Sequence
atgc intronic sequence ATGC exonic sequence...catgagtattgactgcctatttttgtcgacttcacatttcatgatagtcctctatccctcttaatctaattatcatatttttctgctattctatgtgcagTGTGATTCAGTTCTGTGCCACGGCTTTTGCCTACTACGCACAAGCAACTGCAGCTCAAGAGATATTTGGCCACACTTTGCAATCCCTTCGTGGAATTAAG
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GRMZM2G012284_T01 (Zea mays), 3'ss of exon 9
lower sequence: LOC_Os06g03760.2 (Oryza sativa), 3'ss of exon 11
--catgagtattgactgcctatttttgtcgacttcacatttcatgatagtcctctatccctcttaatctaattatcatatttttctgctattctatgtgcagTGTGATTCAGTTCTGTGCCACGGCTTTTGCCTACTACGCACAAGCAACTGCAGCTCAAGAGATATTTGGCCACACTTTGCAATCCCTTCGTGGAATTAAG
| || | | ||| || || | || || ||| | |||| | | | | | | | | | | |||||||||||||||||||||||||| |||||||| || || || ||||||||||||||||| ||||| ||||||||||| ||||||| || ||||||||||||
tttgttggtttcatcaaccttgcttcctccataacatatg-catacctgctgattatctgt-taattttctccactaagaggccatctaaaatcttttgcagTGTGATTCAGTTCTGTGCCACAGCTTTTGCTTATTATGCGCAAGCAACTGCAGCTCAGGAGATCTTTGGCCACACACTGCAATCTCTCCGTGGAATTAAG
upper sequence: GRMZM2G012284_T01 (Zea mays), 3'ss of exon 9
lower sequence: GLYMA01G30400.1 (Glycine max), 3'ss of exon 11
catgagtattgactgcctatttttgtcgacttcacatttcatgatagtcctctatccctcttaatctaattatcatatttttctgctattctatgtgcagTGTGATTCAGTTCTGTGCCACGGCTTTTGCCTACTACGCACAAGCAACTGCAGCTCAAGAGATATTTGGCCACACTTTGCAATCCCTTCGTGGAATTAAG
| ||| || | || | || | | || | | | || | | | | | | | || | | || | | ||||||||| |||||||| |||| || ||||||||||| || |||||||||||||| || || |||||||||||||| ||| |||| ||||||||||||||
actaagttgtgttctatacatagtgaaaaattatggtgctgtcatgataatgtcatgctgtgataacattgctgaaagttcggttgttttaccttttcagTGTGATCCAGTTCTGCTCCACAGCATTTGCCTACTATGCTCAAGCAACTGCAGCACAGGAAATATTTGGCCACACCTTGGAATCTCTTCGTGGAATTAAA
upper sequence: GRMZM2G012284_T01 (Zea mays), 3'ss of exon 9
lower sequence: GLYMA16G19230.1 (Glycine max), 3'ss of exon 10
catgagtattgactgcctatttttgtcg-acttcacatttcatgatagtcctctatccctcttaatctaattatcatatttttctgctattctatgtgcagTGTGATTCAGTTCTGTGCCACGGCTTTTGCCTACTACGCACAAGCAACTGCAGCTCAAGAGATATTTGGCCACACTTTGCAATCCCTTCGTGGAATTAAG
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tatagcgcatagtgttctatttaaagcataaggcacttgttatg-ttgtcatgataatgtgatgctgtacagctcaaagttctattgttttaccttttcagTGTGATCCAGTTCTGCTCCACAGCATTTGCCTACTATGCTCAAGCAACTGCAGCCCAGGAAATATTTGGCCACACTTTGGAGTCTCTTCGAGGAATTAAA
upper sequence: GRMZM2G012284_T01 (Zea mays), 3'ss of exon 9
lower sequence: GLYMA03G07890.1 (Glycine max), 3'ss of exon 11
--catgagtattgactgcctatttttgtcgacttcaca--tttcatgatagtcctctatccctcttaatctaattatcatatttttctgctattctatgtgcagTGTGATTCAGTTCTGTGCCACGGCTTTTGCCTACTACGCACAAGCAACTGCAGCTCAAGAGATATTTGGCCACACTTTGCAATCCCTTCGTGGAATTAAG
| || || || | | | |||||||||| | | | || || | || | || | | ||||||||| |||||||| |||| || ||||||||||| || |||||||||||||| || || |||||||||||||| ||| | || ||||||||||||||
taccaagtcatgttctatacatagtgaaaaattgtggtgctttcatgataatgtcatggtg----tgataacatcgatgaaagttcagttttttaccttttcagTGTGATCCAGTTCTGCTCCACAGCATTTGCCTACTATGCTCAAGCAACTGCAGCACAGGAAATATTTGGCCACACCTTGGAGTCTCTTCGTGGAATTAAA
upper sequence: GRMZM2G012284_T01 (Zea mays), 3'ss of exon 9
lower sequence: GLYMA18G43020.1 (Glycine max), 3'ss of exon 11
ca-tgagtattgactgcctatttttgtcgacttcacatttcatgatagtcctctatccctct-taatctaattatcatatttttctgctattctatgtgcagTGTGATTCAGTTCTGTGCCACGGCTTTTGCCTACTACGCACAAGCAACTGCAGCTCAAGAGATATTTGGCCACACTTTGCAATCCCTTCGTGGAATTAAG
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cacttagtgttctatataaagcgtaaggcacttgttatgttgtcatgataatggggtgctgtacaaccttgctg--aaagttctattgttttaccttttcagTGTGATCCAGTTCTGCTCCACAGCATTTGCCTACTATGCTCAAGCAACTGCAGCCCAGGAAATATTTGGTCACACTTTGGAGTCTCTTCGAGGAATTAAA
upper sequence: GRMZM2G012284_T01 (Zea mays), 3'ss of exon 9
lower sequence: AT5G01460.1 (Arabidopsis thaliana), 3'ss of exon 11
catgagtat-tgactgcctatttttgtcgacttcacatttcatgatagtcctctatcc-ctcttaatctaattatcatatttttctgct-attctatgtgcagTGTGATTCAGTTCTGTGCCACGGCTTTTGCCTACTACGCACAAGCAACTGCAGCTCAAGAGATATTTGGCCACACTTTGCAATCCCTTCGTGGAATTAAG
| | | | | | | || ||| || | | || ||| | | | ||| || ||| ||| | ||| | || ||| | | | | |||||||||||| ||||| ||||| || |||| || || || ||||| || || ||||| ||||||||||||||||||||||| |||||||| || ||||||
-gtaggcttcttagttctcatatttcccgtcagctgatagcatcaaaagtatgtattaacttttattcttacaatcgactattgtggctcactgaaattccagTGTGATTCAATTCTGCGCCACTGCATTTGGATATTATGCTCAAGCCACCGCCGCTCAGGAGATATTTGGCCACACTTTGCAGTCCCTTCGCGGTATTAAG
upper sequence: GRMZM2G012284_T01 (Zea mays), 3'ss of exon 9
lower sequence: AT3G08930.1 (Arabidopsis thaliana), 3'ss of exon 11
-catgag-tattgactgcctatttttgt----cgacttcacatttcatgatagtcctctatccctcttaatctaattatcatatttttctgctattctatgtgcagTGTGATTCAGTTCTGTGCCACGGCTTTTGCCTACTACGCACAAGCAACTGCAGCTCAAGAGATATTTGGCCACACTTTGCAATCCCTTCGTGGAATTAAG
|| || | | | | |||| | || | ||| || || |||| | ||| | || | || ||| | ||||| |||||||| || |||||||| || |||| || ||||| ||||| ||||| || || ||||||||||||||||| ||||| |||||| | |||||||||
ctattagatgtcaaaccaagacttttaatatacagctgctaccctcacaattacatgttaatcctcacagtctgagtaatgtggttc------atttaaaatgcagCGTGATTCAATTTTGTGCCACTGCATTTGGATATTACGCTCAAGCCACTGCTGCCCAGGAGATATTTGGCCACACATTGCAGTCCCTTAGAGGAATTAAG
upper sequence: GRMZM2G012284_T01 (Zea mays), 3'ss of exon 9
lower sequence: Vv08s0007g02270.t01 (Vitis vinifera), 3'ss of exon 11
----------------------------------------------------------catgagtattgactgcctatttttgtcgacttcacatttcatgatagtcctctatccctcttaatctaattatcatatttttctgctattctatgtgcagTGTGATTCAGTTCTGTGCCACGGCTTTTGCCTACTACGCACAAGCAACTGCAGCTCAAGAGATATTTGGCCACACTTTGCAATCCCTTCGTGGAATTAAG
|| || |||| | || | | | || | | || ||| | | || ||||| | ||||| || | ||| || | | |||||||||||| ||||| ||||| || |||| ||||| || ||||||||||| || || || |||||||||||||| || |||| || ||||||||
gtttgcatgtttagtcctctaaattcattaacagatataattgggttgggaccagcaccacaaggggggactcttactgttattttatgtagaatatatttccagaccttggtagatgtttatcta-taatcattgttgttggctcctccaatttcagTGTGATTCAATTCTGCGCCACAGCATTTGGTTACTATGCTCAAGCAACTGCTGCACAGGAAATATTTGGCCACACACTGGAATCTCTCAAAGGAATTAAAMapped 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|76288405|gb|DV027973.1|DV027973EST: ATGAACTCCTTCCTGTTTAATGTTGGGCTCATACTACTTTGCTCCATCAG TGTGATTCAGTTCTGTGCCACGGCTTTTGCCTACTACGCACAAGCAACTGC
genomic: ATGAACTCCTTCCTGTTTAATGTTGGGCTCATACTACTTTGCTCCATCAGgtatgccatc ... ctatgtgcagTGTGATTCAGTTCTGTGCCACGGCTTTTGCCTACTACGCACAAGCAACTGC
EST:
gi|67039856|gb|CO466111.1|CO466111EST: ATGAACTCCTTCCTGTTTAATGTTGGGCTCATACTACTTTGCTCCATCAG TGTGATTCAGTTCTGTGCCACGGCTTTTGCCTACTACGCACAAGCAACTGC
genomic: ATGAACTCCTTCCTGTTTAATGTTGGGCTCATACTACTTTGCTCCATCAGgtatgccatc ... ctatgtgcagTGTGATTCAGTTCTGTGCCACGGCTTTTGCCTACTACGCACAAGCAACTGC
EST:
gi|76288406|gb|DV027974.1|DV027974EST: ATGAACTCCTTCCTGTTTAATGTTGGGCTCATACTACTTTGCTCCATCAG TGTGATTCAGTTCTGTGCCACGGCTTTTGCCTACTACGCACAAGCAACTGC
genomic: ATGAACTCCTTCCTGTTTAATGTTGGGCTCATACTACTTTGCTCCATCAGgtatgccatc ... ctatgtgcagTGTGATTCAGTTCTGTGCCACGGCTTTTGCCTACTACGCACAAGCAACTGC
EST:
gi|38568991|gb|CF974876.1|CF974876EST: ATGAACTCCTTCCTGTTTAATGTTGGGCTCATACTACTTTGCTCCATCAG TGTGATTCAGTTCTGTGCC
genomic: ATGAACTCCTTCCTGTTTAATGTTGGGCTCATACTACTTTGCTCCATCAGgtatgccatc ... ctatgtgcagTGTGATTCAGTTCTGTGCC
EST:
gi|91872772|gb|EB402729.1|EB402729EST: ATGAACTCCTTCCTGTTTAATGTTGGGCTCATACTACTTTGCTCCATCAG TGTGATTCAGTTCTGTGCCACGGCTTTTGCCTACTACGCACAAGCAACTGC
genomic: ATGAACTCCTTCCTGTTTAATGTTGGGCTCATACTACTTTGCTCCATCAGgtatgccatc ... ctatgtgcagTGTGATTCAGTTCTGTGCCACGGCTTTTGCCTACTACGCACAAGCAACTGC
EST:
gi|67024981|gb|CO453730.1|CO453730EST: ATGAACTCCTTCCTGTTTAATGTTGGGCTCATACTACTTTGCTCCATCAG TGTGATTCAGTTCTGTGCCACGGCTTTTGCCTACTACGCACAAGCAACTGC
genomic: ATGAACTCCTTCCTGTTTAATGTTGGGCTCATACTACTTTGCTCCATCAGgtatgccatc ... ctatgtgcagTGTGATTCAGTTCTGTGCCACGGCTTTTGCCTACTACGCACAAGCAACTGC
EST:
gi|71763789|gb|DR961726.1|DR961726EST: ATGAACTCCTTCCTGTTTAATGTTGGGCTCATACTACTTTGCTCCATCAG TGTGATTCAGTTCTGTGCCACGGCTTTTGCCTACTACGCACAAGCAACTGC
genomic: ATGAACTCCTTCCTGTTTAATGTTGGGCTCATACTACTTTGCTCCATCAGgtatgccatc ... ctatgtgcagTGTGATTCAGTTCTGTGCCACGGCTTTTGCCTACTACGCACAAGCAACTGC
EST:
gi|71449543|gb|DR830593.1|DR830593EST: ATGAACTCCTTCCTGTTTAATGTTGGGCTCATACTACTTTGCTCCATCAG TGTGATTCAGTTCTGTGCCACGGCTTTTGCCTACTACGCACAAGCAACTGC
genomic: ATGAACTCCTTCCTGTTTAATGTTGGGCTCATACTACTTTGCTCCATCAGgtatgccatc ... ctatgtgcagTGTGATTCAGTTCTGTGCCACGGCTTTTGCCTACTACGCACAAGCAACTGC
EST:
gi|33942467|gb|CF349067.1|CF349067EST: ATGAACTCCTTCCTGTTTAATGTTGGGCTCATACTACTTTGCTCCATCAG TGTGATTCAGTTCTGTGCCACGGCTTTTGCCTACTACGCACAAGCAACTGC
genomic: ATGAACTCCTTCCTGTTTAATGTTGGGCTCATACTACTTTGCTCCATCAGgtatgccatc ... ctatgtgcagTGTGATTCAGTTCTGTGCCACGGCTTTTGCCTACTACGCACAAGCAACTGC
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:
218ATGGGGAGGCACTTTAATGAACTCCTTCCTGTTTAATGTTGGGCTCATACTACTTTGCTCCATCAGgtatgccatc ... ctatgtgcagTGTGATTCAGTTCTGTGCCACGGCTTTTGCCTACTACGCACAAGCAACTGCAGCTCAAGAGATATTTGGCCACACTTTGCAATCCCTTCGTGGAATTAAG
Block sizes:
49 (upstream exon),
49 (downstream exon)
Score:
214ATGGGGAGGCACTTTAATGAACTCCTTCCTGTTTAATGTTGGGCTCATACTACTTTGCTCCATCAGgtatgccatc ... ctatgtgcagTGTGATTCAGTTCTGTGCCACGGCTTTTGCCTACTACGCACAAGCAACTGCAGCTCAAGAGATATTTGGCCACACTTTGCAATCCCTTCGTGGAATTAAG
Block sizes:
49 (upstream exon),
49 (downstream exon)
Score:
273ATGGGGAGGCACTTTAATGAACTCCTTCCTGTTTAATGTTGGGCTCATACTACTTTGCTCCATCAGgtatgccatc ... ctatgtgcagTGTGATTCAGTTCTGTGCCACGGCTTTTGCCTACTACGCACAAGCAACTGCAGCTCAAGAGATATTTGGCCACACTTTGCAATCCCTTCGTGGAATTAAG
Block sizes:
49 (upstream exon),
49 (downstream exon)
Score:
281ATGGGGAGGCACTTTAATGAACTCCTTCCTGTTTAATGTTGGGCTCATACTACTTTGCTCCATCAGgtatgccatc ... ctatgtgcagTGTGATTCAGTTCTGTGCCACGGCTTTTGCCTACTACGCACAAGCAACTGCAGCTCAAGAGATATTTGGCCACACTTTGCAATCCCTTCGTGGAATTAAG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.agtcctctatccctcttaatctaattatcatatttttctgctattctatgtgcagTGTGATTCAGTTCTGTGCCACGGCTTTTGCCTACTACGCACAAGCAACTGCAGCTCAAGAGATATTTGGCCACACTTTGCAATCCCTTCGTGGAATTAAG
atctaat putative branch site (score: 281)
tttttctgctattct putative PPT
tcttaatctaattatc 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
catgagtattgactgcctatttttgtcgacttcacatttcatgatagtcctctatccctcttaatctaattatcatatttttctgctattctatgtgcagTGTGATTCAGTTCTGTGCCACGGCTTTTGCCTACTACGCACAAGCAACTGCAGCTCAAGAGATATTTGGCCACACTTTGCAATCCCTTCGTGGAATTAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - -tgactgc
- - - - - - - - - - - - - - -cttcaca
- - - - - - - - - - - - - - - - - - tttcatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ttctgct