Sequence
atgc intronic sequence ATGC exonic sequence...tacttgaacagtgtgtacatagtgtggagtttgatgtatcagcttgttttacaaattttatagaatcacaaggttctgaatctggcattaacttttgcagTACACTCCTGCCATTGATATTTGGAGCGTAGGGTGTATATTTGCTGAATTGCTCACAGGGAAGCCACTCTTTCCAGGGAAGAATGTTGTGCATCAGTTGG
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GRMZM2G062761_T02 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os05g50120.1 (Oryza sativa), 3'ss of exon 4
-------------------------------------------------------------------------tacttgaa-cagtgtgtacatagtgtg--gagtttgatgtatcagcttgttttacaaattttatagaatcacaaggttctgaatctggcattaacttttgcagTACACTCCTGCCATTGATATTTGGAGCGTAGGGTGTATATTTGCTGAATTGCTCACAGGGAAGCCACTCTTTCCAGGGAAGAATGTTGTGCATCAGTTGG
| ||| | || ||| | ||||| ||| || | | | || | | || ||| || | | || | | || |||| |||||||||||||| ||||| |||||||||||||| ||||| ||||||||||| || |||| ||||| |||||||||||||||||||| |||||||||||||| ||||
gtaagggaatttccatttaacatggtgatggctatattattttttcttccaacattgttatattactatgatatgtttggatcaatgtagcaacagtgttttgagaatgttctcttagacattgtcgca----ttaggtgatatcttgatttatattttgtcattggcttttgcagTACACCCCTGCAATTGATATTTGGAGTGTAGGATGTATATTTGCAGAGCTGCTTACAGGAAAGCCACTCTTTCCAGGGAAAAATGTTGTGCATCAATTGG
upper sequence: GRMZM2G062761_T02 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA07G11470.1 (Glycine max), 3'ss of exon 4
-tacttgaacagtgtgtacatagtgtggagtttgatgtatcagcttgttt---tacaaattttatagaat-cacaaggttctgaatctggcattaacttttgcagTACACTCCTGCCATTGATATTTGGAGCGTAGGGTGTATATTTGCTGAATTGCTCACAGGGAAGCCACTCTTTCCAGGGAAGAATGTTGTGCATCAGTTGG
| | | | | ||| || | | || |||| ||| | ||| | | || | || || | | | || |||| || ||||||||||| || || || ||||| ||||||||| | || || |||||||| ||| |||||| ||||||||| | ||||| || || ||||| ||||| || ||||
ctcttcaatcctcctctac-caggattgtgtatgatttatgaagttgaatatatttaagtattgcagtacgtgtacgatttcaaatcc----ttgtcttttgcagTATACCCCCGCAATTGACATTTGGAGCATTGGATGCATATTTGCAGAAATGCTCAGTGGGAAGCCATTGTTTCCTGGAAAAAATGTAGTGCACCAATTGG
upper sequence: GRMZM2G062761_T02 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA05G33980.1 (Glycine max), 3'ss of exon 4
------------tacttgaacagtgtgtacatag----tgtggagtttgatgtatc-agcttgttttacaaattttatagaatcacaaggttctgaatctggcattaacttttgcagTACACTCCTGCCATTGATATTTGGAGCGTAGGGTGTATATTTGCTGAATTGCTCACAGGGAAGCCACTCTTTCCAGGGAAGAATGTTGTGCATCAGTTGG
| || |||| | | | | | | | | | | | | || | | || || | | ||| || || || | ||| | || ||||||||||||| ||||| ||||||||||||||| | ||||| |||||||| ||| ||||||| ||||||||| | ||||| ||||| ||||||||||| || ||||
gtaagcttcttttcttttaaca-tattttcttgggttctatataatataagcaattgaacatgcttgatatattgaattatg-catgcaattttaaatttat--ttcctttttgcagTACACCCCTGCAATTGATATTTGGAGCATTGGGTGCATATTTGCAGAAATGCTCACTGGGAAGCCATTGTTTCCTGGGAAAAATGTTGTGCACCAATTGG
upper sequence: GRMZM2G062761_T02 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA09G30790.1 (Glycine max), 3'ss of exon 4
--tacttgaacagtgtgtacatagtgtggagtttgatgtatcagcttgttt---tacaaattttatagaatcacaaggttctgaatctggcattaacttttgcagTACACTCCTGCCATTGATATTTGGAGCGTAGGGTGTATATTTGCTGAATTGCTCACAGGGAAGCCACTCTTTCCAGGGAAGAATGTTGTGCATCAGTTGG
| | | | | ||| | | | || |||| ||| | ||| | | || | || | | || |||| || ||||||||||| || ||||| ||||||||||||||| | || || |||||||| ||| |||||| ||||||||| | ||||| || || ||||| ||||| || ||||
cctcttcaatcctcctctac-cgggattgtgtatgatttatgaagttgaatatatttaagtattgcactagtgtgtaatttcaaatcc----ttgtcttttgcagTATACGCCTGCAATTGATATTTGGAGCATTGGATGCATATTTGCAGAAATGCTCAGTGGGAAGCCATTGTTTCCTGGAAAAAATGTAGTGCACCAATTGG
upper sequence: GRMZM2G062761_T02 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA08G05700.1 (Glycine max), 3'ss of exon 4
--------------tacttgaacagtgtgtacatagtgtggagtttgatgtat-cagcttgttttacaaattttatagaat----cacaaggttctgaatctggcattaacttttgcagTACACTCCTGCCATTGATATTTGGAGCGTAGGGTGTATATTTGCTGAATTGCTCACAGGGAAGCCACTCTTTCCAGGGAAGAATGTTGTGCATCAGTTGG
| || |||| | | | | | | || || | | || || || | ||| | ||| ||| || || | ||| | || |||||||||||||||| || ||||||||||||||| | || || |||||||| ||| ||||||| ||||||||| | ||||| ||||| ||||||||||| || ||||
gtaagtttcttcttttttttaaca-tcttttcttgg-gttgaatataatttaagcaattgaacatacttggtgtattgaaatatgcatgtaattttaaatttat--ttcctttttgcagTACACTCCAGCAATTGATATTTGGAGCATTGGATGCATATTTGCAGAAATGCTCACTGGGAAGCCATTGTTTCCTGGGAAAAATGTTGTGCACCAATTGG
upper sequence: GRMZM2G062761_T02 (Zea mays), 3'ss of exon 4
lower sequence: AT3G18040.2 (Arabidopsis thaliana), 3'ss of exon 3
tacttgaacagtgtgtacatagtgtggagtttgatgtatcagcttgttttacaaatttt---atagaatcacaaggtt----ctgaatctggcattaacttttgcagTACACTCCTGCCATTGATATTTGGAGCGTAGGGTGTATATTTGCTGAATTGCTCACAGGGAAGCCACTCTTTCCAGGGAAGAATGTTGTGCATCAGTTGG
| || | | || | | |||| | | || || ||| ||| | | | | ||||| | || | | || || | ||||||| ||||||||||||||||| |||||| |||| || |||||||| ||| ||||||| ||||||||| | ||||| ||||||||||| ||||| || ||||
---gtaaaatgcaattctctattttcttttttgcaaaagttgtctgattcacatattatgacaccacaacctgaggttaaaacggattattgctttctttgctgcagTATACTCCTGCCATTGATATATGGAGCATAGGATGCATATTTGCAGAAATGCTCACTGGGAAGCCATTGTTTCCTGGGAAGAATGTGGTGCACCAATTGG
upper sequence: GRMZM2G062761_T02 (Zea mays), 3'ss of exon 4
lower sequence: AT1G73670.1 (Arabidopsis thaliana), 3'ss of exon 4
-tacttgaacagtgtgtacatagtgtggagtttgatgtatcagcttgttttacaaattttatagaatcacaaggttctgaatctggcattaacttttgcagTACACTCCTGCCATTGATATTTGGAGCGTAGGGTGTATATTTGCTGAATTGCTCACAGGGAAGCCACTCTTTCCAGGGAAGAATGTTGTGCATCAGTTGG
|||| | || | | | | | || || || || | || ||| | | | | || | ||| || | ||||| || ||||| ||||||||||||||||| || || |||||||||||| |||| ||||||||| || ||||| || || ||||| || || || ||||
ccacttttgta-tgaaggcctgctctagttagctatctacaagtgtgcaggataaggtttgattacagatctgatgctaactctacttttgcgaaatacagTATACCCCTGCGATTGATATTTGGAGCGTTGGTTGCATATTTGCTGAAATGCTATTAGGGAAGCCGCTATTTCCTGGCAAAAATGTGGTTCACCAATTGG
upper sequence: GRMZM2G062761_T02 (Zea mays), 3'ss of exon 4
lower sequence: Vv01s0011g04920.t01 (Vitis vinifera), 3'ss of exon 4
tacttgaacagtgtgtacatagtgtggagtttgatgtatcagcttgttt--tacaaattttatagaatcaca-aggttctgaatctggcattaacttttgcagTACACTCCTGCCATTGATATTTGGAGCGTAGGGTGTATATTTGCTGAATTGCTCACAGGGAAGCCACTCTTTCCAGGGAAGAATGTTGTGCATCAGTTGG
|| | | | | | | | || ||| | | | | | | || | | ||| | || |||| || || | | |||||||||||||| ||||| ||||||||||||||| |||| ||||||||||| ||| |||| || || ||||| | ||||| || || ||||| || || || ||||
-gttttatactaatatctgtgttatttatttcgattgaactgatcatacaccataatccctctgaaatggtacagtttctaaagct--tttcatcttttgcagTACACCCCTGCTATTGATATTTGGAGCATAGGATGTATATTTGCGGAAATGCTTACTGGAAAGCCCTTGTTTCCTGGTAAAAATGTGGTCCAGCAATTGG
upper sequence: GRMZM2G062761_T02 (Zea mays), 3'ss of exon 4
lower sequence: Vv17s0000g02570.t01 (Vitis vinifera), 3'ss of exon 4
----tacttgaacagtgtgtacatagtgtg-gagtttgatgtatcagcttgttttac-aaattttatagaatcacaaggttctgaatctggcattaacttttgcagTACACTCCTGCCATTGATATTTGGAGCGTAGGGTGTATATTTGCTGAATTGCTCACAGGGAAGCCACTCTTTCCAGGGAAGAATGTTGTGCATCAGTTGG
| | || | | | || | | || | || ||||||| ||| | |||| ||| |||| || | | |||| |||||||||||||| ||||||||||||||| |||| || |||||||| ||| |||| ||||| || || || ||||| ||||| ||||| ||||| |||||||
cttttgatgaaatatgacctctttggtttataaaatttaagtggagttatgttttattaaactatatat-----caaatttcttaaaaccttctccattttt-cagTACACTCCTGCGATTGATATTTGGAGCATAGGATGCATATTTGCAGAAATGCTTACAGGAAAACCGCTGTTTCCGGGGAAAAATGTAGTGCACCAGTTGG
upper sequence: GRMZM2G062761_T02 (Zea mays), 3'ss of exon 4
lower sequence: PP1S87_157V6.2 (Physcomitrella patens), 3'ss of exon 4
----------tacttgaacagtgtgtacatagtgtggagtttgatgta--tcagcttgttttacaaattttatagaa---tcacaaggttctgaatctggcattaacttttgcagTACACTCCTGCCATTGATATTTGGAGCGTAGGGTGTATATTTGCTGAATTGCTCACAGGGAAGCCACTCTTTCCAGGGAAGAATGTTGTGCATCAGTTGG
| | | | || | ||||| ||| | | | || ||| |||| || | | | | | || | | |||| ||||| |||||||| || ||||| ||||| |||| ||||||||||| ||| || | || || |||||||| || || |||||||||||||| |||||| |||
gtaacactagtgcgctctcgttcagtggaggtcgtggaccatgacacaagttattgggtagaacatatttgtgagtgattttgaataagtgttgttatgtcccttttttttacagTATACTCCTGCGATCGATATCTGGAGTATAGGCTGTATATTTGCGGAAGTGTTGACCGGAAAGCCACTTTTCCCTGGGAAGAATGTTGTTCATCAGCTGGMapped 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|74245616|gb|DT653530.1|DT653530EST: CCACTAGATGGTATCGAGCTCCAGAATTATGTGGCTCCNNNNNNNCAAAG TACACTCCTGCCATTGATATTTGGAGCGTAGGGTGTATATTTTGCTGA-TT
genomic: CCACTAGATGGTATCGAGCTCCAGAATTATGTGGCTCCTTTTTTTCAAAGgtgatgtctc ... acttttgcagTACACTCCTGCCATTGATATTTGGAGCGTAGGGTGTATATTT-GCTGAATT
EST:
gi|5871276|gb|AW017747.1|AW017747EST: CCACTAGATGGTATCGAGCTCCAGAATTATGTGGCTCCNNNNNNNCAAAG TACACTCCTGCCATTGATATTTGGAGCGTAGGGTGTATATTTGCTGAATTG
genomic: CCACTAGATGGTATCGAGCTCCAGAATTATGTGGCTCCTTTTTTTCAAAGgtgatgtctc ... acttttgcagTACACTCCTGCCATTGATATTTGGAGCGTAGGGTGTATATTTGCTGAATTG
EST:
gi|76934717|gb|DV173988.1|DV173988EST: CCACTAGATGGTATCGAGCTCCAGAATTATGTGGCTCCNNNNNNNCAAAG TACACTCCTGCCATTGATATTTGGAGCGTAGGGTGTATATTTGCTGAATTG
genomic: CCACTAGATGGTATCGAGCTCCAGAATTATGTGGCTCCTTTTTTTCAAAGgtgatgtctc ... acttttgcagTACACTCCTGCCATTGATATTTGGAGCGTAGGGTGTATATTTGCTGAATTG
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),
46 (downstream exon)
Score:
42GATTACGTGGCCACTAGATGGTATCGAGCTCCAGAATTATGTGGCTCCTTTTTTTCAAAGgtgatgtctc ... acttttgcagTACACTCCTGCCATTGATATTTGGAGCGTAGGGTGTATATTTGCTGAATTGCTCACAGGGAAGCCACTCTTTCCAGGGAAGAATGTTGTGCATCAGTTGG
Block sizes:
40 (upstream exon),
45 (downstream exon)
Score:
24GATTACGTGGCCACTAGATGGTATCGAGCTCCAGAATTATGTGGCTCCTTTTTTTCAAAGgtgatgtctc ... acttttgcagTACACTCCTGCCATTGATATTTGGAGCGTAGGGTGTATATTTGCTGAATTGCTCACAGGGAAGCCACTCTTTCCAGGGAAGAATGTTGTGCATCAGTTGG
Block sizes:
48 (upstream exon),
45 (downstream exon)
Score:
12GATTACGTGGCCACTAGATGGTATCGAGCTCCAGAATTATGTGGCTCCTTTTTTTCAAAGgtgatgtctc ... acttttgcagTACACTCCTGCCATTGATATTTGGAGCGTAGGGTGTATATTTGCTGAATTGCTCACAGGGAAGCCACTCTTTCCAGGGAAGAATGTTGTGCATCAGTTGG
Block sizes:
47 (upstream exon),
46 (downstream exon)
Score:
43GATTACGTGGCCACTAGATGGTATCGAGCTCCAGAATTATGTGGCTCCTTTTTTTCAAAGgtgatgtctc ... acttttgcagTACACTCCTGCCATTGATATTTGGAGCGTAGGGTGTATATTTGCTGAATTGCTCACAGGGAAGCCACTCTTTCCAGGGAAGAATGTTGTGCATCAGTTGG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gttttacaaattttatagaatcacaaggttctgaatctggcattaacttttgcagTACACTCCTGCCATTGATATTTGGAGCGTAGGGTGTATATTTGCTGAATTGCTCACAGGGAAGCCACTCTTTCCAGGGAAGAATGTTGTGCATCAGTTGG
cattaac putative branch site (score: 43)
cttttgc CT-rich tract
acaaattttatagaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tacttgaacagtgtgtacatagtgtggagtttgatgtatcagcttgttttacaaattttatagaatcacaaggttctgaatctggcattaacttttgcagTACACTCCTGCCATTGATATTTGGAGCGTAGGGTGTATATTTGCTGAATTGCTCACAGGGAAGCCACTCTTTCCAGGGAAGAATGTTGTGCATCAGTTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - -tttgatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - atcacaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ggttctg