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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AAACATGGTTGACAAAAGGACAGCACTCGAGAATTTGGATATGATCCTATTGTGCCTTGATGAAATTGTTGATGGAGGgtaaatccttatcttactacatacatgatattagggcttcttttcttgttccctttattgtgtacatttattattcttcctttgctctgaaataatctga...

Basic information

species Zea mays
transcript GRMZM2G431350_T01
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G431350_T01 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os05g38610.1 (Oryza sativa), 5'ss of exon 4
AAACATGGTTGACAAAAGGACAGCACTCGAGAATTTGGATATGATCCTATTGTGCCTTGATGAAATTGTTGATGGAGGgtaaatccttatcttactacatacatgatattagggcttcttttctt-----gttc--cctttattgtgtacatttattattcttcctttgctctgaaataatctga
||| |  || |||||||| ||||||||||| ||| ||||| | |||||||||||||| |||||||||||||||||||||||||||||  ||| |||  ||     || ||     | ||||  ||     |||   | || || |    | ||||| ||   |  | ||||||  | ||||    
AAATAACGTCGACAAAAGAACAGCACTCGAAAATCTGGATCTCATCCTATTGTGCCTCGATGAAATTGTTGATGGAGGgtaaatcctagtctcactggatgtcaaatgttcttattcctttcgtttgtatgtttggctttcatggcacgc-tttataatcggttgtctgctct--agtaat----

upper sequence: GRMZM2G431350_T01 (Zea mays), 5'ss of exon 4
lower sequence: GLYMA15G13190.3 (Glycine max), 5'ss of exon 4
AAACATGGTTGACAAAAGGACAGCACTCGAGAATTTGGATATGATCCTATTGTGCCTTGATGAAATTGTTGATGGAGGgtaa-----atccttatcttactacatacatgatattagggcttcttttcttgttccctttattgtgtacatttat-tattcttcctttgctctgaaataatctga
|  ||  || ||||| | |  |||||| ||||| |||||| | || ||||||||| ||||||||||||||||||| |||||      || ||  || ||  | ||  ||    ||  |  || | |  |||||  |||   |   |    | ||  | |   |  || |||  | | ||     
AGGCAATGTAGACAAGAAGGAAGCACTAGAGAACTTGGATCTCATTCTATTGTGCATTGATGAAATTGTTGATGGCGGgtatgctatatgctattcatatgaaatttatctccttcag--ttgtgtgtttgtttgcttctctaaatcttctcatgcacttccctcttcctccaatacaaa----

upper sequence: GRMZM2G431350_T01 (Zea mays), 5'ss of exon 4
lower sequence: GLYMA13G42470.1 (Glycine max), 5'ss of exon 4
AAACATGGTTGACAAAAGGACAGCACTCGAGAATTTGGATATGATCCTATTGTGCCTTGATGAAATTGTTGATGGAGGgtaaatccttatcttactacatacatgatattagggcttcttttcttgttccctttattgtgtacatttattattcttcctttgctctgaaataatctga
 ||||  |||||||||||    || || || || |||||  | || || || ||||||||||| |||||||||||||||||  | | | | ||| ||  ||||   | |||    ||    |   ||     || |  | ||  ||    ||  |||||   |  ||||         
GAACAATGTTGACAAAAGAGAGGCGCTGGAAAACTTGGACCTCATTCTTTTATGCCTTGATGAGATTGTTGATGGAGGgta--tgcatctgttattagttacagtttgtta----tttgcattgcgtaaaagttttgatctattttctaaatatttcctc--ccttgaag--------

upper sequence: GRMZM2G431350_T01 (Zea mays), 5'ss of exon 4
lower sequence: GLYMA09G02270.3 (Glycine max), 5'ss of exon 4
AAACATGGTTGACAAAAGGACAGCACTCGAGAATTTGGATATGATCCTATTGTGCCTTGATGAAATTGTTGATGGAGGgtaaatccttatcttactacatacatgatattagggcttcttttcttgttcccttta--ttgtgtacatttattattcttcctttgctctgaaataatctga---
|  ||  || ||||| | |  |||||| ||||| |||||| | || ||||||||| | ||||||||||||||||| |||||     |     | |||   | |||| |||    |||||||  ||||     |||  || |  | || |  | ||   | |      ||    || ||     
AGGCAATGTGGACAAGAAGGAAGCACTAGAGAACTTGGATCTCATTCTATTGTGCATAGATGAAATTGTTGATGGCGGgtatgctata----tgctattcatatgaaatttat-cttctttagttgtgtttgttagcttctcaaaatcttctcttgcgcttcccacttgttccaacctacaaa

upper sequence: GRMZM2G431350_T01 (Zea mays), 5'ss of exon 4
lower sequence: Vv09s0002g01710.t01 (Vitis vinifera), 5'ss of exon 4
AAACATGGTTGACAAAAGGACAGCACTCGAGAATTTGGATATGATCCTATTGTGCCTTGATGAAATTGTTGATGGAGGgtaaatccttatcttactacataca-tgatattagggcttcttttcttgttccctttattgtgtacatttattattcttcctttgctctgaaataatctga
 ||||   ||||||| |||   ||||| ||||| |||||| | || ||  | ||||||||||| |||||||||||||||||     |   |||   |  | |  |  |  |      | |||     | |||||  ||    |      | |||     | | |||  |   | |  | 
GAACAACATTGACAAGAGGGAGGCACTTGAGAACTTGGATCTCATTCTCCTATGCCTTGATGAGATTGTTGATGGAGGgtatgcaatatgcttctcatgttctctcgtcctttaaaatatttcaaaatgcccttgtttacacatgaacttaatttaggatcttctcatagcaagtgcg-

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|211420227|gb|FL011433.1|FL011433
EST:     GAGAATTTGGATATGATCCTATTGTGCCTTGATGAAATTGTTGATGGAGG                         GATTGTACTTGAAACAGAAGGAAGAGAGATAGCTGAAAAGGTGTCTGGACA
genomic: GAGAATTTGGATATGATCCTATTGTGCCTTGATGAAATTGTTGATGGAGGgtaaatcctt ... gattacacagGATTGTACTTGAAACAGAAGGAAGAGAGATAGCTGAAAAGGTGTCTGGACA
EST: gi|32863613|gb|CF003295.1|CF003295
EST:     GAGAATTTGGATATGATCCTATTGTGCCTTGATGAAATTGTTGATGGAGG                         GATTGTACTTGAAACAGAAGGAAGAGAGATAGCTGA
genomic: GAGAATTTGGATATGATCCTATTGTGCCTTGATGAAATTGTTGATGGAGGgtaaatcctt ... gattacacagGATTGTACTTGAAACAGAAGGAAGAGAGATAGCTGA
EST: gi|22819983|gb|BU500073.1|BU500073
EST:     GAGAATTTGGATATGATCCTATTGTGCCTTGATGAAATTGTTGATGGAGG                         GATTGTACTTGAAACAGAAGGAAGAGAGATAGCTGAAAAGGTGTCTGGACA
genomic: GAGAATTTGGATATGATCCTATTGTGCCTTGATGAAATTGTTGATGGAGGgtaaatcctt ... gattacacagGATTGTACTTGAAACAGAAGGAAGAGAGATAGCTGAAAAGGTGTCTGGACA
EST: gi|22545780|gb|BU098154.1|BU098154
EST:     GAGAATTTGGATATGATCCTATTGTGCCTTGATGAAATTGTTGATGGAGG                         GATTGTACTTGAAACAGAAGGAAGAGAGATAGCTGAAAAGGTGTCTGGACA
genomic: GAGAATTTGGATATGATCCTATTGTGCCTTGATGAAATTGTTGATGGAGGgtaaatcctt ... gattacacagGATTGTACTTGAAACAGAAGGAAGAGAGATAGCTGAAAAGGTGTCTGGACA
EST: gi|30591528|gb|CD052418.1|CD052418
EST:     GAGAATTTGGATATGATCCTATTGTGCCTTGATGAAATTGTTGATGGAGG                         GATTGTACTTGAAACAGAAGGAAGAGAGATAGCTGAAAAGGTGTCTGGACA
genomic: GAGAATTTGGATATGATCCTATTGTGCCTTGATGAAATTGTTGATGGAGGgtaaatcctt ... gattacacagGATTGTACTTGAAACAGAAGGAAGAGAGATAGCTGAAAAGGTGTCTGGACA
EST: gi|211270446|gb|FL011426.1|FL011426
EST:     GAGAATTTGGATATGATCCTATTGTGCCTTGATGAAATTGTTGATGGAGG                         GATTGTACTTGAAACAGAAGGAAGAGAGATAGCTGAAAAGGTGTCTGGACA
genomic: GAGAATTTGGATATGATCCTATTGTGCCTTGATGAAATTGTTGATGGAGGgtaaatcctt ... gattacacagGATTGTACTTGAAACAGAAGGAAGAGAGATAGCTGAAAAGGTGTCTGGACA
EST: gi|71302986|gb|DR787604.1|DR787604
EST:     GAGAATTTGGATATGATCCTATTGTGCCTTGATGAAATTGTTGATGGAGG                         GATTGTACTTGAAACAGAAGGAAAAGAGATAGCTGAAAAGGTGTCTGGACA
genomic: GAGAATTTGGATATGATCCTATTGTGCCTTGATGAAATTGTTGATGGAGGgtaaatcctt ... gattacacagGATTGTACTTGAAACAGAAGGAAGAGAGATAGCTGAAAAGGTGTCTGGACA
EST: gi|6020321|gb|AW065249.1|AW065249
EST:     GAGAATTTGGATATGATCCTATTGTGCCTTGATGAAATTGTTGATGGAGG                         GATTGTACTTGAAACAGAAGGAAGAGAGATAGCTGAAAAGGTGTCTGGACA
genomic: GAGAATTTGGATATGATCCTATTGTGCCTTGATGAAATTGTTGATGGAGGgtaaatcctt ... gattacacagGATTGTACTTGAAACAGAAGGAAGAGAGATAGCTGAAAAGGTGTCTGGACA
EST: gi|86468241|gb|DY234611.1|DY234611
EST:     GAGAATTTGGATATGATCCTATTGTGCCTTGATGAAATTGTTGATGGAGG                         GATTGTACTTGAAACAGAAGGAAGAGAGATAGCTGAAAAGGTGTCT
genomic: GAGAATTTGGATATGATCCTATTGTGCCTTGATGAAATTGTTGATGGAGGgtaaatcctt ... gattacacagGATTGTACTTGAAACAGAAGGAAGAGAGATAGCTGAAAAGGTGTCT
EST: gi|37622066|gb|CF675119.1|CF675119
EST:     GAGAATTTGGATATGATCCTATTGTGCCTTGATGAAATTGTTGATGGAGG                         GATTGTACTTGAAACAGAAGGAAGAGAGATAGCTGAAAAGGTGTCTGGACA
genomic: GAGAATTTGGATATGATCCTATTGTGCCTTGATGAAATTGTTGATGGAGGgtaaatcctt ... gattacacagGATTGTACTTGAAACAGAAGGAAGAGAGATAGCTGAAAAGGTGTCTGGACA
EST: gi|30591531|gb|CD052420.1|CD052420
EST:     GAGAATTTGGATATGATCCTATTGTGCCTTGATGAAATTGTTGATGGAGG                         GATTGTACTTGAAACAGAAGGAAGAGAGATAGCTGAAAAGGTGTCTGGACA
genomic: GAGAATTTGGATATGATCCTATTGTGCCTTGATGAAATTGTTGATGGAGGgtaaatcctt ... gattacacagGATTGTACTTGAAACAGAAGGAAGAGAGATAGCTGAAAAGGTGTCTGGACA
EST: gi|211477577|gb|FL100777.1|FL100777
EST:     GAGAATTTGGATATGATCCTATTGTGCCTTGATGAAATTGTTGATGGAGG                         GATTGTACTTGAAACAGAAGGAAGAGAGATAGCTGAAAAGGTGTCTGGTCA
genomic: GAGAATTTGGATATGATCCTATTGTGCCTTGATGAAATTGTTGATGGAGGgtaaatcctt ... gattacacagGATTGTACTTGAAACAGAAGGAAGAGAGATAGCTGAAAAGGTGTCTGGACA
EST: gi|33093855|gb|CF053849.1|CF053849
EST:     GAGAATTTGGATATGATCCTATTGTGCCTTGATGAAATTGTTGATGGAGG                         GATTGTACTTGAAACAGAAGGAAGAGAGATAGCTGAAAA
genomic: GAGAATTTGGATATGATCCTATTGTGCCTTGATGAAATTGTTGATGGAGGgtaaatcctt ... gattacacagGATTGTACTTGAAACAGAAGGAAGAGAGATAGCTGAAAA
EST: gi|166543611|gb|EG303722.1|EG303722
EST:     ATTTGGATATGATCCTATTGTGCCTTGTATGAAATTGTTGATGGAGG                         GATTGTACTTGAAACAGAAGGAAGAGAGATAGCTGAAAAGGTGTCTGG
genomic: ATTTGGATATGATCCTATTGTGCCTTG-ATGAAATTGTTGATGGAGGgtaaatcctt ... gattacacagGATTGTACTTGAAACAGAAGGAAGAGAGATAGCTGAAAAGGTGTCTGG

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), 48 (downstream exon)
Score: 313

AAACATGGTTGACAAAAGGACAGCACTCGAGAATTTGGATATGATCCTATTGTGCCTTGATGAAATTGTTGATGGAGGgtaaatcctt ... gattacacagGATTGTACTTGAAACAGAAGGAAGAGAGATAGCTGAAAAGGTGTCTGGACATGGATTGGAGGGTGCTTCATCAGCTGAGCAG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 314

AAACATGGTTGACAAAAGGACAGCACTCGAGAATTTGGATATGATCCTATTGTGCCTTGATGAAATTGTTGATGGAGGgtaaatcctt ... gattacacagGATTGTACTTGAAACAGAAGGAAGAGAGATAGCTGAAAAGGTGTCTGGACATGGATTGGAGGGTGCTTCATCAGCTGAGCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 365

AAACATGGTTGACAAAAGGACAGCACTCGAGAATTTGGATATGATCCTATTGTGCCTTGATGAAATTGTTGATGGAGGgtaaatcctt ... gattacacagGATTGTACTTGAAACAGAAGGAAGAGAGATAGCTGAAAAGGTGTCTGGACATGGATTGGAGGGTGCTTCATCAGCTGAGCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 320

AAACATGGTTGACAAAAGGACAGCACTCGAGAATTTGGATATGATCCTATTGTGCCTTGATGAAATTGTTGATGGAGGgtaaatcctt ... gattacacagGATTGTACTTGAAACAGAAGGAAGAGAGATAGCTGAAAAGGTGTCTGGACATGGATTGGAGGGTGCTTCATCAGCTGAGCAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AAACATGGTTGACAAAAGGACAGCACTCGAGAATTTGGATATGATCCTATTGTGCCTTGATGAAATTGTTGATGGAGGgtaaatccttatcttactacatacatgatattagggcttcttttcttgttccctttattgtgtacatttattattcttcctttgctctgaaataatctga

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG