Sequence
atgc intronic sequence ATGC exonic sequencegttcgtactttactgttctgactgattgcctaaaatgattaagcatagctggagcttattgagtgttgtctaaacatgcctactcctcttgcaacagAGGCTGGTTTATGGGGCCAAGGCAGAGGCTGCCATCGCCATTGGATTTGATGACTTCATTGCAGATGCTCTGAGAGGCACTGGGTTCTACCAGAAGGCCA
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GRMZM2G008216_T02 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os07g14150.6 (Oryza sativa), 3'ss of exon 3
gttcgtactttactgttctgactgattgcctaaaatgattaagcatagctggagcttattgagtgttgtctaaacatgcctactcctcttgcaacagAGGCTGGTTTATGGGGCCAAGGCAGAGGCTGCCATCGCCATTGGATTTGATGACTTCATTGCAGATGCTCTGAGAGGCACTGGGTTCTACCAGAAGGCCA
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gtctgcacccgtcaattttc-cta--cgcataacctcatcacaaatatctgacgatttt-----atttaacacaactgctaattcttc--actacagAGGCTGGTGTATGGAGCCAAGGCAGAAGCTGCCATTGCCATTGGATTTGATGACTTCATTGCAGATGCTCTGAGAGGCACTGGGTTTTACCAGAAGGCCA
upper sequence: GRMZM2G008216_T02 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA15G20970.2 (Glycine max), 3'ss of exon 4
gttcgtactttactgttctgactgattgcctaaaatgattaagcatagct---ggagcttatt-----gagtgttgtctaaacatgcctactcctcttgcaacagAGGCTGGTTTATGGGGCCAAGGCAGAGGCTGCCATCGCCATTGGATTTGATGACTTCATTGCAGATGCTCTGAGAGGCACTGGGTTCTACCAGAAGGCCA
|| | | || | || || | | | ||| ||||| || | ||||| | | | ||| | || ||| || | ||||| |||||||||| || ||||||||||| || || || |||||||| |||||||||||| ||||||| || |||||||||| ||||||||||| ||
atttaaaaat--ctttaaagatagagtacatgaaa--attaaatttattttacaatgcttactctcgggcacactttcttacaatattcactttatttata-tagAGGTTGGTTTATGGAGCAAAGGCAGAGGCAGCAATTGCTATTGGATTCGATGACTTCATTTCAGATGCATTGCGAGGCACTGGATTCTACCAGAAAGCAC
upper sequence: GRMZM2G008216_T02 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA09G09440.1 (Glycine max), 3'ss of exon 4
-gttcgtactttactgttctgactgattgcctaaaatgattaagcatagctggagcttattgagt--gttgtctaaacatgcctactcctcttgcaacagAGGCTGGTTTATGGGGCCAAGGCAGAGGCTGCCATCGCCATTGGATTTGATGACT-TCATTGCAGATGCTCTGAGAGGCACTGGGTTCTACCAGAAGGCCA
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tttttatacttaaaatacatgaaaattaaacttatttgacaaattgaagcttattacttttgggcccactttcttgtcacactcaaattattttttatagAGGTTGGTTTATGGAGCGAAGGCAGAGGCAGCAATTGCTATTGGATTCGATGACTATGATTTCAGATGCATTGCGAGGTACTGGATTCTATCAGAAAGCA-
upper sequence: GRMZM2G008216_T02 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA16G22830.1 (Glycine max), 3'ss of exon 8
gttcgta---ctttactgttctgactgattgc--ctaaaatgattaagcatagctggagcttattgagtgttgtctaaacatgcctactcctcttgcaacagAGGCTGGTTTATGGGGCCAAGGCAGAGGCTGCCATCGCCATTGGATTTGATGACTTCATTGCAGATGCTCTGAGAGGCACTGGGTTCTACCAGAAGGCCA
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atttaaaaatctttaaagatagagtacatgaaaattaaattcattttacaatgcttactctcgg-gcacattttcttacaatattcactttatttata-tagAGGTTGGTTTATGGAGCAAAGGCAGAGGCTGCAATTGCTATTGGATTCGATGACTTCATTTCAGATGCATTGCGAGGCACTGGATTCTACCTGAAAGCAC
upper sequence: GRMZM2G008216_T02 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA09G12900.1 (Glycine max), 3'ss of exon 2
-gttcgtactttactgttctgactgattgcctaaaatgattaagcatagctggagcttattgagtgttgtctaaacatgcctac----tcctcttgcaacagAGGCTGGTTTATGGGGCCAAGGCAGAGGCTGCCATCGCCATTGGATTTGATGACTTCATTGCAGATGCTCTGAGAGGCACTGGGTTCTACCAGAAGGCCA
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atttaagataatttctaattaattaatattacatcaaaattgaat-tattttacaatgatt-acttttgggcacacttttttacaatattaaatttatacagAGGTTGGTTTATGGAGCAAAGGCAGAGGCAGCAATTGCTATTAGGTTCGATGACTTCATTTCAGATGCATTGCGAGGTACTGCATTCTATCAGAAGGCAC
upper sequence: GRMZM2G008216_T02 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA20G37210.1 (Glycine max), 3'ss of exon 4
----gttcgtactttactgttctgactgattgcctaaaatgattaagcatagctggagcttattgagtgttgtctaaacatgcctactcctcttgca----acagAGGCTGGTTTATGGGGCCAAGGCAGAGGCTGCCATCGCCATTGGATTTGATGACTTCATTGCAGATGCTCTGAGAGGCACTGGGTTCTACCAGAAGGCCA
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gtgagcctctgccacagccacactattcatattttcctctcaccacatgtttctctagtatttattaaaatgatcacat-tgttcattcctttcacatcaaacagAGACTGGTTTACGGAGCTAAAGCAGAAGCTGCAATAGCAATTGGATTTGATGATTTCATTGCCGATGCACTGAGGGGCACTGGTTTTTATCAGAAGGCTC
upper sequence: GRMZM2G008216_T02 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA17G04720.2 (Glycine max), 3'ss of exon 4
gttcgtactttactgttctgactgattgcctaaaatgattaagcatagctggagcttattgagtgttgtctaaacatgcctactcctcttgcaacagAGGCTGGTTTATGGGGCCAAGGCAGAGGCTGCCATCGCCATTGGATTTGATGACTTCATTGCAGATGCTCTGAGAGGCACTGGGTTCTACCAGAAGGCCA
||| | | | |||| | || || || | | | ||| | | | | || | | || | | || || | || |||||||| |||||||||| || ||||| ||||| || || || ||||| |||||||| |||||||||||||| ||| |||| ||||| ||||| ||||| || |
gttag-aatggcttgttatccctatgtgtctc---ttttataccatgttt--atcctgtttctagctaacttattacat-tattctttttctaacagAGGTTGGTTTATGGAGCGAAGGCTGAGGCAGCAATTGCTATTGGGTTTGATGATTTCATTGCAGATGCACTGCGAGGTACTGGATTCTATCAGAAAGCAA
upper sequence: GRMZM2G008216_T02 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA09G09430.2 (Glycine max), 3'ss of exon 3
gttcgtactttactgttctgactgattgcctaaaatgat-taagcatagctggagcttat--tgagtgttgtctaaacatgcctactcc---tcttgca-----acagAGGCTGGTTTATGGGGCCAAGGCAGAGGCTGCCATCGCCATTGGATTTGATGACTTCATTGCAGATGCTCTGAGAGGCACTGGGTTCTACCAGAAGGCCA
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-------atttaagataatttctaattaattaatattacatcaaaattgaattattttacaatgattact-tttgggcacgctttcttacaatattaaatttatacagAGGTTGGTTTATGGAGCAAAGGCAGAGGCAGCAATTGCTATTGGGTTCGATGACTTCATTTCAGATGCATTGCGAGGTACTGGATTCTATCAGAAGGCAC
upper sequence: GRMZM2G008216_T02 (Zea mays), 3'ss of exon 1
lower sequence: AT5G28050.2 (Arabidopsis thaliana), 3'ss of exon 5
gttcgtactttactgttctgactgattgcctaaaatgattaagcatagctggagcttattgagtgttgtctaaacatgcctactcctcttgcaacagAGGCTGGTTTATGGGGCCAAGGCAGAGGCTGCCATCGCCATTGGATTTGATGACTTCATTGCAGATGCTCTGAGAGGCACTGGGTTCTACCAGAAGGCCA
||| | | | | | ||| || | || | | | || || |||| || || || | |||||||| |||||||||| ||||| || || || || || ||||| || |||||||||||||| || |||||| |||||||||| ||| | |||||||| | |
----gtaagatgtcgaaacaagtctactcacaaacccatctttc-taatcatttcatttatcacaatgagtactcatgtct-ctacttgta-aacagAGGTTGGTTTATGGAGCCAAAGCCGAAGCAGCTATAGCCATCGGGTTTGATGACTTCATAGCTGATGCTTTGAGAGGCACGGGGGTTTACCAGAAATCTAMapped 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|22489218|gb|BU049141.1|BU049141EST: GCGAGCCATGCCCAATGTGCTTTGGTGCAGTTCATCTCTCCCGAATCAAG AGGCTGGTTTATGGGGCCAAGGCAGAGGCTGCCATCGCCATTGGATTTGAT
genomic: GCGAGCCATGCCCAATGTGCTTTGGTGCAGTTCATCTCTCCCGAATCAAGgttcgtactt ... cttgcaacagAGGCTGGTTTATGGGGCCAAGGCAGAGGCTGCCATCGCCATTGGATTTGAT
EST:
gi|6012424|gb|AW061861.1|AW061861EST: GCGAGCCATGCCCAATGTGCTTTGGTGCAGTTCATCTCTCCCGAATCAAG AGGCTGGTTTATGGGGCCAAGGCAGAGGCTGCCATCGCCATTGGATTTGAT
genomic: GCGAGCCATGCCCAATGTGCTTTGGTGCAGTTCATCTCTCCCGAATCAAGgttcgtactt ... cttgcaacagAGGCTGGTTTATGGGGCCAAGGCAGAGGCTGCCATCGCCATTGGATTTGAT
EST:
gi|40303146|gb|CK347533.1|CK347533EST: GCGAGCCATGCCCAATGTGCTTTGGTGCAGTTCATCTCTCCCGAATCAAG AGGCTGGTTTATGGGGCCAAGGCAGAGGCTGCCATCGCCATTGGATTTGAT
genomic: GCGAGCCATGCCCAATGTGCTTTGGTGCAGTTCATCTCTCCCGAATCAAGgttcgtactt ... cttgcaacagAGGCTGGTTTATGGGGCCAAGGCAGAGGCTGCCATCGCCATTGGATTTGAT
EST:
gi|17921800|gb|BM259451.1|BM259451EST: CCAATGTGCTTTGGTGCAGTTCATCTCTCCCGAATCAAG AGGCTGGTTTATGGGGCCAAGGCAGAGGCTGCCATCGCCATTGGATTTGAT
genomic: CCAATGTGCTTTGGTGCAGTTCATCTCTCCCGAATCAAGgttcgtactt ... cttgcaacagAGGCTGGTTTATGGGGCCAAGGCAGAGGCTGCCATCGCCATTGGATTTGAT
EST:
gi|32919559|gb|CF024371.1|CF024371EST: GCGAGCCATGCCCAATGTGCTTTGGTGCAGTTCATCTCTCCCGAATCAAG AGGCTGGTTTATGGGGCCAAGGCAGAGGCTGCCATCGCCATTGGATTTGAT
genomic: GCGAGCCATGCCCAATGTGCTTTGGTGCAGTTCATCTCTCCCGAATCAAGgttcgtactt ... cttgcaacagAGGCTGGTTTATGGGGCCAAGGCAGAGGCTGCCATCGCCATTGGATTTGAT
EST:
gi|17921473|gb|BM259124.1|BM259124EST: CCCAATGTGCTTTGGTGCAGTTCATCTCTCCCGAATCAAG AGGCTGGTTTATGGGGCCAAGGCAGAGGCTGCCATCGCCATTGGATTTGAT
genomic: CCCAATGTGCTTTGGTGCAGTTCATCTCTCCCGAATCAAGgttcgtactt ... cttgcaacagAGGCTGGTTTATGGGGCCAAGGCAGAGGCTGCCATCGCCATTGGATTTGAT
EST:
gi|37394241|gb|CF634392.1|CF634392EST: GCGAGCCATGCCCAATGTGCTTTGGTGCAGTTCATCTCTCCCGAATCAAG AGGCTGGTTTATGGGGCCAAGGCAGAGGCTGCCATCGCCATTGGATTTGAT
genomic: GCGAGCCATGCCCAATGTGCTTTGGTGCAGTTCATCTCTCCCGAATCAAGgttcgtactt ... cttgcaacagAGGCTGGTTTATGGGGCCAAGGCAGAGGCTGCCATCGCCATTGGATTTGAT
EST:
gi|87298774|gb|DY470777.1|DY470777EST: GCGAGCCATGCCCAATGTGCTTTGGTGCAGTTCATCTCTCCCGAATCAAG AGGCTGGTTTATGGGGCCAAGGCAGAGGCTGCCATCGCCATTGGATTTGAT
genomic: GCGAGCCATGCCCAATGTGCTTTGGTGCAGTTCATCTCTCCCGAATCAAGgttcgtactt ... cttgcaacagAGGCTGGTTTATGGGGCCAAGGCAGAGGCTGCCATCGCCATTGGATTTGAT
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),
47 (downstream exon)
Score:
115CAAAAAGCTTGGGAAAATTGAGCTCTCAGACTGCGAAATTTACGCGTCCTGCGAGCCATGCCCAATGTGCTTTGGTGCAGTTCATCTCTCCCGAATCAAGgttcgtactt ... cttgcaacagAGGCTGGTTTATGGGGCCAAGGCAGAGGCTGCCATCGCCATTGGATTTGATGACTTCATTGCAGATGCTCTGAGAGGCACTGGGTTCTACCAGAAGGCCA
Block sizes:
49 (upstream exon),
49 (downstream exon)
Score:
310CAAAAAGCTTGGGAAAATTGAGCTCTCAGACTGCGAAATTTACGCGTCCTGCGAGCCATGCCCAATGTGCTTTGGTGCAGTTCATCTCTCCCGAATCAAGgttcgtactt ... cttgcaacagAGGCTGGTTTATGGGGCCAAGGCAGAGGCTGCCATCGCCATTGGATTTGATGACTTCATTGCAGATGCTCTGAGAGGCACTGGGTTCTACCAGAAGGCCA
Block sizes:
49 (upstream exon),
49 (downstream exon)
Score:
243CAAAAAGCTTGGGAAAATTGAGCTCTCAGACTGCGAAATTTACGCGTCCTGCGAGCCATGCCCAATGTGCTTTGGTGCAGTTCATCTCTCCCGAATCAAGgttcgtactt ... cttgcaacagAGGCTGGTTTATGGGGCCAAGGCAGAGGCTGCCATCGCCATTGGATTTGATGACTTCATTGCAGATGCTCTGAGAGGCACTGGGTTCTACCAGAAGGCCA
Block sizes:
49 (upstream exon),
49 (downstream exon)
Score:
227CAAAAAGCTTGGGAAAATTGAGCTCTCAGACTGCGAAATTTACGCGTCCTGCGAGCCATGCCCAATGTGCTTTGGTGCAGTTCATCTCTCCCGAATCAAGgttcgtactt ... cttgcaacagAGGCTGGTTTATGGGGCCAAGGCAGAGGCTGCCATCGCCATTGGATTTGATGACTTCATTGCAGATGCTCTGAGAGGCACTGGGTTCTACCAGAAGGCCA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gcatagctggagcttattgagtgttgtctaaacatgcctactcctcttgcaacagAGGCTGGTTTATGGGGCCAAGGCAGAGGCTGCCATCGCCATTGGATTTGATGACTTCATTGCAGATGCTCTGAGAGGCACTGGGTTCTACCAGAAGGCCA
gtctaaa putative branch site (score: 227)
tgcctactcctctt putative PPT
ttattga 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttcgtactttactgttctgactgattgcctaaaatgattaagcatagctggagcttattgagtgttgtctaaacatgcctactcctcttgcaacagAGGCTGGTTTATGGGGCCAAGGCAGAGGCTGCCATCGCCATTGGATTTGATGACTTCATTGCAGATGCTCTGAGAGGCACTGGGTTCTACCAGAAGGCCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG