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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtggagctctgtttgttgcatgtatactagttactctacaggtggaaatagataaattgccattttcatcactatatttccaatgtttttctttctatagGTGTTGCATTGCGGAAGTGGCAACAAAAATGCCTTTAAGGCACTTATTGCTGCAGAGTACACTGGAGTCAAGGTCGAGCTGACCAAGAATTTTGAGATGG

Basic information

species Oryza sativa
transcript LOC_Os06g37440.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g37440.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G059580_T02 (Zea mays), 3'ss of exon 1
gtggagctc--tgtttgtt-gcatgtatactagttactctacaggtggaaatagataaattgccattttcatcactatatttccaatgtttttctttctatagGTGTTGCATTGCGGAAGTGGCAACAAAAATGCCTTTAAGGCACTTATTGCTGCAGAGTACACTGGAGTCAAGGTCGAGCTGACCAAGAATTTTGAGATGG
 | ||  ||  ||  |||| |||||  ||||| | | |   || |   ||| |||   ||| |  |||  |  || |||| || | |  ||||  ||| |||||| |||||||  ||   ||| |||||||||||||| |||||||||||||||||||| |||| ||| |||||||| ||| |||||||| ||||||||||||
-tagatgtcattgcctgtttgcatgcgtactattgaattaccatgcacaaacagaggtatttcagtttgtaatacaatatgtctatt--tttttattccatagGTATTGCATTCTGGGGCTGGAAACAAAAATGCCTTCAAGGCACTTATTGCTGCAGAATACAGTGGGGTCAAGGTTGAGTTGACCAAGGATTTTGAGATGG

upper sequence: LOC_Os06g37440.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G122871_T03 (Zea mays), 3'ss of exon 1
gtggagctc-tgtttgttgcatgtatactagttactctacag-gtggaaatagataaattgccattttcatcactatatttccaatgtttttctttctatagGTGTTGCATTGCGGAAGTGGCAACAAAAATGCCTTTAAGGCACTTATTGCTGCAGAGTACACTGGAGTCAAGGTCGAGCTGACCAAGAATTTTGAGATGG
 |  | | | |    | |  | |       ||| |  ||    |    | |   | |||    || ||  | | || | |     | |||||  ||  |||||| |||||| | ||   ||| ||||| |||||||| || ||||||||||||||||| |||| |||  ||||||| ||| |||||||| ||||||||||||
-tttatcgcgtaaaagataaaagggggtcggttgccttatgtcgccttactgccttaataagtatgtttgtaa-tacaatatgtctattttttgttgcatagGTATTGCATAGTGGGGCTGGAAACAAGAATGCCTTCAAAGCACTTATTGCTGCAGAATACAGTGGGATCAAGGTTGAGTTGACCAAGGATTTTGAGATGG
















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|58693057|gb|CK081744.1|CK081744
EST:     TGAGATTTGGATCGGGCGCGAGGCCGGCGGCTCCAGTCGGCATGGCGCTT                         GTGTTGCATTGCGGAAGTGGCAACAAAAATGCCTTTAAGGCACTTATTGCT
genomic: TGAGATTTGGATCGGGCGCGAGGCCGGCGGCTCCAGTCGGCATGGCGCTTgtgagtgtcc ... ctttctatagGTGTTGCATTGCGGAAGTGGCAACAAAAATGCCTTTAAGGCACTTATTGCT
EST: gi|88300178|gb|CI582412.1|CI582412
EST:     TGAGATTTGGATCGGGCGCGAGGCCGGCGGCTCCAGTCGGCATGGCGCTT                         GTGTTGCATTGCGGAAGTGGCAACAAAAATGCCTTTAAGGCACTTATTGCT
genomic: TGAGATTTGGATCGGGCGCGAGGCCGGCGGCTCCAGTCGGCATGGCGCTTgtgagtgtcc ... ctttctatagGTGTTGCATTGCGGAAGTGGCAACAAAAATGCCTTTAAGGCACTTATTGCT
EST: gi|58692670|gb|CK081357.1|CK081357
EST:     TGAGATNTGGATCGGGCGCGAGGCCGGCGGCTCCAGTCGGCATGGCGCTT                         GTGTTGCATTGCGGAAGTGGCAACAAAAATGCCTTTAAGGCACTTATTGCT
genomic: TGAGATTTGGATCGGGCGCGAGGCCGGCGGCTCCAGTCGGCATGGCGCTTgtgagtgtcc ... ctttctatagGTGTTGCATTGCGGAAGTGGCAACAAAAATGCCTTTAAGGCACTTATTGCT
EST: gi|88393909|gb|CI684174.1|CI684174
EST:     TGAGATTTGGATCGGGCGCGAGGCCGGCGGCTCCAGTCGGCATGGCGCTT                         GTGTTGCATTGCGGAAGTGGCAACAAAAATGCCTTTAAGGCACTTATTGCT
genomic: TGAGATTTGGATCGGGCGCGAGGCCGGCGGCTCCAGTCGGCATGGCGCTTgtgagtgtcc ... ctttctatagGTGTTGCATTGCGGAAGTGGCAACAAAAATGCCTTTAAGGCACTTATTGCT
EST: gi|29642157|gb|CB647164.1|CB647164
EST:     TGAGATTTGGATCGGGCGCGAGGCCGGCGGCTCCAGTCGGCATGGCGCTT                         GTGTTGCATTGCGGAAGTGGCAACAAAAATGCCTTTAAGGCACTTATTGCT
genomic: TGAGATTTGGATCGGGCGCGAGGCCGGCGGCTCCAGTCGGCATGGCGCTTgtgagtgtcc ... ctttctatagGTGTTGCATTGCGGAAGTGGCAACAAAAATGCCTTTAAGGCACTTATTGCT
EST: gi|88299640|gb|CI574753.1|CI574753
EST:     TGAGATTTGGATCGGGCGCGAGGCCGGCGGCTCCAGTCGGCATGGCGCTT                         GTGTTGCATTGCGGAAGTGGCAACAAAAATGCCTTTAAGGCACTTATTGCT
genomic: TGAGATTTGGATCGGGCGCGAGGCCGGCGGCTCCAGTCGGCATGGCGCTTgtgagtgtcc ... ctttctatagGTGTTGCATTGCGGAAGTGGCAACAAAAATGCCTTTAAGGCACTTATTGCT
EST: gi|33797048|gb|CF324390.1|CF324390
EST:     TGAGATTTGGATCGGGCGCGAGGCCGGCGGCTCCAGTCGGCATGGCGCTT                         GTGTTGCATTGCGGAAGTGGCAACAAAAATGCCTTTAAGGCACTTATTGCT
genomic: TGAGATTTGGATCGGGCGCGAGGCCGGCGGCTCCAGTCGGCATGGCGCTTgtgagtgtcc ... ctttctatagGTGTTGCATTGCGGAAGTGGCAACAAAAATGCCTTTAAGGCACTTATTGCT
EST: gi|66917477|gb|CX104325.1|CX104325
EST:     TGACATTTGGATCGGGCGCGAGGCCGGCGGCTCCAGTCGGCATGGCGCTT                         GTGTTGCATTGCGGAAGTGGCAACAAAAATGCCTTTAAGGCACTTATTGCT
genomic: TGAGATTTGGATCGGGCGCGAGGCCGGCGGCTCCAGTCGGCATGGCGCTTgtgagtgtcc ... ctttctatagGTGTTGCATTGCGGAAGTGGCAACAAAAATGCCTTTAAGGCACTTATTGCT
EST: gi|88340432|gb|CI659638.1|CI659638
EST:     TGAGATTTGGATCGGGCGCGAGGCCGGCGGCTCCAGTCGGCATGGCGCTT                         GTGTTGCATTGCGGAAGTGGCAACAAAAATGCCTTTAAGGCACTTATTGCT
genomic: TGAGATTTGGATCGGGCGCGAGGCCGGCGGCTCCAGTCGGCATGGCGCTTgtgagtgtcc ... ctttctatagGTGTTGCATTGCGGAAGTGGCAACAAAAATGCCTTTAAGGCACTTATTGCT
EST: gi|88325683|gb|CI648126.1|CI648126
EST:     TGAGATTTGGATCGGGCGCGAGGCCGGCGGCTCCAGTCGGCATGGCGCTT                         GTGTTGCATTGCGGAAGTGGCAACAAAAATGCCTTTAAGGCACTTATTGCT
genomic: TGAGATTTGGATCGGGCGCGAGGCCGGCGGCTCCAGTCGGCATGGCGCTTgtgagtgtcc ... ctttctatagGTGTTGCATTGCGGAAGTGGCAACAAAAATGCCTTTAAGGCACTTATTGCT
EST: gi|88392537|gb|CI625359.1|CI625359
EST:     TGAGATTTGGATCGGGCGCGAGGCCGGCGGCTCCAGTCGGAATGGCGCTT                         GTGTTGCATTGCGGAAGTGGCAACAAAAATGGCTTTAAGGGACTTATTGCT
genomic: TGAGATTTGGATCGGGCGCGAGGCCGGCGGCTCCAGTCGGCATGGCGCTTgtgagtgtcc ... ctttctatagGTGTTGCATTGCGGAAGTGGCAACAAAAATGCCTTTAAGGCACTTATTGCT
EST: gi|88402181|gb|CI615024.1|CI615024
EST:     TGAGATTTGGATCGGGCGCGAGGCCGGCGGCTCCAGTCGGCATGGCGCTT                         GTGTTGCATTGCGGAAGTGG-AACAAAAATGCCTTTAAGGCACTTATTGCT
genomic: TGAGATTTGGATCGGGCGCGAGGCCGGCGGCTCCAGTCGGCATGGCGCTTgtgagtgtcc ... ctttctatagGTGTTGCATTGCGGAAGTGGCAACAAAAATGCCTTTAAGGCACTTATTGCT
EST: gi|58677886|gb|CK066573.1|CK066573
EST:     TGAGATTTGGATCGGGCGCGAGGCCGGCGGCGCCAGTCGGCATGGCGCTT                         GTGTTGCATTGCGGAAGTGGCAACAAAAATGCCTTTAAGGCACTTATTGCT
genomic: TGAGATTTGGATCGGGCGCGAGGCCGGCGGCTCCAGTCGGCATGGCGCTTgtgagtgtcc ... ctttctatagGTGTTGCATTGCGGAAGTGGCAACAAAAATGCCTTTAAGGCACTTATTGCT
EST: gi|88403316|gb|CI573039.1|CI573039
EST:     TGAGATTTGGATCGGGCGCGAGGCCGGCGGCTCCAGTCGGCATGGCGCTT                         GTGTTGCATTGCGGAAGTGGCAACAAAAATGCCTTTAAGGCACTTATTGCT
genomic: TGAGATTTGGATCGGGCGCGAGGCCGGCGGCTCCAGTCGGCATGGCGCTTgtgagtgtcc ... ctttctatagGTGTTGCATTGCGGAAGTGGCAACAAAAATGCCTTTAAGGCACTTATTGCT
EST: gi|88421445|gb|CI618569.1|CI618569
EST:     TGAGATTTGGATCGGGCGCGAGGCCGGCGGCTCCAGTCGGCATGGCGCTT                         GTGTTGCATTGCGGAAGTGGCAACAAAAATGCCTTTAAGGCACTTATTGCT
genomic: TGAGATTTGGATCGGGCGCGAGGCCGGCGGCTCCAGTCGGCATGGCGCTTgtgagtgtcc ... ctttctatagGTGTTGCATTGCGGAAGTGGCAACAAAAATGCCTTTAAGGCACTTATTGCT
EST: gi|88432577|gb|CI567616.1|CI567616
EST:     TGAGATTTGGATCGGGCGCGAGGCCGGCGGCTCCAGTCGGCATGGCGCTT                         GTGTTGCATTGCGGAAGTGGCAACAAAAATGCCTTTAAGGCACTTATTGCT
genomic: TGAGATTTGGATCGGGCGCGAGGCCGGCGGCTCCAGTCGGCATGGCGCTTgtgagtgtcc ... ctttctatagGTGTTGCATTGCGGAAGTGGCAACAAAAATGCCTTTAAGGCACTTATTGCT
EST: gi|33658387|gb|CF281000.1|CF281000
EST:     TGAGATTTGGATCGGGCGCGAGGCCGGCGGCTCCAGTCGGCATGGCGCTT                         GTGTTGCATTGCGGAAGTGGCAACATTTTTTCCTTTAAGGCACTTATTGCT
genomic: TGAGATTTGGATCGGGCGCGAGGCCGGCGGCTCCAGTCGGCATGGCGCTTgtgagtgtcc ... ctttctatagGTGTTGCATTGCGGAAGTGGCAACAAAAATGCCTTTAAGGCACTTATTGCT
EST: gi|33794630|gb|CF323201.1|CF323201
EST:     TGAGATTTGGATCGGGCGCGAGGCCGGCGGCTCCAGTCGGCATGGCGCTT                         GTGTTGCATTGCGGAAGTGGCAACAAAAATGCCTTTAAGGCACTTATTGCT
genomic: TGAGATTTGGATCGGGCGCGAGGCCGGCGGCTCCAGTCGGCATGGCGCTTgtgagtgtcc ... ctttctatagGTGTTGCATTGCGGAAGTGGCAACAAAAATGCCTTTAAGGCACTTATTGCT

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 1 RNA-Seqlibrary.


Block sizes: 75 (upstream exon), 74 (downstream exon)
Score: 124

ATCTGAGATTTGGATCGGGCGCGAGGCCGGCGGCTCCAGTCGGCATGGCGCTTgtgagtgtcc ... ctttctatagGTGTTGCATTGCGGAAGTGGCAACAAAAATGCCTTTAAGGCACTTATTGCTGCAGAGTACACTGGAGTCAAGGTCGAGCTGACCAAGAATTTTGAGATGG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaatagataaattgccattttcatcactatatttccaatgtttttctttctatagGTGTTGCATTGCGGAAGTGGCAACAAAAATGCCTTTAAGGCACTTATTGCTGCAGAGTACACTGGAGTCAAGGTCGAGCTGACCAAGAATTTTGAGATGG
                                      tgtttttctttctat  CT-rich tract
                                        tttttctttctata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtggagctctgtttgttgcatgtatactagttactctacaggtggaaatagataaattgccattttcatcactatatttccaatgtttttctttctatagGTGTTGCATTGCGGAAGTGGCAACAAAAATGCCTTTAAGGCACTTATTGCTGCAGAGTACACTGGAGTCAAGGTCGAGCTGACCAAGAATTTTGAGATGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATG
-tggagct
- - - - ctgtttg
- - - - - - - - tgcatgt
- - - - - - - - - - - - - - - - - - - - - - gaaataga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - caatgtt