Sequence
atgc intronic sequence ATGC exonic sequencegttcggtgctctttcactagtgctatagctgggtgtttttttttcttgtaagtggtcatcctgcttacataagtgtgattttgccttgatgcagATATCCTCCTCCTTGATGTGGCTCCTCTCACCCTGGGTATTGAGACCGTCGGTGGAGTCATGACCAAGTTGATCCCGAGGAACACTGTCATCCCGACCAA
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GRMZM2G415007_T01 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os02g02410.1 (Oryza sativa), 3'ss of exon 5
gttcggtgctctttcactagtgctatagctgggtgtttttttttcttgtaagtggtcatcctgcttaca-taagtgtgattttgccttg--atgcagATATCCTCCTCCTTGATGTGGCTCCTCTCACCCTGGGTATTGAGACCGTCGGTGGAGTCATGACCAAGTTGATCCCGAGGAACACTGTCATCCCGACCAA
||||| || |||| | | || ||| | || | || ||| || | | | ||| ||| ||| | ||||||||||| ||||| |||||||| || || ||||| ||||| ||||| ||||||||||||||||||||||||||||| |||||||| |||||||| |||||
gttcgac-cttgatcacatacatagtcctttgg-gttggtaacaactgcgatcatctgtcttgcatatacttatcgtgctttgattttggtacgcagATATCCTTCTCCTGGATGTGGCACCCCTTACCCTCGGTATCGAGACTGTCGGTGGAGTCATGACCAAGTTGATCCCCAGGAACACCGTCATCCCCACCAA
upper sequence: GRMZM2G415007_T01 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA05G36620.1 (Glycine max), 3'ss of exon 5
------------gttcggt-gctctt---tcactagtgctatagc--tgggtgtttttttttcttgtaagtggt----catcctgcttac--ataagtgtgattttgccttgatgcagATATCCTCCTCCTTGATGTGGCTCCTCTCACCCTGGGTATTGAGACCGTCGGTGGAGTCATGACCAAGTTGATCCCGAGGAACACTGTCATCCCGACCAA
|| || ||| || | ||| || | || | | || ||| | || | | ||| ||| | || |||| | || |||| ||||| ||||| ||||||||||| ||||| || || ||||| || || |||||||||||||| |||||||| || || |||||||| ||||| |||||
gtaccgtagtctgtaatgtagcttttaaattacttgtcccgaagtcataaatattatttacgcaattagattgctaagcataacactttctaatcgttgtgtggcaatatctatccagACATCCTTCTCCTGGATGTGGCTCCCCTCACTCTCGGAATTGAAACTGTTGGTGGAGTCATGACAAAGTTGATTCCCAGAAACACTGTTATCCCAACCAA
upper sequence: GRMZM2G415007_T01 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA08G02940.1 (Glycine max), 3'ss of exon 5
gttcggtgctctttcactagtgctatagctgggtgtttttttttcttgtaagtggtcatcctgcttacataagtgtgattttgccttgatgcagATATCCTCCTCCTTGATGTGGCTCCTCTCACCCTGGGTATTGAGACCGTCGGTGGAGTCATGACCAAGTTGATCCCGAGGAACACTGTCATCCCGACCAA
|| | | ||| | | | ||| ||| || || |||| | | || || || |||| || || |||||||||| ||||| ||||||||||| ||||| || || ||||| || || |||||||||||||| |||||||| || || |||||||| |||||||||||
gtaccatagtctgta---aatattatttatggaagtagattgc-----taagca-ttacactttcta-attgttgtgtggcaatctctatccagATATCCTTCTCCTGGATGTGGCTCCCCTCACTCTCGGAATTGAAACTGTTGGTGGAGTCATGACAAAGTTGATTCCCAGAAACACTGTTATCCCGACCAA
upper sequence: GRMZM2G415007_T01 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA08G02960.1 (Glycine max), 3'ss of exon 5
----------------gttcggtgctctttcactagtgctatagc--tgggtgtttttttttcttgtaagtggt----catcctgct--tacataagtgtgattttgccttgatgcagATATCCTCCTCCTTGATGTGGCTCCTCTCACCCTGGGTATTGAGACCGTCGGTGGAGTCATGACCAAGTTGATCCCGAGGAACACTGTCATCCCGACCAA
| | ||| | ||| || | | | | || ||| | | ||| | || ||| ||| ||| |||| | || ||| |||||||||| ||| | ||||||||||| |||||||| || ||||| || || ||||| || ||||| |||||||| || || |||||||| ||||| |||||
gtactgtagtctgtaatctaacttctcaattacttgtccagaaatcataaatattatttatgcaagtagattgtgacacattacgctgtctcattgttgtgtggctctctggatccagATATCCTTCTCTTGGATGTGGCTCCCCTCACCCTTGGAATTGAAACTGTTGGTGGGGTGATGACGAAGTTGATTCCCAGAAACACTGTTATCCCTACCAA
upper sequence: GRMZM2G415007_T01 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA05G36600.1 (Glycine max), 3'ss of exon 5
---------------gttcggtgctctttcactagtgctatag--ctgggtgtttttttttcttgtaagtggtcatcc------tgcttacataagtgtgattttgccttgatgcagATATCCTCCTCCTTGATGTGGCTCCTCTCACCCTGGGTATTGAGACCGTCGGTGGAGTCATGACCAAGTTGATCCCGAGGAACACTGTCATCCCGACCAA
| | ||| || | | || | || ||| | | ||| | | || | | ||| |||| | || ||| |||||||||| ||| | ||||||||||| |||||||| || ||||| || || ||||| || ||||| |||||||| || || |||||||| ||||| |||||
gtactacagtctgtaatctaacttctcattacttgtccagaaatcctaaatattatttatgcaagtagattgccacgcattacactttctcattgttgtgtggctctctggatccagATATCCTTCTCTTGGATGTGGCTCCCCTCACCCTTGGAATTGAAACTGTTGGTGGGGTGATGACGAAGTTGATTCCCAGAAACACTGTTATCCCTACCAA
upper sequence: GRMZM2G415007_T01 (Zea mays), 3'ss of exon 5
lower sequence: Vv16s0098g01580.t01 (Vitis vinifera), 3'ss of exon 5
gttcggtgctctttc-actagtgctatagctgggtgtttttttttcttgtaagtggtcatcctgcttacataagtgtgattttgccttgatgcagATATCCTCCTCCTTGATGTGGCTCCTCTCACCCTGGGTATTGAGACCGTCGGTGGAGTCATGACCAAGTTGATCCCGAGGAACACTGTCATCCCGACCAA
|| | |||| | | || | || | | || | |||| || || || | | || |||||||||| ||| | ||||||||||| ||||| || |||||||| || || || || || |||||||| ||||| || || ||||| || ||||| |||||
-----gtattatttccatcctcaccatcttcgcagaaccttcaatggcatggttgaaagtt-tgctaactcttgttctgttgtttcatgtatcagATATCCTTCTCTTGGATGTGGCTCCACTCACTCTTGGTATTGAAACGGTTGGCGGGGTGATGACCAAATTGATTCCCAGAAACACCGTTATCCCAACCAA
upper sequence: GRMZM2G415007_T01 (Zea mays), 3'ss of exon 5
lower sequence: Vv02s0025g02140.t01 (Vitis vinifera), 3'ss of exon 5
gttcggtgctctttcactagtgct-atagctgggtgtttttttttcttgtaagtggtcatcctgcttacataagtgtgattttgccttgatgcagATATCCTCCTCCTTGATGTGGCTCCTCTCACCCTGGGTATTGAGACCGTCGGTGGAGTCATGACCAAGTTGATCCCGAGGAACACTGTCATCCCGACCAA
|| | | ||| ||| | | | | | || || | || || || | | | | | |||| || | |||||||||| || ||| | ||||||||||| ||||| || || ||||| ||||| ||||| || |||||||||||||| || ||||||||||| |||||||||||
gtatcatttccattctctatcaatgaccgatagatggttgtgcatcgagtgttgatgaatggtagacatttga-tatgatatttgttccatgcagATATTCTTCTCTTGGATGTGGCTCCGCTCACTCTTGGAATTGAAACCGTTGGTGGGGTGATGACCAAGTTGATTCCTAGGAACACTGTTATCCCGACCAA
upper sequence: GRMZM2G415007_T01 (Zea mays), 3'ss of exon 5
lower sequence: EFJ29073 (Selaginella moellendorffii), 3'ss of exon 5
gttcggtgctctttcactagtgctatagctgggtgtttttttttcttgtaagtggtcatcctgcttacataagtgtgattttgccttgatgcagATATCCTCCTCCTTGATGTGGCTCCTCTCACCCTGGGTATTGAGACCGTCGGTGGAGTCATGACCAAGTTGATCCCGAGGAACACTGTCATCCCGACCAA
|| ||| | || | || | |||||| || |||| || || | | || ||| || || ||| | || || || || || || |||||||| |||||||| |||||||| ||||||||| ||||||| |||||||||||||| ||||||||
----------------------gta-agcaaagacttgtcttcttttgtaatccatc--tgtgctaacgcgcgtc--------catcga--cagGCATTCTTCTCTTGGACGTTGCGCCCCTTACTCTGGGTATCGAGACCGTTGGTGGAGTGATGACCAAGCTGATCCCCAGGAACACTGTCATTCCGACCAAMapped 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|149067539|gb|EE157747.2|EE157747EST: CGCGGTGCAGGGAAGCATCTTGAGCGGCGAGGGTGGTGACGAGACAAAAG ATATCCTCCTCCTTGATGTGGCTCCTCTCACCCTGGGTATTGAGACCGTCG
genomic: CGCGGTGCAGGGAAGCATCTTGAGCGGCGAGGGTGGTGACGAGACAAAAGgttcggtgct ... cttgatgcagATATCCTCCTCCTTGATGTGGCTCCTCTCACCCTGGGTATTGAGACCGTCG
EST:
gi|211197978|gb|FL446530.1|FL446530EST: CGCGGTGCAGGGAAGCATCTTGAGCGGCGAGGGTGGTGACGAGACAAAAG ATATCCTCCTCCTTGATGTGGCTCCTCTCACCCTGGGTATTGAGACCGT
genomic: CGCGGTGCAGGGAAGCATCTTGAGCGGCGAGGGTGGTGACGAGACAAAAGgttcggtgct ... cttgatgcagATATCCTCCTCCTTGATGTGGCTCCTCTCACCCTGGGTATTGAGACCGT
EST:
gi|20300524|gb|BQ163467.1|BQ163467EST: CGCGGTGCAGGGAAGCATCTTGAGCGGCGAGGGTGGTGACGAGACAAAAG ATATCCTCCTCCTTGACGTGGCTCCTCTCACCCTGGGTATTGAGACCGTCG
genomic: CGCGGTGCAGGGAAGCATCTTGAGCGGCGAGGGTGGTGACGAGACAAAAGgttcggtgct ... cttgatgcagATATCCTCCTCCTTGATGTGGCTCCTCTCACCCTGGGTATTGAGACCGTCG
EST:
gi|14529531|gb|BI096664.1|BI096664EST: CGCGGTGCAGGGAAGCATCTTGAGCGGCGAGGGTGGTGACGAGACAAAAG ATATCCTCCTCCTTGACGTGGCTCCTCTCACCCTGGGTATTGAGACCGTCG
genomic: CGCGGTGCAGGGAAGCATCTTGAGCGGCGAGGGTGGTGACGAGACAAAAGgttcggtgct ... cttgatgcagATATCCTCCTCCTTGATGTGGCTCCTCTCACCCTGGGTATTGAGACCGTCG
EST:
gi|87153886|gb|DY398675.1|DY398675EST: CGCGGTGCAGGGAAGCATCTTGAGCGGCGAGGGTGGTGACGAGACAAAAG ATATCCTCCTCCTTGACGTGGCTCCTCTCACCCTGGGTATTGAGACCGTCG
genomic: CGCGGTGCAGGGAAGCATCTTGAGCGGCGAGGGTGGTGACGAGACAAAAGgttcggtgct ... cttgatgcagATATCCTCCTCCTTGATGTGGCTCCTCTCACCCTGGGTATTGAGACCGTCG
EST:
gi|19770559|gb|BQ035280.1|BQ035280EST: CGCGGTGCAGGGAAGCATCTTGAGCGGCGAGGGTGGTGACGAGACAAAAG ATATCCTCCTCCTTGACGTGGCTCCTCTCACCCTGGGTATTGAGACCGTCG
genomic: CGCGGTGCAGGGAAGCATCTTGAGCGGCGAGGGTGGTGACGAGACAAAAGgttcggtgct ... cttgatgcagATATCCTCCTCCTTGATGTGGCTCCTCTCACCCTGGGTATTGAGACCGTCG
EST:
gi|211320987|gb|FL255017.1|FL255017EST: CGCGGTGCAGGGAAGCATCTTGAGCGGCGAGGGTGGTGACGAGACAAAAG ATATCCTCCTCCTTGATGTGGCTCCTCTCACCCTGGGTATTGAGACCGTCG
genomic: CGCGGTGCAGGGAAGCATCTTGAGCGGCGAGGGTGGTGACGAGACAAAAGgttcggtgct ... cttgatgcagATATCCTCCTCCTTGATGTGGCTCCTCTCACCCTGGGTATTGAGACCGTCG
EST:
gi|15198951|gb|BI423577.1|BI423577EST: CGCGGTGCA-GGAAGCATCTTGAGCGGCGAGGGTGGTGACGAGACAAAAG ATATCCTCCTCCTTGACGTGGCTCCTCTCACCCTGGGTATTGAGACCGTCG
genomic: CGCGGTGCAGGGAAGCATCTTGAGCGGCGAGGGTGGTGACGAGACAAAAGgttcggtgct ... cttgatgcagATATCCTCCTCCTTGATGTGGCTCCTCTCACCCTGGGTATTGAGACCGTCG
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:
312AAGGAGCCCAACAAGGGTGTGAACCCTGATGAGGCTGTTGCCTTTGGTGCCGCGGTGCAGGGAAGCATCTTGAGCGGCGAGGGTGGTGACGAGACAAAAGgttcggtgct ... cttgatgcagATATCCTCCTCCTTGATGTGGCTCCTCTCACCCTGGGTATTGAGACCGTCGGTGGAGTCATGACCAAGTTGATCCCGAGGAACACTGTCATCCCGACCAA
Block sizes:
49 (upstream exon),
48 (downstream exon)
Score:
379AAGGAGCCCAACAAGGGTGTGAACCCTGATGAGGCTGTTGCCTTTGGTGCCGCGGTGCAGGGAAGCATCTTGAGCGGCGAGGGTGGTGACGAGACAAAAGgttcggtgct ... cttgatgcagATATCCTCCTCCTTGATGTGGCTCCTCTCACCCTGGGTATTGAGACCGTCGGTGGAGTCATGACCAAGTTGATCCCGAGGAACACTGTCATCCCGACCAA
Block sizes:
47 (upstream exon),
49 (downstream exon)
Score:
323AAGGAGCCCAACAAGGGTGTGAACCCTGATGAGGCTGTTGCCTTTGGTGCCGCGGTGCAGGGAAGCATCTTGAGCGGCGAGGGTGGTGACGAGACAAAAGgttcggtgct ... cttgatgcagATATCCTCCTCCTTGATGTGGCTCCTCTCACCCTGGGTATTGAGACCGTCGGTGGAGTCATGACCAAGTTGATCCCGAGGAACACTGTCATCCCGACCAA
Block sizes:
49 (upstream exon),
49 (downstream exon)
Score:
1545AAGGAGCCCAACAAGGGTGTGAACCCTGATGAGGCTGTTGCCTTTGGTGCCGCGGTGCAGGGAAGCATCTTGAGCGGCGAGGGTGGTGACGAGACAAAAGgttcggtgct ... cttgatgcagATATCCTCCTCCTTGATGTGGCTCCTCTCACCCTGGGTATTGAGACCGTCGGTGGAGTCATGACCAAGTTGATCCCGAGGAACACTGTCATCCCGACCAA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttttcttgtaagtggtcatcctgcttacataagtgtgattttgccttgatgcagATATCCTCCTCCTTGATGTGGCTCCTCTCACCCTGGGTATTGAGACCGTCGGTGGAGTCATGACCAAGTTGATCCCGAGGAACACTGTCATCCCGACCAA
ttttgcctt CT-rich tract
ttacataa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttcggtgctctttcactagtgctatagctgggtgtttttttttcttgtaagtggtcatcctgcttacataagtgtgattttgccttgatgcagATATCCTCCTCCTTGATGTGGCTCCTCTCACCCTGGGTATTGAGACCGTCGGTGGAGTCATGACCAAGTTGATCCCGAGGAACACTGTCATCCCGACCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG