Sequence
atgc intronic sequence ATGC exonic sequencegtatcaccttttctgtttcacacattttttcctctttctgcttgttgatagtgtgttctggcctttttggggtgtaaattttattttgtctggtcaagGTTGTTGCAATAGCATCAAATGCATTGGAGACCTTCAAAAACGACGCCAAAAAGATGGTCGTTGCGCTTGTTGATATGGAACGTGCTTTTGTTCCTCCCC
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GRMZM2G157462_T01 (Zea mays), 3'ss of exon 11
lower sequence: LOC_Os06g13820.1 (Oryza sativa), 3'ss of exon 11
gtatcaccttttctgtttcacacattttttcctctt--tctgcttgttgata--gtgtgttctggcctttttggggtgtaaattttat-tttgtctggtcaagGTTGTTGCAATAGCATCAAATGCATTGGAGACCTTCAAAAACGACGCCAAAAAGATGGTCGTTGCGCTTGTTGATATGGAACGTGCTTTTGTTCCTCCCC
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gtatcacctag-ctattttagagtttctttcctttcgagtttcacgttggtagagtttattgttgactgatgtgagtaaaaaatctatgtttcctttcgcaagGTCATTGCAATAGCATCAAATGCACTAGACAGCTTCAAAAATGATGCAAAAAAGATGGTTGTTGCACTTGTTGATATGGAGCGCGCCTTTGTTCCTCCTC
upper sequence: GRMZM2G157462_T01 (Zea mays), 3'ss of exon 11
lower sequence: GLYMA07G40300.1 (Glycine max), 3'ss of exon 11
gtatcaccttttctgtttcacacattttttcctctttctgcttgttgatagtgtgttctggcctttttggggtgtaaattttattttgtctggtcaagGTTGTTGCAATAGCATCAAATGCATTGGAGACCTTCAAAAACGACGCCAAAAAGATGGTCGTTGCGCTTGTTGATATGGAACGTGCTTTTGTTCCTCCCC
||| || | | | | | | | || | || || || | | | | || | ||| | || || ||| | | |||| ||||| ||| || | ||| | || ||||| || ||||||| ||||| ||||| || ||||||||||| ||||| |||||||||||||
gtaacaatgctgtgctgtaagttacatgtaacttggtttgttttttagaaat-tatcttgctcattt---gttgcaattttca--------------gATTGTGGCAATTGCAAGTTCAGCCCTAGAGGCATTTAAAAATGAATCCAAAAAAATGGTGGTTGCACTAGTTGATATGGAGCGTGCATTTGTTCCTCCCC
upper sequence: GRMZM2G157462_T01 (Zea mays), 3'ss of exon 11
lower sequence: Vv12s0035g01740.t01 (Vitis vinifera), 3'ss of exon 11
------------------gtatcaccttttctgtttcacacattttttcctctt-tctgcttg--ttgatagtgt----gttctggcct------ttttggggtgtaaatt--ttattttg----tctggtcaagGTTGTTGCAATAGCATCAAATGCATTGGAGACCTTCAAAAACGACGCCAAAAAGATGGTCGTTGCGCTTGTTGATATGGAACGTGCTTTTGTTCCTCCCC
| | | |||| | ||| | | ||| |||| | | || || |||||| | | |||| | | ||||| ||| || | || | | | | | ||||||| ||||| ||||| | |||| |||| || || || || || || || ||||| ||||| |||||||||||||| ||||| |||||||| || |
gtaatcatgctgcaaatgctgcccctttttttttttaagagattccctcctttgatatgtttaatttgatatttttcaagttcaagtttgttggcttttgtggtacaactcacttgtcataaatttttaaaccagGTTGTGGCAATTGCATCTACTGCACTGGAAGGGTTTAAGAATGAGGCAAAGAAAATGGTTGTTGCACTTGTTGATATGGAGCGTGCATTTGTTCCCCCTC
upper sequence: GRMZM2G157462_T01 (Zea mays), 3'ss of exon 11
lower sequence: PP1S109_214V6.1 (Physcomitrella patens), 3'ss of exon 11
------------------------------------gtatcaccttttctgttt-cacacatttt-----ttcctctttctgcttg---ttgatagtgtgttctggcctttttggggtgtaaattttattttgtctggtca------agGTTGTTGCAATAGCATCAAATGCATTGGAGACCTTCAAAAACGACGCCAAAAAGATGGTCGTTGCGCTTGTTGATATGGAACGTGCTTTTGTTCCTCCCC
| | || | || | || | ||| | | ||||| | ||| || | | ||| || | || | | || ||| | || | | | || ||||||| || || | ||| |||| | | | || || || || ||||| |||||||||||||||||||| ||||| ||| |||| || |
gtgcttatagatttatctctttctactatcaaatgttcactaaattctgtgactgcaaaaattatagttacccatctttttcattgaatttcacacaatgtgcttgggcttacagtattcaatggttactcggtgttataatcctgcagATTGTTGCCATTGCTACTGCTGCGCTGGATGAGTATAGAGCAGAAGCAAAGAAAATGGTTGTTGCGCTTGTTGATATGGAGCGTGCATTTATTCCCCCTCMapped 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|211286766|gb|FK982432.1|FK982432EST: CCGCAAATGCCACACCAGGACTTGGGAGATATCCTCCATTCAAGCGTGAG GTTGTTGCAATAGCATCAAATGCATTGGAGACCTTCAAAAACGACGCCAAA
genomic: CCGCAAATGCCACACCAGGACTTGGGAGATATCCTCCATTCAAGCGTGAGgtatcacctt ... tctggtcaagGTTGTTGCAATAGCATCAAATGCATTGGAGACCTTCAAAAACGACGCCAAA
EST:
gi|9254689|gb|BE345157.1|BE345157EST: CCGCAAATGCCACACCAGGACTTGGGAGATATCCTCCATTCAAGCGTGAG GTTGTTGCAATAGCATCAAATGCATTGGAGACCTTCAAAAACGACGCCAAA
genomic: CCGCAAATGCCACACCAGGACTTGGGAGATATCCTCCATTCAAGCGTGAGgtatcacctt ... tctggtcaagGTTGTTGCAATAGCATCAAATGCATTGGAGACCTTCAAAAACGACGCCAAA
EST:
gi|211286763|gb|FK982429.1|FK982429EST: CCGCAAATGCCACACCGGGACTTGGGAGATATCCTCCATTCAAGCGTGAG GTTGTTGCAATAGCATCAAATGCATTGGAGACCTTCAAAAACGACGCCAAA
genomic: CCGCAAATGCCACACCAGGACTTGGGAGATATCCTCCATTCAAGCGTGAGgtatcacctt ... tctggtcaagGTTGTTGCAATAGCATCAAATGCATTGGAGACCTTCAAAAACGACGCCAAA
EST:
gi|87155357|gb|DY400146.1|DY400146EST: CCGCAAATGCCACACCAGGACTTGGGAGATATCCTCCATTCAAGCGTGAG GTTGTTGCAATAGCATCAAATGCATTGGAGACCTTCAAAAACGACGCCAAA
genomic: CCGCAAATGCCACACCAGGACTTGGGAGATATCCTCCATTCAAGCGTGAGgtatcacctt ... tctggtcaagGTTGTTGCAATAGCATCAAATGCATTGGAGACCTTCAAAAACGACGCCAAA
EST:
gi|30306992|gb|CD001665.1|CD001665EST: CCGCAAATGCCACACCAGGACTTGGGAGATATCCTCCATTCAAGCGTGAG GTTGTTGCAATAGCATCAAATGCATTGGAGACCTTCAAAAACGACGCCAAA
genomic: CCGCAAATGCCACACCAGGACTTGGGAGATATCCTCCATTCAAGCGTGAGgtatcacctt ... tctggtcaagGTTGTTGCAATAGCATCAAATGCATTGGAGACCTTCAAAAACGACGCCAAA
EST:
gi|211132359|gb|FK982426.1|FK982426EST: CCGCAAATGCCACACCAGGACTTGGGAGATATCCTCCATTCAAGCGTGAG GTTGTTGCAATAGCATCAAATGCATTGGAGACCTTCAAAAACGACGCCAAA
genomic: CCGCAAATGCCACACCAGGACTTGGGAGATATCCTCCATTCAAGCGTGAGgtatcacctt ... tctggtcaagGTTGTTGCAATAGCATCAAATGCATTGGAGACCTTCAAAAACGACGCCAAA
EST:
gi|31361304|gb|CD445661.1|CD445661EST: CCGCAAATGCCACACCAGGACTTGGGAGATATCCTCCATTCAAGCGTGAG GTTGTTGCAATAGCATCAAATGCATTGGAGACCTTGGAGAACGACGCCAAA
genomic: CCGCAAATGCCACACCAGGACTTGGGAGATATCCTCCATTCAAGCGTGAGgtatcacctt ... tctggtcaagGTTGTTGCAATAGCATCAAATGCATTGGAGACCTTCAAAAACGACGCCAAA
EST:
gi|31354322|gb|CD438679.1|CD438679EST: CCGCAAATGCCATACCAGGACTTGGGAGATATCCTCCATTCAAGCGTGAG GTTGTTGCAATAGCATCAAATGCATTGGAGACCTTCAAAAACGACGCCAAA
genomic: CCGCAAATGCCACACCAGGACTTGGGAGATATCCTCCATTCAAGCGTGAGgtatcacctt ... tctggtcaagGTTGTTGCAATAGCATCAAATGCATTGGAGACCTTCAAAAACGACGCCAAA
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:
330GTTCATCGTGTATTGTTAGACATAGTCAATGCTTCCGCAAATGCCACACCAGGACTTGGGAGATATCCTCCATTCAAGCGTGAGgtatcacctt ... tctggtcaagGTTGTTGCAATAGCATCAAATGCATTGGAGACCTTCAAAAACGACGCCAAAAAGATGGTCGTTGCGCTTGTTGATATGGAACGTGCTTTTGTTCCTCCCC
Block sizes:
49 (upstream exon),
49 (downstream exon)
Score:
406GTTCATCGTGTATTGTTAGACATAGTCAATGCTTCCGCAAATGCCACACCAGGACTTGGGAGATATCCTCCATTCAAGCGTGAGgtatcacctt ... tctggtcaagGTTGTTGCAATAGCATCAAATGCATTGGAGACCTTCAAAAACGACGCCAAAAAGATGGTCGTTGCGCTTGTTGATATGGAACGTGCTTTTGTTCCTCCCC
Block sizes:
49 (upstream exon),
49 (downstream exon)
Score:
425GTTCATCGTGTATTGTTAGACATAGTCAATGCTTCCGCAAATGCCACACCAGGACTTGGGAGATATCCTCCATTCAAGCGTGAGgtatcacctt ... tctggtcaagGTTGTTGCAATAGCATCAAATGCATTGGAGACCTTCAAAAACGACGCCAAAAAGATGGTCGTTGCGCTTGTTGATATGGAACGTGCTTTTGTTCCTCCCC
Block sizes:
49 (upstream exon),
49 (downstream exon)
Score:
261GTTCATCGTGTATTGTTAGACATAGTCAATGCTTCCGCAAATGCCACACCAGGACTTGGGAGATATCCTCCATTCAAGCGTGAGgtatcacctt ... tctggtcaagGTTGTTGCAATAGCATCAAATGCATTGGAGACCTTCAAAAACGACGCCAAAAAGATGGTCGTTGCGCTTGTTGATATGGAACGTGCTTTTGTTCCTCCCC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gttgatagtgtgttctggcctttttggggtgtaaattttattttgtctggtcaagGTTGTTGCAATAGCATCAAATGCATTGGAGACCTTCAAAAACGACGCCAAAAAGATGGTCGTTGCGCTTGTTGATATGGAACGTGCTTTTGTTCCTCCCC
tgttgat putative branch site (score: 261)
ttttgtct putative PPT
tgtaaattttattttg 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatcaccttttctgtttcacacattttttcctctttctgcttgttgatagtgtgttctggcctttttggggtgtaaattttattttgtctggtcaagGTTGTTGCAATAGCATCAAATGCATTGGAGACCTTCAAAAACGACGCCAAAAAGATGGTCGTTGCGCTTGTTGATATGGAACGTGCTTTTGTTCCTCCCC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG