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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagctataatctcagtgattttacctgaaaaagattcctttatattttatttttaatatgctcaataaattctttttatatctaattgtagGGTGGAATATATACCCTTCCTAGTCATTTGTCACCTTCAGCGAGGGACTTGATTCCCAGAATGCTGGTTGTTGATCCAATGAAAAGGATTACAATACGTG

Basic information

species Zea mays
transcript GRMZM2G077278_T01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G077278_T01 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os05g45420.3 (Oryza sativa), 3'ss of exon 5
gtgagctataatctcagtgattttacctgaaaaagattcctttatattttatttttaatatgctcaataaattctttttatatcta-attgtagGGTGGAATATATACCCTTCCTAGTCATTTGTCACCTTCAGCGAGGGACTTGATTCCCAGAATGCTGGTTGTTGATCCAATGAAAAGGATTACAATACGTG
|| ||| |  || | |   ||  ||| ||| |||| | |      || |  ||||  || |       ||| ||| |   | |  |  || |||||||| |||||||||||||| ||||||||||||||||  || ||||| ||||||||||||||||| ||||||||||| ||||| ||||| || |||||||
gttagcaaagatgtgatatatcctac-tgataaaggtgctgcctcatctccttttatatgttaaagtaaaactctgtccgttttgatgttctagGGTGGCATATATACCCTTCCCAGTCATTTGTCACCTTTGGCAAGGGATTTGATTCCCAGAATGCTTGTTGTTGATCCCATGAAGAGGATCACCATACGTG
















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|211517180|gb|FL332457.1|FL332457
EST:     CTCTCCCATTTGACGATGAGAATATTCCAAACCTTTTCAAGAAAATAAAG                         GGTGGAATATATACCCTTCCTAGTCATTTGTCACCTTCAGCGAGGGACTTG
genomic: CTCTCCCATTTGACGATGAGAATATTCCAAACCTTTTCAAGAAAATAAAGgtgagctata ... ctaattgtagGGTGGAATATATACCCTTCCTAGTCATTTGTCACCTTCAGCGAGGGACTTG
EST: gi|149013919|gb|EE043417.2|EE043417
EST:     CTCTCCCATTTGACGATGAGAATATTCCAAACCTTTTCAAGAAAATAAAG                         GGTGGAATATATATCCTTTCCTAGTCATTTG
genomic: CTCTCCCATTTGACGATGAGAATATTCCAAACCTTTTCAAGAAAATAAAGgtgagctata ... ctaattgtagGGTGGAATATATACCCTT-CCTAGTCATTTG
EST: gi|148954916|gb|EC900404.2|EC900404
EST:     TCTCCCATTTGACGATGAGAATATTCCAAACCTTTTNCA-GAAAATAAAG                         GGTGGAATATATACCCTTCCTAGTCATTTGTCACCTTCAGCGAGGGACTTG
genomic: TCTCCCATTTGACGATGAGAATATTCCAAACCTTTT-CAAGAAAATAAAGgtgagctata ... ctaattgtagGGTGGAATATATACCCTTCCTAGTCATTTGTCACCTTCAGCGAGGGACTTG
EST: gi|9254260|gb|BE344728.1|BE344728
EST:     CTCTCCCATTTGACGATGAGAATATTCCAAACCTTTTCAAGAAAATAAAG                         GGTGGAATATATACCCTTCCTAGTCATTTGTCACCTTCAGCGAGGGACTTG
genomic: CTCTCCCATTTGACGATGAGAATATTCCAAACCTTTTCAAGAAAATAAAGgtgagctata ... ctaattgtagGGTGGAATATATACCCTTCCTAGTCATTTGTCACCTTCAGCGAGGGACTTG
EST: gi|31352455|gb|CD436812.1|CD436812
EST:     CTCTCCCATTTGACGATGAGAATATTCCAAACCTTTTCAAGAAAATAAAG                         GGTGGAATATATACCCTTCCTAGTCATTTGTCACCTTCAGCGAGGGACTTG
genomic: CTCTCCCATTTGACGATGAGAATATTCCAAACCTTTTCAAGAAAATAAAGgtgagctata ... ctaattgtagGGTGGAATATATACCCTTCCTAGTCATTTGTCACCTTCAGCGAGGGACTTG

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), 46 (downstream exon)
Score: 212

AGTTGACGTCTGGAGCTGTGGAGTTATTCTTTATGCTCTTCTTTGTGGCACTCTCCCATTTGACGATGAGAATATTCCAAACCTTTTCAAGAAAATAAAGgtgagctata ... ctaattgtagGGTGGAATATATACCCTTCCTAGTCATTTGTCACCTTCAGCGAGGGACTTGATTCCCAGAATGCTGGTTGTTGATCCAATGAAAAGGATTACAATACGTG


Block sizes: 48 (upstream exon), 46 (downstream exon)
Score: 179

AGTTGACGTCTGGAGCTGTGGAGTTATTCTTTATGCTCTTCTTTGTGGCACTCTCCCATTTGACGATGAGAATATTCCAAACCTTTTCAAGAAAATAAAGgtgagctata ... ctaattgtagGGTGGAATATATACCCTTCCTAGTCATTTGTCACCTTCAGCGAGGGACTTGATTCCCAGAATGCTGGTTGTTGATCCAATGAAAAGGATTACAATACGTG


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 259

AGTTGACGTCTGGAGCTGTGGAGTTATTCTTTATGCTCTTCTTTGTGGCACTCTCCCATTTGACGATGAGAATATTCCAAACCTTTTCAAGAAAATAAAGgtgagctata ... ctaattgtagGGTGGAATATATACCCTTCCTAGTCATTTGTCACCTTCAGCGAGGGACTTGATTCCCAGAATGCTGGTTGTTGATCCAATGAAAAGGATTACAATACGTG


Block sizes: 49 (upstream exon), 45 (downstream exon)
Score: 139

AGTTGACGTCTGGAGCTGTGGAGTTATTCTTTATGCTCTTCTTTGTGGCACTCTCCCATTTGACGATGAGAATATTCCAAACCTTTTCAAGAAAATAAAGgtgagctata ... ctaattgtagGGTGGAATATATACCCTTCCTAGTCATTTGTCACCTTCAGCGAGGGACTTGATTCCCAGAATGCTGGTTGTTGATCCAATGAAAAGGATTACAATACGTG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cctttatattttatttttaatatgctcaataaattctttttatatctaattgtagGGTGGAATATATACCCTTCCTAGTCATTTGTCACCTTCAGCGAGGGACTTGATTCCCAGAATGCTGGTTGTTGATCCAATGAAAAGGATTACAATACGTG
                                           atctaat  putative branch site (score: 139)
                                 ttctttttatatct  CT-rich tract
     atattttatttttaat  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagctataatctcagtgattttacctgaaaaagattcctttatattttatttttaatatgctcaataaattctttttatatctaattgtagGGTGGAATATATACCCTTCCTAGTCATTTGTCACCTTCAGCGAGGGACTTGATTCCCAGAATGCTGGTTGTTGATCCAATGAAAAGGATTACAATACGTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG