Sequence
atgc intronic sequence ATGC exonic sequencegtaatttcgagctattctcctgttaatatacatcagttagctccaaaggttgctgcgcccctctcctaacagctgtgttactatatgaccttttgcagGTGTATGTGACCATGTACCTGAATGACTGCCAACGCACTGCATTCTATGAGGGAATTGGTCTGGACACCAAAGAATTCGACATGCATGTGATCATCGAGG
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GRMZM2G081462_T02 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os01g17170.1 (Oryza sativa), 3'ss of exon 3
gtaat-ttcgagctattctcctgttaatata---catcagttagctccaaaggttg---ctgcgcccctctcctaacagctgtgttactatatgaccttttgcagGTGTATGTGACCATGTACCTGAATGACTGCCAACGCACTGCATTCTATGAGGGAATTGGTCTGGACACCAAAGAATTCGACATGCATGTGATCATCGAGG
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gtaatctccgagctattccgttgtttgcatggaccaacagttcacactgaagattgttactgtgctcctcttctaacagtt---tttgtgtgtgatcctttgcagGTGTATGTGACCATGTACCTAAATGATTGCCAACGTACTACATTCTATGAAGGGATTGGTCTGGACACCAAAGAATTCGACATGCATGTGATAATTGAG-
upper sequence: GRMZM2G081462_T02 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA03G27380.1 (Glycine max), 3'ss of exon 3
---gtaatttcgagctattctcctgttaatatacatcagttagctccaaaggttgctgcgcccctctcctaacagctgtgttactatatgaccttttgcagGTGTATGTGACCATGTACCTGAATGACTGCCAACGCACTGCATTCTATGAGGGAATTGGTCTGGACACCAAAGAATTCGACATGCATGTGATCATCGAGG
| || || || | || |||| | | || | | | | || | | || ||| | || | ||||||| ||||| || ||||| || ||||| |||||||| || || ||||| || || ||||| || |||| |||||||| ||||||||||| || ||||||
gccgaaacagatcatgtttgtcacatctatcaacataaagttactgttttaatccttcttaactgttacttaaaacttggttgtcaaatt-tgtcctgcagGTTTATGTCACAATGTATCTCAATGATTGCCAACGTACAGCTTTCTACGAAGGCATTGGACTTAACACAAAAGAATTTGACATGCATGTCATTATCGAG-
upper sequence: GRMZM2G081462_T02 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA19G30350.1 (Glycine max), 3'ss of exon 3
gtaatttcgagctattctcctgttaatatacatcagttagctccaaaggttgctgcgcccctc-----tcctaacagctgtgttactatatgaccttttgcagGTGTATGTGACCATGTACCTGAATGACTGCCAACGCACTGCATTCTATGAGGGAATTGGTCTGGACACCAAAGAATTCGACATGCATGTGATCATCGAGG
| || || | | | || |||| | | ||| | || | || | || ||| | | || ||||||||| ||||| || ||||| || ||||| |||||||| || || |||||||| || ||||| || |||| |||||||| ||||||||||| |||||||||
-cagccagaagagatcacatttgtcacatctatcaataaaaagttgctgttttaatccttcttaactgtacttcaaacttggttgccaaat--ttgtttgcagGTTTATGTTACAATGTATCTCAATGATTGCCAACGTACAGCTTTCTATGAAGGCATTGGACTTAACACAAAAGAATTTGACATGCATGTCATCATCGAG-
upper sequence: GRMZM2G081462_T02 (Zea mays), 3'ss of exon 3
lower sequence: Vv08s0040g00390.t01 (Vitis vinifera), 3'ss of exon 3
----------------------------------------------------gtaatttcgagctattctcctgtta-atatacatcagttagctccaaaggttgctgcgcccctctcctaacagctgtgttactatatgacctt---ttgcagGTGTATGTGACCATGTACCTGAATGACTGCCAACGCACTGCATTCTATGAGGGAATTGGTCTGGACACCAAAGAATTCGACATGCATGTGATCATCGAGG
| || | | | || ||| | | || ||| || ||| | | || | || || | | ||| | || |||||||| ||||| || |||||||| ||||| ||||| || || | |||||||| |||||||| || |||| |||||||| ||||||||||||||||| |||
gtaattatagtataataagtttctacattcaattgtatactagattgcaaatattatcttaattttttaccctagtgtgtttaaatct-ttggcttctcgagaacctctgggattcctctggtcctcttatgacttcccaaatttgtcttgcagGTTTATGTAACAATGTACCTCAATGATTGCCAGCGTACGGATTTCTATGAAGGAATTGGGCTCAACACAAAAGAATTTGACATGCATGTGATCATAGAG-
upper sequence: GRMZM2G081462_T02 (Zea mays), 3'ss of exon 3
lower sequence: PP1S97_248V6.1 (Physcomitrella patens), 3'ss of exon 2
------gtaatttcgagctattctcctgttaatatacatcagttagctccaaaggttgctgcgcccctctcctaacagctgtgttactatatgaccttttgcagGTGTATGTGACCATGTACCTGAATGACTGCCAACGCACTGCATTCTATGAGGGAATTGGTCTGGACACCAAAGAATTCGACATGCATGTGATCATCGAGG
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ccatgaccacattggagtgccaaacctaacattagtggaggaatttttttgagtgtagaggacttcttgcctgaatagctggaat-ctactt---tttgtgcagGTGTATGTGACAATGTACCTGAATGATGTTCAAAGAACCTCATTCTATGAGGGGATTGGCCTGAACACCCGCGACTTCGATATGCATGTCATTGTTGAGG
upper sequence: GRMZM2G081462_T02 (Zea mays), 3'ss of exon 3
lower sequence: EFJ28505 (Selaginella moellendorffii), 3'ss of exon 3
gtaatttcgagctattctcctgttaatatacatcagttagctccaaaggttgctgcgcccctctcctaacagctgtgttactatatgaccttttgcagGTGTATGTGACCATGTACCTGAATGACTGCCAACGCACTGCATTCTATGAGGGAATTGGTCTGGACACCAAAGAATTCGACATGCATGTGATCATCGAGG
|| | || | || || || | | | || | | || || |||||||| ||||| |||||||| |||||||||||| | ||||| || || || ||||| || || ||||| ||||| |||||||||||||| |||||||||
---------------------------gtaaagcaa--acctttggctcttcttggaa---tttttagatgctcatgcttccgctcttgctcttccagGTGTACGTGACAATGTACCTAAATGACTGCCAAAGAACTGCCTTTTACGAAGGAATAGGCCTCGACACTAAAGATTTCGACATGCATGTCATCATCGAG-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|78112391|gb|DV530785.1|DV530785EST: TCCTCAATGACTGGAAGGCCAAGCTCTGGTCACGGTTCTTCTGCCTCTCG GTGTATGTGACCATGTACCTGAATGACTGCCAACGCACTGCATTCTATGAG
genomic: TCCTCAATGACTGGAAGGCCAAGCTCTGGTCACGGTTCTTCTGCCTCTCGgtaatttcga ... ccttttgcagGTGTATGTGACCATGTACCTGAATGACTGCCAACGCACTGCATTCTATGAG
EST:
gi|32849293|gb|CD988974.1|CD988974EST: TCCTCAATGACTGGAAGGCCAAGCTCTGGTCACGGTTCTTCTGCCTCTCG GTGTATGTGACCATGT
genomic: TCCTCAATGACTGGAAGGCCAAGCTCTGGTCACGGTTCTTCTGCCTCTCGgtaatttcga ... ccttttgcagGTGTATGTGACCATGT
EST:
gi|76016942|gb|DT944112.1|DT944112EST: TCCTCAATGACTGGAAGGCCAAGCTCTGGTCACGGTTCTTCTGCCTCTCG GTGTATGTGACCATGTACCTGAATGACTGCCAACGCACTGCATTCTATGAG
genomic: TCCTCAATGACTGGAAGGCCAAGCTCTGGTCACGGTTCTTCTGCCTCTCGgtaatttcga ... ccttttgcagGTGTATGTGACCATGTACCTGAATGACTGCCAACGCACTGCATTCTATGAG
EST:
gi|78107168|gb|DV525586.1|DV525586EST: TCCTCAATGACTGGAAGGCCAAGCTCTGGTCACGGTTCTTCTGCCTCTCG GTGTATGTGACCATGTACCTGAATGACTGCCAACGCACTGCATTCTATGAG
genomic: TCCTCAATGACTGGAAGGCCAAGCTCTGGTCACGGTTCTTCTGCCTCTCGgtaatttcga ... ccttttgcagGTGTATGTGACCATGTACCTGAATGACTGCCAACGCACTGCATTCTATGAG
EST:
gi|32849718|gb|CD989399.1|CD989399EST: TCCTCAATGACTGGAAGGCCAAGCTCTGGTCACGGTTCTTCTGCCTCTCG GTGTATGTGACCATGTAC
genomic: TCCTCAATGACTGGAAGGCCAAGCTCTGGTCACGGTTCTTCTGCCTCTCGgtaatttcga ... ccttttgcagGTGTATGTGACCATGTAC
EST:
gi|93016118|gb|EB641638.1|EB641638EST: TCCTCAATGACTGGAAGGCCAAGCTCTGGTCACGGTTCTTCTGCCTCTCG GTGTATGTGACCATGTACCTGAATGACTGCCAACGCACTGCATTCTATGAG
genomic: TCCTCAATGACTGGAAGGCCAAGCTCTGGTCACGGTTCTTCTGCCTCTCGgtaatttcga ... ccttttgcagGTGTATGTGACCATGTACCTGAATGACTGCCAACGCACTGCATTCTATGAG
EST:
gi|149097284|gb|EE183107.2|EE183107EST: CCTNCA-TGACTGGGAGGCCAAGCTCTGGTCACGGTTCTTCTGCCTCTCG GTGTATGTGACCATGTACCTGAATGACTGCCAACGCACTGCATTCTATGAG
genomic: CCT-CAATGACTGGAAGGCCAAGCTCTGGTCACGGTTCTTCTGCCTCTCGgtaatttcga ... ccttttgcagGTGTATGTGACCATGTACCTGAATGACTGCCAACGCACTGCATTCTATGAG
EST:
gi|32845408|gb|CD985089.1|CD985089EST: TCCTCAATGACTGGAAGGCCAAGCTCTGGTCACGGTTCTTCTGCCTCTCG GTGTATGTGACCATGTA
genomic: TCCTCAATGACTGGAAGGCCAAGCTCTGGTCACGGTTCTTCTGCCTCTCGgtaatttcga ... ccttttgcagGTGTATGTGACCATGTA
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),
48 (downstream exon)
Score:
100GAACAGGCACGGCGACTTCTTCTCTGCCCTGCTCAAGGCTCAGCCGCAGTTCCTCAATGACTGGAAGGCCAAGCTCTGGTCACGGTTCTTCTGCCTCTCGgtaatttcga ... ccttttgcagGTGTATGTGACCATGTACCTGAATGACTGCCAACGCACTGCATTCTATGAGGGAATTGGTCTGGACACCAAAGAATTCGACATGCATGTGATCATCGAGG
Block sizes:
49 (upstream exon),
49 (downstream exon)
Score:
902GAACAGGCACGGCGACTTCTTCTCTGCCCTGCTCAAGGCTCAGCCGCAGTTCCTCAATGACTGGAAGGCCAAGCTCTGGTCACGGTTCTTCTGCCTCTCGgtaatttcga ... ccttttgcagGTGTATGTGACCATGTACCTGAATGACTGCCAACGCACTGCATTCTATGAGGGAATTGGTCTGGACACCAAAGAATTCGACATGCATGTGATCATCGAGG
Block sizes:
49 (upstream exon),
45 (downstream exon)
Score:
24GAACAGGCACGGCGACTTCTTCTCTGCCCTGCTCAAGGCTCAGCCGCAGTTCCTCAATGACTGGAAGGCCAAGCTCTGGTCACGGTTCTTCTGCCTCTCGgtaatttcga ... ccttttgcagGTGTATGTGACCATGTACCTGAATGACTGCCAACGCACTGCATTCTATGAGGGAATTGGTCTGGACACCAAAGAATTCGACATGCATGTGATCATCGAGG
Block sizes:
49 (upstream exon),
49 (downstream exon)
Score:
382GAACAGGCACGGCGACTTCTTCTCTGCCCTGCTCAAGGCTCAGCCGCAGTTCCTCAATGACTGGAAGGCCAAGCTCTGGTCACGGTTCTTCTGCCTCTCGgtaatttcga ... ccttttgcagGTGTATGTGACCATGTACCTGAATGACTGCCAACGCACTGCATTCTATGAGGGAATTGGTCTGGACACCAAAGAATTCGACATGCATGTGATCATCGAGG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.caaaggttgctgcgcccctctcctaacagctgtgttactatatgaccttttgcagGTGTATGTGACCATGTACCTGAATGACTGCCAACGCACTGCATTCTATGAGGGAATTGGTCTGGACACCAAAGAATTCGACATGCATGTGATCATCGAGG
tcctaac putative branch site (score: 382)
ccttttgc putative PPT
ttactatat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaatttcgagctattctcctgttaatatacatcagttagctccaaaggttgctgcgcccctctcctaacagctgtgttactatatgaccttttgcagGTGTATGTGACCATGTACCTGAATGACTGCCAACGCACTGCATTCTATGAGGGAATTGGTCTGGACACCAAAGAATTCGACATGCATGTGATCATCGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA