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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatagtatattctttctactctatttttattggcaaggttcagttattgtctccttggaactataatcagttttctggttgccaacttttagGGTTGTACATGTGTTCCACTCCCTGTCCGTCCAAAAGCTTCATCACTTCCTAGAACACCTCCATGTG

Basic information

species Zea mays
transcript GRMZM2G108829_T01
intron # 14
splice site 3'
intron type U2

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|60349468|gb|DN216441.1|DN216441
EST:     CTAGCAAGAGACCAAAGGCCGCAGAAGTCCTCCAGCATACCTTTTTTCAG                         GGTTGTACATGTGTTCCACTCCCTGTCCGTCCAAAAGCTTCATCACTTCCT
genomic: CTAGCAAGAGACCAAAGGCCGCAGAAGTCCTCCAGCATACCTTTTTTCAGgtaatagtat ... caacttttagGGTTGTACATGTGTTCCACTCCCTGTCCGTCCAAAAGCTTCATCACTTCCT
EST: gi|211496287|gb|FL041699.1|FL041699
EST:     CTAGCAAGAGACCAAAGGCCGCAGAAGTCCTCCAGCATACCTTTTTTCAG                         GGTTGTACATGTGTTCCACTCCCTGTCCGTCCAAAAGCTTCATCACTTCCT
genomic: CTAGCAAGAGACCAAAGGCCGCAGAAGTCCTCCAGCATACCTTTTTTCAGgtaatagtat ... caacttttagGGTTGTACATGTGTTCCACTCCCTGTCCGTCCAAAAGCTTCATCACTTCCT
EST: gi|32870331|gb|CF010013.1|CF010013
EST:     CTAGCAAGAGACCAAAGGCCGCAGAAGTCCTCCAGCATACCTTTTTTCAG                         GGTTGTACATGTGTTCCACTCCCTGTCCGTCCAAAAGCTTCATCACTTCCT
genomic: CTAGCAAGAGACCAAAGGCCGCAGAAGTCCTCCAGCATACCTTTTTTCAGgtaatagtat ... caacttttagGGTTGTACATGTGTTCCACTCCCTGTCCGTCCAAAAGCTTCATCACTTCCT
EST: gi|32788458|gb|CD940694.1|CD940694
EST:     CTAGCAAGAGACCAAAGGCCGCAGAAGTCCTCCAGCATACCTTTTTTCAG                         GGTTGTACATGTGTTCCACTCCCTGTCCGTCCAAAAGCTTCATCACTTCCT
genomic: CTAGCAAGAGACCAAAGGCCGCAGAAGTCCTCCAGCATACCTTTTTTCAGgtaatagtat ... caacttttagGGTTGTACATGTGTTCCACTCCCTGTCCGTCCAAAAGCTTCATCACTTCCT
EST: gi|32869779|gb|CF009461.1|CF009461
EST:     CTAGCAAGAGACCAAAGGCCGCAGAAGTCCTCCAGCATACCTTTTTTCAG                         GGTTGTACATGTGTTCCACTCCCTGTCCGTCCAAAAGCTTCATCAC
genomic: CTAGCAAGAGACCAAAGGCCGCAGAAGTCCTCCAGCATACCTTTTTTCAGgtaatagtat ... caacttttagGGTTGTACATGTGTTCCACTCCCTGTCCGTCCAAAAGCTTCATCAC
EST: gi|67011156|gb|CO439905.1|CO439905
EST:     CTAGCAAGAGACCAAAGGCCGCAGAAGTCCTCCAGCATACCTTNTTTCAG                         GGNTGTACATGTGTTCCACTTNCTGTCCGTCCAAAAGCTTCATCACTTNCT
genomic: CTAGCAAGAGACCAAAGGCCGCAGAAGTCCTCCAGCATACCTTTTTTCAGgtaatagtat ... caacttttagGGTTGTACATGTGTTCCACTCCCTGTCCGTCCAAAAGCTTCATCACTTCCT
EST: gi|5325074|gb|AI783265.1|AI783265
EST:     TAGCAAGAGACCAAAGGCCGCAGAAGTCCTCCAGCATACCNNNNNNNCAG                         GGTTGTACATGTGTTCCACTTCCTGTCCGTCCAAAAGCTTCATCACTTCC
genomic: TAGCAAGAGACCAAAGGCCGCAGAAGTCCTCCAGCATACC-TTTTTTCAGgtaatagtat ... caacttttagGGTTGTACATGTGTTCCACTCCCTGTCCGTCCAAAAGCTTCATCACTTCC
EST: gi|5846886|gb|AI999969.1|AI999969
EST:     TAGCAAGAGACCAAAGGCCGCAGAAGTCCTCCAGCATACCNNNNNNNCAG                         GGTTGTACATGTGTTCCACTTCCTGTCCGTCCAAAAGCTTCATCACTTCC
genomic: TAGCAAGAGACCAAAGGCCGCAGAAGTCCTCCAGCATACC-TTTTTTCAGgtaatagtat ... caacttttagGGTTGTACATGTGTTCCACTCCCTGTCCGTCCAAAAGCTTCATCACTTCC

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: 332

TCACTATGCTCATGGGATCCTAGCAAGAGACCAAAGGCCGCAGAAGTCCTCCAGCATACCTTTTTTCAGgtaatagtat ... caacttttagGGTTGTACATGTGTTCCACTCCCTGTCCGTCCAAAAGCTTCATCACTTCCTAGAACACCTCCATGTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 277

TCACTATGCTCATGGGATCCTAGCAAGAGACCAAAGGCCGCAGAAGTCCTCCAGCATACCTTTTTTCAGgtaatagtat ... caacttttagGGTTGTACATGTGTTCCACTCCCTGTCCGTCCAAAAGCTTCATCACTTCCTAGAACACCTCCATGTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 296

TCACTATGCTCATGGGATCCTAGCAAGAGACCAAAGGCCGCAGAAGTCCTCCAGCATACCTTTTTTCAGgtaatagtat ... caacttttagGGTTGTACATGTGTTCCACTCCCTGTCCGTCCAAAAGCTTCATCACTTCCTAGAACACCTCCATGTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 272

TCACTATGCTCATGGGATCCTAGCAAGAGACCAAAGGCCGCAGAAGTCCTCCAGCATACCTTTTTTCAGgtaatagtat ... caacttttagGGTTGTACATGTGTTCCACTCCCTGTCCGTCCAAAAGCTTCATCACTTCCTAGAACACCTCCATGTG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttcagttattgtctccttggaactataatcagttttctggttgccaacttttagGGTTGTACATGTGTTCCACTCCCTGTCCGTCCAAAAGCTTCATCACTTCCTAGAACACCTCCATGTG
                                                ctttt  CT-rich tract
                     aactataat  TA-rich tract