Sequence
atgc intronic sequence ATGC exonic sequencegtattgtatactattctttaatggaaaggtttctagcagattcagtttttaaagaagtttaagatatttggttgatagcatgtaatcaactctatttgcagGTTCAGAAACTTCTTGGCATTTGTTCACAGCATCTTGAGAAAGGTGAAACACACCAAGGGCCAGCTGTCCTTGGAATTGCTCTTATTGCTATGGCTGAAG
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GRMZM5G816609_T01 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os02g05340.1 (Oryza sativa), 3'ss of exon 18
gtattgtatactattctttaatggaaaggtttctagcagattcagtttttaaagaagtttaagatatttggttgatagcatgtaatcaactctatttgcagGTTCAGAAACTTCTTGGCATTTGTTCACAGCATCTTGAGAAAGGTGAAACACACCAAGGGCCAGCTGTCCTTGGAATTGCTCTTATTGCTATGGCTGAAG
||| || || | | | |||| | | |||| || || || || | |||| | || || || ||| | || ||||||||| || || ||||| ||||| |||||||||||||||||||||||||| ||||| |||||||||||||| |||||||| |||||||| ||||||||||
-----gtacttcatgtttaatgcttagaggttcttgtggcttcaagcttgtttaaatttcgaggt-tttgat--at-gcttgg---caattttac--gcagGTTCAAAAGCTCCTTGGGATTTGCTCACAGCATCTTGAGAAAGGTGAAACCCACCAGGGGCCAGCTGTCCTAGGAATTGCGCTTATTGCAATGGCTGAAG
upper sequence: GRMZM5G816609_T01 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA12G13410.1 (Glycine max), 3'ss of exon 18
-------------------gtattgtatactattctttaatggaaaggtttctagcaga---ttcagtttttaaagaagtttaag-atatttggttgatagcatgtaatcaactctattt---gcagGTTCAGAAACTTCTTGGCATTTGTTCACAGCATCTTGAGAAAGGTGAAACACACCAAGGGCCAGCTGTCCTTGGAATTGCTCTTATTGCTATGGCTGAAG
|| | | | || ||||| ||| | | ||| | |||| | | | | | || ||| | | | || | | | | ||| ||||||||| || || | || ||||||||| |||||||| ||||||||||| ||||| || || ||||| |||||||||||| | | |||||||||||||
gtacaatcttgtgatgaattagttatgaagttttttttaaaaatgtaacatctgctacacctttctatgtttataattgctgatgcattttttcatttttgtatttgctgatgcttctttcttgcagGTTCAAAATCTGTTGGGTCATTGTTCACAACATCTTGATAAAGGTGAAACTCACCAGGGTCCTGCTGTGCTTGGAATTGCTATGGTAGCTATGGCTGAAG
upper sequence: GRMZM5G816609_T01 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA06G44340.1 (Glycine max), 3'ss of exon 18
-------------------gtattgtatactattctttaatggaaaggtttctagcaga---ttcagtttttaaagaagttta----agata-------tttggttgatagcatgtaatcaactctat-ttgcagGTTCAGAAACTTCTTGGCATTTGTTCACAGCATCTTGAGAAAGGTGAAACACACCAAGGGCCAGCTGTCCTTGGAATTGCTCTTATTGCTATGGCTGAAG
|| | | | || || || | |||| | ||| | |||| | | | | ||| || || ||| || ||| | ||||||||||| || || | || ||||||||| |||||||| ||||||||||| |||||||| || ||||| |||||||||||| | | |||||||||||||
gtacaatcttgtgataaactggttatgaattttttttaaaaaatgaaacttctgctgcacctttctatgtttataattgctgattgcggatgcatctttttattttaatattttgctggtgcttctttcttgcagGTTCAAAATCTGTTGGGTCATTGTTCACAACATCTTGATAAAGGTGAAACTCACCAAGGTCCTGCTGTGCTTGGAATTGCTATGGTAGCTATGGCTGAAG
upper sequence: GRMZM5G816609_T01 (Zea mays), 3'ss of exon 4
lower sequence: Vv12s0028g03130.t01 (Vitis vinifera), 3'ss of exon 18
gtattgtat-actattctttaatggaaaggtttctagcagattcagtttttaaagaagtttaagatatttggttgatagcatgtaatcaactctatt-tgcagGTTCAGAAACTTCTTGGCATTTGTTCACAGCATCTTGAGAAAGGTGAAACACACCAAGGGCCAGCTGTCCTTGGAATTGCTCTTATTGCTATGGCTGAAG
|| ||| || | || || || | | ||| |||| | | |||| | | || || | | | | | ||| ||||| || | |||||||| ||| | || |||||||| || |||||||| |||||||| |||||||| ||||||||||| | | || ||||||||||
gttttgcattaaagttgattgctgttcaagattcct----attccataaatgaagaggcc---aaccttcttttttcattctttgctttttttaattgcacagGTCCAACACCTTCTTGGTCAGTGTGCCCAACATCTTGAAAAGGGTGAAACCCACCAAGGCCCAGCTGTACTTGGAATTGCAATGGTGGCAATGGCTGAAGMapped 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|87157733|gb|DY402522.1|DY402522EST: ATGTAACACTTATGTCGCTGGCATATGCCGGGACAGGAAATGTGCTTAAG GTTCAGAAACTTCTTGGCATTTGTTCACAGCATCTTGAGAAAGGTGAAACA
genomic: ATGTAACACTTATGTCGCTGGCATATGCCGGGACAGGAAATGTGCTTAAGgtattgtata ... ctatttgcagGTTCAGAAACTTCTTGGCATTTGTTCACAGCATCTTGAGAAAGGTGAAACA
EST:
gi|32911849|gb|CF016661.1|CF016661EST: ATGTAACACTTATGTCGCTGGCATATGCCGGGACAGGAAATGTGCTTAAG GTTCTTAAACTTCTTGGCATTTGTTCACAGCATCTTGAGAAAGGTGAAACA
genomic: ATGTAACACTTATGTCGCTGGCATATGCCGGGACAGGAAATGTGCTTAAGgtattgtata ... ctatttgcagGTTCAGAAACTTCTTGGCATTTGTTCACAGCATCTTGAGAAAGGTGAAACA
EST:
gi|26559722|gb|CA831957.1|CA831957EST: TGTAACACTTATGTCGCTGGCATATGCCGGGACAGGAAATGTCGCTTAAG GTTCAGAAACTTCTTGGCATTTGTTCACAGCATCTTGAGAAAGGTGAAAC
genomic: TGTAACACTTATGTCGCTGGCATATGCCGGGACAGGAAATGT-GCTTAAGgtattgtata ... ctatttgcagGTTCAGAAACTTCTTGGCATTTGTTCACAGCATCTTGAGAAAGGTGAAAC
EST:
gi|67041940|gb|CO468195.1|CO468195EST: ATGTAACACTTATGTCGCTGGCATATGCCGGGACAGGAAATGTGCTTAAG GTTCAGAAACTTCTTGGCATTTGTTCACAGCATCTTGAGAAAGGTGAAACA
genomic: ATGTAACACTTATGTCGCTGGCATATGCCGGGACAGGAAATGTGCTTAAGgtattgtata ... ctatttgcagGTTCAGAAACTTCTTGGCATTTGTTCACAGCATCTTGAGAAAGGTGAAACA
EST:
gi|22819353|gb|BU499443.1|BU499443EST: ATGTAACACTTATGTCGCTGGCATATGCCGGGACAGGAAACGTGCTTAAG GTTCAGAAACTTCTTGGCATTTGTTCACAGCATCTTGAGAAAGGTGAAACA
genomic: ATGTAACACTTATGTCGCTGGCATATGCCGGGACAGGAAATGTGCTTAAGgtattgtata ... ctatttgcagGTTCAGAAACTTCTTGGCATTTGTTCACAGCATCTTGAGAAAGGTGAAACA
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),
49 (downstream exon)
Score:
484TACCGCAGAGGTCTCTAAAACATTTGATGAAAAGATAGGGAAGTACTGTGATGTAACACTTATGTCGCTGGCATATGCCGGGACAGGAAATGTGCTTAAGgtattgtata ... ctatttgcagGTTCAGAAACTTCTTGGCATTTGTTCACAGCATCTTGAGAAAGGTGAAACACACCAAGGGCCAGCTGTCCTTGGAATTGCTCTTATTGCTATGGCTGAAG
Block sizes:
49 (upstream exon),
48 (downstream exon)
Score:
373TACCGCAGAGGTCTCTAAAACATTTGATGAAAAGATAGGGAAGTACTGTGATGTAACACTTATGTCGCTGGCATATGCCGGGACAGGAAATGTGCTTAAGgtattgtata ... ctatttgcagGTTCAGAAACTTCTTGGCATTTGTTCACAGCATCTTGAGAAAGGTGAAACACACCAAGGGCCAGCTGTCCTTGGAATTGCTCTTATTGCTATGGCTGAAG
Block sizes:
48 (upstream exon),
49 (downstream exon)
Score:
388TACCGCAGAGGTCTCTAAAACATTTGATGAAAAGATAGGGAAGTACTGTGATGTAACACTTATGTCGCTGGCATATGCCGGGACAGGAAATGTGCTTAAGgtattgtata ... ctatttgcagGTTCAGAAACTTCTTGGCATTTGTTCACAGCATCTTGAGAAAGGTGAAACACACCAAGGGCCAGCTGTCCTTGGAATTGCTCTTATTGCTATGGCTGAAG
Block sizes:
49 (upstream exon),
49 (downstream exon)
Score:
450TACCGCAGAGGTCTCTAAAACATTTGATGAAAAGATAGGGAAGTACTGTGATGTAACACTTATGTCGCTGGCATATGCCGGGACAGGAAATGTGCTTAAGgtattgtata ... ctatttgcagGTTCAGAAACTTCTTGGCATTTGTTCACAGCATCTTGAGAAAGGTGAAACACACCAAGGGCCAGCTGTCCTTGGAATTGCTCTTATTGCTATGGCTGAAG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttttaaagaagtttaagatatttggttgatagcatgtaatcaactctatttgcagGTTCAGAAACTTCTTGGCATTTGTTCACAGCATCTTGAGAAAGGTGAAACACACCAAGGGCCAGCTGTCCTTGGAATTGCTCTTATTGCTATGGCTGAAG
ggttgat putative branch site (score: 450)
ctctattt putative PPT
aagtttaagatattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtattgtatactattctttaatggaaaggtttctagcagattcagtttttaaagaagtttaagatatttggttgatagcatgtaatcaactctatttgcagGTTCAGAAACTTCTTGGCATTTGTTCACAGCATCTTGAGAAAGGTGAAACACACCAAGGGCCAGCTGTCCTTGGAATTGCTCTTATTGCTATGGCTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG