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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacgtttcttgtactagaatcttctatagatccaccatggagtacaacgtgcttgctatcttaatgtgatttagctgatgtatcgattcatgttttgtgttttacagCCTTCGGCGAGTTTATAGAGCTCATGAAGAGCAACAGATTGTAAGAAAGGGGATCAGGGGAGTACTTGAAAAGGTCAATAATTGTATTGGTGCTCCCTCG

Basic information

species Zea mays
transcript GRMZM2G029573_T02
intron # 10
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|32913902|gb|CF018714.1|CF018714
EST:     TCTCCAGTACCATCCCGAGTCTTCCCCTGGTCCGCATGACTCCGACACAG                         CCTTCGGCGAGTTTATAGAGCTCATGAAGAGCAACAGATTGTAAGATAGGG
genomic: TCTCCAGTACCATCCCGAGTCTTCCCCTGGTCCGCATGACTCCGACACAGgtacgtttct ... tgttttacagCCTTCGGCGAGTTTATAGAGCTCATGAAGAGCAACAGATTGTAAGAAAGGG
EST: gi|14244956|gb|BG842894.2|BG842894
EST:     TCTCCAGTACCATCCCGAGTCTTCCCCTGGTCCGCATGACTCCGACACAG                         CCTTCGGCGAGTTTATAGAGCTCATGAAGAGCAACAGATTGTAAGAAAGGG
genomic: TCTCCAGTACCATCCCGAGTCTTCCCCTGGTCCGCATGACTCCGACACAGgtacgtttct ... tgttttacagCCTTCGGCGAGTTTATAGAGCTCATGAAGAGCAACAGATTGTAAGAAAGGG
EST: gi|31362536|gb|CD446893.1|CD446893
EST:     TCTCCAGTACCATCCCGAGTCTTCCCCTGGTCCGCATGACTCCGACACAG                         CCTTCGGCGAGTTTATAGAGCTCATGAAGAGCAACAGATTGTAAGAAAGGG
genomic: TCTCCAGTACCATCCCGAGTCTTCCCCTGGTCCGCATGACTCCGACACAGgtacgtttct ... tgttttacagCCTTCGGCGAGTTTATAGAGCTCATGAAGAGCAACAGATTGTAAGAAAGGG
EST: gi|71760287|gb|DR958224.1|DR958224
EST:     TCTCCAGTACCATCCCGAGTCTTCCCCTGGTCCGCATGACTCCGACACAG                         CCTTCGGCGAGTTTATAGAGCTCATGAAGAGCAACAGATTGTAAGAAAGGG
genomic: TCTCCAGTACCATCCCGAGTCTTCCCCTGGTCCGCATGACTCCGACACAGgtacgtttct ... tgttttacagCCTTCGGCGAGTTTATAGAGCTCATGAAGAGCAACAGATTGTAAGAAAGGG
EST: gi|211106984|gb|FL115271.1|FL115271
EST:     TCTCCAGTACCATCCCGAGTCTTCCCCTGGTCCGCATGACTCCGACACAG                         CCTTCGGCGAGTTTATAGAGCTCATGAAGAGC
genomic: TCTCCAGTACCATCCCGAGTCTTCCCCTGGTCCGCATGACTCCGACACAGgtacgtttct ... tgttttacagCCTTCGGCGAGTTTATAGAGCTCATGAAGAGC
EST: gi|37401297|gb|CF638011.1|CF638011
EST:     TCTCCAGTACCATCCCGAGTCTTCCCCTGGTCCGCATGACTCCGACACAG                         CCTTCGGCGAGTTTATAGAGCTCATGAAGAGCAACAGATTGTAAGAAAGGG
genomic: TCTCCAGTACCATCCCGAGTCTTCCCCTGGTCCGCATGACTCCGACACAGgtacgtttct ... tgttttacagCCTTCGGCGAGTTTATAGAGCTCATGAAGAGCAACAGATTGTAAGAAAGGG
EST: gi|211518595|gb|FL052563.1|FL052563
EST:     CTCCAGTACCATCCCGAGTCTTCCCCTGGTCCGCATGACTCCGACANCA-                         C-TTCGGCGAGTTTATAGAGCTCATGAAGAGCAACAGATTGTAAGAAAGG
genomic: CTCCAGTACCATCCCGAGTCTTCCCCTGGTCCGCATGACTCCGACA-CAGgtacgtttct ... tgttttacagCCTTCGGCGAGTTTATAGAGCTCATGAAGAGCAACAGATTGTAAGAAAGG
EST: gi|6342748|gb|AW165572.1|AW165572
EST:     TCTCCAGTACCATCCCGAGTCTTCCCCTGGTCCGCATGACTCCGACACAG                         CCTTCGGCGAGTTTATAGAGCTCATGAAGAGCAACAGATTGTAAGAAAGGG
genomic: TCTCCAGTACCATCCCGAGTCTTCCCCTGGTCCGCATGACTCCGACACAGgtacgtttct ... tgttttacagCCTTCGGCGAGTTTATAGAGCTCATGAAGAGCAACAGATTGTAAGAAAGGG
EST: gi|67018136|gb|CO446885.1|CO446885
EST:     TCTCCAGTACCATCCCGAGTCTTCCCCTGGTCCGCATGACTCCGACACAG                         CCTTCGGCGAGTTTATAGAGCTCATGAAGAGCAACAGATTGTAAGAAAGGG
genomic: TCTCCAGTACCATCCCGAGTCTTCCCCTGGTCCGCATGACTCCGACACAGgtacgtttct ... tgttttacagCCTTCGGCGAGTTTATAGAGCTCATGAAGAGCAACAGATTGTAAGAAAGGG
EST: gi|33091813|gb|CF051807.1|CF051807
EST:     TCTCCAGTACCATCCCGAGTCTTCCCCTGGTCCGCATGACTCCGACACAG                         CCTTCGGCGAGTTTATAGAGCTCATGAAGAGCAACAGATTGTAAGAAAGGG
genomic: TCTCCAGTACCATCCCGAGTCTTCCCCTGGTCCGCATGACTCCGACACAGgtacgtttct ... tgttttacagCCTTCGGCGAGTTTATAGAGCTCATGAAGAGCAACAGATTGTAAGAAAGGG
EST: gi|211038354|gb|FL445366.1|FL445366
EST:     CTCCAGTACCATCCCGAGTCTTCCCCTGGTCCGCATGACTCCGACANCA-                         C-TTCGGCGAGTTTATAGAGCTCATGAAGAGCAACAGATTGTAAGAAAGG
genomic: CTCCAGTACCATCCCGAGTCTTCCCCTGGTCCGCATGACTCCGACA-CAGgtacgtttct ... tgttttacagCCTTCGGCGAGTTTATAGAGCTCATGAAGAGCAACAGATTGTAAGAAAGG
EST: gi|60343079|gb|DN210052.1|DN210052
EST:     TCTCCAGTACCATCCCGAGTCTTCCCCTGGTCCGCATGACTCCGACACAG                         CCTTCGGCGAGTTTATAGAGCTCATGAAGAGCAACAGATTGTAAGAAAGGG
genomic: TCTCCAGTACCATCCCGAGTCTTCCCCTGGTCCGCATGACTCCGACACAGgtacgtttct ... tgttttacagCCTTCGGCGAGTTTATAGAGCTCATGAAGAGCAACAGATTGTAAGAAAGGG
EST: gi|31356811|gb|CD441168.1|CD441168
EST:     TCTCCAGTACCATCCCGAGTCTTCCCCTGGTCCGCATGACTCCGACACAG                         CCTTCGGCGAGTTTATAGAGCTCATGAAGAGCAACAGATTGTAAGAAAGGG
genomic: TCTCCAGTACCATCCCGAGTCTTCCCCTGGTCCGCATGACTCCGACACAGgtacgtttct ... tgttttacagCCTTCGGCGAGTTTATAGAGCTCATGAAGAGCAACAGATTGTAAGAAAGGG
EST: gi|6012497|gb|AW061934.1|AW061934
EST:     TCTCCAGTACCATCCCGAGTCTTCCCCTGGTCCGCATGACTCCGACACAG                         CCTTCGGCGAGTTTATAGAGCTCATGAAGAGCAACAGATTGTAAGAAAGGG
genomic: TCTCCAGTACCATCCCGAGTCTTCCCCTGGTCCGCATGACTCCGACACAGgtacgtttct ... tgttttacagCCTTCGGCGAGTTTATAGAGCTCATGAAGAGCAACAGATTGTAAGAAAGGG
EST: gi|88751312|gb|DY535453.1|DY535453
EST:     TCTCCAGTACCATCCCGAGTCTTCCCCTGGTCCGCATGACTCCGACACAG                         CCTTCGGCGAGTTTATAGAGCTCATGAAGAGCAACAGATTGTAAGAAAGGG
genomic: TCTCCAGTACCATCCCGAGTCTTCCCCTGGTCCGCATGACTCCGACACAGgtacgtttct ... tgttttacagCCTTCGGCGAGTTTATAGAGCTCATGAAGAGCAACAGATTGTAAGAAAGGG
EST: gi|71764309|gb|DR962246.1|DR962246
EST:     TCTCCAGTACCATCCCGAGTCTTCCCCTGGTCCGCATGACTCCGACACAG                         CCTTCGGCGAGTTTATAGAGCTCATGAAGAGCAACAGATTGTAAGAAAGGG
genomic: TCTCCAGTACCATCCCGAGTCTTCCCCTGGTCCGCATGACTCCGACACAGgtacgtttct ... tgttttacagCCTTCGGCGAGTTTATAGAGCTCATGAAGAGCAACAGATTGTAAGAAAGGG
EST: gi|37379091|gb|CF626275.1|CF626275
EST:     TCTCCAGTACCATCCCGAGTCTTCCCCTGGTCCGCATGACTCCGACACAG                         CCTTCGGCGAGTTTATAGAGCTCATGAAGAGCAACAGATTGTAAGAAAGGG
genomic: TCTCCAGTACCATCCCGAGTCTTCCCCTGGTCCGCATGACTCCGACACAGgtacgtttct ... tgttttacagCCTTCGGCGAGTTTATAGAGCTCATGAAGAGCAACAGATTGTAAGAAAGGG
EST: gi|211287671|gb|FL254549.1|FL254549
EST:     TCTCCAGTACCATCCCGAGTCTTCCCCTGGTCCGCATGACTCCGAC-CAG                         CCCTTCGGCGAGTTTATAGAGCTCATGAAGAGCA-CAGATTGTTAGGAAGG
genomic: TCTCCAGTACCATCCCGAGTCTTCCCCTGGTCCGCATGACTCCGACACAGgtacgtttct ... tgttttacagCC-TTCGGCGAGTTTATAGAGCTCATGAAGAGCAACAGATTGTAAGAAAGG

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: 142

AACGATAATAGTTGCGCTGGCCTCCAGTACTCCAAGATGAAGCTTATGTCTCTCCAGTACCATCCCGAGTCTTCCCCTGGTCCGCATGACTCCGACACAGgtacgtttct ... tgttttacagCCTTCGGCGAGTTTATAGAGCTCATGAAGAGCAACAGATTGTAAGAAAGGGGATCAGGGGAGTACTTGAAAAGGTCAATAATTGTATTGGTGCTCCCTCG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 176

AACGATAATAGTTGCGCTGGCCTCCAGTACTCCAAGATGAAGCTTATGTCTCTCCAGTACCATCCCGAGTCTTCCCCTGGTCCGCATGACTCCGACACAGgtacgtttct ... tgttttacagCCTTCGGCGAGTTTATAGAGCTCATGAAGAGCAACAGATTGTAAGAAAGGGGATCAGGGGAGTACTTGAAAAGGTCAATAATTGTATTGGTGCTCCCTCG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 160

AACGATAATAGTTGCGCTGGCCTCCAGTACTCCAAGATGAAGCTTATGTCTCTCCAGTACCATCCCGAGTCTTCCCCTGGTCCGCATGACTCCGACACAGgtacgtttct ... tgttttacagCCTTCGGCGAGTTTATAGAGCTCATGAAGAGCAACAGATTGTAAGAAAGGGGATCAGGGGAGTACTTGAAAAGGTCAATAATTGTATTGGTGCTCCCTCG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 71

AACGATAATAGTTGCGCTGGCCTCCAGTACTCCAAGATGAAGCTTATGTCTCTCCAGTACCATCCCGAGTCTTCCCCTGGTCCGCATGACTCCGACACAGgtacgtttct ... tgttttacagCCTTCGGCGAGTTTATAGAGCTCATGAAGAGCAACAGATTGTAAGAAAGGGGATCAGGGGAGTACTTGAAAAGGTCAATAATTGTATTGGTGCTCCCTCG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgctatcttaatgtgatttagctgatgtatcgattcatgttttgtgttttacagCCTTCGGCGAGTTTATAGAGCTCATGAAGAGCAACAGATTGTAAGAAAGGGGATCAGGGGAGTACTTGAAAAGGTCAATAATTGTATTGGTGCTCCCTCG
     atcttaat  TA-rich tract