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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtcagttttatttcatggactttcccatgttttccattgtaaattagtaattgatcttcaggtcatatgcttatcagaattctctcagtagGTTGGAATTGGTGTTGCAGTTGTTATATTTGGACTAGTCTTCGCTTTTGGGGATTTCCTGCCTTATGGAAG

Basic information

species Zea mays
transcript GRMZM5G863152_T02
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G863152_T01 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os07g18720.1 (Oryza sativa), 3'ss of exon 6
gtcagttttatttcatggactttcccatgttttccattgtaaattagtaattgatcttcaggtcatatgcttatcagaattctctcagtagGTTGGAATTGGTGTTGCAGTTGTTATATTTGGACTAGTCTTCGCTTTTGGGGATTTCCTGCCTTATGGAAG
|||||| ||  ||     |   |      ||| |     ||| ||  ||  |    |     |||||| || || | || | || ||| |||||||||||||  | || ||  |  | |||||| ||||||||||||||||||||||||| || ||||||||
gtcagtatttattataaaatggttttgcatttcc----ataatttgttagctagctt----atcatatactaataaaaaatttcccagcagGTTGGAATTGGCATAGCTGTCATGGTCTTTGGATTAGTCTTCGCTTTTGGGGATTTCCTTCCATATGGAAG
















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|166596764|gb|EG145516.1|EG145516
EST:     TAAAAGTACTATTGGCTTTGGTACTAGG                         GTTGGAATTGGTGTTGCAGTTGTTATATTTGGACTAGTCTTCGCTTTTGGG
genomic: TAAAAGTACTATTGGCTTTGGTACTAGGgtcagtttta ... ctctcagtagGTTGGAATTGGTGTTGCAGTTGTTATATTTGGACTAGTCTTCGCTTTTGGG
EST: gi|166654390|gb|EG123193.1|EG123193
EST:     TAAAAGTACTATTGGCTTTGGTACTAGG                         GTTGGAATTGGTGTTGCAGTTGTTATATTTGGACTAGTCTTCGCTTTTGGG
genomic: TAAAAGTACTATTGGCTTTGGTACTAGGgtcagtttta ... ctctcagtagGTTGGAATTGGTGTTGCAGTTGTTATATTTGGACTAGTCTTCGCTTTTGGG
EST: gi|71305070|gb|DR788672.1|DR788672
EST:     ATGATGCTCCAATTGAGTCAGATAAAAGTACTATTGGCTTTGGTACTAGG                         GTTGGAATTGGTGTTGCAGTTGTTATATTTGGACTAGTCTTCGCTTTTGGG
genomic: ATGATGCTCCAATTGAGTCAGATAAAAGTACTATTGGCTTTGGTACTAGGgtcagtttta ... ctctcagtagGTTGGAATTGGTGTTGCAGTTGTTATATTTGGACTAGTCTTCGCTTTTGGG
EST: gi|211226055|gb|FL296371.1|FL296371
EST:     ATGATGCTCCAATTGAGTCAGATAAAAGTACTATTGGCTTTGGTACTAGG                         GTTGGAATTGGTG
genomic: ATGATGCTCCAATTGAGTCAGATAAAAGTACTATTGGCTTTGGTACTAGGgtcagtttta ... ctctcagtagGTTGGAATTGGTG
EST: gi|211223997|gb|FL296365.1|FL296365
EST:     ATGATGCTCCAATTGAGTCAGATAAAAGTACTATTGGCTTTGGTACTAGG                         GTTGGGAATTGGTGTTGCAGTTGTTATATTTGGACTAGTCTTCGCTTTTGG
genomic: ATGATGCTCCAATTGAGTCAGATAAAAGTACTATTGGCTTTGGTACTAGGgtcagtttta ... ctctcagtagGTTGG-AATTGGTGTTGCAGTTGTTATATTTGGACTAGTCTTCGCTTTTGG
EST: gi|76920373|gb|DV168136.1|DV168136
EST:     ATGATGCTCCAATTGAGTCAGATAAAAGTACTATTGGCTTTGGTACTAGG                         GTTGGAATTGGTGTTGCAGTTGTTATATTTGGACTAGTCTTCGCTTTTGGG
genomic: ATGATGCTCCAATTGAGTCAGATAAAAGTACTATTGGCTTTGGTACTAGGgtcagtttta ... ctctcagtagGTTGGAATTGGTGTTGCAGTTGTTATATTTGGACTAGTCTTCGCTTTTGGG
EST: gi|211226058|gb|FL296374.1|FL296374
EST:     ATGATGCTCCAATTGAGTCAGATAAAAGTACTATTGGCTTGGGTACTAGG                         GTTGGAAATTGGTGTTGCAGGTGTTTATATTTGGACTAGTCNNTCGCTTTT
genomic: ATGATGCTCCAATTGAGTCAGATAAAAGTACTATTGGCTTTGGTACTAGGgtcagtttta ... ctctcagtagGTTGGAA-TTGGTGTTGCAGTTGTT-ATATTTGGACTAGTCT-TCGCTTTT
EST: gi|71432424|gb|DR813474.1|DR813474
EST:     ATGATGCTCCAATTGAGTCAGATAAAAGTACTATTGGCTTTGGTACTAGG                         GTTGGAATTGGTGTTGCAGTTGTTATATTTGGACTAGTCTTCGCTTTTGGG
genomic: ATGATGCTCCAATTGAGTCAGATAAAAGTACTATTGGCTTTGGTACTAGGgtcagtttta ... ctctcagtagGTTGGAATTGGTGTTGCAGTTGTTATATTTGGACTAGTCTTCGCTTTTGGG
EST: gi|78081578|gb|DV509990.1|DV509990
EST:     ATGATGCTCCAATTGAGTCAGATAAAAGTACTATTGGCTTTGGTACTAGG                         GTTGGAATTGGTGTTGCAGTTGTTATATTTGGACTAGTCTTCGCTTTTGGG
genomic: ATGATGCTCCAATTGAGTCAGATAAAAGTACTATTGGCTTTGGTACTAGGgtcagtttta ... ctctcagtagGTTGGAATTGGTGTTGCAGTTGTTATATTTGGACTAGTCTTCGCTTTTGGG

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: 89

TCTTGAGAAAAAGAAAGCTGAAGAGAACAAAGATTATCAAGCTATTGATTATGATGCTCCAATTGAGTCAGATAAAAGTACTATTGGCTTTGGTACTAGGgtcagtttta ... ctctcagtagGTTGGAATTGGTGTTGCAGTTGTTATATTTGGACTAGTCTTCGCTTTTGGGGATTTCCTGCCTTATGGAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 133

TCTTGAGAAAAAGAAAGCTGAAGAGAACAAAGATTATCAAGCTATTGATTATGATGCTCCAATTGAGTCAGATAAAAGTACTATTGGCTTTGGTACTAGGgtcagtttta ... ctctcagtagGTTGGAATTGGTGTTGCAGTTGTTATATTTGGACTAGTCTTCGCTTTTGGGGATTTCCTGCCTTATGGAAG


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

TCTTGAGAAAAAGAAAGCTGAAGAGAACAAAGATTATCAAGCTATTGATTATGATGCTCCAATTGAGTCAGATAAAAGTACTATTGGCTTTGGTACTAGGgtcagtttta ... ctctcagtagGTTGGAATTGGTGTTGCAGTTGTTATATTTGGACTAGTCTTCGCTTTTGGGGATTTCCTGCCTTATGGAAG


Block sizes: 47 (upstream exon), 48 (downstream exon)
Score: 69

TCTTGAGAAAAAGAAAGCTGAAGAGAACAAAGATTATCAAGCTATTGATTATGATGCTCCAATTGAGTCAGATAAAAGTACTATTGGCTTTGGTACTAGGgtcagtttta ... ctctcagtagGTTGGAATTGGTGTTGCAGTTGTTATATTTGGACTAGTCTTCGCTTTTGGGGATTTCCTGCCTTATGGAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgtaaattagtaattgatcttcaggtcatatgcttatcagaattctctcagtagGTTGGAATTGGTGTTGCAGTTGTTATATTTGGACTAGTCTTCGCTTTTGGGGATTTCCTGCCTTATGGAAG
            aattgat  putative branch site (score: 69)
                                           ttctctc  putative PPT
     aattagtaattgat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtcagttttatttcatggactttcccatgttttccattgtaaattagtaattgatcttcaggtcatatgcttatcagaattctctcagtagGTTGGAATTGGTGTTGCAGTTGTTATATTTGGACTAGTCTTCGCTTTTGGGGATTTCCTGCCTTATGGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG