagagaatcacttttcagctactatcaccatcatcattttgttgcttttcgggtgcttatagccagctgtactgcctgtatattcttctttgtacattagacatctctctcatttagtcagtcaaataatgaa--agtatctatttatgatctattttagAGATCCTGGTGCTGAACAAAAGTTCAAGGATATCAGTAATGCTTATGAG
|| |||  |  | |||  |   | ||||    ||||||||||    ||  ||   || ||| | |||||    | |||     |   | ||   ||||  || |  |  |||  |||||  | | | ||  |  ||   | ||||||||  ||    |||   | | |  | |  |||||||||||||||||||||||||||||||||||||| || ||||||||||||
gtaagtactaaccattatat--gggaattgtgtttcagctac----ac--tcgatatattgcttctttttc--tcctttcgatccattataa-acctgagtactagttgttg--catta--cctttttcataactacataatcaaataagcaattgttatgcttgtgtatttttctttagAGATCCTGGTGCTGAACAAAAGTTCAAGGATATTAGCAATGCTTATGAG
















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|61119026|gb|DN559987.1|DN559987
EST:     GAAGCTTGCTAGGAGCTATCATCCAGATGTAAACAA                         AGATCCTGGTGCTGAACAAAAGTTCAAGGATATCAGTAATGCTTATGAG
genomic: GAAGCTTGCTAGGAGCTATCATCCAGATGTAAACAAgtgagttggc ... tctattttagAGATCCTGGTGCTGAACAAAAGTTCAAGGATATCAGTAATGCTTATGAG
EST: gi|148950667|gb|EC896255.2|EC896255
EST:     CCTATCGGAAGCTTGCTAGGAGCTATCATCCAGATGTAAACAA                         AGATCCTGGTGCTGAACAAAAGTTCAAGGATATCAGTAATGCTTATGAG
genomic: CCTATCGGAAGCTTGCTAGGAGCTATCATCCAGATGTAAACAAgtgagttggc ... tctattttagAGATCCTGGTGCTGAACAAAAGTTCAAGGATATCAGTAATGCTTATGAG
EST: gi|148955679|gb|EC901358.2|EC901358
EST:     CCTATCGGAAGCTTGCTAGGAGCTATCATCCAGATGTAAACAA                         AGATCCTGGTGCTGAACAAAAGTTCAAGGATATCAGTAATGCTTATGAG
genomic: CCTATCGGAAGCTTGCTAGGAGCTATCATCCAGATGTAAACAAgtgagttggc ... tctattttagAGATCCTGGTGCTGAACAAAAGTTCAAGGATATCAGTAATGCTTATGAG
EST: gi|211525859|gb|FL340350.1|FL340350
EST:     CCTATCGGAAGCTTGCTAGGAGCTATCATCCAGATGTAAACAA                         AGATCCTGGTGCTGAACAAAAGTTCAAGGATATCAGTAATGCTTATGAG
genomic: CCTATCGGAAGCTTGCTAGGAGCTATCATCCAGATGTAAACAAgtgagttggc ... tctattttagAGATCCTGGTGCTGAACAAAAGTTCAAGGATATCAGTAATGCTTATGAG
EST: gi|149051735|gb|EE155859.2|EE155859
EST:     CCTATCGGAAGCTTGCTAGGAGCTATCATCCAGATGTAAACAA                         AGATCCTGGTGCTGAACAAAAGTTCAAGGATATCAGTAATGCTTATGAG
genomic: CCTATCGGAAGCTTGCTAGGAGCTATCATCCAGATGTAAACAAgtgagttggc ... tctattttagAGATCCTGGTGCTGAACAAAAGTTCAAGGATATCAGTAATGCTTATGAG
EST: gi|211152737|gb|FL348042.1|FL348042
EST:     CCTATCGGAAGCTTGCTAGGAGCTATCATCCAGATGTAAACAA                         AGATCCTGGTGCTGAACAAAAGTTCAAGGATATCAGTAATGCTTATGAG
genomic: CCTATCGGAAGCTTGCTAGGAGCTATCATCCAGATGTAAACAAgtgagttggc ... tctattttagAGATCCTGGTGCTGAACAAAAGTTCAAGGATATCAGTAATGCTTATGAG
EST: gi|71769003|gb|DR966940.1|DR966940
EST:     CCTATCGGAAGCTTGCTAGGAGCTATCATCCAGATGTAAACAA                         AGATCCTGGTGCTGAACAAAAGTTCAAGGATATCAGTAATGCTTATGAG
genomic: CCTATCGGAAGCTTGCTAGGAGCTATCATCCAGATGTAAACAAgtgagttggc ... tctattttagAGATCCTGGTGCTGAACAAAAGTTCAAGGATATCAGTAATGCTTATGAG

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: 48 (upstream exon), 49 (downstream exon)
Score: 87

CCTATCGGAAGCTTGCTAGGAGCTATCATCCAGATGTAAACAAgtgagttggc ... tctattttagAGATCCTGGTGCTGAACAAAAGTTCAAGGATATCAGTAATGCTTATGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 224

CCTATCGGAAGCTTGCTAGGAGCTATCATCCAGATGTAAACAAgtgagttggc ... tctattttagAGATCCTGGTGCTGAACAAAAGTTCAAGGATATCAGTAATGCTTATGAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 87

CCTATCGGAAGCTTGCTAGGAGCTATCATCCAGATGTAAACAAgtgagttggc ... tctattttagAGATCCTGGTGCTGAACAAAAGTTCAAGGATATCAGTAATGCTTATGAG


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 144

CCTATCGGAAGCTTGCTAGGAGCTATCATCCAGATGTAAACAAgtgagttggc ... tctattttagAGATCCTGGTGCTGAACAAAAGTTCAAGGATATCAGTAATGCTTATGAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctctctcatttagtcagtcaaataatgaaagtatctatttatgatctattttagAGATCCTGGTGCTGAACAAAAGTTCAAGGATATCAGTAATGCTTATGAG
                                             tctatttt  CT-rich tract
                    aaataatgaaagtatc  TA-rich tract