Sequence
atgc intronic sequence ATGC exonic sequence...attcaactcagtattttattttgtaagttataactggtcgctaatagttgatgctagaacggcattgatatcatgttgttgatattcattctgtttgcagTGAGCAATGGTCCACCCAAGCTGGTGATCCTTCATATGAACATGGCTCTTCATGTCTTTGATGATATAATGAGGATGACTGAGAACTTGAGTGAGAAATA
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GRMZM5G809695_T03 (Zea mays), 3'ss of exon 23
lower sequence: LOC_Os06g10230.1 (Oryza sativa), 3'ss of exon 24
-------------------------------------------------------------------------------attcaactcagtattttattttgtaagttata-actggtcgctaatagttgatgctagaacggcattgatatcatgttgttgatattcattctgtttgcagTGAGCAATGGTCCACCCAAGCTGGTGATCCTTCATATGAACATGGCTCTTCATGTCTTTGATGATATAATGAGGATGACTGAGAACTTGAGTGAGAAATA
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gtaatgcatctgcaaggagttttgctcaacaaatcaactcatttctctcctgccaagttcaatattaggatactatcttgtccagca-attattgtatttagtcaattgtttgtttttacctgataactgg-gttaatggtagagcaacactaaagcgctg-tatatttgctgtc-acagTGAGCAATGTTCCCCCCAAGCTGGTTATCCTTCATATGAACCTTTCCCTTCTTGTATACGAGGATATAATGACGATGACTGAAAACCTGAGTGAGAAGTA
upper sequence: GRMZM5G809695_T03 (Zea mays), 3'ss of exon 23
lower sequence: GLYMA17G34380.2 (Glycine max), 3'ss of exon 23
-attcaactcagtattttattttgtaagttataactggtcgctaatagttgatgctagaacggcattgatatcatgttgttgatat---tcattctgtttgcagTGAGCAATGGTCCACCCAAGCTGGTGATCCTTCATATGAACATGGCTCTTCATGTCTTTGATGATATAATGAGGATGACTGAGAACTTGAGTGAGAAATA
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tgccggattttgtagt--gtttgatatattataatggtatcattctgcctattg--aaacttaagttgacaagttactgactgcataagctatgctattgacagTTAATTTCTCCCCCCCAAAGCTAGTGATTCTTCATATGAATATGGCACTACATGTGTATGAAGATATCATGAGGATGACTGAAAACCTGAGTGAGAAGTA
upper sequence: GRMZM5G809695_T03 (Zea mays), 3'ss of exon 23
lower sequence: GLYMA14G11220.2 (Glycine max), 3'ss of exon 24
attcaactcagtattttattttgta-agttataactggtcgctaatagttgatgctagaacggcattgatatcatgttgttgatat---tcattctgtttgcagTGAGCAATGGTCCACCCAAGCTGGTGATCCTTCATATGAACATGGCTCTTCATGTCTTTGATGATATAATGAGGATGACTGAGAACTTGAGTGAGAAATA
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----tttgtagtgtttcatttattataatggtattttattatcattctgcctatttaaacttaagttgacaagttactgactgcataagctatgttattgacagTTAATTTCTCCCCTCCAAAGCTAGTGATTCTTCATATGAATATGGCACTACATGTGTATGAAGATATCATGAGGATGACTGAAAACCTAAGTGAGAAGTA
upper sequence: GRMZM5G809695_T03 (Zea mays), 3'ss of exon 23
lower sequence: GLYMA06G05900.1 (Glycine max), 3'ss of exon 25
attcaactcagtattttattttgtaagttataactggtcgctaatagttgatgctagaacggcattgatatcatg-ttgttgatattcattctgtttgcagTGAGCAATGGTCCACCCAAGCTGGTGATCCTTCATATGAACATGGCTCTTCATGTCTTTGATGATATAATGAGGATGACTGAGAACTTGAGTGAGAAATA
||| | || || | || |||| || | | | |||| || ||||| ||| | | |||| | | || || ||||| ||||| ||||| || || ||| | |||||||| | ||||||||| |||||||||||||| ||| | |||||||| ||
----------------------gtacttcat--cttaactgtacctattgaaactgaa--gatgataatatgctgattgttcatacttgaaa-atcgacagTCAATTACTCACCTCCGAAGCTAGTGATTCTTCACATTAATATGACACTTCATGTGTATGATGATATCATGAGGATGACTGAAAACCTAAGTGAGAAGTA
upper sequence: GRMZM5G809695_T03 (Zea mays), 3'ss of exon 23
lower sequence: GLYMA04G05910.1 (Glycine max), 3'ss of exon 16
attcaactcagtattttattttgtaagttataactggtcgctaatagttgatgctagaacggcattgatatcatgttgttgatattcattctgtttgcagTGAGCAATGGTCCACCCAAGCTGGTGATCCTTCATATGAACATGGCTCTTCATGTCTTTGATGATATAATGAGGATGACTGAGAACTTGAGTGAGAAATA
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----------gtactttatctt---aactgtaccta----ttgaaactgaagactgtaaca-tgctgat----tgttcttgct-tgaaaattgt---cagTTAATTACTCACCTCCAAAGCTAGTGATTCTTCACATGAATATGGCACTTCATGTGTATGATGATATCATGAGGATGACCGAAAACCTAAGTGAGAAGTA
upper sequence: GRMZM5G809695_T03 (Zea mays), 3'ss of exon 23
lower sequence: Vv04s0008g01970.t01 (Vitis vinifera), 3'ss of exon 24
attcaactcagtattttattttgtaagttataactggtcgctaatagttgatgcta-gaacggcattgatatcatgttgttgatattcattctgtttgcagTGAGCA-ATGGTC--CACCCAAGCTGGTGATCCTTCATATGAACATGGCTCTTCATGTCTTTGATGATATAATGAGGATGACTGAGAACTTGAGTGAGAAATA
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--ttatatctgtatcccttaatatattttgaaaaatgt-gttactattttcccttttgaaacttctctccatctactaactaatgta-gtttgctaaacaacagTTACATACTCAACACCGAAGCTGGTGATCCTTCACATGAATATGGCACTGCATGTGTACGAGGATATCATGAGAATGACGGAAAACTTGAGTGAGAAGTAMapped 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|71769229|gb|DR967166.1|DR967166EST: CAGGCCACACCATCCACCTGCTTTTAAAGATGCCACTGTAAGCAAGCCAG TGAGCAATGGTCCACCCAAGCTGGTGATCCTTCATATGAACATGGCTCTTC
genomic: CAGGCCACACCATCCACCTGCTTTTAAAGATGCCACTGTAAGCAAGCCAGgtaatgcatt ... ctgtttgcagTGAGCAATGGTCCACCCAAGCTGGTGATCCTTCATATGAACATGGCTCTTC
EST:
gi|28873715|gb|CB329664.1|CB329664EST: CAGGCCACACCATCCACCTGCTTTTAAAGATGCCACTGTAAGCAAGCCAG TGAGCAATGGTCCACCCAAGCTGGTGATCCTTCATATGAACATGGCTCTTC
genomic: CAGGCCACACCATCCACCTGCTTTTAAAGATGCCACTGTAAGCAAGCCAGgtaatgcatt ... ctgtttgcagTGAGCAATGGTCCACCCAAGCTGGTGATCCTTCATATGAACATGGCTCTTC
EST:
gi|211403947|gb|FL320399.1|FL320399EST: CAGGCCACACCATCCACCTGCTTTTAAAGATGCCACTGTAAGCAAGCCAG TGAGCAATGGTCCACCCAAGCTGGTGATCCTTCATATGAACATGGCTCTTC
genomic: CAGGCCACACCATCCACCTGCTTTTAAAGATGCCACTGTAAGCAAGCCAGgtaatgcatt ... ctgtttgcagTGAGCAATGGTCCACCCAAGCTGGTGATCCTTCATATGAACATGGCTCTTC
EST:
gi|32164946|gb|CD670264.1|CD670264EST: CAGGCCACACCATCCACCTGCTTTTAAAGATGCCACTGTAAGCAAGCCAG TGAGCAATGGTCCACCCAAGCTGG
genomic: CAGGCCACACCATCCACCTGCTTTTAAAGATGCCACTGTAAGCAAGCCAGgtaatgcatt ... ctgtttgcagTGAGCAATGGTCCACCCAAGCTGG
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 3 RNA-Seq libraries.
Block sizes:
49 (upstream exon),
48 (downstream exon)
Score:
927GTTGCTGTGGGTGGACTTGTTATCCTCCTGATGATCTTAGTAGCTGTATGCAGGCCACACCATCCACCTGCTTTTAAAGATGCCACTGTAAGCAAGCCAGgtaatgcatt ... ctgtttgcagTGAGCAATGGTCCACCCAAGCTGGTGATCCTTCATATGAACATGGCTCTTCATGTCTTTGATGATATAATGAGGATGACTGAGAACTTGAGTGAGAAATA
Block sizes:
49 (upstream exon),
49 (downstream exon)
Score:
30GTTGCTGTGGGTGGACTTGTTATCCTCCTGATGATCTTAGTAGCTGTATGCAGGCCACACCATCCACCTGCTTTTAAAGATGCCACTGTAAGCAAGCCAGgtaatgcatt ... ctgtttgcagTGAGCAATGGTCCACCCAAGCTGGTGATCCTTCATATGAACATGGCTCTTCATGTCTTTGATGATATAATGAGGATGACTGAGAACTTGAGTGAGAAATA
Block sizes:
49 (upstream exon),
40 (downstream exon)
Score:
46GTTGCTGTGGGTGGACTTGTTATCCTCCTGATGATCTTAGTAGCTGTATGCAGGCCACACCATCCACCTGCTTTTAAAGATGCCACTGTAAGCAAGCCAGgtaatgcatt ... ctgtttgcagTGAGCAATGGTCCACCCAAGCTGGTGATCCTTCATATGAACATGGCTCTTCATGTCTTTGATGATATAATGAGGATGACTGAGAACTTGAGTGAGAAATA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.agttgatgctagaacggcattgatatcatgttgttgatattcattctgtttgcagTGAGCAATGGTCCACCCAAGCTGGTGATCCTTCATATGAACATGGCTCTTCATGTCTTTGATGATATAATGAGGATGACTGAGAACTTGAGTGAGAAATA
tgttgat putative branch site (score: 46)
ttcattct CT-rich tract
atattcatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
attcaactcagtattttattttgtaagttataactggtcgctaatagttgatgctagaacggcattgatatcatgttgttgatattcattctgtttgcagTGAGCAATGGTCCACCCAAGCTGGTGATCCTTCATATGAACATGGCTCTTCATGTCTTTGATGATATAATGAGGATGACTGAGAACTTGAGTGAGAAATA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG