Sequence
atgc intronic sequence ATGC exonic sequence...tgtagaaaaattagctgcacgaaaattgtgggtccctgatcttgcttttggttactgatataaaagtaatcatgtccctaatattccttgtcccttgcagGTATTTGATTTGTTTGACACAAAGCACAATGGAATTTTAGGATTTGAAGAATTTGCTCGTGCTCTCTCAGTATTTCATCCTAATGCTCCCCTTGATGAGA
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GRMZM2G007555_T01 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os12g40510.1 (Oryza sativa), 3'ss of exon 4
-------tgtagaaaaattagctgcacgaaaattgtgggtccctgatcttgcttttggttac-tgatataaaagtaatcatgtccctaatattccttgt-cccttgcagGTATTTGATTTGTTTGACACAAAGCACAATGGAATTTTAGGATTTGAAGAATTTGCTCGTGCTCTCTCAGTATTTCATCCTAATGCTCCCCTTGATGAGA
||||||||||| ||||| | || | ||| || | ||| |||| ||| | | || | |||||| | |||||||| | | ||| |||||||||||||||||||||||||| ||||||||||||||||||||||| |||||||||||||| ||||||||||||||||| | |||||| ||||||||||
aattctttgtagaaaaat-agctgtatgatagatgtcagtgca-gattttgcctttatctccgtgctgcc-------tcatgttcttaatattctccctgctcttacagGTATTTGATTTGTTTGACACAAAACACAATGGAATTTTAGGATTTGATGAATTTGCTCGTGCACTCTCAGTATTTCATCCAAGTGCTCCACTTGATGAGA
upper sequence: GRMZM2G007555_T01 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA07G39940.1 (Glycine max), 3'ss of exon 4
-tgtagaaaaattagctgcacgaaaattgtgggtccctgatct-tgcttttggttactgatataaaagtaatcatgtccctaatattccttgtcccttgcagGTATTTGATTTGTTTGACACAAAGCACAATGGAATTTTAGGATTTGAAGAATTTGCTCGTGCTCTCTCAGTATTTCATCCTAATGCTCCCCTTGATGAGA
| | | | | | || | | ||| | | | || || || | | | || ||| | | || | | || |||| ||||| |||||||| |||||||||||||| || | | |||||||| ||||| ||||||||||| || |||||||| ||||| || ||||||| |
atatttatgatctgattacaagttagttgcataccgtatacatatggggttaaccttagaatttgtatttgtcctgttcatgat--tttgtactgtctgtagGTGTTTGACTTGTTTGATACAAAGCACAATGGGATACTTGATTTTGAAGAGTTTGCACGTGCTCTCTCTGTCTTTCATCCCAATGCACCAATTGATGATA
upper sequence: GRMZM2G007555_T01 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA18G08230.1 (Glycine max), 3'ss of exon 5
tgtagaaaaattagctgcacgaaaattgtgggtccctgatcttgcttttggttactgatataaaagtaatcatgtccctaatattccttgtcccttgcagGTATTTGATTTGTTTGACACAAAGCACAATGGAATTTTAGGATTTGAAGAATTTGCTCGTGCTCTCTCAGTATTTCATCCTAATGCTCCCCTTGATGAGA-
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tgtttacgtatta-tttcaacattatattttgttcaaaaattgattcacaattcaacttgtgattggaatctaatatgaacttctctctaactctattaggTATTTGATTTATTTGACACAAAGCACAATGGGATACTAGGTTTTGAAGAGTTTGCTCGTGCTCTCTCCGTTTTTCATCCAAATGCCCCTATTGATGATAA
upper sequence: GRMZM2G007555_T01 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA08G44580.1 (Glycine max), 3'ss of exon 4
------tgtagaaaaattagctgcacgaaaattgtgggtccctgatcttgcttttggttactgatataaaagtaatcatgtccctaatattccttgtcccttgcagGTATTTGATTTGTTTGACACAAAGCACAATGGAATTTTAGGATTTGAAGAATTTGCTCGTGCTCTCTCAGTATTTCATCCTAATGCTCCCCTTGATGAGA
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tatatctgtttacgtatttttcaatattatattttg---ttcaaaaattgattcacattact--ccttgtggttggtatctcatatgaacttctc-tctaacttagGTATTTGATTTATTTGACACAAAACACAATGGGATACTGGGTTTTGAAGAGTTTGCTCGTGCTCTCTCCGTTTTCCATCCTAATGCCCCCATTGATGATA
upper sequence: GRMZM2G007555_T01 (Zea mays), 3'ss of exon 4
lower sequence: AT4G26570.1 (Arabidopsis thaliana), 3'ss of exon 5
tgtagaaaaattagctgcacgaaaattgtgggtccctgatcttgct-tttggttactgatataaaagtaatcatgtccctaatattccttg------tcccttgcagGTATTTGATTTGTTTGACACAAAGCACAATGGAATTTTAGGATTTGAAGAATTTGCTCGTGCTCTCTCAGTATTTCATCCTAATGCTCCCCTTGATGAGA
| | || | | | ||| || |||| || | | ||| | | || || |||| | | |||||||| |||||||||||||||||||| |||||||| | || ||||| || ||||| ||||||||||| || |||||||| ||||||||| | || || |
--------------------gtatgttcttcttttttaatcaaaagactttgttatccatttgccaa-gatcctttttgaaagataacttgacagtaccaatcacagGTATTCGATTTGTTTGACACAAAGCATAATGGAATACTGGGGTTTGAGGAGTTTGCGCGTGCTCTCTCTGTCTTTCATCCAAATGCTCCCATAGAAGACA
upper sequence: GRMZM2G007555_T01 (Zea mays), 3'ss of exon 4
lower sequence: AT5G55990.1 (Arabidopsis thaliana), 3'ss of exon 5
tgtagaaaaattagctgcacgaaaattgtgggtccctgatcttgcttttggtta---ctgatataaaagtaatcatgtccctaatattccttgtcccttgcagGTATTTGATTTGTTTGACACAAAGCACAATGGAATTTTAGGATTTGAAGAATTTGCTCGTGCTCTCTCAGTATTTCATCCTAATGCTCCCCTTGATGAGA
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-gtaatgtttctttcttcacatta--taagtgttcttaaacccatttttgtcaagatcaagtttagaagaaatgctga----aatatgtgattttgtttctagGTTTTCGATTTGTTTGATACAAAGCACAATGGAATACTGGGGTTTGAGGAATTTGCTCGTGCTCTCTCCGTCTTTCACCCAAATGCGCCTATAGATGACA
upper sequence: GRMZM2G007555_T01 (Zea mays), 3'ss of exon 4
lower sequence: AT4G26570.2 (Arabidopsis thaliana), 3'ss of exon 5
tgtagaaaaattagctgcacgaaaattgtgggtccctgatcttgct-tttggttactgatataaaagtaatcatgtccctaatattccttg------tcccttgcagGTATTTGATTTGTTTGACACAAAGCACAATGGAATTTTAGGATTTGAAGAATTTGCTCGTGCTCTCTCAGTATTTCATCCTAATGCTCCCCTTGATGAGA
| | || | | | ||| || |||| || | | ||| | | || || |||| | | |||||||| |||||||||||||||||||| |||||||| | || ||||| || ||||| ||||||||||| || |||||||| |||||||
--------------------gtatgttcttcttttttaatcaaaagactttgttatccatttgccaa-gatcctttttgaaagataacttgacagTACCAATCACAGGTATTCGATTTGTTTGACACAAAGCATAATGGAATACTGGGGTTTGAGGAGTTTGCGCGTGCTCTCTCTGTCTTTCATCCAAATGCTC------------
upper sequence: GRMZM2G007555_T01 (Zea mays), 3'ss of exon 4
lower sequence: Vv00s1569g00020.t01 (Vitis vinifera), 3'ss of exon 3
-tgtagaaaaattagctgcacgaaaattgtgggtccctgatcttgcttttggttactgatataaaagtaatcatgtccctaatattccttgtc---ccttgcagGTATTTGATTTGTTTGACACAAAGCACAATGGAATTTTAGGATTTGAAGAATTTGCTCGTGCTCTCTCAGTATTTCATCCTAATGCTCCCCTTGATGAGA
||| ||||| || | | || | | || | | | | | ||| || || | | || || || |||| |||||||||| |||||||||||||||||||||||||| ||| |||||||| ||||| ||||| ||||| || |||||||| ||||| ||| |||| || |
atgttccttcattagttggcttgtagtc----ttctttcagttttttcaaaatgagtccaaataaattattcctacaatttatgcctctattcaaatcttgtagGTATTTGACTTGTTTGACACAAAGCACAATGGAATACTAGATTTTGAAGAGTTTGCGCGTGCCCTCTCTGTCTTTCATCCCAATGCACCCATTGAAGACA
upper sequence: GRMZM2G007555_T01 (Zea mays), 3'ss of exon 4
lower sequence: Vv19s0015g01070.t01 (Vitis vinifera), 3'ss of exon 3
tgtagaaaaattagctgcacgaaaattgtgggtccctgatcttgcttttggttactgatataaaagtaatcatgtccc-taatat------tccttgtcccttgcagGTATTTGATTTGTTTGACACAAAGCACAATGGAATTTTAGGATTTGAAGAATTTGCTCGTGCTCTCTCAGTATTTCATCCTAATGCTCCCCTTGATGAGA
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------aactcttgcatcattgaattggtagtttcattggatatttttggaagagttcca-aaagacgctcatttgccattgtatatgtaatgctaatcaattgtagGTATTTGACTTGTTTGACACAAAGCATAACGGAATACTTGGCTTTGAGGAGTTTGCTCGTGCTCTATCTGTTTTTCACCCCAACGCACCTATCGACGACAMapped 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|149111971|gb|EE191131.2|EE191131EST: AGTTGGCACTATTTAAGACCAGCAAGAAGGAGAGCCTGTTCGCAGACCGC GTATTTGATTTGTTTGACACAAAGCACAATGGAATTTTAGGATTTGAAGAA
genomic: AGTTGGCACTATTTAAGACCAGCAAGAAGGAGAGCCTGTTCGCAGACCGCgtgagtccct ... tcccttgcagGTATTTGATTTGTTTGACACAAAGCACAATGGAATTTTAGGATTTGAAGAA
EST:
gi|149077489|gb|EE166185.2|EE166185EST: AGTTGGCACTATTTAAGACCAGCAAGAAGGAGAGCCTGTTCGCAGACCGC GTATTTGATTTGTTTGACACAAAGCACAATGGAATTTTAGGATTTGAAGAA
genomic: AGTTGGCACTATTTAAGACCAGCAAGAAGGAGAGCCTGTTCGCAGACCGCgtgagtccct ... tcccttgcagGTATTTGATTTGTTTGACACAAAGCACAATGGAATTTTAGGATTTGAAGAA
EST:
gi|71319028|gb|DR796259.1|DR796259EST: AGTTGGCACTATTTAAGACCAGCAAGAAGGAGAGCCTGTTCGCAGACCGC GTATTTGATTTGTTTGACACAAAGCACAATGGAATTTTAGGATTTGAAGAA
genomic: AGTTGGCACTATTTAAGACCAGCAAGAAGGAGAGCCTGTTCGCAGACCGCgtgagtccct ... tcccttgcagGTATTTGATTTGTTTGACACAAAGCACAATGGAATTTTAGGATTTGAAGAA
EST:
gi|148944608|gb|EC889738.2|EC889738EST: AGTTGGCACTATTTAAGACCAGCAAGAAGGAGAGCCTGTTCGCAGACCGC GTATTTGATTTGTTTGACACAAAGCACAATGGAATTTTAGGATTTGAAGAA
genomic: AGTTGGCACTATTTAAGACCAGCAAGAAGGAGAGCCTGTTCGCAGACCGCgtgagtccct ... tcccttgcagGTATTTGATTTGTTTGACACAAAGCACAATGGAATTTTAGGATTTGAAGAA
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:
146GAGGAGTTTCAGTTGGCACTATTTAAGACCAGCAAGAAGGAGAGCCTGTTCGCAGACCGCgtgagtccct ... tcccttgcagGTATTTGATTTGTTTGACACAAAGCACAATGGAATTTTAGGATTTGAAGAATTTGCTCGTGCTCTCTCAGTATTTCATCCTAATGCTCCCCTTGATGAGA
Block sizes:
49 (upstream exon),
48 (downstream exon)
Score:
131GAGGAGTTTCAGTTGGCACTATTTAAGACCAGCAAGAAGGAGAGCCTGTTCGCAGACCGCgtgagtccct ... tcccttgcagGTATTTGATTTGTTTGACACAAAGCACAATGGAATTTTAGGATTTGAAGAATTTGCTCGTGCTCTCTCAGTATTTCATCCTAATGCTCCCCTTGATGAGA
Block sizes:
49 (upstream exon),
48 (downstream exon)
Score:
130GAGGAGTTTCAGTTGGCACTATTTAAGACCAGCAAGAAGGAGAGCCTGTTCGCAGACCGCgtgagtccct ... tcccttgcagGTATTTGATTTGTTTGACACAAAGCACAATGGAATTTTAGGATTTGAAGAATTTGCTCGTGCTCTCTCAGTATTTCATCCTAATGCTCCCCTTGATGAGA
Block sizes:
49 (upstream exon),
49 (downstream exon)
Score:
81GAGGAGTTTCAGTTGGCACTATTTAAGACCAGCAAGAAGGAGAGCCTGTTCGCAGACCGCgtgagtccct ... tcccttgcagGTATTTGATTTGTTTGACACAAAGCACAATGGAATTTTAGGATTTGAAGAATTTGCTCGTGCTCTCTCAGTATTTCATCCTAATGCTCCCCTTGATGAGA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttttggttactgatataaaagtaatcatgtccctaatattccttgtcccttgcagGTATTTGATTTGTTTGACACAAAGCACAATGGAATTTTAGGATTTGAAGAATTTGCTCGTGCTCTCTCAGTATTTCATCCTAATGCTCCCCTTGATGAGA
tattccttgtccctt CT-rich tract
atataaaagtaatcat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tgtagaaaaattagctgcacgaaaattgtgggtccctgatcttgcttttggttactgatataaaagtaatcatgtccctaatattccttgtcccttgcagGTATTTGATTTGTTTGACACAAAGCACAATGGAATTTTAGGATTTGAAGAATTTGCTCGTGCTCTCTCAGTATTTCATCCTAATGCTCCCCTTGATGAGA
- -agaaaaa
- - - - - - -gctgcac
- - - - - - - - - - - - - - - - - - - - - - - - - - tactgat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaaagtaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - catgtcc