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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacatctaaatcttcactcacatgttctgtttgtgtaattaaccatttcatgctgaggcagttggcatgacaagctacgttccgttttgcagAACATGTATGCGCAACTGCTTCCTCTTGCCCTGCCTGCTCCGCCAATGCCCGGCATGGGTGGCCCTCCACCTCCGATGGGCGGAATGGGCATGCCTCCGA

Basic information

species Zea mays
transcript GRMZM5G822591_T01
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G822591_T01 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os12g01390.1 (Oryza sativa), 3'ss of exon 29
gtacatctaaatcttcactcacatgttctgtttgtgtaattaaccatttcatgctgaggcagttggcatgacaagc-----tacgttccgttttgcagAACATGTATGCGCAACTGCTTCCTCTTGCCCTGCCTGCTCCGCCAATGCCCGGCATGGGTGGCCCTCCACCTCCGATGGGCGGAATGGGCATGCCTCCGA------
         |||||  |   |    |  | |||  || ||||  |  ||  |  | ||  ||   ||||||| ||      ||| ||   |  |||||||||||||||| ||| |||||||||||||| |||||||||| ||       || ||||| || |||||||| || |||||      ||||||||||||||      
-------gtaatctatagagattgctcttcttttggttattattctgttattatttag-taggcagcatgacgagtggtattacattgtatggtgcagAACATGTATGCCCAATTGCTTCCTCTTGCCTTGCCTGCTCCTCC------TGGTATGGGCGGTCCTCCACCGCCAATGGGGATGCCGGGCATGCCTCCGATGGGCG

upper sequence: GRMZM5G822591_T01 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os11g01380.1 (Oryza sativa), 3'ss of exon 29
---gtacatctaaatcttcactcacatg-ttctgtttgtgtaattaaccatttcatgctgaggcagttggcatgacaagctacgttccgttttgcagAACATGTATGCGCAACTGCTTCCTCTTGCCCTGCCTGCTCCGCCAATGCCCGGCATGGGTGGCCCTCCACCTCCGATGGGCGGAATGGGCATGCCTCCGA------
    |  ||  | ||      ||   || || |  || ||| ||||   | |         | |    || || |||      |||   |  |||||||||||||||| ||| |||||||||| ||| |||||||||| ||       || ||||| || |||||||| || |||||      ||||||||||||||      
gtaatctatagagattgctcttcttttggttattattctgttattatttagtaggcagcatgacgagcggtattacat----tgttgtatggtgcagAACATGTATGCCCAATTGCTTCCTCTCGCCTTGCCTGCTCCACC------TGGTATGGGCGGTCCTCCACCGCCAATGGGGATGCCGGGCATGCCTCCGATGGGCG

upper sequence: GRMZM5G822591_T01 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA14G06340.2 (Glycine max), 3'ss of exon 27
gtacatctaaatcttcactcacatgttctgtttgtgtaattaaccatttcatgctgaggcagt--tggcatga-caagctacgttccgttttgcagAACATGTATGCGCAACTGCTTCCTCTTGCCCTGCCTGCTCCGCCAATGCCCGGCATGGGTGGC------CCTCCACCTCCGATGGGCGGAATGGGCATGCCTCCGA-------------------------------------------------------
                                                          | |||  ||  ||||   || |  | |   | ||||||||||||||||| ||| || | ||||||||  ||||||| || |||||||| || ||||| |||      ||||| ||||| ||||| ||| |||| ||||| || |                                                       
---------------------------------------------------------agtagtactgatatgaatgagatgtgctttttgttgcagaacatgtatgctcaattgttgcctcttgctttgcctgcaccaccaatgcctggaatgggagGCTTTGCTCCTCCCCCTCCAATGGGTGGACTGGGGATGCCCCCAATGCCTCCTTATGGTATGCCACCCATGGGCAGCAGTTTTTGAAGAGTATAGCATGA

upper sequence: GRMZM5G822591_T01 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA14G06340.1 (Glycine max), 3'ss of exon 29
-----------------------------------------------------------------gtacatctaaatcttcactcacatgttctgtttgtgtaattaacc-atttcatgctgaggcagt--tggcatga-caagctacgttccgttttgcagAACATGTATGCGCAACTGCTTCCTCTTGCCCTGCCTGCTCCGCCAATGCCCGGCATGGGTGGC------CCTCCACCTCCGATGGGCGGAATGGGCATGCCTCCGA
                                                                  || |||   |||||      |||      |     |  | |||  |||  |   |   | |||  ||  ||||   || |  | |   | ||||||||||||||||| ||| || | ||||||||  ||||||| || |||||||| || ||||| |||      ||||| ||||| ||||| ||| |||| ||||      
gtaattattttatgtcatgctgtcactctgtcagcagtttgagtgttctgaaatgtttgttgttgataaatcctcatctttcgcatcattcatcctcgactttctcaacagattgaacattagagtagtactgatatgaatgagatgtgctttttgttgcagAACATGTATGCTCAATTGTTGCCTCTTGCTTTGCCTGCACCACCAATGCCTGGAATGGGAGGCTTTGCTCCTCCCCCTCCAATGGGTGGACTGGGGATGC------

upper sequence: GRMZM5G822591_T01 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA02G42560.1 (Glycine max), 3'ss of exon 29
---------------------------------------------------gtacatctaaatc---ttcactcacatgttctgtttgtgtaatt---aacc-atttcatgctgaggcagt--tggcatga-caagctacgttccgttttgcagAACATGTATGCGCAACTGCTTCCTCTTGCCCTGCCTGCTCCGCCAATGCCCGGCATGGGTGGCCCTCCACCTCCGATGGGCGGAATGGGCATGCCTCCGA
                                                    |     ||||||   |||  || |||  |   |       |||   |||  |||  |   |   | |||  ||  ||||   || |  | |   | ||||||||||||||||| ||| || | ||||||||  ||||||| || |||||||| || ||||| |||||   |  |  |   || ||  | |     || ||  
gtaattattttatgttgtgctgtcagcagtttgagtgttcagaaatgtttgttgttgataaatcctcttctttcgcatccttcatcctcaacattctcaacagattgaacattagagtagtactgatatgaatgagatgtgctttttgttgcagAACATGTATGCTCAATTGTTGCCTCTTGCTTTGCCTGCACCACCAATGCCTGGAATGGGAGGCCCAGGAGGTATGGGAGGAGGCTTTGCTCCTCCCCCTC

upper sequence: GRMZM5G822591_T01 (Zea mays), 3'ss of exon 6
lower sequence: EFJ24508 (Selaginella moellendorffii), 3'ss of exon 29
gtacatctaaatcttcactcacatgttctgtttgtgtaattaaccatttcatgctgaggcagttggcatgacaagctacgttccgttttgcagAACATGTATGCGCAACTGCTTCCTCTTGCCCTGCCTGCTCCGCCAATGCCCGGCATGGGTGGCCCTCCACCTCCGATGGGCGGAATGGGCATGCCTCCGA---
                                 || |   |   ||  ||||  ||  |||  |      | |  ||   |||  | |||||||||||||| || || || |||||||| || ||||| ||||| || |||||||||||||| |||  |   |||||      |     ||||||||| ||     
---------------------------------gtttgtctcctcacctcat-ttgctgcaact------atagactgaattcgatcttgcagAACATGTACGCTCAGCTCCTTCCTCTGGCGCTGCCCGCTCCTCCGATGCCCGGCATGGGAGGCGGT---CCTCCAGGATTCAACCCGGGCATGCCACCTCCTT

upper sequence: GRMZM5G822591_T01 (Zea mays), 3'ss of exon 6
lower sequence: EFJ13237 (Selaginella moellendorffii), 3'ss of exon 29
gtacatctaaatcttcactcacatgttctgtttgtgtaattaacc-atttcatgctgaggcagttggcat---gacaagctacgttccgttttgcagAACATGTATGCGCAACTGCTTCCTCTTGCCCTGCCTGCTCCGCCAATGCCCGGCATGGGTGGCCCTCCACCTCCGATGGGCGGAATGGGCATGCCTCCGA---
                             |||||| |  | | || ||||  |||      ||   | ||     |  | || |   | | |||||||||||||| || || || |||||||| || ||||| ||||| || |||||||||||||| |||  |   |||||      |     ||| ||||| ||     
-----------------------------gtttgtctcctcaccccatttgctgcaactatagactgaattcgatctggatatgcaac-tcttgcagAACATGTACGCTCAGCTCCTTCCTCTGGCTCTGCCCGCTCCTCCGATGCCCGGCATGGGAGGCGGT---CCTCCAGGATTCAACCCGGGAATGCCACCTCCAT

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|211415580|gb|FL028984.1|FL028984
EST:     ATGAAGAAAGAGCCAAAGAGAAGGAGGAGAAAGATCTTGTGGCTCAGCAG                         AACATGTATGCGCAACTGCTTCCTCTTGCCCTGCCTGCTCCGCCAATGCCC
genomic: ATGAAGAAAGAGCCAAAGAGAAGGAGGAGAAAGATCTTGTGGCTCAGCAGgtacatctaa ... cgttttgcagAACATGTATGCGCAACTGCTTCCTCTTGCCCTGCCTGCTCCGCCAATGCCC
EST: gi|37375445|gb|CF624160.1|CF624160
EST:     ATGAAGAAAGAGCCAAAGAGAAGGAGGAGAAAGATCTTGTGGCTCAGCAG                         AACATGTATGCGCAACTGCTTCCTCTTGCTCTGCCTGCTCCGCCAATGCCC
genomic: ATGAAGAAAGAGCCAAAGAGAAGGAGGAGAAAGATCTTGTGGCTCAGCAGgtacatctaa ... cgttttgcagAACATGTATGCGCAACTGCTTCCTCTTGCCCTGCCTGCTCCGCCAATGCCC
EST: gi|31664357|gb|CD573082.1|CD573082
EST:     ATGAAGAAAGAGCCAAAGAGAAGGAGGAGAAAGATCTTGTGGCTCAGCAG                         AACATGTATGCGCAACTGCTTCCTCTTGCCCTGCCTGCTCCGCCAATGCCC
genomic: ATGAAGAAAGAGCCAAAGAGAAGGAGGAGAAAGATCTTGTGGCTCAGCAGgtacatctaa ... cgttttgcagAACATGTATGCGCAACTGCTTCCTCTTGCCCTGCCTGCTCCGCCAATGCCC
EST: gi|60399410|gb|DN232222.1|DN232222
EST:     ATGAAGAAAGAGCCAAAGAGAAGGAGGAGAAAGATCTTGTGGCTCAGCAG                         AACATGTATGCGCAACTGCTTCCTCTTGCCCTGCCTGCTCCGCCAATGCCC
genomic: ATGAAGAAAGAGCCAAAGAGAAGGAGGAGAAAGATCTTGTGGCTCAGCAGgtacatctaa ... cgttttgcagAACATGTATGCGCAACTGCTTCCTCTTGCCCTGCCTGCTCCGCCAATGCCC
EST: gi|60395619|gb|DN228489.1|DN228489
EST:     ATGAAGAAAGAGCCAAAGAGAAGGAGGAGAAAGATCTTGTGGCTCAGCAG                         AACATGTATGCGCAACTGCTTCCTCTTGCCCTGCCTGCTCCGCCAATGCCC
genomic: ATGAAGAAAGAGCCAAAGAGAAGGAGGAGAAAGATCTTGTGGCTCAGCAGgtacatctaa ... cgttttgcagAACATGTATGCGCAACTGCTTCCTCTTGCCCTGCCTGCTCCGCCAATGCCC
EST: gi|67016082|gb|CO444831.1|CO444831
EST:     TGAAGAAAGAGCCANAGAGAAGGAGGGAGAA-GATCTTGTGGCTCAGCAG                         AACATGTATGCGCAACTGCTTCCTCTTGCCCTGCCTGCTNCGCCAATGCCC
genomic: TGAAGAAAGAGCCAAAGAGAAGGAGG-AGAAAGATCTTGTGGCTCAGCAGgtacatctaa ... cgttttgcagAACATGTATGCGCAACTGCTTCCTCTTGCCCTGCCTGCTCCGCCAATGCCC
EST: gi|18178279|gb|BM379489.1|BM379489
EST:     GAGAAGGAGGAGAAAGATCTTGTGGCTCAGCAG                         AACATGTATGCGCAACTGCTTCCTCTTGCCCTGCCTGCTCCGCCAATGCCC
genomic: GAGAAGGAGGAGAAAGATCTTGTGGCTCAGCAGgtacatctaa ... cgttttgcagAACATGTATGCGCAACTGCTTCCTCTTGCCCTGCCTGCTCCGCCAATGCCC
EST: gi|29945571|gb|CB815707.1|CB815707
EST:     ATGAAGAAAGAGCCAAAGAGAAGGAGGAGAAAGATCTTGTGGCTCAGCAG                         AACATGTATGCGCAACTGCTTCCTCTTGCCCTGCCTGCTCCGCCAATGCCC
genomic: ATGAAGAAAGAGCCAAAGAGAAGGAGGAGAAAGATCTTGTGGCTCAGCAGgtacatctaa ... cgttttgcagAACATGTATGCGCAACTGCTTCCTCTTGCCCTGCCTGCTCCGCCAATGCCC
EST: gi|29129934|gb|CB380638.1|CB380638
EST:     ATGAAGAAAGAGCCAAAGAGAAGGAGGAGAAAGATCTTGTGGCTCAGCAG                         AACATGTATGCGCAACTGCTTCCTCTTGCCCTGCCTGCTCCGCCAATGCCC
genomic: ATGAAGAAAGAGCCAAAGAGAAGGAGGAGAAAGATCTTGTGGCTCAGCAGgtacatctaa ... cgttttgcagAACATGTATGCGCAACTGCTTCCTCTTGCCCTGCCTGCTCCGCCAATGCCC

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), 48 (downstream exon)
Score: 299

ATACACTAGCAAGGTGGATGATTTAGTGAAGGACAAAATCGAGTCACAGAATGAAGAAAGAGCCAAAGAGAAGGAGGAGAAAGATCTTGTGGCTCAGCAGgtacatctaa ... cgttttgcagAACATGTATGCGCAACTGCTTCCTCTTGCCCTGCCTGCTCCGCCAATGCCCGGCATGGGTGGCCCTCCACCTCCGATGGGCGGAATGGGCATGCCTCCGA


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 243

ATACACTAGCAAGGTGGATGATTTAGTGAAGGACAAAATCGAGTCACAGAATGAAGAAAGAGCCAAAGAGAAGGAGGAGAAAGATCTTGTGGCTCAGCAGgtacatctaa ... cgttttgcagAACATGTATGCGCAACTGCTTCCTCTTGCCCTGCCTGCTCCGCCAATGCCCGGCATGGGTGGCCCTCCACCTCCGATGGGCGGAATGGGCATGCCTCCGA


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 383

ATACACTAGCAAGGTGGATGATTTAGTGAAGGACAAAATCGAGTCACAGAATGAAGAAAGAGCCAAAGAGAAGGAGGAGAAAGATCTTGTGGCTCAGCAGgtacatctaa ... cgttttgcagAACATGTATGCGCAACTGCTTCCTCTTGCCCTGCCTGCTCCGCCAATGCCCGGCATGGGTGGCCCTCCACCTCCGATGGGCGGAATGGGCATGCCTCCGA


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 296

ATACACTAGCAAGGTGGATGATTTAGTGAAGGACAAAATCGAGTCACAGAATGAAGAAAGAGCCAAAGAGAAGGAGGAGAAAGATCTTGTGGCTCAGCAGgtacatctaa ... cgttttgcagAACATGTATGCGCAACTGCTTCCTCTTGCCCTGCCTGCTCCGCCAATGCCCGGCATGGGTGGCCCTCCACCTCCGATGGGCGGAATGGGCATGCCTCCGA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attaaccatttcatgctgaggcagttggcatgacaagctacgttccgttttgcagAACATGTATGCGCAACTGCTTCCTCTTGCCCTGCCTGCTCCGCCAATGCCCGGCATGGGTGGCCCTCCACCTCCGATGGGCGGAATGGGCATGCCTCCGA
 aattaac  putative branch site (score: 296)
                                          ttccgtttt  putative PPT
       atttcat  TA-rich tract