Sequence
atgc intronic sequence ATGC exonic sequenceATGCAATGTTAAGATTGCAGATTTTGGCTTAAGTAATGTTATGCGGGATGGTCATTTTCTGAAGACAAGTTGTGGTAGCCCAAATTATGCTGCTCCTGAGgtaagctttctataataggtcaaagatataaagaggacccattagatcagtatggccgtatttcctacccctttgttggcaggcagtacagtatccttttattttctgcag
Basic information
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|DR966887EST: GTCATTTTCTGAAGACAAGTTGTGGTAGCCCAAATTATGCTGCTCCTGAG GTGATATCTGGTAAACTATATGCTGGACCTGAAGTTGATGTGTGGAGCTGT
genomic: GTCATTTTCTGAAGACAAGTTGTGGTAGCCCAAATTATGCTGCTCCTGAGgtaagctttc ... ttttctgcagGTGATATCTGGTAAACTATATGCTGGACCTGAAGTTGATGTGTGGAGCTGT
EST:
gi|211439527|gb|FL064919.1|FL064919EST: TCATTTTCTGAAGACAAGTTGTGGTAGCCCAAATTATGCTGCTCCTGGAG -TGATATCTGGGTAA-CTATATGCTGGACCTGAAGTTGATGTGTGGAGCT
genomic: TCATTTTCTGAAGACAAGTTGTGGTAGCCCAAATTATGCTGCTCCTG-AGgtaagctttc ... ttttctgcagGTGATATCTGG-TAAACTATATGCTGGACCTGAAGTTGATGTGTGGAGCT
EST:
gi|148969836|gb|EE020728.2|EE020728EST: GTCATTTTCTGAAGACAAGTTGTGGTAGCCCAAATTATGCTGCTCCTGAG GTGATATCTGGTAAACTATATGCTGGACCTGAAGTTGATGTGTGGAGCTGT
genomic: GTCATTTTCTGAAGACAAGTTGTGGTAGCCCAAATTATGCTGCTCCTGAGgtaagctttc ... ttttctgcagGTGATATCTGGTAAACTATATGCTGGACCTGAAGTTGATGTGTGGAGCTGT
EST:
gi|149088708|gb|EE177828.2|EE177828EST: GTCATTTTCTGAAGACAAGTTGTGGTAGCCCAAATTATGCTGCTCCTGAG GTGATATCTGGTAAACTATATGCTGGACCTGAAGTTGATGTGTGGAGCTGT
genomic: GTCATTTTCTGAAGACAAGTTGTGGTAGCCCAAATTATGCTGCTCCTGAGgtaagctttc ... ttttctgcagGTGATATCTGGTAAACTATATGCTGGACCTGAAGTTGATGTGTGGAGCTGT
EST:
gi|149088317|gb|EE177414.2|EE177414EST: GTCATTTTCTGAAGACAAGTTGTGGTAGCCCAAATTATGCTGCTCCTGAG GTGATATCTGGTAAACTATATGCTGGACCTGAAGTTGATGTGTGGAGCTGT
genomic: GTCATTTTCTGAAGACAAGTTGTGGTAGCCCAAATTATGCTGCTCCTGAGgtaagctttc ... ttttctgcagGTGATATCTGGTAAACTATATGCTGGACCTGAAGTTGATGTGTGGAGCTGT
EST:
gi|211006231|gb|FL064937.1|FL064937EST: GTCATTTTCTGAAGACAAGTTGTGGTAGCCCAAAT-ATGCTGCTCCTGAG GTGATATCTGGTAAACTATATGCTGGACCTGAAAGT-GATGTGT
genomic: GTCATTTTCTGAAGACAAGTTGTGGTAGCCCAAATTATGCTGCTCCTGAGgtaagctttc ... ttttctgcagGTGATATCTGGTAAACTATATGCTGGACCTGAA-GTTGATGTGT
EST:
gi|148974739|gb|EE025550.2|EE025550EST: GTCATTTTCTGAAGACAAGTTGTGGTAGCCCAAATTATGCTGCTCCTGAG GTGATATCTGGTAAACTATATGCTGGACCTGAAGTTGATGTGTGGAGCTGT
genomic: GTCATTTTCTGAAGACAAGTTGTGGTAGCCCAAATTATGCTGCTCCTGAGgtaagctttc ... ttttctgcagGTGATATCTGGTAAACTATATGCTGGACCTGAAGTTGATGTGTGGAGCTGT
EST:
gi|211324790|gb|FL345978.1|FL345978EST: 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:
321ATGCAATGTTAAGATTGCAGATTTTGGCTTAAGTAATGTTATGCGGGATGGTCATTTTCTGAAGACAAGTTGTGGTAGCCCAAATTATGCTGCTCCTGAGgtaagctttc ... ttttctgcagGTGATATCTGGTAAACTATATGCTGGACCTGAAGTTGATGTGTGGAGCTGTGGGGTTATTCTTTATGCTCTTTTATGTGGTACTCTGCCATTTGATGACG
Block sizes:
49 (upstream exon),
48 (downstream exon)
Score:
193ATGCAATGTTAAGATTGCAGATTTTGGCTTAAGTAATGTTATGCGGGATGGTCATTTTCTGAAGACAAGTTGTGGTAGCCCAAATTATGCTGCTCCTGAGgtaagctttc ... ttttctgcagGTGATATCTGGTAAACTATATGCTGGACCTGAAGTTGATGTGTGGAGCTGTGGGGTTATTCTTTATGCTCTTTTATGTGGTACTCTGCCATTTGATGACG
Block sizes:
48 (upstream exon),
48 (downstream exon)
Score:
173ATGCAATGTTAAGATTGCAGATTTTGGCTTAAGTAATGTTATGCGGGATGGTCATTTTCTGAAGACAAGTTGTGGTAGCCCAAATTATGCTGCTCCTGAGgtaagctttc ... ttttctgcagGTGATATCTGGTAAACTATATGCTGGACCTGAAGTTGATGTGTGGAGCTGTGGGGTTATTCTTTATGCTCTTTTATGTGGTACTCTGCCATTTGATGACG
Block sizes:
48 (upstream exon),
49 (downstream exon)
Score:
429ATGCAATGTTAAGATTGCAGATTTTGGCTTAAGTAATGTTATGCGGGATGGTCATTTTCTGAAGACAAGTTGTGGTAGCCCAAATTATGCTGCTCCTGAGgtaagctttc ... 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