Sequence
atgc intronic sequence ATGC exonic sequencegtaatagtcggcaacttttttctgtctactggatctaatctatatatccttgtttcatacacgtttcaaatgtacagACAAGGACTGGGACGACATTAAGTTTGGTGTGGATAATCAAGTTGATTACTATGCTGTTTCCTTTGTGAAAGATGCTCAAGTTGTCCACGAACTCAAGGA
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GRMZM2G152686_T01 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os01g47080.1 (Oryza sativa), 3'ss of exon 4
gtaatagtcggcaacttttttctgtctactggatctaatctatatatccttgtttcatacacgttt--caaatgtacagACAAGGACTGGGACGACATTAAGTTTGGTGTGGATAATCAAGTTGATTACTATGCTGTTTCCTTTGTGAAAGATGCTCAAGTTGTCCACGAACTCAAGGA
||||||||| || ||| | |||| || | || | | | |||||||||| | | ||| || | |||||||||| ||||| || ||||||||||||||||| ||||||||||| |||||||| ||||| ||||| ||||||||||||||||| || ||| | |||||
gtaatagtcaaca------ttcatttcactgaatattat--aaacactcttgtttcattctcattttctgaacttgcagACAAGGATTGGGATGATATTAAGTTTGGTGTGGAGAATCAAGTTGACTACTATGCCGTTTCTTTTGTCAAAGATGCTCAAGTTGTGCATGAATTGAAGGA
upper sequence: GRMZM2G152686_T01 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA20G30430.1 (Glycine max), 3'ss of exon 4
--------------------------------------------------------------------------------gtaatagtcggcaacttttttctgtctactggatctaatctatatatccttg---tttcatacacgtttcaaatg--tacagACAAGGACTGGGACGACATTAAGTTTGGTGTGGATAATCAAGTTGATTACTATGCTGTTTCCTTTGTGAAAGATGCTCAAGTTGTCCACGAACTCAAGGA
| ||||| | | | || | | | | | | | | | | ||| || | | | |||||| ||||| ||||| ||||| || ||||| |||||||| ||||||| | |||||||||||| ||||| || ||||| ||||| || || ||||| ||| |
gttagattctggatcattattcctatacttgattgtttttttaattttaaaccatttcttctacatgcctctccatatgtttgggtactggcaaatgggtgaggatta--aggttttgttggtttcccaaggacatataatatttgtgttgatttgctacagAGAAGGATTGGGATGACATCAAATTTGGAGTGGATAACAAAGTTGACTTCTATGCTGTTTCTTTTGTTAAGGATGCACAAGTAGTTCATGAACTGAAGAA
upper sequence: GRMZM2G152686_T01 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA09G23150.1 (Glycine max), 3'ss of exon 4
----------------------------------------------------------------------gtaatagtcggcaacttttttctgtctactggatctaatctatatatccttgtttcatacacgtttcaaatgtacagACAAGGACTGGGACGACATTAAGTTTGGTGTGGATAATCAAGTTGATTACTATGCTGTTTCCTTTGTGAAAGATGCTCAAGTTGTCCACGAACTCAAGGA
|| | || | | | | | || || ||| | || ||| || | |||| ||||| ||||| || || |||||||| |||||||| ||||||| | ||||||||||||||||| || |||||| ||||||| || || || ||| |
gtcagaattcagattattgatcccaatcttgacgatgctctggtgtctatttctttgtgtgcctctagttgtgtgggagggtagttgctcaggattgatgttatggtggcttcctatggacataatattcacattaatttgttgcagAGAAGGATTGGGATGATATCAAGTTTGGAGTGGATAACAAAGTTGACTTTTATGCTGTTTCCTTTGTTAAGGATGCTGAAGTTGTTCATGAGCTGAAGAA
upper sequence: GRMZM2G152686_T01 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA10G37210.1 (Glycine max), 3'ss of exon 4
-------------------------------------------------------------------------gtaatagtcggcaacttttttctgtctactggatctaatctatatatcctt--------gtttcatacacgtttcaaatg--tacagACAAGGACTGGGACGACATTAAGTTTGGTGTGGATAATCAAGTTGATTACTATGCTGTTTCCTTTGTGAAAGATGCTCAAGTTGTCCACGAACTCAAGGA
||| | || ||| ||| | || | | | | | | | ||| || | | | |||||| ||||| ||||| ||||| || ||||| |||||||| ||||||| | |||||||||||| ||||| |||||||| ||||| || || ||||| ||| |
gttagattccggattattatttctatcttgattatttcttttaatgtttgtccatttcttctacatgcctctccatatatttgggtactgacaactgggtgagggttaaggttttgttggtttcccaaggacatataatatttgtgttgatttgctacagAGAAGGATTGGGATGACATCAAATTTGGAGTGGATAACAAAGTTGACTTCTATGCTGTTTCTTTTGTTAAAGATGCACAAGTAGTTCATGAACTGAAGAA
upper sequence: GRMZM2G152686_T01 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA16G28980.1 (Glycine max), 3'ss of exon 4
----------------------------------------------------------------------gtaatagtcggcaacttttttctgtctactggatctaatctatatatccttgtttcatacacgtttcaaatgtacagACAAGGACTGGGACGACATTAAGTTTGGTGTGGATAATCAAGTTGATTACTATGCTGTTTCCTTTGTGAAAGATGCTCAAGTTGTCCACGAACTCAAGGA
| | || | | | | | || | ||| | || ||| || | |||| ||||| ||||| || || |||||||| |||||||| ||||||| | |||||||||||||||||| || |||||| ||||||| || ||||| ||| |
gtcagaattcagattatgaatcccaatcttgacaatgctctagtgtctatttctttgtgtgccttgagttgcgtgggagggtagttgctcaggattgatgttatggtggtttcctatggacataatattcacattaatttgttgcagAGAAGGATTGGGATGATATCAAGTTTGGAGTGGATAACAAAGTTGACTTCTATGCTGTTTCCTTTGTTAAGGATGCTGAAGTTGTTCATGAACTGAAGAA
upper sequence: GRMZM2G152686_T01 (Zea mays), 3'ss of exon 4
lower sequence: AT5G52920.1 (Arabidopsis thaliana), 3'ss of exon 4
------------------------------------------gtaatagtcg----gcaacttttttctgtctactggatctaatctatatatccttgtttcatacacgtttcaaatgtacagACAAGGACTGGGACGACATTAAGTTTGGTGTGGATAATCAAGTTGATTACTATGCTGTTTCCTTTGTGAAAGATGCTCAAGTTGTCCACGAACTCAAGGA
| | || | | | | ||| |||| ||||| | || | ||| || ||| |||| ||||||||||| || ||||| ||||| ||||| || ||||||| | ||||| ||||||||||| ||||||||||||||||| ||||| | ||| |
gttcgaattttctgtttaccctctttttcactttttcttgttgctttggttgaagtgttgcatatttaagtctgaaagatcttactctgatgcttattttttgtaattattttcttgccgcagAGAAGGACTGGGAGGATATTAAATTTGGAGTGGAGAACAAAGTTGACTTTTATGCAGTTTCCTTTGTCAAAGATGCTCAAGTTGTACACGAGTTGAAGAAMapped 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|5296084|gb|AI782959.1|AI782959EST: GCGCCATCTGAATGTTCGTGGAAAGAGTGCAACCTTGCCATCAATAACTG ACAAGGACTGGGACGACATTAAGTTTGGNGTGGATAATCAAGTTGATTACT
genomic: GCGCCATCTGAATGTTCGTGGAAAGAGTGCAACCTTGCCATCAATAACTGgtaatagtcg ... aaatgtacagACAAGGACTGGGACGACATTAAGTTTGGTGTGGATAATCAAGTTGATTACT
EST:
gi|71426208|gb|DR807258.1|DR807258EST: CGCCATCTGAATGTTCGTGGGAAGAGTGCAACCTTGCCATNCA-TAACTG ACAAGGACTGGGACG
genomic: CGCCATCTGAATGTTCGTGGAAAGAGTGCAACCTTGCCAT-CAATAACTGgtaatagtcg ... aaatgtacagACAAGGACTGGGACG
EST:
gi|211141481|gb|FL154590.1|FL154590EST: GCGCCATCTGAATGTTCGTGGAAAGAGTGCAACCTTGCCATCAATAACTG ACAAGGACTGGGACGACATTAAGTTTGGTGTGGATAATCAAGTTGATTACT
genomic: GCGCCATCTGAATGTTCGTGGAAAGAGTGCAACCTTGCCATCAATAACTGgtaatagtcg ... aaatgtacagACAAGGACTGGGACGACATTAAGTTTGGTGTGGATAATCAAGTTGATTACT
EST:
gi|67025561|gb|CO454310.1|CO454310EST: GCGCCATCTGAATGTTCGTGGAAAGAGTGCAACCTTGCCATCAATAACTG ACAAGGACTGGGACGACATTAAGTTTGGTGTGGATAATCAAGTTGATTACT
genomic: GCGCCATCTGAATGTTCGTGGAAAGAGTGCAACCTTGCCATCAATAACTGgtaatagtcg ... aaatgtacagACAAGGACTGGGACGACATTAAGTTTGGTGTGGATAATCAAGTTGATTACT
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:
444GAAGATTCTGTGAAATGTGAAGTTATTGACGGTGGTGAATTGAAATCTAGGCGCCATCTGAATGTTCGTGGAAAGAGTGCAACCTTGCCATCAATAACTGgtaatagtcg ... aaatgtacagACAAGGACTGGGACGACATTAAGTTTGGTGTGGATAATCAAGTTGATTACTATGCTGTTTCCTTTGTGAAAGATGCTCAAGTTGTCCACGAACTCAAGGA
Block sizes:
49 (upstream exon),
47 (downstream exon)
Score:
343GAAGATTCTGTGAAATGTGAAGTTATTGACGGTGGTGAATTGAAATCTAGGCGCCATCTGAATGTTCGTGGAAAGAGTGCAACCTTGCCATCAATAACTGgtaatagtcg ... aaatgtacagACAAGGACTGGGACGACATTAAGTTTGGTGTGGATAATCAAGTTGATTACTATGCTGTTTCCTTTGTGAAAGATGCTCAAGTTGTCCACGAACTCAAGGA
Block sizes:
49 (upstream exon),
48 (downstream exon)
Score:
220GAAGATTCTGTGAAATGTGAAGTTATTGACGGTGGTGAATTGAAATCTAGGCGCCATCTGAATGTTCGTGGAAAGAGTGCAACCTTGCCATCAATAACTGgtaatagtcg ... aaatgtacagACAAGGACTGGGACGACATTAAGTTTGGTGTGGATAATCAAGTTGATTACTATGCTGTTTCCTTTGTGAAAGATGCTCAAGTTGTCCACGAACTCAAGGA
Block sizes:
49 (upstream exon),
49 (downstream exon)
Score:
865GAAGATTCTGTGAAATGTGAAGTTATTGACGGTGGTGAATTGAAATCTAGGCGCCATCTGAATGTTCGTGGAAAGAGTGCAACCTTGCCATCAATAACTGgtaatagtcg ... aaatgtacagACAAGGACTGGGACGACATTAAGTTTGGTGTGGATAATCAAGTTGATTACTATGCTGTTTCCTTTGTGAAAGATGCTCAAGTTGTCCACGAACTCAAGGA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgtctactggatctaatctatatatccttgtttcatacacgtttcaaatgtacagACAAGGACTGGGACGACATTAAGTTTGGTGTGGATAATCAAGTTGATTACTATGCTGTTTCCTTTGTGAAAGATGCTCAAGTTGTCCACGAACTCAAGGA
atctaat putative branch site (score: 865)
atctaatctatatat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaatagtcggcaacttttttctgtctactggatctaatctatatatccttgtttcatacacgtttcaaatgtacagACAAGGACTGGGACGACATTAAGTTTGGTGTGGATAATCAAGTTGATTACTATGCTGTTTCCTTTGTGAAAGATGCTCAAGTTGTCCACGAACTCAAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG