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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gaacggaatgttcaaaagaagaggaaaacaaaccttttcctattggagaatttctgtactgaccgcttcgtaatttttggcccattcctttgtcatacagGTAAACATTGGCAAGAAGTGGAAGGATGTCATCGACTACAACGACAAGATCACGTACACTTTCCAT

Basic information

species Zea mays
transcript GRMZM2G022019_T01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G022019_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os10g32970.1 (Oryza sativa), 3'ss of exon 3
gaacggaatgttcaaaagaagaggaaaacaaaccttttcctattggagaatttctgtactgaccgcttcgtaatttttggcc--------cattcctttgtcatacagGTAAACATTGGCAAGAAGTGGAAGGATGTCATCGACTACAACGACAAGATCACGTACACTTTCCAT
        | |            || |    | | || ||| ||| |  ||  ||  |   |  |     | ||   | |          ||| ||||||   | |||||||||||||||||||| ||||||||  |  | |||||||| || |||||    ||||  ||||||
--------tatgtgtttttttttgagatttgagcattaccttttgaaacatggcttcaaccatagaccaatgataactagagaaaactaacatgcctttgctttgcagGTAAACATTGGCAAGAAATGGAAGGAGATTGTTGACTACAATGATAAGATGGTCTACAGCTTCCAT
















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|18169348|gb|BM339188.1|BM339188
EST:     GAGATAAGCTGGCATTATGGACTAGGACTGCCAGCAATGAAGCTGTCCAG                         GTAAACATTGGCAAGAAGTGGAAGGATGTCATCGACTACAACGACAAGATC
genomic: GAGATAAGCTGGCATTATGGACTAGGACTGCCAGCAATGAAGCTGTCCAGgttggttttg ... tgtcatacagGTAAACATTGGCAAGAAGTGGAAGGATGTCATCGACTACAACGACAAGATC
EST: gi|87157574|gb|DY402363.1|DY402363
EST:     GAGATAAGCTGGCATTATGGACTAGGACTGCCAGCAATGAAGCTGTCCAG                         GTAAACATTGGCAAGAAGTGGAAGGATGTCATCGACTACAACGACAAGATC
genomic: GAGATAAGCTGGCATTATGGACTAGGACTGCCAGCAATGAAGCTGTCCAGgttggttttg ... tgtcatacagGTAAACATTGGCAAGAAGTGGAAGGATGTCATCGACTACAACGACAAGATC
EST: gi|31250200|gb|CD219224.1|CD219224
EST:     GAGATAAGCTGGCATTATGGACTAGGACTGCCAGCAATGAAGCTGTCCAG                         GTAAACATTGGCAAGAAGTAGAAGGATGTCATCGACTACAACGACAAGATC
genomic: GAGATAAGCTGGCATTATGGACTAGGACTGCCAGCAATGAAGCTGTCCAGgttggttttg ... tgtcatacagGTAAACATTGGCAAGAAGTGGAAGGATGTCATCGACTACAACGACAAGATC
EST: gi|26558254|gb|CA830489.1|CA830489
EST:     GAGATAAGCTGGCATTATGGACTAGGACTGCCAGCAATGAAGCTGTCCAG                         GTAAACATTGGCAAGAAGTGGAAGGATGTCATCGACTACAACGACAAGATC
genomic: GAGATAAGCTGGCATTATGGACTAGGACTGCCAGCAATGAAGCTGTCCAGgttggttttg ... tgtcatacagGTAAACATTGGCAAGAAGTGGAAGGATGTCATCGACTACAACGACAAGATC
EST: gi|17931403|gb|BM268363.1|BM268363
EST:     GAGATAAGCTGGCATTATGGACTAGGACTGCCAGCAATGAAGCTGTCCAG                         GTAAACATTGGCAAGAAGTGGAAGGATGTCATCGACTACAACGACAAGATC
genomic: GAGATAAGCTGGCATTATGGACTAGGACTGCCAGCAATGAAGCTGTCCAGgttggttttg ... tgtcatacagGTAAACATTGGCAAGAAGTGGAAGGATGTCATCGACTACAACGACAAGATC
EST: gi|17931601|gb|BM268561.1|BM268561
EST:     GAGATAAGCTGGCATTATGGACTAGGACTGCCAGCAATGAAGCTGTCCAG                         GTAAACATTGGCAAGAAGTGGAAGGATGTCATCGACTACAACGACAAGATC
genomic: GAGATAAGCTGGCATTATGGACTAGGACTGCCAGCAATGAAGCTGTCCAGgttggttttg ... tgtcatacagGTAAACATTGGCAAGAAGTGGAAGGATGTCATCGACTACAACGACAAGATC
EST: gi|50336177|gb|CO531303.1|CO531303
EST:     GAGATAAGCTGGCATTATGGACTAGGACTGCCAGCAATGAAGCTGTCCAG                         GTAAACATTGGCAAGAAGTGGAAGGATGTCATCGACTACAACGACAAGATC
genomic: GAGATAAGCTGGCATTATGGACTAGGACTGCCAGCAATGAAGCTGTCCAGgttggttttg ... tgtcatacagGTAAACATTGGCAAGAAGTGGAAGGATGTCATCGACTACAACGACAAGATC
EST: gi|21987193|gb|BQ778721.1|BQ778721
EST:     GAGATAAGCTGGCATTATGGACTAGGACTGCCAGCAATGAAGCTGTCCAG                         GTAAACATTGGCAAGAAGTGGAAGGATGTCATCGACTACAACGACAAGATC
genomic: GAGATAAGCTGGCATTATGGACTAGGACTGCCAGCAATGAAGCTGTCCAGgttggttttg ... tgtcatacagGTAAACATTGGCAAGAAGTGGAAGGATGTCATCGACTACAACGACAAGATC
EST: gi|211062307|gb|FL474478.1|FL474478
EST:     GAGATAAGCTGGCATTATGGACTAGGACTGCCAGCAATGAAGCTGTCCAG                         GTAAACATTGGCAAGAAGTGGAAGGATGTCATCGACTACAACGACAAGATC
genomic: GAGATAAGCTGGCATTATGGACTAGGACTGCCAGCAATGAAGCTGTCCAGgttggttttg ... tgtcatacagGTAAACATTGGCAAGAAGTGGAAGGATGTCATCGACTACAACGACAAGATC
EST: gi|18163629|gb|BM333468.1|BM333468
EST:     GAGATAAGCTGGCATTATGGACTAGGACTGCCAGCAATGAAGCTGTCCAG                         GTAAACATTGGCAAGAAGTGGAAGGATGTCATCGACTACAACGACAAGATC
genomic: GAGATAAGCTGGCATTATGGACTAGGACTGCCAGCAATGAAGCTGTCCAGgttggttttg ... tgtcatacagGTAAACATTGGCAAGAAGTGGAAGGATGTCATCGACTACAACGACAAGATC
EST: gi|4887347|gb|AI677446.1|AI677446
EST:     GAGATAAGCTGGCATTATGGACTAGGACTGCCAGCAATGAAGCTGTCCAG                         GTAAACATTGGCAAGAAGTGGAAGGATGTCATCGACTACAACGACAAGATC
genomic: GAGATAAGCTGGCATTATGGACTAGGACTGCCAGCAATGAAGCTGTCCAGgttggttttg ... tgtcatacagGTAAACATTGGCAAGAAGTGGAAGGATGTCATCGACTACAACGACAAGATC
EST: gi|32851639|gb|CD991320.1|CD991320
EST:     AGATAAGCTGGCATTATGGACTAGGACTGCCAGCAATGGAAGCTGTCCAG                         GTAAACATTGGCAAGAAGGGGAAGGATGTCATCGACTACAACGACAAGATC
genomic: AGATAAGCTGGCATTATGGACTAGGACTGCCAGCAATG-AAGCTGTCCAGgttggttttg ... tgtcatacagGTAAACATTGGCAAGAAGTGGAAGGATGTCATCGACTACAACGACAAGATC
EST: gi|50322671|gb|CO517797.1|CO517797
EST:     GAGATAAGCTGGCATTATGGACTAGGACTGCCAGCAATGAAGCTGTCCAG                         GTAAACATTGGCAAGAAGTGGAAGGATGTCATCGACTACAACGACAAGATC
genomic: GAGATAAGCTGGCATTATGGACTAGGACTGCCAGCAATGAAGCTGTCCAGgttggttttg ... tgtcatacagGTAAACATTGGCAAGAAGTGGAAGGATGTCATCGACTACAACGACAAGATC
EST: gi|76010904|gb|DT938074.1|DT938074
EST:     GAGATAAGCTGGCATTATGGACTAGGACTGCCAGCAATGAAGCTGTCCAG                         GTAAACATTGGCAAGAAGTGGAAGGATGTCATCGACTACAACGACAAGATC
genomic: GAGATAAGCTGGCATTATGGACTAGGACTGCCAGCAATGAAGCTGTCCAGgttggttttg ... tgtcatacagGTAAACATTGGCAAGAAGTGGAAGGATGTCATCGACTACAACGACAAGATC
EST: gi|78026174|gb|DV494561.1|DV494561
EST:     GAGATAAGCTGGCATTATGGACTAGGACTGCCAGCAATGAAGCTGTCCAG                         GTAAACATTGGCAAGAAGTGGAAGGATGTCATCGACTACAACGACAAGATC
genomic: GAGATAAGCTGGCATTATGGACTAGGACTGCCAGCAATGAAGCTGTCCAGgttggttttg ... tgtcatacagGTAAACATTGGCAAGAAGTGGAAGGATGTCATCGACTACAACGACAAGATC
EST: gi|16918090|gb|BM073572.1|BM073572
EST:     GAGATAAGCTGGCATTATGGACTAGGACTGCCAGCAATGAAGCTGTCCAG                         GTAAACATTGGCAAGAAGTGGAAGGATGTCATCGACTACAACGACAAGATC
genomic: GAGATAAGCTGGCATTATGGACTAGGACTGCCAGCAATGAAGCTGTCCAGgttggttttg ... tgtcatacagGTAAACATTGGCAAGAAGTGGAAGGATGTCATCGACTACAACGACAAGATC
EST: gi|71437159|gb|DR818209.1|DR818209
EST:     GAGATAAGCTGGCATTATGGACTAGGACTGCCAGCAATGAAGCTGTCCAG                         GTAAACATTGGCAAGAAGTGGAAGGATGTCATCGACTACAACGACAAGATC
genomic: GAGATAAGCTGGCATTATGGACTAGGACTGCCAGCAATGAAGCTGTCCAGgttggttttg ... tgtcatacagGTAAACATTGGCAAGAAGTGGAAGGATGTCATCGACTACAACGACAAGATC
EST: gi|76010903|gb|DT938073.1|DT938073
EST:     GAGATAAGCTGGCATTATGGACTAGGACTGCCAGCAATGAAGCTGTCCAG                         GTAAACATTGGCAAGAAGTGGAAGGATGTCATCGACTACAACGACAAGATC
genomic: GAGATAAGCTGGCATTATGGACTAGGACTGCCAGCAATGAAGCTGTCCAGgttggttttg ... tgtcatacagGTAAACATTGGCAAGAAGTGGAAGGATGTCATCGACTACAACGACAAGATC
EST: gi|50322672|gb|CO517798.1|CO517798
EST:     GAGATAAGCTGGCATTATGGACTAGGACTGCCAGCAATGAAGCTGTCCAG                         GTAAACATTGGCAAGAAGTGGAAGGATGTCATCGACTACAACGACAAGATC
genomic: GAGATAAGCTGGCATTATGGACTAGGACTGCCAGCAATGAAGCTGTCCAGgttggttttg ... tgtcatacagGTAAACATTGGCAAGAAGTGGAAGGATGTCATCGACTACAACGACAAGATC
EST: gi|32164823|gb|CD670141.1|CD670141
EST:     GAGATAAGCTGGCATTATGGACTAGGACTGCCAGCAATGAAGCTGTCCAG                         GTAAACATTGGCAAGAAGTGGAAGGATGTCATCGACTACAACGACAAGATC
genomic: GAGATAAGCTGGCATTATGGACTAGGACTGCCAGCAATGAAGCTGTCCAGgttggttttg ... tgtcatacagGTAAACATTGGCAAGAAGTGGAAGGATGTCATCGACTACAACGACAAGATC
EST: gi|71758459|gb|DR956396.1|DR956396
EST:     GAGATAAGCTGGCATTATGGACTAGGACTGCCAGCAATGAAGCTGTCCAG                         GTAAACATTGGCAAGAAGTGGAAGGATGTCATCGACTACAACGACAAGATC
genomic: GAGATAAGCTGGCATTATGGACTAGGACTGCCAGCAATGAAGCTGTCCAGgttggttttg ... tgtcatacagGTAAACATTGGCAAGAAGTGGAAGGATGTCATCGACTACAACGACAAGATC
EST: gi|18168337|gb|BM338177.1|BM338177
EST:     GAGATAAGCTGGCATTATGGACTAGGACTGCCAGCAATGAAGCTGTCCAG                         GTAAACATTGGCAAGAAGTGGAAGGATGTCATCGACTACAACGACAAGATC
genomic: GAGATAAGCTGGCATTATGGACTAGGACTGCCAGCAATGAAGCTGTCCAGgttggttttg ... tgtcatacagGTAAACATTGGCAAGAAGTGGAAGGATGTCATCGACTACAACGACAAGATC
EST: gi|31558353|gb|CD527565.1|CD527565
EST:     GAGATAAGCTGGCATTATGGACTAGGACTGCCAGCAATGAAGCTGTCCAG                         GTAAACATTGGCAAGAAGTGGAAGGATGTCATCGACTACAACGACAAGATC
genomic: GAGATAAGCTGGCATTATGGACTAGGACTGCCAGCAATGAAGCTGTCCAGgttggttttg ... tgtcatacagGTAAACATTGGCAAGAAGTGGAAGGATGTCATCGACTACAACGACAAGATC
EST: gi|31250144|gb|CD219168.1|CD219168
EST:     GAGATAAGCTGGCATTATGGACTAGGACTGCCAGCAATGAAGCTGTCCAG                         GTAAACATTGGCAAGAAGTAGAAGGATGTCATCGACTACAACGACAAGATC
genomic: GAGATAAGCTGGCATTATGGACTAGGACTGCCAGCAATGAAGCTGTCCAGgttggttttg ... tgtcatacagGTAAACATTGGCAAGAAGTGGAAGGATGTCATCGACTACAACGACAAGATC
EST: gi|32933632|gb|CF038444.1|CF038444
EST:     GAGATAAGCTGGCATTATGGACTAGGACTGCCAGCAATGAAGCTGTCCAG                         GTAAACATTGGCAAGAAGTGGAAGGATGTCATCGACTACAACGACAAGATC
genomic: GAGATAAGCTGGCATTATGGACTAGGACTGCCAGCAATGAAGCTGTCCAGgttggttttg ... tgtcatacagGTAAACATTGGCAAGAAGTGGAAGGATGTCATCGACTACAACGACAAGATC
EST: gi|16925812|gb|BM078880.1|BM078880
EST:     GAGATAAGCTGGCATTATGGACTAGGACTGCCAGCAATGAAGCTGTCCAG                         GTAAACATTGGCAAGAAGTGGAAGGATGTCATCGACTACAACGACAAGATC
genomic: GAGATAAGCTGGCATTATGGACTAGGACTGCCAGCAATGAAGCTGTCCAGgttggttttg ... tgtcatacagGTAAACATTGGCAAGAAGTGGAAGGATGTCATCGACTACAACGACAAGATC
EST: gi|22935572|gb|BU571847.1|BU571847
EST:     GAGATAAGCTGGCATTATGGACTAGGACTGCCAGCAATGAAGCTGTCCAG                         GTAAACATTGGCAAGAAGTGGAAGGATGTCATCGACTACAACGAC
genomic: GAGATAAGCTGGCATTATGGACTAGGACTGCCAGCAATGAAGCTGTCCAGgttggttttg ... tgtcatacagGTAAACATTGGCAAGAAGTGGAAGGATGTCATCGACTACAACGAC
EST: gi|91049925|gb|EB160343.1|EB160343
EST:     GAGATAAGCTGGCATTATGGACTAGGACTGCCAGCAATGAAGCTGTCCAG                         GTAAACATTGGCAAGAAGTGGAAGGATGTCATCGACTACAACGACAAGATC
genomic: GAGATAAGCTGGCATTATGGACTAGGACTGCCAGCAATGAAGCTGTCCAGgttggttttg ... tgtcatacagGTAAACATTGGCAAGAAGTGGAAGGATGTCATCGACTACAACGACAAGATC

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), 48 (downstream exon)
Score: 208

TGATGAAACAGAGGACATTTGTGGAATTGTTGCTAGTGTCCGTGCAAGAGGAGATAAGCTGGCATTATGGACTAGGACTGCCAGCAATGAAGCTGTCCAGgttggttttg ... tgtcatacagGTAAACATTGGCAAGAAGTGGAAGGATGTCATCGACTACAACGACAAGATCACGTACACTTTCCAT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 219

TGATGAAACAGAGGACATTTGTGGAATTGTTGCTAGTGTCCGTGCAAGAGGAGATAAGCTGGCATTATGGACTAGGACTGCCAGCAATGAAGCTGTCCAGgttggttttg ... tgtcatacagGTAAACATTGGCAAGAAGTGGAAGGATGTCATCGACTACAACGACAAGATCACGTACACTTTCCAT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 253

TGATGAAACAGAGGACATTTGTGGAATTGTTGCTAGTGTCCGTGCAAGAGGAGATAAGCTGGCATTATGGACTAGGACTGCCAGCAATGAAGCTGTCCAGgttggttttg ... tgtcatacagGTAAACATTGGCAAGAAGTGGAAGGATGTCATCGACTACAACGACAAGATCACGTACACTTTCCAT


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 166

TGATGAAACAGAGGACATTTGTGGAATTGTTGCTAGTGTCCGTGCAAGAGGAGATAAGCTGGCATTATGGACTAGGACTGCCAGCAATGAAGCTGTCCAGgttggttttg ... tgtcatacagGTAAACATTGGCAAGAAGTGGAAGGATGTCATCGACTACAACGACAAGATCACGTACACTTTCCAT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gagaatttctgtactgaccgcttcgtaatttttggcccattcctttgtcatacagGTAAACATTGGCAAGAAGTGGAAGGATGTCATCGACTACAACGACAAGATCACGTACACTTTCCAT
           tactgac  putative branch site (score: 166)
                                   cccattcctttgtc  putative PPT
                         taattttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gaacggaatgttcaaaagaagaggaaaacaaaccttttcctattggagaatttctgtactgaccgcttcgtaatttttggcccattcctttgtcatacagGTAAACATTGGCAAGAAGTGGAAGGATGTCATCGACTACAACGACAAGATCACGTACACTTTCCAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA
- - - - - - -aaaagaa
- - - - - - - - - - - - -aaacaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - tgtactg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ccgcttc