Sequence
atgc intronic sequence ATGC exonic sequencegtctttatgccttctctggaatttttaattgtaattcatcgtagctgcattagcataaacgttttttttcatactagGTTGCAATCAAATTTGAACATCGAACCAGCAAAGGTTGCAACTATGGTGCTCCTTATGAGTGGCAAGTTTACAA
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GRMZM2G116151_T03 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os05g11140.1 (Oryza sativa), 3'ss of exon 2
-------------gtctttatgccttctctggaatttttaattgtaattcatcgtagctgcattagcataaacgttttttttcatactagGTTGCAATCAAATTTGAACATCGAACCAGCAAAGGTTGCAACTATGGTGCTCCTTATGAGTGGCAAGTTTACAA
|| ||| ||| | |||| | | ||| ||| ||| |||||| || ||| |||| || |||| |||| ||||| |||||||||||||||||||||||||| ||||| ||||| ||||| ||||||||||||||||||||
gtcagctcttctaatccggatgtctttttc---atttccatatttaaaatatcatagttgcatttatattcacgcttttctttataccagGTGGCAATAAAATTTGAACATCGAACCAGCAAAGGCTGCAATTATGGAGCTCCCTATGAGTGGCAAGTTTACAA
upper sequence: GRMZM2G116151_T03 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA06G09190.1 (Glycine max), 3'ss of exon 2
-----------------gtctttatgccttctc---tggaatttttaattgtaattcatcgtagctgcattagcataaacgtttt----ttttcatactagGTTGCAATCAAATTTGAACATCGAACCAGCAAAGGTTGCAACTATGGTGCTCCTTATGAGTGGCAAGTTTACAA
|| || || | | | | | || | || ||| | | | | || |||| || | || || ||||| || | |||||||| ||| ||| |||||| || ||||| ||||| |||| ||||||||||| ||||||||
gtatggtgttggttagtgtgttgatatttatttggttaaagagtgtatgatttatgcatattggatttgtcgttattgacgtattgctctattgattgtagGTAGCCTTAAAATTTGAGCATAGAAGCAGCAAGGGGTGCAATTATGGACCTCCATATGAGTGGCAGGTTTACAA
upper sequence: GRMZM2G116151_T03 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA04G09080.1 (Glycine max), 3'ss of exon 2
-------------gtctttatgccttctctggaatt---tttaattgtaattcatcgtagctgcattagcataaacgtttt----ttttcatactagGTTGCAATCAAATTTGAACATCGAACCAGCAAAGGTTGCAACTATGGTGCTCCTTATGAGTGGCAAGTTTACAA
|| || || | | | | ||| |||| || ||| | | | | | || |||| || | || || ||||| || | |||||||| ||| ||| ||||||||| ||||| ||||| |||| ||||||||||| ||||||||
gtatggtgttagcgtgttgatatttggttaaagagtgtgtttgattg--atgcatattggatttgtcattattgacgtattgctctattgattgtagGTAGCCTTAAAATTTGAGCATAGAAGCAGCAAAGGGTGCAATTATGGACCTCCATATGAGTGGCAGGTTTACAA
upper sequence: GRMZM2G116151_T03 (Zea mays), 3'ss of exon 2
lower sequence: AT2G25760.2 (Arabidopsis thaliana), 3'ss of exon 2
-----------gtctttatgccttctctggaatttttaattgtaattcatcgtagctgcattagcataaacgttttttttcatactagGTTGCAATCAAATTTGAACATCGAACCAGCAAAGGTTGCAACTATGGTGCTCCTTATGAGTGGCAAGTTTACAA
|| ||| || || | || || | || | | | | | | | || | | | ||||| || | || ||||| ||| ||||||||||||| || |||||||| | || ||||||||||||||||||||
gtatgctgtttgtgtttgcaagtttacttgctttcttt-tggttttctgtgatctgtaatgtgattttgatgtgtccacttttg-tagGTGGCTTTGAAGTTTGAGCATAGAACCAGCAAAGGATGTAACTATGGGCCACCGTATGAGTGGCAAGTTTACAA
upper sequence: GRMZM2G116151_T03 (Zea mays), 3'ss of exon 2
lower sequence: Vv04s0008g00160.t01 (Vitis vinifera), 3'ss of exon 2
-----gtctttatgccttctc--tggaatttttaattgta---attcatcgtagctgcattagcataaacgtttttt------ttcata----ctagGTTGCAATCAAATTTGAACATCGAACCAGCAAAGGTTGCAACTATGGTGCTCCTTATGAGTGGCAAGTTTACAA
|||||| ||| | ||| | | ||| || || | | | | | || | |||| ||||| |||||||| | |||||||| ||| ||| ||||||||| ||||| ||||| | || ||||||||||||||||||||
gtgtaacatttatgactttgtggtacaatcactcaatgtggtgatctatgctgggttttatcttgttaatatgttttctgatcttcatgaattttagGTTGCCTTAAAATTTGAGCATAGAAGCAGCAAAGGGTGCAATTATGGACCACCATATGAGTGGCAAGTTTACAA
upper sequence: GRMZM2G116151_T03 (Zea mays), 3'ss of exon 2
lower sequence: PP1S66_174V6.1 (Physcomitrella patens), 3'ss of exon 2
------------------------------gtctttatgccttctctggaatttttaa--ttgtaatt----------catcgtagctgcatt------agcataaac---gtttt-ttttcatact---agGTTGCAATCAAATTTGAACATCGAACCAGCAAAGGTTGCAACTATGGTGCTCCTTATGAGTGGCAAGTTTACAA
||| | | ||| | | | | |||| ||| ||| | ||| | || | |||| || || ||||| | || |||| || | || ||||||||||| | |||||| |||||||| |||||| ||||||| |||||||||||||||||
gtactctttactctaattcgttgaggtccggtcgtgtcgtattccgtatagtgccgagggttgtgattatttagcgagtatctttgctttgtgtctggaagtacaaactgagtcttgttttcgtgctcgcagGTAGCTTTAAAGTTTGAACATCGGAGCAGCAAGGGTTGCAATTATGGTCCTCCTTACGAGTGGCAAGTTTACAA
upper sequence: GRMZM2G116151_T03 (Zea mays), 3'ss of exon 2
lower sequence: PP1S131_16V6.1 (Physcomitrella patens), 3'ss of exon 2
--------------------------------------------------------------gtctttatgccttctctggaatttttaattgtaattcatcgtagctgcattagcataaacgtt---ttttttcatactagGTTGCAATCAAATTTGAACATCGAACCAGCAAAGGTTGCAACTATGGTGCTCCTTATGAGTGGCAAGTTTACAA
||| || || | || | ||| || | ||| || | || | || | || | | ||||||| | || || || ||||| | || || || ||||| |||||| |||||||||||||||| |||||||
gtattcaatttcttacaatttgttctgctctacttctttcgcagcagcatgtttggaagatactctgcatattgcatcgaggtcttgtgatt----tttaatgtaataagttttgtattcatattgaactcgtttgtgc-agGTTGCGTTGAAGTTCGAGCATCGGAGTAGTAAGGGCTGCAATTATGGTCCTCCTTATGAGTGGCAGGTTTACAC
upper sequence: GRMZM2G116151_T03 (Zea mays), 3'ss of exon 2
lower sequence: EFJ38433 (Selaginella moellendorffii), 3'ss of exon 2
gtctttatgccttctctggaatttttaattgtaattcatcgtagctgcattagcataaacgttttttttcatactagGTTGCAATCAAATTTGAACATCGAACCAGCAAAGGTTGCAACTATGGTGCTCCTTATGAGTGGCAAGTTTACAA
|| | | || || | | | ||| | || || | | | | || ||||||| | || |||||||| ||| ||| ||||| ||||||||||| |||| |||||||||||||||||||
----gtagactgttcgaagatttgctcagttggattggctcttttctcagcggc-tgatcaaagatgtt---gtcagGTTGCTTTGAAGTTTGAACACAGAAGCAGTAAAGGATGCAACTATGGGCCTCCGTATGAGTGGCAAGTTTACAC
upper sequence: GRMZM2G116151_T03 (Zea mays), 3'ss of exon 2
lower sequence: EFJ19085 (Selaginella moellendorffii), 3'ss of exon 2
gtctttatgccttctctggaatttttaattgtaattcatcgtagctgcattagcataaacgttttttttcatactagGTTGCAATCAAATTTGAACATCGAACCAGCAAAGGTTGCAACTATGGTGCTCCTTATGAGTGGCAAGTTTACAA
| || | | || | || || | | || | || ||| |||| | ||| | ||||||| |||| || || ||| | | ||||||||||||||||||||| ||||||| || ||||| |||||| |
--gtcggtggcgtttcc----tcttctttttttgcttatgctgattgtgtta----taacgctcgtttgcgc---agGTTGCTCTCAAGTTCGAGCATAGGAGCAGCAAAGGTTGCAACTATGGGCCTCCTTACGAATGGCAGGTTTACGA
upper sequence: GRMZM2G116151_T03 (Zea mays), 3'ss of exon 2
lower sequence: EFJ31718 (Selaginella moellendorffii), 3'ss of exon 2
gtctttatgccttctctggaatttttaattgtaattcatcgtagctgcattagcataaacgttttttttcatactagGTTGCAATCAAATTTGAACATCGAACCAGCAAAGGTTGCAACTATGGTGCTCCTTATGAGTGGCAAGTTTACAA
|| | | || ||| | | | ||| || | || || || | | | | || ||||||| | || |||||||| ||| ||| ||||| ||||||||||| |||| |||||||||||||||||||
----gtagactgttcgaagattttctcagttggattgctcttttct-cagcggc-tgatcaaagatgtt---gtcagGTTGCTTTGAAGTTTGAACACAGAAGCAGTAAAGGATGCAACTATGGGCCTCCGTATGAGTGGCAAGTTTACACMapped 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|30306558|gb|CD001231.1|CD001231EST: TTTCCTCTCCTAGTGTTAGTGACAGGACGCCCGGTGCGAATGCTTTAGAG GTTGCAATCAAATTTGAACATCGAACCAGCAAAGGTTGCAACTATGGTGCT
genomic: TTTCCTCTCCTAGTGTTAGTGACAGGACGCCCGGTGCGAATGCTTTAGAGgtctttatgc ... ttcatactagGTTGCAATCAAATTTGAACATCGAACCAGCAAAGGTTGCAACTATGGTGCT
EST:
gi|101387539|gb|EB815784.1|EB815784EST: TTTCCTCTCCTAGTGTTAGTGACAGGACGCCCGGTGCGAATGCTTTAGAG GTTGCAATCAAATTTGAACATCGAACCAGCAAAGGTTGCAACTATGGTGCT
genomic: TTTCCTCTCCTAGTGTTAGTGACAGGACGCCCGGTGCGAATGCTTTAGAGgtctttatgc ... ttcatactagGTTGCAATCAAATTTGAACATCGAACCAGCAAAGGTTGCAACTATGGTGCT
EST:
gi|211200248|gb|FK978072.1|FK978072EST: TTTCCTCTCCTAGTGTTAGTGACAGGACGCCCGGTGTGAATGCTTTAGAG GTTGCAATCAAATTTGAACATCGAACCAGCAAAGGTTGCAACTATGGTGCT
genomic: TTTCCTCTCCTAGTGTTAGTGACAGGACGCCCGGTGCGAATGCTTTAGAGgtctttatgc ... ttcatactagGTTGCAATCAAATTTGAACATCGAACCAGCAAAGGTTGCAACTATGGTGCT
EST:
gi|71767696|gb|DR965633.1|DR965633EST: TTTCCTCTCCTAGTGTTAGTGACAGGACGCCCGGTGCGAATGCTTTAGAG GTTGCAATCAAATTTGAACATCGAACCAGCAAAGGTTGCAACTATGGTGCT
genomic: TTTCCTCTCCTAGTGTTAGTGACAGGACGCCCGGTGCGAATGCTTTAGAGgtctttatgc ... ttcatactagGTTGCAATCAAATTTGAACATCGAACCAGCAAAGGTTGCAACTATGGTGCT
EST:
gi|78112677|gb|DV531071.1|DV531071EST: TTTCCTCTCCTAGTGTTAGTGACAGGACGCCCGGTGCGAATGCTTTAGAG GTTGCAATCAAATTTGAACATCGAACCAGCAAAGGTTGCAACTATGGTGCT
genomic: TTTCCTCTCCTAGTGTTAGTGACAGGACGCCCGGTGCGAATGCTTTAGAGgtctttatgc ... ttcatactagGTTGCAATCAAATTTGAACATCGAACCAGCAAAGGTTGCAACTATGGTGCT
EST:
gi|211200247|gb|FK978071.1|FK978071EST: TTTCCTCTCCTAGTGTTAGTGACAGGACGCCCGGTGCGAATGCTTTAGAG GTTGCAATCAAATTTGAACATCGAACCAGCAAAGGTTGCAACTATGGTGCT
genomic: TTTCCTCTCCTAGTGTTAGTGACAGGACGCCCGGTGCGAATGCTTTAGAGgtctttatgc ... ttcatactagGTTGCAATCAAATTTGAACATCGAACCAGCAAAGGTTGCAACTATGGTGCT
EST:
gi|149078987|gb|EE167841.2|EE167841EST: TTTCCTCTCCTAGTGTTAGTGACAGGACGCCCGGTGCGAATGCTTTAGAG GTTGCAATCAAATTTGAACATCGAACCAGCAAAGGTTGCAACTATGGTGCT
genomic: TTTCCTCTCCTAGTGTTAGTGACAGGACGCCCGGTGCGAATGCTTTAGAGgtctttatgc ... ttcatactagGTTGCAATCAAATTTGAACATCGAACCAGCAAAGGTTGCAACTATGGTGCT
EST:
gi|30031898|gb|CB833749.1|CB833749EST: TTTCCTCTCCTAGTGTTAGTGACAGGACGCCCGGTGCGAATGCTTTAGAG GTTGCAATCAAATTTGAACATCGAACCAGCAAAGGTTGCAACTATGGTGCT
genomic: TTTCCTCTCCTAGTGTTAGTGACAGGACGCCCGGTGCGAATGCTTTAGAGgtctttatgc ... ttcatactagGTTGCAATCAAATTTGAACATCGAACCAGCAAAGGTTGCAACTATGGTGCT
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:
47 (upstream exon),
49 (downstream exon)
Score:
124CAGAAAGCTTGGAAAGGGAGGGTTTGGGCAAGTATATGTTGGTCGTCGCATTTCCTCTCCTAGTGTTAGTGACAGGACGCCCGGTGCGAATGCTTTAGAGgtctttatgc ... ttcatactagGTTGCAATCAAATTTGAACATCGAACCAGCAAAGGTTGCAACTATGGTGCTCCTTATGAGTGGCAAGTTTACAA
Block sizes:
36 (upstream exon),
44 (downstream exon)
Score:
34CAGAAAGCTTGGAAAGGGAGGGTTTGGGCAAGTATATGTTGGTCGTCGCATTTCCTCTCCTAGTGTTAGTGACAGGACGCCCGGTGCGAATGCTTTAGAGgtctttatgc ... ttcatactagGTTGCAATCAAATTTGAACATCGAACCAGCAAAGGTTGCAACTATGGTGCTCCTTATGAGTGGCAAGTTTACAA
Block sizes:
47 (upstream exon),
49 (downstream exon)
Score:
36CAGAAAGCTTGGAAAGGGAGGGTTTGGGCAAGTATATGTTGGTCGTCGCATTTCCTCTCCTAGTGTTAGTGACAGGACGCCCGGTGCGAATGCTTTAGAGgtctttatgc ... ttcatactagGTTGCAATCAAATTTGAACATCGAACCAGCAAAGGTTGCAACTATGGTGCTCCTTATGAGTGGCAAGTTTACAA
Block sizes:
28 (upstream exon),
46 (downstream exon)
Score:
53CAGAAAGCTTGGAAAGGGAGGGTTTGGGCAAGTATATGTTGGTCGTCGCATTTCCTCTCCTAGTGTTAGTGACAGGACGCCCGGTGCGAATGCTTTAGAGgtctttatgc ... ttcatactagGTTGCAATCAAATTTGAACATCGAACCAGCAAAGGTTGCAACTATGGTGCTCCTTATGAGTGGCAAGTTTACAA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttttaattgtaattcatcgtagctgcattagcataaacgttttttttcatactagGTTGCAATCAAATTTGAACATCGAACCAGCAAAGGTTGCAACTATGGTGCTCCTTATGAGTGGCAAGTTTACAA
ttttaat putative branch site (score: 53)
ttttttttcatact putative PPT
ataaacgtttttttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtctttatgccttctctggaatttttaattgtaattcatcgtagctgcattagcataaacgttttttttcatactagGTTGCAATCAAATTTGAACATCGAACCAGCAAAGGTTGCAACTATGGTGCTCCTTATGAGTGGCAAGTTTACAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG