Sequence
atgc intronic sequence ATGC exonic sequencegtatgctagtgaaaaatacatgttagctgctggagcttctttttttggcaacttgggtttagtgaaatatttattaatgccctttcagGTTCTGTTCGGTTTAATCTGGATCCCTTTAATGAGCACAATGATGCGGACCTCTGGGAGGCTCTGGAAAGGGCTCATCTAAAAGATGTTATAAGGAGGAA
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GRMZM2G084181_T01 (Zea mays), 3'ss of exon 23
lower sequence: LOC_Os04g52900.2 (Oryza sativa), 3'ss of exon 24
gtatgctagtgaaaaatacatgttagctgctggagcttctttttttggcaacttgggtttagtgaaatatttattaatgccctttcagGTTCTGTTCGGTTTAATCTGGATCCCTTTAATGAGCACAATGATGCGGACCTCTGGGAGGCTCTGGAAAGGGCTCATCTAAAAGATGTTATAAGGAGGAA
|| || | ||||||| |||||| || | | | || |||| | || | | | || | ||| || | | ||||||||||||| |||||||||||||| ||||||||||||||||||||||| |||||||| || || ||||||||||||||||||||||| |||||||||||
gtttgtttgtgaaaa-tacatgatatatcttctcgtttgcttttcttacatcata-----aatgttttttttggtactattgtc-cagGTTCTGTTCGATTTAATCTGGATCCTTTTAATGAGCACAATGATGCGGATCTCTGGGAAGCGCTTGAAAGGGCTCATCTAAAAGATGTCATAAGGAGGAA
upper sequence: GRMZM2G084181_T01 (Zea mays), 3'ss of exon 23
lower sequence: GLYMA06G46940.1 (Glycine max), 3'ss of exon 25
---gtatgctagtgaaaaatacatgttagctgctggagcttctttttttggcaacttgggtttag---------tgaaatatttattaatgcc-ctttcagGTTCTGTTCGGTTTAATCTGGATCCCTTTAATGAGCACAATGATGCGGACCTCTGGGAGGCTCTGGAAAGGGCTCATCTAAAAGATGTTATAAGGAGGAA
| | || ||| | || | || || | | || ||| | ||| || | | || | |||| | | || | ||| ||||||| || ||||| ||||| |||||||| ||||||||||| ||||| ||| | ||| | |||||||| ||| | || ||||| ||||| || ||
acattgtattatcttaaattttcccttggttg-tgaataaacattgtttattagcttcagtaaaacttctcccttctaaaaattatcactctttctcttagGAACTGTTCGTTTCAATCTTGATCCATTTAATGAACACAATGATGCTGACCTATGGCAAGCTTTAGAAAGGGCGCATTTGAAGGATGTAATAAGAAGAAA
upper sequence: GRMZM2G084181_T01 (Zea mays), 3'ss of exon 23
lower sequence: GLYMA13G29180.1 (Glycine max), 3'ss of exon 23
-------gtatgctagtgaaaaatacat--gttagctgctggagcttctttttttggcaacttgggtttagtgaaat---atttattaatgccctttcagGTTCTGTTCGGTTTAATCTGGATCCCTTTAATGAGCACAATGATGCGGACCTCTGGGAGGCTCTGGAAAGGGCTCATCTAAAAGATGTTATAAGGAGGAA
| | | || | | || | | || | | || | | || | | || | | | || ||| |||| | |||||||| ||||| |||||||| ||||||||||| |||||||||||||||||||| ||||| ||| | || ||||| ||| |||||||
tcatttaacttctgaatcaatgttttgtaggtaattaattagaatataaaaatcaaataatgtcattgtaataatattaagctcaccttactctttatagGAACTGTGAGATTTAATCTTGATCCATTTAATGAACACAATGATGCTGACCTCTGGGAGGCTCTGGAGAGGGCACATTTGAAGGATGTGATACGGAGGAA
upper sequence: GRMZM2G084181_T01 (Zea mays), 3'ss of exon 23
lower sequence: GLYMA15G09900.1 (Glycine max), 3'ss of exon 23
---gtatgctag-tgaaaaatacatgtt-----agctgctggagcttctttttttggcaacttgggtttagtgaaat---atttattaatgccctttcagGTTCTGTTCGGTTTAATCTGGATCCCTTTAATGAGCACAATGATGCGGACCTCTGGGAGGCTCTGGAAAGGGCTCATCTAAAAGATGTTATAAGGAGGAA
||| || | ||| ||||| | || | | ||| || | | || | | || | || | | ||| |||| | |||||||| ||||| || ||||| ||||||||||| |||||||||||||||||||| ||||| ||| | || ||||| ||| |||||||
agaatattttaacttctgaattaatgttttgcaggtaattgaaatataaaatttaaataatgtcattgtaataatattaagctcatcttacacttcatagGAACTGTGAGATTTAATCTCGATCCATTCAATGAACACAATGATGCTGACCTCTGGGAGGCTCTGGAGAGGGCACATTTGAAGGATGTGATACGGAGGAA
upper sequence: GRMZM2G084181_T01 (Zea mays), 3'ss of exon 23
lower sequence: AT1G30410.1 (Arabidopsis thaliana), 3'ss of exon 25
gtatgctagtgaaaa-atacatgttagctgctggagcttctttttttggcaacttgggtttagtgaaatatttattaatgccctt-tcagGTTCTGTTCGGTTTAATCTGGATCCCTTTAATGAGCACAATGATGCGGACCTCTGGGAGGCTCTGGAAAGGGCTCATCTAAAAGATGTTATAAGGAGGAA
| | ||| || | | | | || | || || | ||| | |||| | || ||| | || | ||| | || | || || | ||||| |||| ||||||||||||||| | ||||||||||||||| | || || ||| |||||||||| || || |||||
----gttcgtgtgtgtatttaagacaacattgtaagtctgttcttgcattatgttgctcattgtgaga-atcaatttttttttttgttagGGACGGTGAGATTCAACATTGATCCATTTAGTGAGCACAATGATGCTGGCCTCTGGGAGGCTCTTCACAGAGCGCATATAAAAGATGTCATCAGCAGGAA
upper sequence: GRMZM2G084181_T01 (Zea mays), 3'ss of exon 23
lower sequence: AT1G30420.1 (Arabidopsis thaliana), 3'ss of exon 23
gtatgctagtgaaaaatacatgt-tagctgctggagcttctttttttggcaacttgggtttagtgaaatatttattaatgccctttcagGTTCTGTTCGGTTTAATCTGGATCCCTTTAATGAGCACAATGATGCGGACCTCTGGGAGGCTCTGGAAAGGGCTCATCTAAAAGATGTTATAAGGAGGAA
| ||| ||| | | | | | | | | | || || | |||| | || || | | | ||| | || | || ||| | ||||| |||| ||| ||||||||||| ||||||||||||||||| |||||||| ||| |||||||||| || |||||
---------------gtttgtgtgtagtttaagacgatattgtaagtatgatcctgaattctgagaaacagttctt-----cttgttagGGACGGTGAGATTCAATATCGATCCATTTAGTGAACACAATGATGCTGACCTCTGGGAGGCTCTAGAAAGGGCGCATATAAAAGATGTCATCGATAGGAA
upper sequence: GRMZM2G084181_T01 (Zea mays), 3'ss of exon 23
lower sequence: Vv10s0003g04460.t01 (Vitis vinifera), 3'ss of exon 5
-------gtatgctagtgaaaaatacatgttagctgctggagcttctttttttggcaacttgggtttagtgaaatatttattaatgccctttca-----gGTTCTGTTCGGTTTAATCTGGATCCCTTTAATGAGCACAATGATGCGGACCTCTGGGAGGCTCTGGAAAGGGCTCATCTAAAAGATGTTATAAGGAGGAA
|| | | ||| | | | | | | | | ||||| | | | || ||| | ||| || | ||| |||| | |||||||| ||||| || ||||||||||||||||| ||||| ||| ||||||| | || || ||||| || || | || |||| |||
tttcacggtgaaacaaaacatgataaaaatcattttcctcaacatatttttctttccgagaatatactgtataattctaattgtcatttttataatgtagGTACTGTGAGATTTAATCTTGATCCTTTCAATGAGCACAATGATGCTGACCTTTGGAAGGCTCTAAAGAGAGCACATCTCAAGGACTTCATTAGGATGAA
upper sequence: GRMZM2G084181_T01 (Zea mays), 3'ss of exon 23
lower sequence: Vv10s0003g04390.t01 (Vitis vinifera), 3'ss of exon 23
---------------gtatgctagtgaaa-aatacatgttagctgctggagcttctttttttggcaacttgggtttagtgaaatatttattaatgccctttcagGTTCTGTTCGGTTTAATCTGGATCCCTTTAATGAGCACAATGATGCGGACCTCTGGGAGGCTCTGGAAAGGGCTCATCTAAAAGATGTTATAAGGAGGAA
|| | || | ||||||| |||| | | | | |||||| || || | ||| | ||| | | | | | ||| |||| || || ||||| ||||| || || |||||||||||||| ||||||||||||||| | || ||||| ||| | || |||||||| ||||||||
attactgataagatcctaagttatcaattcaatacattttagttaataaa---ttttttttaatgaagtttgtgttattctaatgatcacttgt-ttcacatagGAACTGTGCGATTCAATCTTGATCCTTTCAACGAGCACAATGATGCTGACCTCTGGGAGGCTTTAGAGAGGGCACATTTGAAGGATGTTATCAGGAGGAAMapped 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|32930284|gb|CF035096.1|CF035096EST: AGTTCTATTCTCAG GTTCTGTTCGGTTTAATCTGGATCCCTTTAATGAGCACAATGATGCGGACC
genomic: AGTTCTATTCTCAGgtatgctagt ... gccctttcagGTTCTGTTCGGTTTAATCTGGATCCCTTTAATGAGCACAATGATGCGGACC
EST:
gi|87152295|gb|DY397084.1|DY397084EST: GGAATAATACCACAGGCACCAGTTCTATTCTCAG GTTCTGTTCGGTTTAATCTGGATCCCTTTAATGAGCACAATGATGCGGACC
genomic: GGAATAATACCACAGGCACCAGTTCTATTCTCAGgtatgctagt ... gccctttcagGTTCTGTTCGGTTTAATCTGGATCCCTTTAATGAGCACAATGATGCGGACC
EST:
gi|22490706|gb|BU050629.1|BU050629EST: GGAATAATACCACAGGCACCAGTTCTATTCTCAG GTTCTGTTCGGTTTAATCTGGATCCCTTTAATGAGCACAATGATGCGGACC
genomic: GGAATAATACCACAGGCACCAGTTCTATTCTCAGgtatgctagt ... gccctttcagGTTCTGTTCGGTTTAATCTGGATCCCTTTAATGAGCACAATGATGCGGACC
EST:
gi|19058756|gb|BM737423.1|BM737423EST: AGGCACCAGTTCTATTCTCAAG GTTCTGTTCGGTTTAATCTGGATCCCTTTAATGAGCACAATGATGCGGAC
genomic: AGGCACCAGTTCTATTCTC-AGgtatgctagt ... gccctttcagGTTCTGTTCGGTTTAATCTGGATCCCTTTAATGAGCACAATGATGCGGAC
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:
46 (upstream exon),
49 (downstream exon)
Score:
189GGGAGAATATTAATTGATGATTGTGACACTTCTAAGTTTGGAATTTGGGACTTGCGCAAAGTTCTAGGAATAATACCACAGGCACCAGTTCTATTCTCAGgtatgctagt ... gccctttcagGTTCTGTTCGGTTTAATCTGGATCCCTTTAATGAGCACAATGATGCGGACCTCTGGGAGGCTCTGGAAAGGGCTCATCTAAAAGATGTTATAAGGAGGAA
Block sizes:
47 (upstream exon),
49 (downstream exon)
Score:
542GGGAGAATATTAATTGATGATTGTGACACTTCTAAGTTTGGAATTTGGGACTTGCGCAAAGTTCTAGGAATAATACCACAGGCACCAGTTCTATTCTCAGgtatgctagt ... gccctttcagGTTCTGTTCGGTTTAATCTGGATCCCTTTAATGAGCACAATGATGCGGACCTCTGGGAGGCTCTGGAAAGGGCTCATCTAAAAGATGTTATAAGGAGGAA
Block sizes:
49 (upstream exon),
49 (downstream exon)
Score:
845GGGAGAATATTAATTGATGATTGTGACACTTCTAAGTTTGGAATTTGGGACTTGCGCAAAGTTCTAGGAATAATACCACAGGCACCAGTTCTATTCTCAGgtatgctagt ... gccctttcagGTTCTGTTCGGTTTAATCTGGATCCCTTTAATGAGCACAATGATGCGGACCTCTGGGAGGCTCTGGAAAGGGCTCATCTAAAAGATGTTATAAGGAGGAA
Block sizes:
48 (upstream exon),
49 (downstream exon)
Score:
191GGGAGAATATTAATTGATGATTGTGACACTTCTAAGTTTGGAATTTGGGACTTGCGCAAAGTTCTAGGAATAATACCACAGGCACCAGTTCTATTCTCAGgtatgctagt ... gccctttcagGTTCTGTTCGGTTTAATCTGGATCCCTTTAATGAGCACAATGATGCGGACCTCTGGGAGGCTCTGGAAAGGGCTCATCTAAAAGATGTTATAAGGAGGAA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.agcttctttttttggcaacttgggtttagtgaaatatttattaatgccctttcagGTTCTGTTCGGTTTAATCTGGATCCCTTTAATGAGCACAATGATGCGGACCTCTGGGAGGCTCTGGAAAGGGCTCATCTAAAAGATGTTATAAGGAGGAA
tattaat putative branch site (score: 191)
tgccctttc CT-rich tract
tttagtgaaatattta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatgctagtgaaaaatacatgttagctgctggagcttctttttttggcaacttgggtttagtgaaatatttattaatgccctttcagGTTCTGTTCGGTTTAATCTGGATCCCTTTAATGAGCACAATGATGCGGACCTCTGGGAGGCTCTGGAAAGGGCTCATCTAAAAGATGTTATAAGGAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA