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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tcagccaaggccatcttgctttcaaggataagcttagggctctcagatccgtaatacctgaagtgccatattattttaacttgcaatattttgtatatagGTCATTGATCTGGCAACTTCTCTTGCAAAAGTTGCGGATGTGGATAGAAATCTTGGTAACGAAAGTACCGCAGTTGAGGGTTTTGAGGAAGCAATTCGAT

Basic information

species Zea mays
transcript GRMZM2G049672_T01
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G049672_T01 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os02g55200.2 (Oryza sativa), 3'ss of exon 6
----tcagccaaggccatcttgctttcaaggataagcttagggctctcagatccgtaatacctgaagtgccatattattttaacttgcaatattttgtatatagGTCATTGATCTGGCAACTTCTCTTGCAAAAGTTGCGGATGTGGATAGAAATCTTGGTAACGAAAGTACCGCAGTTGAGGGTTTTGAGGAAGCAATTCGAT
    |  |  | |       ||||     | | |  | ||    |||    |   |  | | | |  ||||    | |  | |  ||     ||||| ||||||||||||||| | |||||||||||||| |||||||||||||| |||||||||||||| |||||||| |  |||||||||||||||||||||||||||  ||
agattgtggtaggatttagctgctacatggaacagacata---ttcttgagtgtttt-tcctttagctgccgctatttcatgatctgtctacttttggatatagGTCATTGATGTAGCAACTTCTCTTGCCAAAGTTGCGGATGTCGATAGAAATCTTGGGAACGAAAGCATGGCAGTTGAGGGTTTTGAGGAAGCAATTAAAT

upper sequence: GRMZM2G049672_T01 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os01g01420.3 (Oryza sativa), 3'ss of exon 6
tcagccaaggccatcttgctttcaaggataagcttagggctctcagatccgtaatacctgaagtgccatattattt-taacttgcaatattttgtatatagGTCATTGATCTGGCAACTTCTCTTGCAAAAGTTGCGGATGTGGATAGAAATCTTGGTAACGAAAGTACCGCAGTTGAGGGTTTTGAGGAAGCAATTCGAT
|     |||    |  |    |  ||      | | |  |   || || | | |    |    |    |  | ||  | |  ||     || || ||||||||||||||| | |||||||||||||| |||||||||||||| |||||||||||||| |||||||| |  |||||||||||||||||||||||||||  ||
ttttgtaagattgtggtaggctttagctgctacatggaacagacatattcttga-gtgttttttcttttgctgttcatgatctgtctacttgtggatatagGTCATTGATGTAGCAACTTCTCTTGCCAAAGTTGCGGATGTCGATAGAAATCTTGGGAACGAAAGCATGGCAGTTGAGGGTTTTGAGGAAGCAATTAAAT

upper sequence: GRMZM2G049672_T01 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA06G47010.1 (Glycine max), 3'ss of exon 6
tcagccaaggccatcttgctttcaaggataagcttagggctctcagatccg-taatacctgaagtgccatattatt--ttaacttgcaatattttgtatatagGTCATTGATCTGGCAACTTCTCTTGCAAAAGTTGCGGATGTGGATAGAAATCTTGGTAACGAAAGTACCGCAGTTGAGGGTTTTGAGGAAGCAATTCGAT
 ||   ||    |  |||     || |   |   |||  |    |  |  | | |||    || |  ||| || ||  ||   ||  |||  ||| | | |||||  | ||  | ||    |||||||||||||||||||||||||| |||||||| ||  | ||||     ||   ||| || ||| | ||||| ||    |
-catgtaaa-taaggttgtacaaaatggccactgtagaacaagtatcttggcttatattgaaactaacatttttttcattgttttctaatgatttattt-tagGTGTTAGACGTTGCTGTCTCTCTTGCAAAAGTTGCGGATGTGGACAGAAATCTAGGGGATGAAAAGTTAGCTACTGATGGATTTCAAGAAGCCATAGACT

upper sequence: GRMZM2G049672_T01 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA04G15130.1 (Glycine max), 3'ss of exon 6
tcagccaaggccatcttgctttca-aggataagcttagggctctcagatccgtaa----tacctgaagtgccatattattttaacttgcaatattttgtatatagGTCATTGATCTGGCAACTTCTCTTGCAAAAGTTGCGGATGTGGATAGAAATCTTGGTAACGAAAGTACCGCAGTTGAGGGTTTTGAGGAAGCAATTCGAT
    | ||    |  | |   | | |  ||   |   |        | ||| ||     ||    || |  | | ||   ||   ||  |||  ||| | | |||||  | ||| | ||    |||||||| ||||||||||||||||| |||||||| ||  | ||||     ||    || || ||| | ||||| ||    |
----caaatattaggtggtccttacaaaattgccactgcagaacatgttccttagcttttattgaaattaacctttttcgttgttttctaatgatttattt-tagGTTTTAGATGTTGCTGTCTCTCTTGCGAAAGTTGCGGATGTGGACAGAAATCTAGGGGATGAAAAGTTAGCTACAGATGGATTTCAAGAAGCCATAGATT

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|60340202|gb|DN207175.1|DN207175
EST:     TGGATGTTCGCAGAAATGCAGTAAAAGAACACTCTGCTGTGGCTTCCCAG                         GTCATTGATCTAGCAACTTCTCTTGCAAAAGTTGCGGATGTGGATAGAAAT
genomic: TGGATGTTCGCAGAAATGCAGTAAAAGAACACTCTGCTGTGGCTTCCCAGgtaaattgta ... ttgtatatagGTCATTGATCTGGCAACTTCTCTTGCAAAAGTTGCGGATGTGGATAGAAAT
EST: gi|12972826|gb|BG268175.1|BG268175
EST:     TGGATGTTCGCAGAAATGCAGTAAAAGAACACTCTGCTGTGGCTTCCCAG                         GTCATTGATCTAGCAACTTCTCTTGCAAAAGTTGCGGATGTGGATAGAAAT
genomic: TGGATGTTCGCAGAAATGCAGTAAAAGAACACTCTGCTGTGGCTTCCCAGgtaaattgta ... ttgtatatagGTCATTGATCTGGCAACTTCTCTTGCAAAAGTTGCGGATGTGGATAGAAAT
EST: gi|149087898|gb|EE287177.2|EE287177
EST:     TGGATGTTCGCAGAAATGCAGTAAAAGAACACTCTGCTGTGGCTTCCCAG                         GTCATTGATCTGGCAACTTCTCTTGCAAAAGTTGCGGATGTGGATAGAAAT
genomic: TGGATGTTCGCAGAAATGCAGTAAAAGAACACTCTGCTGTGGCTTCCCAGgtaaattgta ... ttgtatatagGTCATTGATCTGGCAACTTCTCTTGCAAAAGTTGCGGATGTGGATAGAAAT
EST: gi|211393982|gb|FL446401.1|FL446401
EST:     TGGATGTTCGCAGAAATGCAGTAAAAGAACACTCTGCTGTGGCTTCCCAG                         GTCATTGATCTAGCAACTTCTCTTGCAAAAGTTGCGGATGTGGATAGAAAT
genomic: TGGATGTTCGCAGAAATGCAGTAAAAGAACACTCTGCTGTGGCTTCCCAGgtaaattgta ... ttgtatatagGTCATTGATCTGGCAACTTCTCTTGCAAAAGTTGCGGATGTGGATAGAAAT
EST: gi|78179829|gb|DV550202.1|DV550202
EST:     TGGATGTTCGCAGAAATGCAGTAAAAGAACACTCTGCTGTGGCTTCCCAG                         GTCATTGATCTAGCAACTTCTCTTGCAAAAGTTGCGGATGTGGATAGAAAT
genomic: TGGATGTTCGCAGAAATGCAGTAAAAGAACACTCTGCTGTGGCTTCCCAGgtaaattgta ... ttgtatatagGTCATTGATCTGGCAACTTCTCTTGCAAAAGTTGCGGATGTGGATAGAAAT
EST: gi|78025114|gb|DV493501.1|DV493501
EST:     TGGATGTTCGCAGAAATGCAGTAAAAGAACACTCTGCTGTGGCTTCCCAG                         GTCATTGATCTGGCAACTTCTCTTGCAAAAGTTGCGGATGTGGATAGAAAT
genomic: TGGATGTTCGCAGAAATGCAGTAAAAGAACACTCTGCTGTGGCTTCCCAGgtaaattgta ... ttgtatatagGTCATTGATCTGGCAACTTCTCTTGCAAAAGTTGCGGATGTGGATAGAAAT
EST: gi|13516136|gb|BG518412.1|BG518412
EST:     TGGCTTCCCAG                         GTCATTGATCTGGCAACTTCTCTTGCAAAAGTTGCGGATGTGGATAGAAAT
genomic: TGGCTTCCCAGgtaaattgta ... ttgtatatagGTCATTGATCTGGCAACTTCTCTTGCAAAAGTTGCGGATGTGGATAGAAAT
EST: gi|67021056|gb|CO449805.1|CO449805
EST:     TGGATGTTCGCAGAAATGCAGTAAAAGAACACTCTGCTGTGGCTTCCCAG                         GTCATTGATCTAGCAACTTCTCTTGCAAAAGTTGCGGATGTGGATAGAAAT
genomic: TGGATGTTCGCAGAAATGCAGTAAAAGAACACTCTGCTGTGGCTTCCCAGgtaaattgta ... ttgtatatagGTCATTGATCTGGCAACTTCTCTTGCAAAAGTTGCGGATGTGGATAGAAAT
EST: gi|148999090|gb|EE028420.2|EE028420
EST:     TGGATGTTCGCAGAAATGCAGTAAAAGAACACTCTGCTGTGGCTTCCCAG                         GTCATTGATCTGGCAACTTCTCTTGCAAAAGTTGCGGATGTGGATAGAAAT
genomic: TGGATGTTCGCAGAAATGCAGTAAAAGAACACTCTGCTGTGGCTTCCCAGgtaaattgta ... ttgtatatagGTCATTGATCTGGCAACTTCTCTTGCAAAAGTTGCGGATGTGGATAGAAAT
EST: gi|32863820|gb|CF003502.1|CF003502
EST:     TGGATGTTCGCAGAAATGCAGTAAAAGAACACTCTGCTGTGGCTTCCCAG                         GTCATTGATCTAGCAACTTCTCTTGCAAAAGTTGCGGATGTGGATAGAAAT
genomic: TGGATGTTCGCAGAAATGCAGTAAAAGAACACTCTGCTGTGGCTTCCCAGgtaaattgta ... ttgtatatagGTCATTGATCTGGCAACTTCTCTTGCAAAAGTTGCGGATGTGGATAGAAAT
EST: gi|148958312|gb|EC904534.2|EC904534
EST:     TGGATGTTCGCAGAAATGCAGTAAAAGAACACTCTGCTGTGGCTTCCCAG                         GTCATTGATCTGGCAACTTCTCTTGCAAAAGTTGCGGATGTGGATAGAAAT
genomic: TGGATGTTCGCAGAAATGCAGTAAAAGAACACTCTGCTGTGGCTTCCCAGgtaaattgta ... ttgtatatagGTCATTGATCTGGCAACTTCTCTTGCAAAAGTTGCGGATGTGGATAGAAAT
EST: gi|149051662|gb|EE155775.2|EE155775
EST:     TGGATGTTCGCAGAAATGCAGTAAAAGAACACTCTGCTGTGGCTTCCCAG                         GTCATTGATCTGGCAACTTCTCTTGCAAAAGTTGCGGATGTGGATAGAAAT
genomic: TGGATGTTCGCAGAAATGCAGTAAAAGAACACTCTGCTGTGGCTTCCCAGgtaaattgta ... ttgtatatagGTCATTGATCTGGCAACTTCTCTTGCAAAAGTTGCGGATGTGGATAGAAAT
EST: gi|13150752|gb|BG321074.1|BG321074
EST:     TGGATGTTCGCAGAAATGCAGTAAAAGAACACTCTGCTGTGGCTTCCCAG                         GTCATTGATCTAGCAACTTCTCTTGCAAAAGTTGCGGATGTGGATAGAAAT
genomic: TGGATGTTCGCAGAAATGCAGTAAAAGAACACTCTGCTGTGGCTTCCCAGgtaaattgta ... ttgtatatagGTCATTGATCTGGCAACTTCTCTTGCAAAAGTTGCGGATGTGGATAGAAAT
EST: gi|33094944|gb|CF054938.1|CF054938
EST:     TGGATGTTCGCAGAAATGCAGTAAAAGAACACTCTGCTGTGGCTTCCCAG                         GTCATTGATCTAGCAACTTCTCTTGCAAAAGTTGCGGATGTGGATAGAAAT
genomic: TGGATGTTCGCAGAAATGCAGTAAAAGAACACTCTGCTGTGGCTTCCCAGgtaaattgta ... ttgtatatagGTCATTGATCTGGCAACTTCTCTTGCAAAAGTTGCGGATGTGGATAGAAAT
EST: gi|18655055|gb|BM499860.1|BM499860
EST:     TGGATGTTCGCAGAAATGCAGTAAAAGAACACTCTGCTGTGGCTTCCCAG                         GTCATTGATCTAGCAACTTCTCTTGCAAAAGTTGCGGATGTGGATAGAAAT
genomic: TGGATGTTCGCAGAAATGCAGTAAAAGAACACTCTGCTGTGGCTTCCCAGgtaaattgta ... ttgtatatagGTCATTGATCTGGCAACTTCTCTTGCAAAAGTTGCGGATGTGGATAGAAAT
EST: gi|22490004|gb|BU049927.1|BU049927
EST:     TGGATGTTCGCAGAAATGCAGTAAAAGAACACTCTGCTGTGGCTTCCCAG                         GTCATTGATCTAGCAACTTCTCTTGCAAAAGTTGCGGATGTGGATAGAAAT
genomic: TGGATGTTCGCAGAAATGCAGTAAAAGAACACTCTGCTGTGGCTTCCCAGgtaaattgta ... ttgtatatagGTCATTGATCTGGCAACTTCTCTTGCAAAAGTTGCGGATGTGGATAGAAAT
EST: gi|211234748|gb|FL433592.1|FL433592
EST:     TGGATGTTCGCAGAAATGCAGTAAAAGAACACTCTGCTGTGGCTTCCCAG                         GTCATTGATCTAGCAACTTCTCTTGCAAAAGTTGCGGATGTGGATAGAAAT
genomic: TGGATGTTCGCAGAAATGCAGTAAAAGAACACTCTGCTGTGGCTTCCCAGgtaaattgta ... ttgtatatagGTCATTGATCTGGCAACTTCTCTTGCAAAAGTTGCGGATGTGGATAGAAAT
EST: gi|6022117|gb|AW067045.1|AW067045
EST:     TGGATGTTCGCAGAAATGCAGTAAAAGAACACTCTGCTGTGGCTTCCCAG                         GTCATTGATCTGGCAACTTCTCTTGCAAAAGTTGCGGATGTGGATAGAAAT
genomic: TGGATGTTCGCAGAAATGCAGTAAAAGAACACTCTGCTGTGGCTTCCCAGgtaaattgta ... ttgtatatagGTCATTGATCTGGCAACTTCTCTTGCAAAAGTTGCGGATGTGGATAGAAAT
EST: gi|32909333|gb|CF014145.1|CF014145
EST:     TGGATGTTCGCAGAAATGCAGTAAAAGAACACTCTGCTGTGGCTTCCCAG                         GTCATTGATCTAGCAACTTCTCTTGCAAAAGTTGCGGATGTGGATAGAAAT
genomic: TGGATGTTCGCAGAAATGCAGTAAAAGAACACTCTGCTGTGGCTTCCCAGgtaaattgta ... ttgtatatagGTCATTGATCTGGCAACTTCTCTTGCAAAAGTTGCGGATGTGGATAGAAAT
EST: gi|14244109|gb|BG841797.2|BG841797
EST:     TGGATGTTCGCAGAAATGCAGTAAAAGAACACTCTGCTGTGGCTTCCCAG                         GTCATTGATCTGGCAACTTCTCTTGCAAAAGTTGCGGATGTGGATAGAAAT
genomic: TGGATGTTCGCAGAAATGCAGTAAAAGAACACTCTGCTGTGGCTTCCCAGgtaaattgta ... ttgtatatagGTCATTGATCTGGCAACTTCTCTTGCAAAAGTTGCGGATGTGGATAGAAAT
EST: gi|83278529|gb|DV942537.1|DV942537
EST:     TGGATGTTCGCAGAAATGCAGTAAAAGAACACTCTGCTGTGGCTTCCCAG                         GTCATTGATCTAGCAACTTCTCTTGCAAAAGTTGCGGATGTGGATAGAAAT
genomic: TGGATGTTCGCAGAAATGCAGTAAAAGAACACTCTGCTGTGGCTTCCCAGgtaaattgta ... ttgtatatagGTCATTGATCTGGCAACTTCTCTTGCAAAAGTTGCGGATGTGGATAGAAAT
EST: gi|32909332|gb|CF014144.1|CF014144
EST:     TGGATGTTCGCAGAAATGCAGTAAAAGAACACTCTGCTGTGGCTTCCCAG                         GTCATTGATCTAGCAACTTCTCTTGCAAAAGTTGCGGATGTGGATAGAAAT
genomic: TGGATGTTCGCAGAAATGCAGTAAAAGAACACTCTGCTGTGGCTTCCCAGgtaaattgta ... ttgtatatagGTCATTGATCTGGCAACTTCTCTTGCAAAAGTTGCGGATGTGGATAGAAAT
EST: gi|16925308|gb|BM078376.1|BM078376
EST:     TGGATGTTCGCAGAAATGCAGTAAAAGAACACTCTGCTGTGGCTTCCCAG                         GTCATTGATCTGGCAACTTCTCTTGCAAAAGTTGCGGATGTGGATAGAAAT
genomic: TGGATGTTCGCAGAAATGCAGTAAAAGAACACTCTGCTGTGGCTTCCCAGgtaaattgta ... ttgtatatagGTCATTGATCTGGCAACTTCTCTTGCAAAAGTTGCGGATGTGGATAGAAAT

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), 49 (downstream exon)
Score: 150

CTACTATGATGGCGACCTCCAATCTGCAAGAAACTATTATGCCCGTTCATTGGATGTTCGCAGAAATGCAGTAAAAGAACACTCTGCTGTGGCTTCCCAGgtaaattgta ... ttgtatatagGTCATTGATCTGGCAACTTCTCTTGCAAAAGTTGCGGATGTGGATAGAAATCTTGGTAACGAAAGTACCGCAGTTGAGGGTTTTGAGGAAGCAATTCGAT


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 162

CTACTATGATGGCGACCTCCAATCTGCAAGAAACTATTATGCCCGTTCATTGGATGTTCGCAGAAATGCAGTAAAAGAACACTCTGCTGTGGCTTCCCAGgtaaattgta ... ttgtatatagGTCATTGATCTGGCAACTTCTCTTGCAAAAGTTGCGGATGTGGATAGAAATCTTGGTAACGAAAGTACCGCAGTTGAGGGTTTTGAGGAAGCAATTCGAT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 137

CTACTATGATGGCGACCTCCAATCTGCAAGAAACTATTATGCCCGTTCATTGGATGTTCGCAGAAATGCAGTAAAAGAACACTCTGCTGTGGCTTCCCAGgtaaattgta ... ttgtatatagGTCATTGATCTGGCAACTTCTCTTGCAAAAGTTGCGGATGTGGATAGAAATCTTGGTAACGAAAGTACCGCAGTTGAGGGTTTTGAGGAAGCAATTCGAT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 197

CTACTATGATGGCGACCTCCAATCTGCAAGAAACTATTATGCCCGTTCATTGGATGTTCGCAGAAATGCAGTAAAAGAACACTCTGCTGTGGCTTCCCAGgtaaattgta ... ttgtatatagGTCATTGATCTGGCAACTTCTCTTGCAAAAGTTGCGGATGTGGATAGAAATCTTGGTAACGAAAGTACCGCAGTTGAGGGTTTTGAGGAAGCAATTCGAT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gatccgtaatacctgaagtgccatattattttaacttgcaatattttgtatatagGTCATTGATCTGGCAACTTCTCTTGCAAAAGTTGCGGATGTGGATAGAAATCTTGGTAACGAAAGTACCGCAGTTGAGGGTTTTGAGGAAGCAATTCGAT
                            ttttaac  putative branch site (score: 197)
                      atattattttaacttg  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tcagccaaggccatcttgctttcaaggataagcttagggctctcagatccgtaatacctgaagtgccatattattttaacttgcaatattttgtatatagGTCATTGATCTGGCAACTTCTCTTGCAAAAGTTGCGGATGTGGATAGAAATCTTGGTAACGAAAGTACCGCAGTTGAGGGTTTTGAGGAAGCAATTCGAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
tcagcca
- - - - - - - - tgctttc
- - - - - - - - - - - - - - - - - - - - - - - - - - - -acctgaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgccata
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - acttgca