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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gaacgtcaaaaaatttcttttccccaactcttcagggaaaagtccaatcttttgtgtcactttctatatgtacttcatatactgccatctgaaactttctttgttgatctgcagAAGCCATGATACCTTCCGTGAGGCTCTCTCCTGGTCCTGCAGCCTTCTCAGGCTCCAGCCTACGCTCAAAATTACCGTCAATTCCATCCATCTCCAGTCT

Basic information

species Zea mays
transcript GRMZM2G180720_T03
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G180720_T03 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os08g08840.2 (Oryza sativa), 3'ss of exon 1
gaacgtcaaaaaatttcttttccccaactcttcagggaaaagtccaatcttttgtgtcactttctatatgtacttcatatactgccatctgaaactttctttgttgatctgcagAAGCCATGATACCTTCCGTGAGGCTCTCTCCTGGTCCTGCAGCCTTCTCAGGCTCCAGCCTACGCTCAAAATTACCGTCAATTCCATCCATCTCCAGTCT---
    |  |  ||||  | | |       | ||    || |  |   ||  |||   |   || |||  |||           || ||| |  || ||| ||  ||||| ||||||||||||| ||||| | |||| |||||||||||| ||||  |||||| | ||| |||  ||||| || | || | | ||  || ||||  |||| |||||   
----gaaaggaaatggcctgttttgttttatttgatgacagat--gatgctttaaattgtttcctacctgt-----------tgtcatgtacaattttgttctttgatttgcagaagCCATGCTACCTGCTGTGAAGCTCTCTCCTGGCCCTGTGGCCTTCGCTGGCACCAATCTACGGTCCAGATCAGCTTCGGTTTCATCTGTCTCAAGTCTCAA

upper sequence: GRMZM2G180720_T03 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os08g08840.1 (Oryza sativa), 3'ss of exon 1
gaacgtcaaaaaatttcttttccccaactcttcagggaaaagtccaatcttttgtgtcactttctatatgtacttcatatactgccatctgaaactttctttgttgatctgcagAAGCCATGATACCTTCCGTGAGGCTCTCTCCTGGTCCTGCAGCCTTCTCAGGCTCCAGCCTACGCTCAAAATTACCGTCAATTCCATCCATCTCCAGTCT
    |  |  ||||  | | |       | ||    || |  |   ||  |||   |   || |||  |||           || ||| |  || ||| ||  ||||| ||||||||||||| ||||| | |||| |||||||||||| ||||  |||||| | ||| |||  ||||| || | || | | ||  || ||||  |||| |||||
-gttgaaaggaaatggcctgttttgttttatttgatgacagat--gatgctttaaattgtttcctacctgt-----------tgtcatgtacaattttgttctttgatttgcagAAGCCATGCTACCTGCTGTGAAGCTCTCTCCTGGCCCTGTGGCCTTCGCTGGCACCAATCTACGGTCCAGATCAGCTTCGGTTTCATCTGTCTCAAGTCT
















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|76294308|gb|DV033876.1|DV033876
EST:     AAAGCGCTGGTGCATTCTTTTACAACTCAAAGCAATGTTTTATTCAGAAG                         AAGCCATGATACCTTCCGTGAGGCTCTCTCCTGGTCCTGCAGCCTTCTCAG
genomic: AAAGCGCTGGTGCATTCTTTTACAACTCAAAGCAATGTTTTATTCAGAAGgaacgtcaaa ... tgatctgcagAAGCCATGATACCTTCCGTGAGGCTCTCTCCTGGTCCTGCAGCCTTCTCAG




















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 2 RNA-Seq libraries.


Block sizes: 20 (upstream exon), 49 (downstream exon)
Score: 27

CTAGTCTTCAGAAGAAAAATTTCATACCGTTTTCTGTGTACTAAAGCGCTGGTGCATTCTTTTACAACTCAAAGCAATGTTTTATTCAGAAGgaacgtcaaa ... tgatctgcagAAGCCATGATACCTTCCGTGAGGCTCTCTCCTGGTCCTGCAGCCTTCTCAGGCTCCAGCCTACGCTCAAAATTACCGTCAATTCCATCCATCTCCAGTCT


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 41

CTAGTCTTCAGAAGAAAAATTTCATACCGTTTTCTGTGTACTAAAGCGCTGGTGCATTCTTTTACAACTCAAAGCAATGTTTTATTCAGAAGgaacgtcaaa ... tgatctgcagAAGCCATGATACCTTCCGTGAGGCTCTCTCCTGGTCCTGCAGCCTTCTCAGGCTCCAGCCTACGCTCAAAATTACCGTCAATTCCATCCATCTCCAGTCT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctttctatatgtacttcatatactgccatctgaaactttctttgttgatctgcagAAGCCATGATACCTTCCGTGAGGCTCTCTCCTGGTCCTGCAGCCTTCTCAGGCTCCAGCCTACGCTCAAAATTACCGTCAATTCCATCCATCTCCAGTCT
                                          tgttgat  putative branch site (score: 41)
                                   ctttctttgtt  CT-rich tract
     tatatgta  TA-rich tract