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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATGCAATGTTAAGATTGCAGATTTTGGCTTAAGTAATGTTATGCGGGATGGTCATTTTCTGAAGACAAGTTGTGGTAGCCCAAATTATGCTGCTCCTGAGgtaagctttctataataggtcaaagatataaagaggacccattagatcagtatggccgtatttcctacccctttgttggcaggcagtacagtatccttttattttctgcag

Basic information

species Zea mays
transcript GRMZM2G180704_T01
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G180704_T01 (Zea mays), 5'ss of exon 4
lower sequence: GLYMA18G49770.1 (Glycine max), 5'ss of exon 5
ATGCAATGTTAAGATTGCAGATTTTGGCTTAAGTAATGTTATGCGGGATGGTCATTTTCTGAAGACAAGTTGTGGTAGCCCAAATTATGCTGCTCCTGAGgtaagctttctataataggtcaaagata--taaagaggacccattagatcagtatggccgtatttcctacccctttgttggcaggcagtacagtatccttttattttctgcag
||| ||||| |||||||| ||||||||||| || || | ||||| |||||||| ||||| || ||||||||||| ||||| || ||||| ||||||||||| | | | | | | ||| || | ||||| || | | || || || || ||| | ||| || ||||
ATGTAATGTCAAGATTGCTGATTTTGGCTTGAGCAACATCATGCGTGATGGTCACTTTCTTAAAACAAGTTGTGGAAGCCCTAACTATGCAGCTCCTGAGgtttgtaatggaatacacggcaacaattattgttgaggatatat-atgtgtgtgtgtgtgtcttggttacacttttt----catttttcacag--------------------

upper sequence: GRMZM2G180704_T01 (Zea mays), 5'ss of exon 4
lower sequence: GLYMA08G26180.1 (Glycine max), 5'ss of exon 4
ATGCAATGTTAAGATTGCAGATTTTGGCTTAAGTAATGTTATGCGGGATGGTCATTTTCTGAAGACAAGTTGTGGTAGCCCAAATTATGCTGCTCCTGAGgtaagctttctataataggtcaaagatataaagaggacccattagatcagtatggccgtatttcctacccctttgttggcaggcagta-cagtatccttttattttctgcag
||| ||||| |||||||| ||||||||||| || || | ||||| ||||| || ||||| || ||||||||||| ||||| || ||||| ||||||||||| | |||| | || | || || | ||| | | || || ||| | | | | || | | | ||| ||||| |||
ATGTAATGTCAAGATTGCTGATTTTGGCTTGAGCAACATCATGCGTGATGGCCACTTTCTTAAAACAAGTTGTGGAAGCCCTAACTATGCAGCTCCTGAGgt-------ttgtaatgg----aatacatggcgaaaatt-att-gttgaggatatatatatattgtctcttgtgattcatatttcttggttacactttttcatttttcacag

upper sequence: GRMZM2G180704_T01 (Zea mays), 5'ss of exon 4
lower sequence: GLYMA13G05700.1 (Glycine max), 5'ss of exon 4
ATGCAATGTTAAGATTGCAGATTTTGGCTTAAGTAATGTTATGCGGGATGGTCATTTTCTGAAGACAAGTTGTGGTAGCCCAAATTATGCTGCTCCTGAGgtaagctttctataataggtcaaagatataaagaggacccattag-atcagtatggccgtatttcctacccctttgttggcaggcagtacagt-atccttttattttctgcag----------------------------
|| || | |||||||| |||||||| || || || | ||||| |||||||| ||||| |||||||||||||| ||||| |||||||| ||||| ||||| | || | | || | ||| |||| | | ||| | | | || | || | | || | |||| | | | || | | |
ATTTAACATCAAGATTGCTGATTTTGGGTTGAGCAACATCATGCGTGATGGTCACTTTCTTAAGACAAGTTGTGGAAGCCCTAATTATGCGGCTCCAGAGgtttgtaaataattaaattgtaacggaataggatattattattaatgttattattattat-tattatatcactacttctg-agactttacatttacctccttgtgattaataaatcaaggataaactgttgtttttcacag

upper sequence: GRMZM2G180704_T01 (Zea mays), 5'ss of exon 4
lower sequence: AT3G01090.2 (Arabidopsis thaliana), 5'ss of exon 4
ATGCAATGTTAAGATTGCAGATTTTGGCTTAAGTAATGTTATGCGGGATGGTCATTTTCTGAAGACAAGTTGTGGTAGCCCAAATTATGCTGCTCCTGAGgtaagctttctataataggtcaaagatataaagaggacccattagatcagtatggccgtatttcctacccctttgttggcaggcagtacagtatccttttattttctgcag
||||||||| |||||||| ||||||||| | || || | ||||| |||||||||||| |||||||||||||||| || ||||||||||| ||||| |||||||| | | ||| || | | || || || | || | || | | || | | | | || | || ||| |
ATGCAATGTAAAGATTGCTGATTTTGGCCTGAGCAACATAATGCGAGATGGTCATTTTTTGAAGACAAGTTGTGGAAGTCCAAATTATGCCGCTCCAGAGgtaagtgcttcagccc---tcaggtatctgaggaatact------ataattaggcttgtttcaaatgataggttatagtcgagatctataa-attgtttcag---------

upper sequence: GRMZM2G180704_T01 (Zea mays), 5'ss of exon 4
lower sequence: AT3G29160.2 (Arabidopsis thaliana), 5'ss of exon 4
ATGCAATGTTAAGATTGCAGATTTTGGCTTAAGTAATGTTATGCGGGATGGTCATTTTCTGAAGACAAGTTGTGGTAGCCCAAATTATGCTGCTCCTGAGgtaagctttctataataggtcaaagatataaagaggacccattagatcagtatggccgtatttcctacccctttgttggcaggcagtacagtatccttttattttctgcag
|| ||| ||||||||||||| ||||| || ||||||||||||||||||||||||||||| ||||| |||||||| ||||| || || |||||||| |||||| |||| | |||| || | | || | | | || | | | || | | ||| | || | || | | || || ||
GTGTAATATTAAGATTGCAGACTTTGGGTTGAGTAATGTTATGCGGGATGGTCATTTTCTAAAGACGAGTTGTGGAAGCCCCAACTACGCTGCTCCCGAGgta-------tatagtttagtaaagttactgaattgtt---tttcacctatgtgactatgtctcgtttctctt-----atgagt-gtcttatctcttacttcttgttgtag

upper sequence: GRMZM2G180704_T01 (Zea mays), 5'ss of exon 4
lower sequence: AT5G39440.1 (Arabidopsis thaliana), 5'ss of exon 3
ATGCAATGTTAAGATTGCAGATTTTGGCTTAAGTAATGTTATGCGGGATGGTCATTTTCTGAAGACAAGTTGTGGTAGCCCAAATTATGCTGCTCCTGAGgtaagctttctataataggtcaaagatataaagaggacccattagatcagtatggccgtatttcctacccctttgttggcaggcagtacagtatccttttattttctgcag
|||||| | ||||||| || ||||| || |||||||| |||| |||||||||||| | ||||| |||||||| ||||| |||||||||||||| |||||| ||| || | || |||| ||| || | | ||| ||| | | | || | | | || |||
ATGCAACATAAAGATTGTTGACTTTGGATTGAGTAATGTCATGCATGATGGTCATTTTTTAAAGACTAGTTGTGGAAGCCCTAATTATGCTGCTCCAGAGgta---------taagagattaac-atattcttcatttttatttcatgaatttggatatatatttgaagtatcaattactcacacctgaaacttatttatatag-------

upper sequence: GRMZM2G180704_T01 (Zea mays), 5'ss of exon 4
lower sequence: Vv14s0108g01230.t01 (Vitis vinifera), 5'ss of exon 4
ATGCAATGTTAAGATTGCAGATTTTGGCTTAAGTAATGTTATGCGGGATGGTCATTTTCTGAAGACAAGTTGTGGTAGCCCAAATTATGCTGCTCCTGAGgtaagctttctataataggtcaaagatataaagaggacccatt--------agatcagtatggccgtatttcctacccctttgttggcaggcagtacagtatcc----ttttattttctgcag----------
||||||||| |||||||| |||||||| ||||||||| | ||| | |||||||||||| |||||||||||||||| ||||||||||||||||| || |||||||| | | | | | || ||| | | | ||| ||| | | | || || ||| | || || | | | | || || || || ||
ATGCAATGTGAAGATTGCTGATTTTGGTTTAAGTAATATCATGAGAGATGGTCATTTTTTGAAGACAAGTTGTGGAAGCCCAAATTATGCTGCCCCAGAGgtaaggagtttgcagcat-tataatataagacaattcctaatttttggttgagagatgagttacaatactttctaata-tatgatgataatggttgaaatttctaaggttctaattagtgtcccattttatag

upper sequence: GRMZM2G180704_T01 (Zea mays), 5'ss of exon 4
lower sequence: Vv08s0040g00720.t01 (Vitis vinifera), 5'ss of exon 5
ATGCAATGTTAAGATTGCAGATTTTGGCTTAAGTAATGTTATGCGGGATGGTCATTTTCTGAAGACAAGTTGTGGTAGCCCAAATTATGCTGCTCCTGAGgtaagctttctataataggtcaaa--gatataaagaggacccattagatca-gtatggccgtatttcctacccctttgttggcaggcagtacagtatccttttattttctgcag
| ||||||| || ||||||| ||||| | || ||||| ||||| |||||||||||||| || ||||| ||||| || |||||||||||||||||||||||| | |||||| | |||| | || || | | | || | | | | | | | || |||
ACGCAATGTCAAAGTTGCAGACTTTGGACTCAGCAATGTGATGCGTGATGGTCATTTTCTCAAAACAAGCTGTGGAAGTCCAAATTATGCTGCTCCTGAGgta------------tgggtcaacttgttatataagttgccaatgaacttgtgaataattatgctctgtgtacaatgaaatactgcttgtgcag--------------------

upper sequence: GRMZM2G180704_T01 (Zea mays), 5'ss of exon 4
lower sequence: PP1S28_12V6.1 (Physcomitrella patens), 5'ss of exon 3
ATGCAATGTTAAGATTGCAGATTTTGGCTTAAGTAATGTTATGCGGGATGGTCATTTTCTGAAGACAAGTTGTGGTAGCCCAAATTATGCTGCTCCTGAGgtaa-gctttcta--taataggtcaaa--gatataaagaggacccattagatcagtatggc-cgtatttcctacccctttgttggcaggcagtacagtatccttttattttctgcag-----------------------------------------------
| || || |||||||| |||||||| ||| ||||||||| |||| |||||||| || || || || ||||| || ||||||||||||||||| ||||| ||| | | | || | || | | | | | | | | || | | | |||| || |||||| | | | || | | |||||||
GTCTAACGTCAAGATTGCTGATTTTGGGTTATCCAATGTTATGAGGGACGGTCATTTCCTCAAAACTAGCTGTGGAAGTCCAAATTATGCTGCTCCAGAGgttttgctctatgcctgattgccttgtttgacactgttttaattcgtcatgtgattgtgtcacatgtttctgttttctgtgttgggtgcctgaaccaagttgtag-gttttctgtgcccggacacactcctgcttgttgactgttgatattgttgaacatgcag

upper sequence: GRMZM2G180704_T01 (Zea mays), 5'ss of exon 4
lower sequence: PP1S7_365V6.1 (Physcomitrella patens), 5'ss of exon 3
ATGCAATGTTAAGATTGCAGATTTTGGCTTAAGTAATGTTATGCGGGATGGTCATTTTCTGAAGACAAGTTGTGGTAGCCCAAATTATGCTGCTCCTGAGgtaagctttc-tataataggtcaaagatataaagaggacccattagatcagtatggccgtatttcctacccctttgttggcaggcagtacagtatccttttattttctgcag
||| || || ||||| || ||||| || | ||| ||||| |||||||||| ||||| || || ||||| || ||||| |||||||||||||| ||||| | | | | | | |||| | | | | | | | | || | | | | | | || ||||||
ATGGAACGTCAAGATAGCTGATTTCGGACTGTCCAATATTATGAGGGATGGTCACTTTCTCAAAACTAGTTGCGGAAGCCCCAATTATGCTGCTCCAGAGgttttcctccatgccttttcctttaaatatgacaaccttctctgatactactttgtatatgatgtgcttctgatattaaactttagataaagtatctcag------------

upper sequence: GRMZM2G180704_T01 (Zea mays), 5'ss of exon 4
lower sequence: EFJ35371 (Selaginella moellendorffii), 5'ss of exon 3
ATGCAATGTTAAGATTGCAGATTTTGGCTTAAGTAATGTTATGCGGGATGGTCATTTTCTGAAGACAAGTTGTGGTAGCCCAAATTATGCTGCTCCTGAGgtaagctttctataataggtcaaagatataaagaggacccattagatcagtatggccgtatttcctacccctttgttggcaggcagtacagtatccttttattttctgcag
|||||||| |||||||| || |||||||| |||||| | ||||| ||||| || |||||||| || || ||||| || ||||| ||||| ||||| ||||||||||| | | || |||| | || ||||
GTGCAATGTGAAGATTGCGGACTTTGGCTTGAGTAATATCATGCGAGATGGACACTTTCTGAAAACGAGCTGTGGAAGTCCAAACTATGCCGCTCCAGAGgtaagcttcgactttcttttttcctctagaaagccttttcctt---tcag-------------------------------------------------------------

upper sequence: GRMZM2G180704_T01 (Zea mays), 5'ss of exon 4
lower sequence: EFJ10631 (Selaginella moellendorffii), 5'ss of exon 4
ATGCAATGTTAAGATTGCAGATTTTGGCTTAAGTAATGTTATGCGGGATGGTCATTTTCTGAAGACAAGTTGTGGTAGCCCAAATTATGCTGCTCCTGAGgtaagctttctataataggtcaaagatataaagaggacccattagatcagtatggccgtatttcctacccctttgttggcaggcagtacagtatccttttattttctgcag
|||||||| |||||||| || ||||||||||||||| | ||||| ||||| || |||||||| || || ||||| || ||||| ||||| ||||| ||||||||||| | | | | | | | | | | ||||
GTGCAATGTGAAGATTGCGGACTTTGGCTTAAGTAATATCATGCGAGATGGACACTTTCTGAAAACGAGCTGTGGAAGTCCAAACTATGCCGCTCCAGAGgtaagctt-cgacatt--cttttttcctctagaaagccttttcctttcag-------------------------------------------------------------

upper sequence: GRMZM2G180704_T01 (Zea mays), 5'ss of exon 4
lower sequence: EFJ17922 (Selaginella moellendorffii), 5'ss of exon 3
ATGCAATGTTAAGATTGCAGATTTTGGCTTAAGTAATGTTATGCGGGATGGTCATTTTCTGAAGACAAGTTGTGGTAGCCCAAATTATGCTGCTCCTGAGgtaagctttctataataggtcaaagatataaagaggacccattagatcagtatggccgtatttcctacccctttgttggcaggcagtacagtatccttttattttctgcag
||||| ||| ||||| || ||||||||| | || || ||||||| || ||||| |||||||| ||||| ||||| || || || ||||||||||| ||||| || | | ||| || | | | | | | | | | || |||| | |
ATGCAGTGTCAAGATCGCGGATTTTGGCCTGAGCAACATTATGCGAGACGGTCACTTTCTGAAAACAAGCTGTGGAAGTCCGAACTATGCTGCTCCAGAGgtcagtatatcaggataagt------tttgtcataggctcgtcattctaa----gttgtctttctcaatcacag-------------------------------------

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|71768950|gb|DR966887.1|DR966887
EST:     GTCATTTTCTGAAGACAAGTTGTGGTAGCCCAAATTATGCTGCTCCTGAG                         GTGATATCTGGTAAACTATATGCTGGACCTGAAGTTGATGTGTGGAGCTGT
genomic: GTCATTTTCTGAAGACAAGTTGTGGTAGCCCAAATTATGCTGCTCCTGAGgtaagctttc ... ttttctgcagGTGATATCTGGTAAACTATATGCTGGACCTGAAGTTGATGTGTGGAGCTGT
EST: gi|211439527|gb|FL064919.1|FL064919
EST:     TCATTTTCTGAAGACAAGTTGTGGTAGCCCAAATTATGCTGCTCCTGGAG                         -TGATATCTGGGTAA-CTATATGCTGGACCTGAAGTTGATGTGTGGAGCT
genomic: TCATTTTCTGAAGACAAGTTGTGGTAGCCCAAATTATGCTGCTCCTG-AGgtaagctttc ... ttttctgcagGTGATATCTGG-TAAACTATATGCTGGACCTGAAGTTGATGTGTGGAGCT
EST: gi|148969836|gb|EE020728.2|EE020728
EST:     GTCATTTTCTGAAGACAAGTTGTGGTAGCCCAAATTATGCTGCTCCTGAG                         GTGATATCTGGTAAACTATATGCTGGACCTGAAGTTGATGTGTGGAGCTGT
genomic: GTCATTTTCTGAAGACAAGTTGTGGTAGCCCAAATTATGCTGCTCCTGAGgtaagctttc ... ttttctgcagGTGATATCTGGTAAACTATATGCTGGACCTGAAGTTGATGTGTGGAGCTGT
EST: gi|149088708|gb|EE177828.2|EE177828
EST:     GTCATTTTCTGAAGACAAGTTGTGGTAGCCCAAATTATGCTGCTCCTGAG                         GTGATATCTGGTAAACTATATGCTGGACCTGAAGTTGATGTGTGGAGCTGT
genomic: GTCATTTTCTGAAGACAAGTTGTGGTAGCCCAAATTATGCTGCTCCTGAGgtaagctttc ... ttttctgcagGTGATATCTGGTAAACTATATGCTGGACCTGAAGTTGATGTGTGGAGCTGT
EST: gi|149088317|gb|EE177414.2|EE177414
EST:     GTCATTTTCTGAAGACAAGTTGTGGTAGCCCAAATTATGCTGCTCCTGAG                         GTGATATCTGGTAAACTATATGCTGGACCTGAAGTTGATGTGTGGAGCTGT
genomic: GTCATTTTCTGAAGACAAGTTGTGGTAGCCCAAATTATGCTGCTCCTGAGgtaagctttc ... ttttctgcagGTGATATCTGGTAAACTATATGCTGGACCTGAAGTTGATGTGTGGAGCTGT
EST: gi|211006231|gb|FL064937.1|FL064937
EST:     GTCATTTTCTGAAGACAAGTTGTGGTAGCCCAAAT-ATGCTGCTCCTGAG                         GTGATATCTGGTAAACTATATGCTGGACCTGAAAGT-GATGTGT
genomic: GTCATTTTCTGAAGACAAGTTGTGGTAGCCCAAATTATGCTGCTCCTGAGgtaagctttc ... ttttctgcagGTGATATCTGGTAAACTATATGCTGGACCTGAA-GTTGATGTGT
EST: gi|148974739|gb|EE025550.2|EE025550
EST:     GTCATTTTCTGAAGACAAGTTGTGGTAGCCCAAATTATGCTGCTCCTGAG                         GTGATATCTGGTAAACTATATGCTGGACCTGAAGTTGATGTGTGGAGCTGT
genomic: GTCATTTTCTGAAGACAAGTTGTGGTAGCCCAAATTATGCTGCTCCTGAGgtaagctttc ... ttttctgcagGTGATATCTGGTAAACTATATGCTGGACCTGAAGTTGATGTGTGGAGCTGT
EST: gi|211324790|gb|FL345978.1|FL345978
EST:     GTCATTTTCTGAAGACAAGTTGTGGTAGCCCAAATTATGCTGCTCCTGAG                         GTGATATCTGGTAAACTATATGCTGGACCTGAAGTTGATGTGTGGAGCTGT
genomic: GTCATTTTCTGAAGACAAGTTGTGGTAGCCCAAATTATGCTGCTCCTGAGgtaagctttc ... ttttctgcagGTGATATCTGGTAAACTATATGCTGGACCTGAAGTTGATGTGTGGAGCTGT

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: 47 (upstream exon), 48 (downstream exon)
Score: 321

ATGCAATGTTAAGATTGCAGATTTTGGCTTAAGTAATGTTATGCGGGATGGTCATTTTCTGAAGACAAGTTGTGGTAGCCCAAATTATGCTGCTCCTGAGgtaagctttc ... ttttctgcagGTGATATCTGGTAAACTATATGCTGGACCTGAAGTTGATGTGTGGAGCTGTGGGGTTATTCTTTATGCTCTTTTATGTGGTACTCTGCCATTTGATGACG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 193

ATGCAATGTTAAGATTGCAGATTTTGGCTTAAGTAATGTTATGCGGGATGGTCATTTTCTGAAGACAAGTTGTGGTAGCCCAAATTATGCTGCTCCTGAGgtaagctttc ... ttttctgcagGTGATATCTGGTAAACTATATGCTGGACCTGAAGTTGATGTGTGGAGCTGTGGGGTTATTCTTTATGCTCTTTTATGTGGTACTCTGCCATTTGATGACG


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 173

ATGCAATGTTAAGATTGCAGATTTTGGCTTAAGTAATGTTATGCGGGATGGTCATTTTCTGAAGACAAGTTGTGGTAGCCCAAATTATGCTGCTCCTGAGgtaagctttc ... ttttctgcagGTGATATCTGGTAAACTATATGCTGGACCTGAAGTTGATGTGTGGAGCTGTGGGGTTATTCTTTATGCTCTTTTATGTGGTACTCTGCCATTTGATGACG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 429

ATGCAATGTTAAGATTGCAGATTTTGGCTTAAGTAATGTTATGCGGGATGGTCATTTTCTGAAGACAAGTTGTGGTAGCCCAAATTATGCTGCTCCTGAGgtaagctttc ... ttttctgcagGTGATATCTGGTAAACTATATGCTGGACCTGAAGTTGATGTGTGGAGCTGTGGGGTTATTCTTTATGCTCTTTTATGTGGTACTCTGCCATTTGATGACG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATGCAATGTTAAGATTGCAGATTTTGGCTTAAGTAATGTTATGCGGGATGGTCATTTTCTGAAGACAAGTTGTGGTAGCCCAAATTATGCTGCTCCTGAGgtaagctttctataataggtcaaagatataaagaggacccattagatcagtatggccgtatttcctacccctttgttggcaggcagtacagtatccttttattttctgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT